Starting phenix.real_space_refine on Sat Nov 16 13:33:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8izr_35869/11_2024/8izr_35869_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8izr_35869/11_2024/8izr_35869.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8izr_35869/11_2024/8izr_35869.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8izr_35869/11_2024/8izr_35869.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8izr_35869/11_2024/8izr_35869_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8izr_35869/11_2024/8izr_35869_neut.cif" } resolution = 3.62 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 57 5.16 5 C 7213 2.51 5 N 1842 2.21 5 O 2004 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 67 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 11116 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 11116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1400, 11116 Classifications: {'peptide': 1400} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 43, 'TRANS': 1356} Chain breaks: 3 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Time building chain proxies: 6.77, per 1000 atoms: 0.61 Number of scatterers: 11116 At special positions: 0 Unit cell: (100.58, 119.84, 166.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 57 16.00 O 2004 8.00 N 1842 7.00 C 7213 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 6 " - pdb=" SG CYS A 26 " distance=2.04 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: 2.92 Conformation dependent library (CDL) restraints added in 1.4 seconds 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2650 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 6 sheets defined 74.4% alpha, 3.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.50 Creating SS restraints... Processing helix chain 'A' and resid 2 through 7 Processing helix chain 'A' and resid 12 through 18 removed outlier: 4.099A pdb=" N LEU A 16 " --> pdb=" O ASN A 12 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASP A 17 " --> pdb=" O SER A 13 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N SER A 18 " --> pdb=" O SER A 14 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 12 through 18' Processing helix chain 'A' and resid 24 through 30 Processing helix chain 'A' and resid 30 through 43 Proline residue: A 36 - end of helix Processing helix chain 'A' and resid 43 through 55 Processing helix chain 'A' and resid 62 through 68 Processing helix chain 'A' and resid 70 through 91 removed outlier: 3.599A pdb=" N VAL A 86 " --> pdb=" O GLU A 82 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 122 Proline residue: A 104 - end of helix removed outlier: 3.844A pdb=" N TYR A 107 " --> pdb=" O ASN A 103 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLN A 122 " --> pdb=" O GLN A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 157 removed outlier: 4.241A pdb=" N PHE A 145 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N GLN A 146 " --> pdb=" O CYS A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 184 removed outlier: 3.693A pdb=" N LEU A 167 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLY A 173 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N PHE A 184 " --> pdb=" O ILE A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 197 removed outlier: 3.589A pdb=" N SER A 196 " --> pdb=" O ASN A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 205 Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 209 through 219 removed outlier: 4.121A pdb=" N LYS A 218 " --> pdb=" O LEU A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 233 Processing helix chain 'A' and resid 234 through 267 removed outlier: 3.545A pdb=" N SER A 240 " --> pdb=" O LYS A 236 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N HIS A 245 " --> pdb=" O LYS A 241 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N MET A 246 " --> pdb=" O PHE A 242 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG A 248 " --> pdb=" O THR A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 323 removed outlier: 3.649A pdb=" N LYS A 312 " --> pdb=" O SER A 308 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N PHE A 318 " --> pdb=" O LEU A 314 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N MET A 320 " --> pdb=" O LYS A 316 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N VAL A 321 " --> pdb=" O THR A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 337 removed outlier: 3.807A pdb=" N PHE A 337 " --> pdb=" O ASP A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 352 removed outlier: 3.899A pdb=" N GLN A 341 " --> pdb=" O PHE A 337 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU A 345 " --> pdb=" O GLN A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 405 removed outlier: 4.064A pdb=" N GLY A 360 " --> pdb=" O TYR A 356 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR A 361 " --> pdb=" O LEU A 357 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLN A 374 " --> pdb=" O ALA A 370 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N SER A 375 " --> pdb=" O ALA A 371 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR A 401 " --> pdb=" O MET A 397 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LYS A 402 " --> pdb=" O ALA A 398 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LYS A 403 " --> pdb=" O SER A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 413 Processing helix chain 'A' and resid 416 through 426 removed outlier: 3.934A pdb=" N MET A 424 " --> pdb=" O THR A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 437 removed outlier: 3.567A pdb=" N LEU A 431 " --> pdb=" O ASP A 427 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE A 437 " --> pdb=" O ASP A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 460 removed outlier: 4.292A pdb=" N VAL A 445 " --> pdb=" O LEU A 441 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N SER A 451 " --> pdb=" O GLN A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 508 removed outlier: 3.638A pdb=" N GLY A 466 " --> pdb=" O SER A 462 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL A 469 " --> pdb=" O ALA A 465 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N MET A 470 " --> pdb=" O GLY A 466 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE A 474 " --> pdb=" O MET A 470 " (cutoff:3.500A) Proline residue: A 475 - end of helix removed outlier: 3.649A pdb=" N LYS A 493 " --> pdb=" O VAL A 489 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ASN A 494 " --> pdb=" O LYS A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 516 Processing helix chain 'A' and resid 517 through 552 removed outlier: 3.602A pdb=" N ASP A 523 " --> pdb=" O PRO A 519 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLN A 524 " --> pdb=" O SER A 520 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS A 531 " --> pdb=" O ASN A 527 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL A 546 " --> pdb=" O LEU A 542 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N VAL A 549 " --> pdb=" O VAL A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 569 removed outlier: 3.736A pdb=" N LEU A 556 " --> pdb=" O LEU A 552 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N SER A 558 " --> pdb=" O PRO A 554 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR A 565 " --> pdb=" O THR A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 617 removed outlier: 3.659A pdb=" N THR A 581 " --> pdb=" O GLN A 577 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE A 588 " --> pdb=" O THR A 584 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N PHE A 591 " --> pdb=" O ASN A 587 " (cutoff:3.500A) Proline residue: A 592 - end of helix removed outlier: 3.511A pdb=" N MET A 595 " --> pdb=" O PHE A 591 " (cutoff:3.500A) Proline residue: A 597 - end of helix removed outlier: 3.563A pdb=" N ILE A 600 " --> pdb=" O LEU A 596 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU A 604 " --> pdb=" O ILE A 600 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N SER A 607 " --> pdb=" O MET A 603 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N VAL A 608 " --> pdb=" O LEU A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 685 removed outlier: 3.707A pdb=" N SER A 682 " --> pdb=" O SER A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 721 Processing helix chain 'A' and resid 726 through 738 Processing helix chain 'A' and resid 738 through 746 removed outlier: 4.660A pdb=" N ASP A 742 " --> pdb=" O ALA A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 752 Processing helix chain 'A' and resid 766 through 778 removed outlier: 4.134A pdb=" N ALA A 774 " --> pdb=" O SER A 770 " (cutoff:3.500A) Processing helix chain 'A' and resid 792 through 805 Processing helix chain 'A' and resid 824 through 828 removed outlier: 3.711A pdb=" N GLN A 827 " --> pdb=" O PHE A 824 " (cutoff:3.500A) Processing helix chain 'A' and resid 844 through 850 Processing helix chain 'A' and resid 854 through 861 Processing helix chain 'A' and resid 964 through 975 removed outlier: 3.693A pdb=" N TYR A 970 " --> pdb=" O ILE A 966 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY A 975 " --> pdb=" O LEU A 971 " (cutoff:3.500A) Processing helix chain 'A' and resid 975 through 1011 removed outlier: 3.697A pdb=" N ALA A 992 " --> pdb=" O MET A 988 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N SER A1007 " --> pdb=" O TRP A1003 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N LYS A1008 " --> pdb=" O THR A1004 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ILE A1009 " --> pdb=" O SER A1005 " (cutoff:3.500A) Processing helix chain 'A' and resid 1016 through 1067 removed outlier: 3.695A pdb=" N TYR A1027 " --> pdb=" O ARG A1023 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE A1055 " --> pdb=" O HIS A1051 " (cutoff:3.500A) Processing helix chain 'A' and resid 1068 through 1075 removed outlier: 3.801A pdb=" N PHE A1072 " --> pdb=" O PRO A1068 " (cutoff:3.500A) Processing helix chain 'A' and resid 1076 through 1084 removed outlier: 3.955A pdb=" N ILE A1080 " --> pdb=" O PRO A1076 " (cutoff:3.500A) Processing helix chain 'A' and resid 1085 through 1094 removed outlier: 3.535A pdb=" N SER A1089 " --> pdb=" O ALA A1085 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR A1094 " --> pdb=" O THR A1090 " (cutoff:3.500A) Processing helix chain 'A' and resid 1094 through 1120 removed outlier: 4.113A pdb=" N ARG A1100 " --> pdb=" O PRO A1096 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N SER A1101 " --> pdb=" O GLN A1097 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N TRP A1102 " --> pdb=" O SER A1098 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ILE A1103 " --> pdb=" O LEU A1099 " (cutoff:3.500A) Processing helix chain 'A' and resid 1123 through 1169 removed outlier: 3.715A pdb=" N VAL A1127 " --> pdb=" O PHE A1123 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ILE A1128 " --> pdb=" O THR A1124 " (cutoff:3.500A) Proline residue: A1129 - end of helix removed outlier: 3.706A pdb=" N LEU A1151 " --> pdb=" O GLN A1147 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASP A1152 " --> pdb=" O LEU A1148 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N SER A1153 " --> pdb=" O ARG A1149 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N SER A1157 " --> pdb=" O SER A1153 " (cutoff:3.500A) Proline residue: A1158 - end of helix Processing helix chain 'A' and resid 1169 through 1176 Processing helix chain 'A' and resid 1178 through 1229 removed outlier: 3.526A pdb=" N PHE A1182 " --> pdb=" O HIS A1178 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS A1184 " --> pdb=" O GLN A1180 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLU A1187 " --> pdb=" O LEU A1183 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N VAL A1188 " --> pdb=" O LYS A1184 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASN A1193 " --> pdb=" O ARG A1189 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG A1205 " --> pdb=" O ILE A1201 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG A1210 " --> pdb=" O TRP A1206 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL A1227 " --> pdb=" O ALA A1223 " (cutoff:3.500A) Processing helix chain 'A' and resid 1234 through 1247 removed outlier: 4.155A pdb=" N VAL A1238 " --> pdb=" O SER A1234 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLY A1239 " --> pdb=" O GLY A1235 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ASN A1247 " --> pdb=" O SER A1243 " (cutoff:3.500A) Processing helix chain 'A' and resid 1247 through 1266 removed outlier: 3.877A pdb=" N THR A1251 " --> pdb=" O ASN A1247 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASN A1253 " --> pdb=" O THR A1249 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL A1256 " --> pdb=" O LEU A1252 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLU A1263 " --> pdb=" O THR A1259 " (cutoff:3.500A) Processing helix chain 'A' and resid 1266 through 1277 removed outlier: 3.570A pdb=" N THR A1276 " --> pdb=" O ILE A1272 " (cutoff:3.500A) Processing helix chain 'A' and resid 1293 through 1298 removed outlier: 3.560A pdb=" N GLY A1298 " --> pdb=" O PRO A1295 " (cutoff:3.500A) Processing helix chain 'A' and resid 1339 through 1348 removed outlier: 4.126A pdb=" N THR A1344 " --> pdb=" O LYS A1340 " (cutoff:3.500A) Processing helix chain 'A' and resid 1364 through 1368 Processing helix chain 'A' and resid 1369 through 1377 removed outlier: 3.839A pdb=" N LYS A1376 " --> pdb=" O ASP A1372 " (cutoff:3.500A) Processing helix chain 'A' and resid 1390 through 1396 Processing helix chain 'A' and resid 1402 through 1413 removed outlier: 4.094A pdb=" N LYS A1408 " --> pdb=" O GLU A1404 " (cutoff:3.500A) Processing helix chain 'A' and resid 1415 through 1422 removed outlier: 3.841A pdb=" N VAL A1419 " --> pdb=" O LEU A1415 " (cutoff:3.500A) Processing helix chain 'A' and resid 1424 through 1428 removed outlier: 3.677A pdb=" N SER A1427 " --> pdb=" O LEU A1424 " (cutoff:3.500A) Processing helix chain 'A' and resid 1431 through 1435 Processing helix chain 'A' and resid 1438 through 1454 removed outlier: 3.806A pdb=" N CYS A1446 " --> pdb=" O ARG A1442 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU A1447 " --> pdb=" O GLN A1443 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS A1454 " --> pdb=" O ALA A1450 " (cutoff:3.500A) Processing helix chain 'A' and resid 1463 through 1466 removed outlier: 4.494A pdb=" N ALA A1466 " --> pdb=" O ALA A1463 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1463 through 1466' Processing helix chain 'A' and resid 1468 through 1482 removed outlier: 4.034A pdb=" N LEU A1474 " --> pdb=" O GLU A1470 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE A1475 " --> pdb=" O THR A1471 " (cutoff:3.500A) Processing helix chain 'A' and resid 1494 through 1500 removed outlier: 3.919A pdb=" N ASP A1500 " --> pdb=" O HIS A1496 " (cutoff:3.500A) Processing helix chain 'A' and resid 1517 through 1524 Processing helix chain 'A' and resid 1526 through 1535 Processing sheet with id=AA1, first strand: chain 'A' and resid 627 through 629 removed outlier: 3.683A pdb=" N ARG A 628 " --> pdb=" O ILE A 695 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ILE A 697 " --> pdb=" O ARG A 628 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 654 through 657 removed outlier: 5.975A pdb=" N ALA A 642 " --> pdb=" O ASP A 656 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 701 through 704 removed outlier: 5.959A pdb=" N ALA A 702 " --> pdb=" O LEU A 783 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N ASP A 785 " --> pdb=" O ALA A 702 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N VAL A 704 " --> pdb=" O ASP A 785 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N VAL A 818 " --> pdb=" O LEU A 784 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N ALA A 668 " --> pdb=" O VAL A 832 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N LEU A 834 " --> pdb=" O ALA A 668 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N GLY A 835 " --> pdb=" O ILE A 839 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N ILE A 839 " --> pdb=" O GLY A 835 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1300 through 1301 removed outlier: 4.294A pdb=" N ILE A1300 " --> pdb=" O ILE A1324 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1305 through 1308 removed outlier: 7.211A pdb=" N VAL A1307 " --> pdb=" O ARG A1318 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N ARG A1318 " --> pdb=" O VAL A1307 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1378 through 1379 removed outlier: 6.886A pdb=" N THR A1378 " --> pdb=" O VAL A1459 " (cutoff:3.500A) removed outlier: 8.411A pdb=" N ASP A1461 " --> pdb=" O THR A1378 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N LEU A1458 " --> pdb=" O ILE A1489 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N ILE A1491 " --> pdb=" O LEU A1458 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LEU A1460 " --> pdb=" O ILE A1491 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N ILE A1330 " --> pdb=" O THR A1490 " (cutoff:3.500A) 667 hydrogen bonds defined for protein. 1953 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: 4.42 Time building geometry restraints manager: 3.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1782 1.31 - 1.44: 2994 1.44 - 1.56: 6480 1.56 - 1.69: 0 1.69 - 1.82: 94 Bond restraints: 11350 Sorted by residual: bond pdb=" CA SER A 129 " pdb=" CB SER A 129 " ideal model delta sigma weight residual 1.539 1.469 0.070 1.36e-02 5.41e+03 2.61e+01 bond pdb=" CA SER A1111 " pdb=" CB SER A1111 " ideal model delta sigma weight residual 1.529 1.450 0.079 1.55e-02 4.16e+03 2.60e+01 bond pdb=" CA SER A 996 " pdb=" CB SER A 996 " ideal model delta sigma weight residual 1.528 1.452 0.077 1.56e-02 4.11e+03 2.43e+01 bond pdb=" CA SER A1101 " pdb=" CB SER A1101 " ideal model delta sigma weight residual 1.528 1.450 0.078 1.59e-02 3.96e+03 2.40e+01 bond pdb=" CA SER A1145 " pdb=" CB SER A1145 " ideal model delta sigma weight residual 1.528 1.452 0.076 1.56e-02 4.11e+03 2.38e+01 ... (remaining 11345 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.55: 12567 2.55 - 5.10: 2515 5.10 - 7.65: 260 7.65 - 10.20: 39 10.20 - 12.75: 8 Bond angle restraints: 15389 Sorted by residual: angle pdb=" N PRO A1291 " pdb=" CA PRO A1291 " pdb=" C PRO A1291 " ideal model delta sigma weight residual 110.70 99.93 10.77 1.22e+00 6.72e-01 7.79e+01 angle pdb=" N ILE A1350 " pdb=" CA ILE A1350 " pdb=" C ILE A1350 " ideal model delta sigma weight residual 110.62 102.23 8.39 1.02e+00 9.61e-01 6.76e+01 angle pdb=" N ILE A 994 " pdb=" CA ILE A 994 " pdb=" C ILE A 994 " ideal model delta sigma weight residual 110.62 102.23 8.39 1.02e+00 9.61e-01 6.76e+01 angle pdb=" C PRO A 597 " pdb=" CA PRO A 597 " pdb=" CB PRO A 597 " ideal model delta sigma weight residual 113.06 100.31 12.75 1.59e+00 3.96e-01 6.43e+01 angle pdb=" C THR A 561 " pdb=" CA THR A 561 " pdb=" CB THR A 561 " ideal model delta sigma weight residual 110.90 98.26 12.64 1.58e+00 4.01e-01 6.40e+01 ... (remaining 15384 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.11: 5855 17.11 - 34.22: 614 34.22 - 51.34: 225 51.34 - 68.45: 69 68.45 - 85.56: 8 Dihedral angle restraints: 6771 sinusoidal: 2688 harmonic: 4083 Sorted by residual: dihedral pdb=" C ASN A 103 " pdb=" N ASN A 103 " pdb=" CA ASN A 103 " pdb=" CB ASN A 103 " ideal model delta harmonic sigma weight residual -122.60 -142.20 19.60 0 2.50e+00 1.60e-01 6.15e+01 dihedral pdb=" C HIS A1042 " pdb=" N HIS A1042 " pdb=" CA HIS A1042 " pdb=" CB HIS A1042 " ideal model delta harmonic sigma weight residual -122.60 -141.95 19.35 0 2.50e+00 1.60e-01 5.99e+01 dihedral pdb=" C THR A 420 " pdb=" N THR A 420 " pdb=" CA THR A 420 " pdb=" CB THR A 420 " ideal model delta harmonic sigma weight residual -122.00 -138.95 16.95 0 2.50e+00 1.60e-01 4.60e+01 ... (remaining 6768 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.144: 1329 0.144 - 0.288: 419 0.288 - 0.433: 50 0.433 - 0.577: 5 0.577 - 0.721: 2 Chirality restraints: 1805 Sorted by residual: chirality pdb=" CA ASN A 103 " pdb=" N ASN A 103 " pdb=" C ASN A 103 " pdb=" CB ASN A 103 " both_signs ideal model delta sigma weight residual False 2.51 1.79 0.72 2.00e-01 2.50e+01 1.30e+01 chirality pdb=" CA HIS A1042 " pdb=" N HIS A1042 " pdb=" C HIS A1042 " pdb=" CB HIS A1042 " both_signs ideal model delta sigma weight residual False 2.51 1.80 0.71 2.00e-01 2.50e+01 1.27e+01 chirality pdb=" CA THR A 420 " pdb=" N THR A 420 " pdb=" C THR A 420 " pdb=" CB THR A 420 " both_signs ideal model delta sigma weight residual False 2.53 1.97 0.56 2.00e-01 2.50e+01 7.71e+00 ... (remaining 1802 not shown) Planarity restraints: 1909 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A1230 " -0.470 9.50e-02 1.11e+02 2.10e-01 2.71e+01 pdb=" NE ARG A1230 " 0.027 2.00e-02 2.50e+03 pdb=" CZ ARG A1230 " 0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG A1230 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A1230 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A1207 " -0.017 2.00e-02 2.50e+03 3.38e-02 1.14e+01 pdb=" C LEU A1207 " 0.059 2.00e-02 2.50e+03 pdb=" O LEU A1207 " -0.022 2.00e-02 2.50e+03 pdb=" N ALA A1208 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A1364 " -0.016 2.00e-02 2.50e+03 3.30e-02 1.09e+01 pdb=" C ASP A1364 " 0.057 2.00e-02 2.50e+03 pdb=" O ASP A1364 " -0.021 2.00e-02 2.50e+03 pdb=" N ILE A1365 " -0.020 2.00e-02 2.50e+03 ... (remaining 1906 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.88: 5011 2.88 - 3.39: 11368 3.39 - 3.89: 17867 3.89 - 4.40: 21270 4.40 - 4.90: 31976 Nonbonded interactions: 87492 Sorted by model distance: nonbonded pdb=" C THR A1344 " pdb=" OG1 THR A1344 " model vdw 2.376 2.616 nonbonded pdb=" C SER A1143 " pdb=" OG SER A1143 " model vdw 2.403 2.616 nonbonded pdb=" O ILE A1358 " pdb=" N ASP A1364 " model vdw 2.406 3.120 nonbonded pdb=" CZ ARG A1335 " pdb=" O HIS A1493 " model vdw 2.409 3.270 nonbonded pdb=" NH2 ARG A1066 " pdb=" O ALA A1282 " model vdw 2.411 3.120 ... (remaining 87487 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.460 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 28.460 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 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 : 0.013 0.079 11350 Z= 0.831 Angle : 1.999 12.754 15389 Z= 1.527 Chirality : 0.135 0.721 1805 Planarity : 0.009 0.210 1909 Dihedral : 17.092 85.558 4118 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.09 % Favored : 96.77 % Rotamer: Outliers : 14.34 % Allowed : 13.38 % Favored : 72.28 % Cbeta Deviations : 2.87 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.21), residues: 1392 helix: 0.64 (0.16), residues: 889 sheet: 0.44 (0.94), residues: 33 loop : -0.42 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP A 208 HIS 0.007 0.002 HIS A 439 PHE 0.035 0.003 PHE A 515 TYR 0.034 0.003 TYR A 119 ARG 0.008 0.001 ARG A 815 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 178 poor density : 276 time to evaluate : 1.280 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: A 156 GLN cc_start: 0.8522 (OUTLIER) cc_final: 0.8263 (mp10) REVERT: A 219 ARG cc_start: 0.7434 (OUTLIER) cc_final: 0.7209 (ptt90) REVERT: A 246 MET cc_start: 0.8579 (ptt) cc_final: 0.8248 (ptp) REVERT: A 248 ARG cc_start: 0.8912 (OUTLIER) cc_final: 0.8612 (ttm-80) REVERT: A 309 TRP cc_start: 0.8771 (p-90) cc_final: 0.8339 (p-90) REVERT: A 419 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7663 (tt0) REVERT: A 424 MET cc_start: 0.8185 (OUTLIER) cc_final: 0.7645 (tmm) REVERT: A 429 GLN cc_start: 0.8264 (OUTLIER) cc_final: 0.7631 (tt0) REVERT: A 447 GLN cc_start: 0.8293 (OUTLIER) cc_final: 0.7880 (tt0) REVERT: A 457 ARG cc_start: 0.8151 (OUTLIER) cc_final: 0.7728 (ptt180) REVERT: A 458 GLU cc_start: 0.8255 (mm-30) cc_final: 0.7679 (mt-10) REVERT: A 470 MET cc_start: 0.8199 (mmt) cc_final: 0.7992 (mmt) REVERT: A 521 PHE cc_start: 0.8634 (OUTLIER) cc_final: 0.7650 (m-80) REVERT: A 969 GLU cc_start: 0.8876 (OUTLIER) cc_final: 0.8081 (mp0) REVERT: A 1010 PHE cc_start: 0.7856 (m-80) cc_final: 0.7619 (m-10) REVERT: A 1030 LEU cc_start: 0.9282 (mt) cc_final: 0.8999 (mt) REVERT: A 1093 ASP cc_start: 0.7719 (m-30) cc_final: 0.7034 (t0) REVERT: A 1193 ASN cc_start: 0.7607 (OUTLIER) cc_final: 0.7335 (t0) REVERT: A 1438 SER cc_start: 0.8327 (OUTLIER) cc_final: 0.7707 (p) outliers start: 178 outliers final: 72 residues processed: 416 average time/residue: 0.2352 time to fit residues: 138.8051 Evaluate side-chains 276 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 192 time to evaluate : 1.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LYS Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 15 PHE Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 101 TYR Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 111 TRP Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 156 GLN Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 219 ARG Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 248 ARG Chi-restraints excluded: chain A residue 311 MET Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 419 GLU Chi-restraints excluded: chain A residue 424 MET Chi-restraints excluded: chain A residue 429 GLN Chi-restraints excluded: chain A residue 438 MET Chi-restraints excluded: chain A residue 440 MET Chi-restraints excluded: chain A residue 447 GLN Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 521 PHE Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 575 ASP Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 594 SER Chi-restraints excluded: chain A residue 595 MET Chi-restraints excluded: chain A residue 638 GLN Chi-restraints excluded: chain A residue 648 HIS Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain A residue 710 ILE Chi-restraints excluded: chain A residue 760 ASN Chi-restraints excluded: chain A residue 784 LEU Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 838 THR Chi-restraints excluded: chain A residue 859 LEU Chi-restraints excluded: chain A residue 969 GLU Chi-restraints excluded: chain A residue 996 SER Chi-restraints excluded: chain A residue 1007 SER Chi-restraints excluded: chain A residue 1032 LEU Chi-restraints excluded: chain A residue 1050 VAL Chi-restraints excluded: chain A residue 1061 LEU Chi-restraints excluded: chain A residue 1094 THR Chi-restraints excluded: chain A residue 1099 LEU Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1112 THR Chi-restraints excluded: chain A residue 1143 SER Chi-restraints excluded: chain A residue 1155 THR Chi-restraints excluded: chain A residue 1158 PRO Chi-restraints excluded: chain A residue 1188 VAL Chi-restraints excluded: chain A residue 1193 ASN Chi-restraints excluded: chain A residue 1218 THR Chi-restraints excluded: chain A residue 1242 LEU Chi-restraints excluded: chain A residue 1260 SER Chi-restraints excluded: chain A residue 1267 VAL Chi-restraints excluded: chain A residue 1318 ARG Chi-restraints excluded: chain A residue 1341 SER Chi-restraints excluded: chain A residue 1344 THR Chi-restraints excluded: chain A residue 1358 ILE Chi-restraints excluded: chain A residue 1365 ILE Chi-restraints excluded: chain A residue 1368 ILE Chi-restraints excluded: chain A residue 1379 ILE Chi-restraints excluded: chain A residue 1386 LEU Chi-restraints excluded: chain A residue 1414 HIS Chi-restraints excluded: chain A residue 1415 LEU Chi-restraints excluded: chain A residue 1438 SER Chi-restraints excluded: chain A residue 1458 LEU Chi-restraints excluded: chain A residue 1467 VAL Chi-restraints excluded: chain A residue 1474 LEU Chi-restraints excluded: chain A residue 1487 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 118 optimal weight: 20.0000 chunk 106 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 71 optimal weight: 6.9990 chunk 56 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 chunk 81 optimal weight: 0.0060 chunk 127 optimal weight: 0.4980 overall best weight: 1.0400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 118 GLN A 447 GLN A 524 GLN A 551 GLN A 577 GLN A 694 HIS A 711 GLN A 732 GLN A 760 ASN A1185 HIS A1194 GLN A1216 ASN A1371 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7077 moved from start: 0.3446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11350 Z= 0.239 Angle : 0.709 8.410 15389 Z= 0.384 Chirality : 0.044 0.248 1805 Planarity : 0.005 0.061 1909 Dihedral : 11.374 77.222 1652 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 8.22 % Allowed : 18.45 % Favored : 73.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.21), residues: 1392 helix: 1.17 (0.16), residues: 933 sheet: -0.55 (0.77), residues: 42 loop : -0.55 (0.28), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 358 HIS 0.005 0.001 HIS A1042 PHE 0.031 0.002 PHE A1240 TYR 0.022 0.002 TYR A1141 ARG 0.011 0.001 ARG A1349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 222 time to evaluate : 1.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 LEU cc_start: 0.9006 (mt) cc_final: 0.8800 (tt) REVERT: A 248 ARG cc_start: 0.8695 (OUTLIER) cc_final: 0.8412 (mtm-85) REVERT: A 312 LYS cc_start: 0.8604 (OUTLIER) cc_final: 0.8214 (mptt) REVERT: A 419 GLU cc_start: 0.7593 (OUTLIER) cc_final: 0.7215 (tp30) REVERT: A 552 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8185 (tt) REVERT: A 638 GLN cc_start: 0.8033 (OUTLIER) cc_final: 0.7445 (tm-30) REVERT: A 677 LYS cc_start: 0.7531 (OUTLIER) cc_final: 0.7248 (ptmm) REVERT: A 766 LYS cc_start: 0.7715 (pttt) cc_final: 0.7505 (pttp) REVERT: A 814 THR cc_start: 0.7165 (OUTLIER) cc_final: 0.6956 (m) REVERT: A 824 PHE cc_start: 0.7017 (m-80) cc_final: 0.6714 (m-80) REVERT: A 982 ILE cc_start: 0.9240 (mt) cc_final: 0.8983 (mt) REVERT: A 1149 ARG cc_start: 0.7108 (OUTLIER) cc_final: 0.6630 (ptm160) REVERT: A 1207 LEU cc_start: 0.8968 (tp) cc_final: 0.8625 (tp) outliers start: 102 outliers final: 57 residues processed: 298 average time/residue: 0.2354 time to fit residues: 101.0455 Evaluate side-chains 237 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 172 time to evaluate : 1.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LYS Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 101 TYR Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 111 TRP Chi-restraints excluded: chain A residue 130 TRP Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 248 ARG Chi-restraints excluded: chain A residue 311 MET Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 419 GLU Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 440 MET Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 575 ASP Chi-restraints excluded: chain A residue 595 MET Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain A residue 638 GLN Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 648 HIS Chi-restraints excluded: chain A residue 677 LYS Chi-restraints excluded: chain A residue 710 ILE Chi-restraints excluded: chain A residue 814 THR Chi-restraints excluded: chain A residue 838 THR Chi-restraints excluded: chain A residue 859 LEU Chi-restraints excluded: chain A residue 1007 SER Chi-restraints excluded: chain A residue 1032 LEU Chi-restraints excluded: chain A residue 1069 MET Chi-restraints excluded: chain A residue 1094 THR Chi-restraints excluded: chain A residue 1099 LEU Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1143 SER Chi-restraints excluded: chain A residue 1149 ARG Chi-restraints excluded: chain A residue 1218 THR Chi-restraints excluded: chain A residue 1242 LEU Chi-restraints excluded: chain A residue 1260 SER Chi-restraints excluded: chain A residue 1273 THR Chi-restraints excluded: chain A residue 1318 ARG Chi-restraints excluded: chain A residue 1344 THR Chi-restraints excluded: chain A residue 1358 ILE Chi-restraints excluded: chain A residue 1365 ILE Chi-restraints excluded: chain A residue 1379 ILE Chi-restraints excluded: chain A residue 1414 HIS Chi-restraints excluded: chain A residue 1415 LEU Chi-restraints excluded: chain A residue 1437 LEU Chi-restraints excluded: chain A residue 1454 LYS Chi-restraints excluded: chain A residue 1455 SER Chi-restraints excluded: chain A residue 1458 LEU Chi-restraints excluded: chain A residue 1467 VAL Chi-restraints excluded: chain A residue 1474 LEU Chi-restraints excluded: chain A residue 1488 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 70 optimal weight: 20.0000 chunk 39 optimal weight: 0.9990 chunk 105 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 127 optimal weight: 0.8980 chunk 137 optimal weight: 20.0000 chunk 113 optimal weight: 4.9990 chunk 126 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 102 optimal weight: 3.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN A 118 GLN A 551 GLN A 638 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7069 moved from start: 0.4351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11350 Z= 0.204 Angle : 0.625 9.637 15389 Z= 0.334 Chirality : 0.041 0.171 1805 Planarity : 0.004 0.046 1909 Dihedral : 8.887 71.020 1577 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 6.20 % Allowed : 21.92 % Favored : 71.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.22), residues: 1392 helix: 1.40 (0.17), residues: 929 sheet: -0.10 (0.81), residues: 42 loop : -0.41 (0.28), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 358 HIS 0.005 0.001 HIS A 794 PHE 0.023 0.002 PHE A1240 TYR 0.017 0.001 TYR A1141 ARG 0.004 0.000 ARG A1449 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 201 time to evaluate : 1.346 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 GLN cc_start: 0.8588 (OUTLIER) cc_final: 0.8380 (tp40) REVERT: A 112 LEU cc_start: 0.9011 (mt) cc_final: 0.8710 (tp) REVERT: A 312 LYS cc_start: 0.8622 (OUTLIER) cc_final: 0.8345 (mptt) REVERT: A 419 GLU cc_start: 0.7528 (OUTLIER) cc_final: 0.5854 (tm-30) REVERT: A 552 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.7872 (tt) REVERT: A 677 LYS cc_start: 0.7519 (OUTLIER) cc_final: 0.7218 (ptmm) REVERT: A 814 THR cc_start: 0.6914 (OUTLIER) cc_final: 0.6530 (p) REVERT: A 845 TYR cc_start: 0.6102 (t80) cc_final: 0.5765 (t80) REVERT: A 1149 ARG cc_start: 0.6918 (OUTLIER) cc_final: 0.6564 (ptm160) REVERT: A 1207 LEU cc_start: 0.8985 (tp) cc_final: 0.8711 (tp) outliers start: 77 outliers final: 45 residues processed: 256 average time/residue: 0.2219 time to fit residues: 83.6527 Evaluate side-chains 224 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 172 time to evaluate : 1.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LYS Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 69 GLN Chi-restraints excluded: chain A residue 101 TYR Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 111 TRP Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 130 TRP Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 409 ASN Chi-restraints excluded: chain A residue 419 GLU Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 575 ASP Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 648 HIS Chi-restraints excluded: chain A residue 677 LYS Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 814 THR Chi-restraints excluded: chain A residue 838 THR Chi-restraints excluded: chain A residue 990 SER Chi-restraints excluded: chain A residue 1032 LEU Chi-restraints excluded: chain A residue 1094 THR Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1112 THR Chi-restraints excluded: chain A residue 1149 ARG Chi-restraints excluded: chain A residue 1164 SER Chi-restraints excluded: chain A residue 1242 LEU Chi-restraints excluded: chain A residue 1273 THR Chi-restraints excluded: chain A residue 1285 VAL Chi-restraints excluded: chain A residue 1287 ASP Chi-restraints excluded: chain A residue 1343 LEU Chi-restraints excluded: chain A residue 1344 THR Chi-restraints excluded: chain A residue 1358 ILE Chi-restraints excluded: chain A residue 1365 ILE Chi-restraints excluded: chain A residue 1379 ILE Chi-restraints excluded: chain A residue 1426 LEU Chi-restraints excluded: chain A residue 1455 SER Chi-restraints excluded: chain A residue 1488 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 125 optimal weight: 0.9980 chunk 95 optimal weight: 0.9980 chunk 66 optimal weight: 7.9990 chunk 14 optimal weight: 1.9990 chunk 60 optimal weight: 10.0000 chunk 85 optimal weight: 1.9990 chunk 127 optimal weight: 8.9990 chunk 135 optimal weight: 7.9990 chunk 121 optimal weight: 8.9990 chunk 36 optimal weight: 0.7980 chunk 112 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN A1414 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7089 moved from start: 0.4762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11350 Z= 0.225 Angle : 0.631 12.226 15389 Z= 0.332 Chirality : 0.041 0.184 1805 Planarity : 0.004 0.044 1909 Dihedral : 7.459 71.002 1531 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 5.88 % Allowed : 23.69 % Favored : 70.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.22), residues: 1392 helix: 1.45 (0.17), residues: 927 sheet: -0.07 (0.80), residues: 42 loop : -0.52 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1407 HIS 0.005 0.001 HIS A1042 PHE 0.023 0.001 PHE A1240 TYR 0.021 0.001 TYR A 565 ARG 0.004 0.000 ARG A1318 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 185 time to evaluate : 1.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 LEU cc_start: 0.8546 (tt) cc_final: 0.8304 (tp) REVERT: A 112 LEU cc_start: 0.8969 (mt) cc_final: 0.8667 (tp) REVERT: A 312 LYS cc_start: 0.8616 (OUTLIER) cc_final: 0.8381 (mptt) REVERT: A 419 GLU cc_start: 0.7517 (OUTLIER) cc_final: 0.5840 (tm-30) REVERT: A 677 LYS cc_start: 0.7554 (OUTLIER) cc_final: 0.7224 (ptmm) REVERT: A 786 ASP cc_start: 0.7982 (OUTLIER) cc_final: 0.7499 (t70) REVERT: A 814 THR cc_start: 0.6961 (OUTLIER) cc_final: 0.6521 (p) REVERT: A 1149 ARG cc_start: 0.6930 (OUTLIER) cc_final: 0.6548 (ptm160) REVERT: A 1393 MET cc_start: 0.8069 (ptm) cc_final: 0.7788 (tmm) outliers start: 73 outliers final: 54 residues processed: 237 average time/residue: 0.2150 time to fit residues: 76.1109 Evaluate side-chains 222 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 162 time to evaluate : 1.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LYS Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 101 TYR Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 111 TRP Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 130 TRP Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 333 ASP Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 409 ASN Chi-restraints excluded: chain A residue 419 GLU Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 438 MET Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 575 ASP Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 648 HIS Chi-restraints excluded: chain A residue 677 LYS Chi-restraints excluded: chain A residue 786 ASP Chi-restraints excluded: chain A residue 814 THR Chi-restraints excluded: chain A residue 838 THR Chi-restraints excluded: chain A residue 990 SER Chi-restraints excluded: chain A residue 1032 LEU Chi-restraints excluded: chain A residue 1064 ILE Chi-restraints excluded: chain A residue 1069 MET Chi-restraints excluded: chain A residue 1094 THR Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1112 THR Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain A residue 1149 ARG Chi-restraints excluded: chain A residue 1164 SER Chi-restraints excluded: chain A residue 1217 LEU Chi-restraints excluded: chain A residue 1273 THR Chi-restraints excluded: chain A residue 1285 VAL Chi-restraints excluded: chain A residue 1287 ASP Chi-restraints excluded: chain A residue 1306 GLN Chi-restraints excluded: chain A residue 1343 LEU Chi-restraints excluded: chain A residue 1344 THR Chi-restraints excluded: chain A residue 1350 ILE Chi-restraints excluded: chain A residue 1358 ILE Chi-restraints excluded: chain A residue 1365 ILE Chi-restraints excluded: chain A residue 1379 ILE Chi-restraints excluded: chain A residue 1414 HIS Chi-restraints excluded: chain A residue 1426 LEU Chi-restraints excluded: chain A residue 1455 SER Chi-restraints excluded: chain A residue 1488 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 76 optimal weight: 2.9990 chunk 1 optimal weight: 8.9990 chunk 100 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 115 optimal weight: 9.9990 chunk 93 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 69 optimal weight: 10.0000 chunk 121 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 118 GLN ** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1019 GLN A1244 ASN A1371 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7160 moved from start: 0.4841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 11350 Z= 0.327 Angle : 0.683 11.354 15389 Z= 0.358 Chirality : 0.043 0.274 1805 Planarity : 0.004 0.050 1909 Dihedral : 7.257 71.838 1527 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 7.25 % Allowed : 23.13 % Favored : 69.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.22), residues: 1392 helix: 1.12 (0.17), residues: 933 sheet: -0.28 (0.79), residues: 42 loop : -0.76 (0.28), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 208 HIS 0.014 0.002 HIS A1414 PHE 0.031 0.002 PHE A1240 TYR 0.026 0.002 TYR A 565 ARG 0.004 0.000 ARG A1318 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 180 time to evaluate : 1.320 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: A 4 LYS cc_start: 0.8858 (OUTLIER) cc_final: 0.7897 (pptt) REVERT: A 112 LEU cc_start: 0.9016 (mt) cc_final: 0.8691 (tp) REVERT: A 312 LYS cc_start: 0.8662 (OUTLIER) cc_final: 0.8422 (mptt) REVERT: A 419 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.6071 (tm-30) REVERT: A 599 MET cc_start: 0.7380 (mmp) cc_final: 0.6680 (mmt) REVERT: A 688 MET cc_start: 0.7583 (mtm) cc_final: 0.7373 (ttm) REVERT: A 766 LYS cc_start: 0.7633 (pttm) cc_final: 0.7351 (pttp) REVERT: A 980 PHE cc_start: 0.7635 (m-80) cc_final: 0.7367 (t80) REVERT: A 1039 PHE cc_start: 0.8279 (t80) cc_final: 0.8045 (t80) REVERT: A 1149 ARG cc_start: 0.7011 (OUTLIER) cc_final: 0.6645 (ptm160) outliers start: 90 outliers final: 66 residues processed: 248 average time/residue: 0.2151 time to fit residues: 78.7989 Evaluate side-chains 233 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 163 time to evaluate : 1.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LYS Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 101 TYR Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 111 TRP Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 130 TRP Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 333 ASP Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 409 ASN Chi-restraints excluded: chain A residue 419 GLU Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 438 MET Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 575 ASP Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 648 HIS Chi-restraints excluded: chain A residue 838 THR Chi-restraints excluded: chain A residue 990 SER Chi-restraints excluded: chain A residue 1032 LEU Chi-restraints excluded: chain A residue 1050 VAL Chi-restraints excluded: chain A residue 1064 ILE Chi-restraints excluded: chain A residue 1069 MET Chi-restraints excluded: chain A residue 1094 THR Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1112 THR Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain A residue 1135 VAL Chi-restraints excluded: chain A residue 1149 ARG Chi-restraints excluded: chain A residue 1164 SER Chi-restraints excluded: chain A residue 1188 VAL Chi-restraints excluded: chain A residue 1217 LEU Chi-restraints excluded: chain A residue 1218 THR Chi-restraints excluded: chain A residue 1273 THR Chi-restraints excluded: chain A residue 1278 VAL Chi-restraints excluded: chain A residue 1285 VAL Chi-restraints excluded: chain A residue 1287 ASP Chi-restraints excluded: chain A residue 1306 GLN Chi-restraints excluded: chain A residue 1343 LEU Chi-restraints excluded: chain A residue 1344 THR Chi-restraints excluded: chain A residue 1350 ILE Chi-restraints excluded: chain A residue 1358 ILE Chi-restraints excluded: chain A residue 1365 ILE Chi-restraints excluded: chain A residue 1379 ILE Chi-restraints excluded: chain A residue 1386 LEU Chi-restraints excluded: chain A residue 1426 LEU Chi-restraints excluded: chain A residue 1437 LEU Chi-restraints excluded: chain A residue 1488 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 121 optimal weight: 9.9990 chunk 26 optimal weight: 0.6980 chunk 79 optimal weight: 20.0000 chunk 33 optimal weight: 1.9990 chunk 135 optimal weight: 5.9990 chunk 112 optimal weight: 2.9990 chunk 62 optimal weight: 9.9990 chunk 11 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 71 optimal weight: 9.9990 chunk 130 optimal weight: 1.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 118 GLN A1244 ASN A1371 HIS A1394 ASN A1414 HIS A1443 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7132 moved from start: 0.5167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 11350 Z= 0.251 Angle : 0.647 11.756 15389 Z= 0.333 Chirality : 0.041 0.220 1805 Planarity : 0.004 0.046 1909 Dihedral : 7.015 67.515 1527 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 6.37 % Allowed : 24.09 % Favored : 69.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.22), residues: 1392 helix: 1.14 (0.17), residues: 941 sheet: -0.19 (0.68), residues: 54 loop : -0.75 (0.29), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A1407 HIS 0.004 0.001 HIS A1051 PHE 0.022 0.001 PHE A1240 TYR 0.020 0.002 TYR A 565 ARG 0.004 0.000 ARG A1146 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 182 time to evaluate : 1.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 LYS cc_start: 0.8852 (OUTLIER) cc_final: 0.7933 (pptt) REVERT: A 112 LEU cc_start: 0.8966 (mt) cc_final: 0.8654 (tp) REVERT: A 312 LYS cc_start: 0.8643 (OUTLIER) cc_final: 0.8389 (mptt) REVERT: A 419 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.6123 (tm-30) REVERT: A 814 THR cc_start: 0.6905 (OUTLIER) cc_final: 0.6501 (p) REVERT: A 834 LEU cc_start: 0.7036 (tt) cc_final: 0.6644 (pp) REVERT: A 980 PHE cc_start: 0.7544 (OUTLIER) cc_final: 0.7300 (t80) REVERT: A 982 ILE cc_start: 0.9262 (mt) cc_final: 0.8916 (mt) REVERT: A 1039 PHE cc_start: 0.8238 (t80) cc_final: 0.8012 (t80) REVERT: A 1149 ARG cc_start: 0.7115 (OUTLIER) cc_final: 0.6740 (ptm160) outliers start: 79 outliers final: 65 residues processed: 242 average time/residue: 0.2135 time to fit residues: 76.8614 Evaluate side-chains 242 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 171 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LYS Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 101 TYR Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 111 TRP Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 130 TRP Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 333 ASP Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 409 ASN Chi-restraints excluded: chain A residue 419 GLU Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 438 MET Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 575 ASP Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 648 HIS Chi-restraints excluded: chain A residue 814 THR Chi-restraints excluded: chain A residue 838 THR Chi-restraints excluded: chain A residue 980 PHE Chi-restraints excluded: chain A residue 990 SER Chi-restraints excluded: chain A residue 1032 LEU Chi-restraints excluded: chain A residue 1050 VAL Chi-restraints excluded: chain A residue 1064 ILE Chi-restraints excluded: chain A residue 1069 MET Chi-restraints excluded: chain A residue 1094 THR Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1112 THR Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain A residue 1143 SER Chi-restraints excluded: chain A residue 1149 ARG Chi-restraints excluded: chain A residue 1164 SER Chi-restraints excluded: chain A residue 1273 THR Chi-restraints excluded: chain A residue 1278 VAL Chi-restraints excluded: chain A residue 1285 VAL Chi-restraints excluded: chain A residue 1287 ASP Chi-restraints excluded: chain A residue 1343 LEU Chi-restraints excluded: chain A residue 1344 THR Chi-restraints excluded: chain A residue 1350 ILE Chi-restraints excluded: chain A residue 1358 ILE Chi-restraints excluded: chain A residue 1365 ILE Chi-restraints excluded: chain A residue 1371 HIS Chi-restraints excluded: chain A residue 1379 ILE Chi-restraints excluded: chain A residue 1386 LEU Chi-restraints excluded: chain A residue 1426 LEU Chi-restraints excluded: chain A residue 1437 LEU Chi-restraints excluded: chain A residue 1443 GLN Chi-restraints excluded: chain A residue 1455 SER Chi-restraints excluded: chain A residue 1488 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 15 optimal weight: 0.7980 chunk 77 optimal weight: 10.0000 chunk 98 optimal weight: 0.0670 chunk 76 optimal weight: 3.9990 chunk 114 optimal weight: 1.9990 chunk 75 optimal weight: 7.9990 chunk 134 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 82 optimal weight: 10.0000 chunk 62 optimal weight: 10.0000 chunk 83 optimal weight: 0.9990 overall best weight: 1.5724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 118 GLN A1138 GLN A1371 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7125 moved from start: 0.5333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 11350 Z= 0.240 Angle : 0.664 13.543 15389 Z= 0.337 Chirality : 0.041 0.248 1805 Planarity : 0.004 0.046 1909 Dihedral : 6.915 66.298 1527 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 6.45 % Allowed : 24.66 % Favored : 68.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.22), residues: 1392 helix: 1.22 (0.17), residues: 942 sheet: -0.25 (0.68), residues: 54 loop : -0.75 (0.29), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 208 HIS 0.015 0.001 HIS A1371 PHE 0.031 0.001 PHE A1348 TYR 0.020 0.001 TYR A 565 ARG 0.008 0.000 ARG A1318 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 185 time to evaluate : 1.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 LYS cc_start: 0.8856 (OUTLIER) cc_final: 0.7927 (pptt) REVERT: A 112 LEU cc_start: 0.8970 (mt) cc_final: 0.8651 (tp) REVERT: A 312 LYS cc_start: 0.8633 (OUTLIER) cc_final: 0.8377 (mptt) REVERT: A 419 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.6128 (tm-30) REVERT: A 766 LYS cc_start: 0.7641 (pttm) cc_final: 0.7374 (pttp) REVERT: A 814 THR cc_start: 0.6933 (OUTLIER) cc_final: 0.6502 (p) REVERT: A 834 LEU cc_start: 0.6924 (tt) cc_final: 0.6685 (pp) REVERT: A 982 ILE cc_start: 0.9271 (mt) cc_final: 0.8952 (mt) REVERT: A 1149 ARG cc_start: 0.7069 (OUTLIER) cc_final: 0.6714 (ptm160) outliers start: 80 outliers final: 62 residues processed: 240 average time/residue: 0.2294 time to fit residues: 83.1009 Evaluate side-chains 240 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 173 time to evaluate : 1.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LYS Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 101 TYR Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 130 TRP Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 333 ASP Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 409 ASN Chi-restraints excluded: chain A residue 419 GLU Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 438 MET Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 575 ASP Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 648 HIS Chi-restraints excluded: chain A residue 814 THR Chi-restraints excluded: chain A residue 990 SER Chi-restraints excluded: chain A residue 1032 LEU Chi-restraints excluded: chain A residue 1050 VAL Chi-restraints excluded: chain A residue 1064 ILE Chi-restraints excluded: chain A residue 1094 THR Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain A residue 1143 SER Chi-restraints excluded: chain A residue 1149 ARG Chi-restraints excluded: chain A residue 1164 SER Chi-restraints excluded: chain A residue 1217 LEU Chi-restraints excluded: chain A residue 1273 THR Chi-restraints excluded: chain A residue 1278 VAL Chi-restraints excluded: chain A residue 1285 VAL Chi-restraints excluded: chain A residue 1287 ASP Chi-restraints excluded: chain A residue 1343 LEU Chi-restraints excluded: chain A residue 1344 THR Chi-restraints excluded: chain A residue 1350 ILE Chi-restraints excluded: chain A residue 1358 ILE Chi-restraints excluded: chain A residue 1365 ILE Chi-restraints excluded: chain A residue 1386 LEU Chi-restraints excluded: chain A residue 1393 MET Chi-restraints excluded: chain A residue 1426 LEU Chi-restraints excluded: chain A residue 1437 LEU Chi-restraints excluded: chain A residue 1443 GLN Chi-restraints excluded: chain A residue 1455 SER Chi-restraints excluded: chain A residue 1488 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 53 optimal weight: 0.9990 chunk 80 optimal weight: 6.9990 chunk 40 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 chunk 85 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 66 optimal weight: 10.0000 chunk 12 optimal weight: 8.9990 chunk 106 optimal weight: 0.8980 chunk 122 optimal weight: 6.9990 chunk 129 optimal weight: 6.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 118 GLN A 122 GLN A1371 HIS A1443 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7108 moved from start: 0.5540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11350 Z= 0.221 Angle : 0.668 14.320 15389 Z= 0.339 Chirality : 0.041 0.259 1805 Planarity : 0.004 0.047 1909 Dihedral : 6.568 59.950 1521 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 5.80 % Allowed : 25.95 % Favored : 68.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.23), residues: 1392 helix: 1.29 (0.17), residues: 938 sheet: -0.30 (0.63), residues: 67 loop : -0.75 (0.30), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 646 HIS 0.004 0.001 HIS A1178 PHE 0.034 0.001 PHE A1348 TYR 0.018 0.001 TYR A 565 ARG 0.004 0.000 ARG A1318 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 181 time to evaluate : 1.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 LYS cc_start: 0.8832 (OUTLIER) cc_final: 0.7950 (pptt) REVERT: A 101 TYR cc_start: 0.6140 (OUTLIER) cc_final: 0.5823 (t80) REVERT: A 112 LEU cc_start: 0.8962 (mt) cc_final: 0.8643 (tp) REVERT: A 312 LYS cc_start: 0.8601 (OUTLIER) cc_final: 0.8373 (mptt) REVERT: A 419 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.6104 (tm-30) REVERT: A 766 LYS cc_start: 0.7698 (pttm) cc_final: 0.7411 (pttp) REVERT: A 834 LEU cc_start: 0.7025 (tt) cc_final: 0.6797 (pp) REVERT: A 980 PHE cc_start: 0.7515 (OUTLIER) cc_final: 0.7212 (t80) REVERT: A 982 ILE cc_start: 0.9242 (mt) cc_final: 0.8824 (mt) REVERT: A 1045 SER cc_start: 0.8926 (m) cc_final: 0.8537 (t) REVERT: A 1149 ARG cc_start: 0.6943 (OUTLIER) cc_final: 0.6738 (ptm160) outliers start: 72 outliers final: 53 residues processed: 232 average time/residue: 0.2130 time to fit residues: 74.4450 Evaluate side-chains 234 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 175 time to evaluate : 1.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LYS Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 101 TYR Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 130 TRP Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain A residue 333 ASP Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 409 ASN Chi-restraints excluded: chain A residue 419 GLU Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 648 HIS Chi-restraints excluded: chain A residue 980 PHE Chi-restraints excluded: chain A residue 990 SER Chi-restraints excluded: chain A residue 1032 LEU Chi-restraints excluded: chain A residue 1050 VAL Chi-restraints excluded: chain A residue 1064 ILE Chi-restraints excluded: chain A residue 1094 THR Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1143 SER Chi-restraints excluded: chain A residue 1149 ARG Chi-restraints excluded: chain A residue 1164 SER Chi-restraints excluded: chain A residue 1217 LEU Chi-restraints excluded: chain A residue 1273 THR Chi-restraints excluded: chain A residue 1278 VAL Chi-restraints excluded: chain A residue 1285 VAL Chi-restraints excluded: chain A residue 1287 ASP Chi-restraints excluded: chain A residue 1344 THR Chi-restraints excluded: chain A residue 1350 ILE Chi-restraints excluded: chain A residue 1358 ILE Chi-restraints excluded: chain A residue 1365 ILE Chi-restraints excluded: chain A residue 1371 HIS Chi-restraints excluded: chain A residue 1386 LEU Chi-restraints excluded: chain A residue 1393 MET Chi-restraints excluded: chain A residue 1426 LEU Chi-restraints excluded: chain A residue 1443 GLN Chi-restraints excluded: chain A residue 1455 SER Chi-restraints excluded: chain A residue 1488 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 117 optimal weight: 6.9990 chunk 125 optimal weight: 3.9990 chunk 129 optimal weight: 3.9990 chunk 75 optimal weight: 20.0000 chunk 54 optimal weight: 1.9990 chunk 98 optimal weight: 0.7980 chunk 38 optimal weight: 3.9990 chunk 113 optimal weight: 0.9980 chunk 118 optimal weight: 30.0000 chunk 82 optimal weight: 3.9990 chunk 132 optimal weight: 4.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1371 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7155 moved from start: 0.5508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 11350 Z= 0.310 Angle : 0.720 14.384 15389 Z= 0.365 Chirality : 0.043 0.260 1805 Planarity : 0.004 0.046 1909 Dihedral : 6.616 59.987 1519 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 6.29 % Allowed : 25.79 % Favored : 67.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.22), residues: 1392 helix: 1.12 (0.17), residues: 942 sheet: -0.43 (0.61), residues: 67 loop : -0.79 (0.30), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 208 HIS 0.006 0.001 HIS A1051 PHE 0.036 0.002 PHE A1348 TYR 0.024 0.002 TYR A 565 ARG 0.003 0.000 ARG A1374 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 176 time to evaluate : 1.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 LYS cc_start: 0.8855 (OUTLIER) cc_final: 0.7975 (pptt) REVERT: A 101 TYR cc_start: 0.6211 (OUTLIER) cc_final: 0.5894 (t80) REVERT: A 112 LEU cc_start: 0.8997 (mt) cc_final: 0.8658 (tp) REVERT: A 312 LYS cc_start: 0.8653 (OUTLIER) cc_final: 0.8418 (mptt) REVERT: A 419 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.6161 (tm-30) REVERT: A 744 GLU cc_start: 0.8184 (mm-30) cc_final: 0.7769 (mm-30) REVERT: A 766 LYS cc_start: 0.7801 (pttm) cc_final: 0.7424 (pttp) REVERT: A 827 GLN cc_start: 0.6404 (tm-30) cc_final: 0.6144 (tm-30) REVERT: A 834 LEU cc_start: 0.6955 (tt) cc_final: 0.6730 (pp) REVERT: A 980 PHE cc_start: 0.7566 (OUTLIER) cc_final: 0.7281 (t80) REVERT: A 982 ILE cc_start: 0.9308 (mt) cc_final: 0.8990 (mt) REVERT: A 1149 ARG cc_start: 0.7057 (OUTLIER) cc_final: 0.6729 (ptm160) REVERT: A 1258 MET cc_start: 0.8059 (mmt) cc_final: 0.7678 (mmm) outliers start: 78 outliers final: 65 residues processed: 233 average time/residue: 0.2079 time to fit residues: 72.1458 Evaluate side-chains 241 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 170 time to evaluate : 1.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LYS Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 101 TYR Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 130 TRP Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 311 MET Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 333 ASP Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 409 ASN Chi-restraints excluded: chain A residue 419 GLU Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 648 HIS Chi-restraints excluded: chain A residue 710 ILE Chi-restraints excluded: chain A residue 859 LEU Chi-restraints excluded: chain A residue 980 PHE Chi-restraints excluded: chain A residue 990 SER Chi-restraints excluded: chain A residue 1032 LEU Chi-restraints excluded: chain A residue 1050 VAL Chi-restraints excluded: chain A residue 1064 ILE Chi-restraints excluded: chain A residue 1094 THR Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1135 VAL Chi-restraints excluded: chain A residue 1143 SER Chi-restraints excluded: chain A residue 1149 ARG Chi-restraints excluded: chain A residue 1188 VAL Chi-restraints excluded: chain A residue 1217 LEU Chi-restraints excluded: chain A residue 1218 THR Chi-restraints excluded: chain A residue 1273 THR Chi-restraints excluded: chain A residue 1278 VAL Chi-restraints excluded: chain A residue 1285 VAL Chi-restraints excluded: chain A residue 1287 ASP Chi-restraints excluded: chain A residue 1323 ASP Chi-restraints excluded: chain A residue 1344 THR Chi-restraints excluded: chain A residue 1350 ILE Chi-restraints excluded: chain A residue 1358 ILE Chi-restraints excluded: chain A residue 1365 ILE Chi-restraints excluded: chain A residue 1371 HIS Chi-restraints excluded: chain A residue 1379 ILE Chi-restraints excluded: chain A residue 1386 LEU Chi-restraints excluded: chain A residue 1393 MET Chi-restraints excluded: chain A residue 1426 LEU Chi-restraints excluded: chain A residue 1443 GLN Chi-restraints excluded: chain A residue 1455 SER Chi-restraints excluded: chain A residue 1488 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 81 optimal weight: 4.9990 chunk 63 optimal weight: 9.9990 chunk 92 optimal weight: 3.9990 chunk 139 optimal weight: 10.0000 chunk 128 optimal weight: 0.9990 chunk 111 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 85 optimal weight: 0.6980 chunk 68 optimal weight: 0.3980 chunk 88 optimal weight: 0.6980 chunk 118 optimal weight: 20.0000 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 118 GLN A1371 HIS A1443 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7089 moved from start: 0.5780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11350 Z= 0.201 Angle : 0.680 15.741 15389 Z= 0.343 Chirality : 0.041 0.301 1805 Planarity : 0.004 0.047 1909 Dihedral : 6.497 59.567 1519 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 4.19 % Allowed : 28.12 % Favored : 67.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.23), residues: 1392 helix: 1.34 (0.17), residues: 949 sheet: -0.57 (0.61), residues: 68 loop : -0.85 (0.30), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 208 HIS 0.007 0.001 HIS A1371 PHE 0.036 0.001 PHE A1348 TYR 0.016 0.001 TYR A 565 ARG 0.007 0.000 ARG A1449 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 185 time to evaluate : 1.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 LYS cc_start: 0.8830 (OUTLIER) cc_final: 0.8017 (pptt) REVERT: A 112 LEU cc_start: 0.8947 (mt) cc_final: 0.8607 (tp) REVERT: A 312 LYS cc_start: 0.8613 (OUTLIER) cc_final: 0.8389 (mptt) REVERT: A 419 GLU cc_start: 0.7669 (OUTLIER) cc_final: 0.6098 (tm-30) REVERT: A 744 GLU cc_start: 0.8159 (mm-30) cc_final: 0.7764 (mm-30) REVERT: A 827 GLN cc_start: 0.6266 (tm-30) cc_final: 0.6002 (tm-30) REVERT: A 834 LEU cc_start: 0.7007 (tt) cc_final: 0.6785 (pp) REVERT: A 980 PHE cc_start: 0.7465 (OUTLIER) cc_final: 0.7156 (t80) REVERT: A 982 ILE cc_start: 0.9234 (mt) cc_final: 0.8826 (mt) REVERT: A 1045 SER cc_start: 0.8903 (m) cc_final: 0.8590 (t) outliers start: 52 outliers final: 45 residues processed: 223 average time/residue: 0.2306 time to fit residues: 75.3243 Evaluate side-chains 221 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 172 time to evaluate : 1.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LYS Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 130 TRP Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 333 ASP Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 409 ASN Chi-restraints excluded: chain A residue 419 GLU Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 648 HIS Chi-restraints excluded: chain A residue 980 PHE Chi-restraints excluded: chain A residue 990 SER Chi-restraints excluded: chain A residue 1032 LEU Chi-restraints excluded: chain A residue 1064 ILE Chi-restraints excluded: chain A residue 1094 THR Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1143 SER Chi-restraints excluded: chain A residue 1188 VAL Chi-restraints excluded: chain A residue 1217 LEU Chi-restraints excluded: chain A residue 1278 VAL Chi-restraints excluded: chain A residue 1285 VAL Chi-restraints excluded: chain A residue 1287 ASP Chi-restraints excluded: chain A residue 1344 THR Chi-restraints excluded: chain A residue 1350 ILE Chi-restraints excluded: chain A residue 1358 ILE Chi-restraints excluded: chain A residue 1365 ILE Chi-restraints excluded: chain A residue 1371 HIS Chi-restraints excluded: chain A residue 1379 ILE Chi-restraints excluded: chain A residue 1426 LEU Chi-restraints excluded: chain A residue 1443 GLN Chi-restraints excluded: chain A residue 1455 SER Chi-restraints excluded: chain A residue 1488 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 34 optimal weight: 2.9990 chunk 102 optimal weight: 0.5980 chunk 16 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 111 optimal weight: 0.0570 chunk 46 optimal weight: 5.9990 chunk 114 optimal weight: 6.9990 chunk 14 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 97 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN A1304 ASN A1371 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.160720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.119932 restraints weight = 21097.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.119529 restraints weight = 10941.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.120201 restraints weight = 8199.386| |-----------------------------------------------------------------------------| r_work (final): 0.3795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.5995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11350 Z= 0.188 Angle : 0.693 15.875 15389 Z= 0.345 Chirality : 0.041 0.323 1805 Planarity : 0.004 0.048 1909 Dihedral : 6.253 58.621 1517 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.95 % Allowed : 29.09 % Favored : 66.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.23), residues: 1392 helix: 1.43 (0.17), residues: 949 sheet: -0.42 (0.63), residues: 63 loop : -0.82 (0.30), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1206 HIS 0.006 0.001 HIS A1371 PHE 0.039 0.001 PHE A1348 TYR 0.014 0.001 TYR A 565 ARG 0.004 0.000 ARG A1449 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2439.23 seconds wall clock time: 45 minutes 15.41 seconds (2715.41 seconds total)