Starting phenix.real_space_refine on Sun Apr 7 03:27:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f4b_28854/04_2024/8f4b_28854_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f4b_28854/04_2024/8f4b_28854.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f4b_28854/04_2024/8f4b_28854.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f4b_28854/04_2024/8f4b_28854.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f4b_28854/04_2024/8f4b_28854_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f4b_28854/04_2024/8f4b_28854_updated.pdb" } resolution = 3.27 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= 0.003 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 48 5.16 5 C 6140 2.51 5 N 1585 2.21 5 O 1714 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 544": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 594": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 632": "NH1" <-> "NH2" Residue "A ASP 657": "OD1" <-> "OD2" Residue "A ARG 723": "NH1" <-> "NH2" Residue "A ARG 730": "NH1" <-> "NH2" Residue "A ARG 758": "NH1" <-> "NH2" Residue "A ARG 780": "NH1" <-> "NH2" Residue "A ARG 1065": "NH1" <-> "NH2" Residue "A PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1203": "OE1" <-> "OE2" Residue "A ARG 1221": "NH1" <-> "NH2" Residue "A TYR 1235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1262": "NH1" <-> "NH2" Residue "A GLU 1270": "OE1" <-> "OE2" Residue "A ARG 1291": "NH1" <-> "NH2" Residue "A ARG 1295": "NH1" <-> "NH2" Residue "A ARG 1300": "NH1" <-> "NH2" Residue "A GLU 1349": "OE1" <-> "OE2" Residue "A ARG 1366": "NH1" <-> "NH2" Residue "A ARG 1384": "NH1" <-> "NH2" Residue "A PHE 1410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1434": "NH1" <-> "NH2" Residue "A ARG 1441": "NH1" <-> "NH2" Residue "A GLU 1454": "OE1" <-> "OE2" Residue "A ARG 1486": "NH1" <-> "NH2" Residue "A ARG 1495": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 9487 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 9323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1182, 9323 Classifications: {'peptide': 1182} Link IDs: {'PTRANS': 41, 'TRANS': 1140} Chain breaks: 3 Chain: "B" Number of atoms: 164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 164 Unusual residues: {'ACE': 1} Classifications: {'peptide': 17, 'undetermined': 1} Modifications used: {'PEPT-D': 1} Link IDs: {'TRANS': 16, None: 1} Not linked: pdbres="CYS B 17 " pdbres="ACE B 18 " Time building chain proxies: 5.71, per 1000 atoms: 0.60 Number of scatterers: 9487 At special positions: 0 Unit cell: (147.29, 112.27, 84.46, 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 48 16.00 O 1714 8.00 N 1585 7.00 C 6140 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.73 Conformation dependent library (CDL) restraints added in 2.0 seconds 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DTY B 1 " Number of C-beta restraints generated: 2258 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 45 helices and 5 sheets defined 61.8% alpha, 5.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.91 Creating SS restraints... Processing helix chain 'A' and resid 215 through 220 Processing helix chain 'A' and resid 222 through 233 removed outlier: 4.495A pdb=" N GLY A 226 " --> pdb=" O TRP A 223 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VAL A 229 " --> pdb=" O GLY A 226 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLN A 230 " --> pdb=" O MET A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 267 Proline residue: A 255 - end of helix removed outlier: 3.831A pdb=" N LYS A 267 " --> pdb=" O LYS A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 339 removed outlier: 4.122A pdb=" N MET A 327 " --> pdb=" O PRO A 323 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N SER A 328 " --> pdb=" O TYR A 324 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N PHE A 329 " --> pdb=" O PHE A 325 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N LEU A 330 " --> pdb=" O LEU A 326 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE A 331 " --> pdb=" O MET A 327 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU A 337 " --> pdb=" O ALA A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 354 removed outlier: 3.686A pdb=" N LEU A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 409 removed outlier: 3.521A pdb=" N PHE A 365 " --> pdb=" O GLN A 362 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU A 370 " --> pdb=" O THR A 367 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ILE A 372 " --> pdb=" O LEU A 369 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER A 373 " --> pdb=" O LEU A 370 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU A 376 " --> pdb=" O SER A 373 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLN A 377 " --> pdb=" O ALA A 374 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N THR A 378 " --> pdb=" O CYS A 375 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU A 379 " --> pdb=" O LEU A 376 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL A 380 " --> pdb=" O GLN A 377 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU A 381 " --> pdb=" O THR A 378 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N PHE A 385 " --> pdb=" O HIS A 382 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ILE A 387 " --> pdb=" O TYR A 384 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N VAL A 390 " --> pdb=" O ILE A 387 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER A 391 " --> pdb=" O CYS A 388 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLY A 392 " --> pdb=" O PHE A 389 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG A 394 " --> pdb=" O SER A 391 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N THR A 397 " --> pdb=" O ARG A 394 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ILE A 400 " --> pdb=" O THR A 397 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL A 403 " --> pdb=" O ILE A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 415 No H-bonds generated for 'chain 'A' and resid 412 through 415' Processing helix chain 'A' and resid 420 through 428 Processing helix chain 'A' and resid 430 through 461 removed outlier: 3.595A pdb=" N PHE A 434 " --> pdb=" O ASP A 430 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N MET A 435 " --> pdb=" O ALA A 431 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASP A 436 " --> pdb=" O GLN A 432 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA A 438 " --> pdb=" O PHE A 434 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N THR A 439 " --> pdb=" O MET A 435 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR A 440 " --> pdb=" O ASP A 436 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N ASN A 442 " --> pdb=" O ALA A 438 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N MET A 443 " --> pdb=" O THR A 439 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ILE A 444 " --> pdb=" O TYR A 440 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N TRP A 445 " --> pdb=" O ILE A 441 " (cutoff:3.500A) Proline residue: A 448 - end of helix Processing helix chain 'A' and resid 464 through 510 removed outlier: 3.828A pdb=" N ALA A 471 " --> pdb=" O ALA A 468 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N MET A 473 " --> pdb=" O VAL A 470 " (cutoff:3.500A) Proline residue: A 478 - end of helix removed outlier: 3.564A pdb=" N VAL A 482 " --> pdb=" O LEU A 479 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N MET A 483 " --> pdb=" O ASN A 480 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N THR A 487 " --> pdb=" O ALA A 484 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR A 489 " --> pdb=" O LYS A 486 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL A 492 " --> pdb=" O THR A 489 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LYS A 496 " --> pdb=" O ALA A 493 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASP A 499 " --> pdb=" O LYS A 496 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASN A 500 " --> pdb=" O SER A 497 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LYS A 503 " --> pdb=" O ASN A 500 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASN A 506 " --> pdb=" O LYS A 503 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU A 509 " --> pdb=" O ASN A 506 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASN A 510 " --> pdb=" O GLU A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 518 removed outlier: 3.749A pdb=" N LEU A 517 " --> pdb=" O LYS A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 571 removed outlier: 3.665A pdb=" N ILE A 531 " --> pdb=" O LYS A 527 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLU A 534 " --> pdb=" O ALA A 530 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N VAL A 538 " --> pdb=" O GLU A 534 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL A 548 " --> pdb=" O TYR A 544 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TRP A 553 " --> pdb=" O GLY A 549 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL A 554 " --> pdb=" O THR A 550 " (cutoff:3.500A) Proline residue: A 557 - end of helix removed outlier: 3.623A pdb=" N ALA A 561 " --> pdb=" O PRO A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 620 removed outlier: 4.193A pdb=" N VAL A 584 " --> pdb=" O GLN A 580 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N PHE A 594 " --> pdb=" O ASN A 590 " (cutoff:3.500A) Proline residue: A 595 - end of helix Proline residue: A 600 - end of helix Processing helix chain 'A' and resid 627 through 629 No H-bonds generated for 'chain 'A' and resid 627 through 629' Processing helix chain 'A' and resid 684 through 691 removed outlier: 4.442A pdb=" N LEU A 688 " --> pdb=" O LYS A 684 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N SER A 689 " --> pdb=" O SER A 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 722 through 727 Processing helix chain 'A' and resid 734 through 743 Processing helix chain 'A' and resid 747 through 750 No H-bonds generated for 'chain 'A' and resid 747 through 750' Processing helix chain 'A' and resid 762 through 764 No H-bonds generated for 'chain 'A' and resid 762 through 764' Processing helix chain 'A' and resid 770 through 784 Processing helix chain 'A' and resid 800 through 809 removed outlier: 3.506A pdb=" N HIS A 805 " --> pdb=" O HIS A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 834 No H-bonds generated for 'chain 'A' and resid 832 through 834' Processing helix chain 'A' and resid 852 through 857 Processing helix chain 'A' and resid 861 through 866 Processing helix chain 'A' and resid 959 through 969 Processing helix chain 'A' and resid 971 through 998 Processing helix chain 'A' and resid 1012 through 1056 removed outlier: 3.553A pdb=" N GLY A1022 " --> pdb=" O TYR A1018 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR A1028 " --> pdb=" O SER A1024 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE A1041 " --> pdb=" O SER A1037 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU A1056 " --> pdb=" O LEU A1052 " (cutoff:3.500A) Processing helix chain 'A' and resid 1060 through 1065 Processing helix chain 'A' and resid 1068 through 1110 removed outlier: 3.506A pdb=" N PHE A1075 " --> pdb=" O LEU A1071 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N LEU A1079 " --> pdb=" O PHE A1075 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASP A1080 " --> pdb=" O SER A1076 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N ILE A1086 " --> pdb=" O VAL A1082 " (cutoff:3.500A) Proline residue: A1087 - end of helix removed outlier: 3.937A pdb=" N LYS A1091 " --> pdb=" O PRO A1087 " (cutoff:3.500A) Processing helix chain 'A' and resid 1112 through 1146 Proline residue: A1119 - end of helix removed outlier: 3.542A pdb=" N GLY A1122 " --> pdb=" O PRO A1119 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU A1123 " --> pdb=" O PRO A1120 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE A1126 " --> pdb=" O LEU A1123 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL A1128 " --> pdb=" O TYR A1125 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLN A1129 " --> pdb=" O PHE A1126 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N PHE A1131 " --> pdb=" O VAL A1128 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N VAL A1133 " --> pdb=" O ARG A1130 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA A1134 " --> pdb=" O PHE A1131 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N SER A1136 " --> pdb=" O VAL A1133 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ARG A1137 " --> pdb=" O ALA A1134 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS A1140 " --> pdb=" O ARG A1137 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL A1145 " --> pdb=" O LEU A1142 " (cutoff:3.500A) Processing helix chain 'A' and resid 1148 through 1159 Processing helix chain 'A' and resid 1161 through 1166 Processing helix chain 'A' and resid 1170 through 1219 removed outlier: 3.522A pdb=" N LYS A1180 " --> pdb=" O GLN A1176 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ALA A1187 " --> pdb=" O GLU A1183 " (cutoff:3.500A) Proline residue: A1190 - end of helix removed outlier: 3.726A pdb=" N ASN A1195 " --> pdb=" O SER A1191 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL A1218 " --> pdb=" O SER A1214 " (cutoff:3.500A) Processing helix chain 'A' and resid 1226 through 1263 removed outlier: 3.890A pdb=" N GLN A1238 " --> pdb=" O SER A1234 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL A1239 " --> pdb=" O TYR A1235 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N THR A1240 " --> pdb=" O SER A1236 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N THR A1241 " --> pdb=" O LEU A1237 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N TYR A1242 " --> pdb=" O GLN A1238 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASN A1244 " --> pdb=" O THR A1240 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TRP A1245 " --> pdb=" O THR A1241 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N VAL A1258 " --> pdb=" O GLU A1254 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ALA A1259 " --> pdb=" O THR A1255 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N VAL A1260 " --> pdb=" O ASN A1256 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU A1261 " --> pdb=" O ILE A1257 " (cutoff:3.500A) Processing helix chain 'A' and resid 1265 through 1267 No H-bonds generated for 'chain 'A' and resid 1265 through 1267' Processing helix chain 'A' and resid 1286 through 1288 No H-bonds generated for 'chain 'A' and resid 1286 through 1288' Processing helix chain 'A' and resid 1333 through 1339 removed outlier: 3.602A pdb=" N GLY A1338 " --> pdb=" O LEU A1335 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU A1339 " --> pdb=" O THR A1336 " (cutoff:3.500A) Processing helix chain 'A' and resid 1362 through 1368 removed outlier: 3.899A pdb=" N LYS A1368 " --> pdb=" O ASP A1364 " (cutoff:3.500A) Processing helix chain 'A' and resid 1383 through 1387 Processing helix chain 'A' and resid 1395 through 1404 Processing helix chain 'A' and resid 1431 through 1445 removed outlier: 3.905A pdb=" N GLN A1435 " --> pdb=" O VAL A1431 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU A1436 " --> pdb=" O GLY A1432 " (cutoff:3.500A) Processing helix chain 'A' and resid 1463 through 1474 removed outlier: 3.680A pdb=" N THR A1473 " --> pdb=" O SER A1469 " (cutoff:3.500A) Processing helix chain 'A' and resid 1487 through 1491 Processing helix chain 'A' and resid 1510 through 1516 removed outlier: 3.644A pdb=" N GLN A1515 " --> pdb=" O SER A1511 " (cutoff:3.500A) Processing helix chain 'A' and resid 1519 through 1527 Processing sheet with id= A, first strand: chain 'A' and resid 644 through 647 Processing sheet with id= B, first strand: chain 'A' and resid 846 through 851 removed outlier: 7.128A pdb=" N VAL A 840 " --> pdb=" O SER A 847 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N MET A 849 " --> pdb=" O ILE A 838 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ILE A 838 " --> pdb=" O MET A 849 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL A 837 " --> pdb=" O LEU A 673 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ARG A 822 " --> pdb=" O VAL A 674 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N VAL A 676 " --> pdb=" O ARG A 822 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N LEU A 824 " --> pdb=" O VAL A 676 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N TYR A 789 " --> pdb=" O LEU A 823 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N VAL A 825 " --> pdb=" O TYR A 789 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N LEU A 791 " --> pdb=" O VAL A 825 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 1314 through 1316 Processing sheet with id= D, first strand: chain 'A' and resid 1506 through 1508 removed outlier: 3.708A pdb=" N ARG A1495 " --> pdb=" O LYS A1321 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N VAL A1480 " --> pdb=" O VAL A1322 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N ILE A1324 " --> pdb=" O VAL A1480 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N THR A1482 " --> pdb=" O ILE A1324 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU A1452 " --> pdb=" O LEU A1481 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N THR A1370 " --> pdb=" O VAL A1451 " (cutoff:3.500A) removed outlier: 8.646A pdb=" N ASP A1453 " --> pdb=" O THR A1370 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ILE A1372 " --> pdb=" O ASP A1453 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 661 through 664 removed outlier: 6.181A pdb=" N ALA A 649 " --> pdb=" O GLY A 663 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N GLU A 699 " --> pdb=" O THR A 650 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N THR A 652 " --> pdb=" O LYS A 697 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N LYS A 697 " --> pdb=" O THR A 652 " (cutoff:3.500A) 468 hydrogen bonds defined for protein. 1146 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: 3.31 Time building geometry restraints manager: 3.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1767 1.33 - 1.45: 2318 1.45 - 1.58: 5522 1.58 - 1.70: 0 1.70 - 1.82: 80 Bond restraints: 9687 Sorted by residual: bond pdb=" N GLN A 234 " pdb=" CA GLN A 234 " ideal model delta sigma weight residual 1.453 1.490 -0.037 8.30e-03 1.45e+04 2.02e+01 bond pdb=" N THR A 556 " pdb=" CA THR A 556 " ideal model delta sigma weight residual 1.462 1.495 -0.033 7.70e-03 1.69e+04 1.84e+01 bond pdb=" N ILE A 829 " pdb=" CA ILE A 829 " ideal model delta sigma weight residual 1.455 1.497 -0.042 1.04e-02 9.25e+03 1.59e+01 bond pdb=" N VAL A 668 " pdb=" CA VAL A 668 " ideal model delta sigma weight residual 1.460 1.495 -0.035 9.30e-03 1.16e+04 1.42e+01 bond pdb=" N ILE A1369 " pdb=" CA ILE A1369 " ideal model delta sigma weight residual 1.457 1.499 -0.043 1.15e-02 7.56e+03 1.37e+01 ... (remaining 9682 not shown) Histogram of bond angle deviations from ideal: 100.19 - 107.06: 269 107.06 - 113.94: 5389 113.94 - 120.81: 4226 120.81 - 127.68: 3181 127.68 - 134.55: 71 Bond angle restraints: 13136 Sorted by residual: angle pdb=" C MET A 476 " pdb=" N VAL A 477 " pdb=" CA VAL A 477 " ideal model delta sigma weight residual 120.33 125.50 -5.17 8.00e-01 1.56e+00 4.18e+01 angle pdb=" C ILE A1360 " pdb=" N GLY A1361 " pdb=" CA GLY A1361 " ideal model delta sigma weight residual 120.10 125.65 -5.55 9.50e-01 1.11e+00 3.41e+01 angle pdb=" C LYS A1408 " pdb=" N GLY A1409 " pdb=" CA GLY A1409 " ideal model delta sigma weight residual 120.03 125.87 -5.84 1.12e+00 7.97e-01 2.72e+01 angle pdb=" CA GLY A 700 " pdb=" C GLY A 700 " pdb=" O GLY A 700 " ideal model delta sigma weight residual 122.37 118.61 3.76 7.30e-01 1.88e+00 2.65e+01 angle pdb=" C GLN A1025 " pdb=" N GLY A1026 " pdb=" CA GLY A1026 " ideal model delta sigma weight residual 119.98 125.56 -5.58 1.11e+00 8.12e-01 2.53e+01 ... (remaining 13131 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.79: 5203 15.79 - 31.58: 456 31.58 - 47.37: 104 47.37 - 63.15: 17 63.15 - 78.94: 3 Dihedral angle restraints: 5783 sinusoidal: 2290 harmonic: 3493 Sorted by residual: dihedral pdb=" CA TYR A 318 " pdb=" C TYR A 318 " pdb=" N LYS A 319 " pdb=" CA LYS A 319 " ideal model delta harmonic sigma weight residual 180.00 154.66 25.34 0 5.00e+00 4.00e-02 2.57e+01 dihedral pdb=" CA ASN B 5 " pdb=" C ASN B 5 " pdb=" N LEU B 6 " pdb=" CA LEU B 6 " ideal model delta harmonic sigma weight residual 180.00 160.46 19.54 0 5.00e+00 4.00e-02 1.53e+01 dihedral pdb=" CA VAL A 810 " pdb=" C VAL A 810 " pdb=" N ILE A 811 " pdb=" CA ILE A 811 " ideal model delta harmonic sigma weight residual -180.00 -160.91 -19.09 0 5.00e+00 4.00e-02 1.46e+01 ... (remaining 5780 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 499 0.045 - 0.089: 468 0.089 - 0.134: 390 0.134 - 0.179: 143 0.179 - 0.223: 24 Chirality restraints: 1524 Sorted by residual: chirality pdb=" CA ILE A1003 " pdb=" N ILE A1003 " pdb=" C ILE A1003 " pdb=" CB ILE A1003 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CA ILE A1316 " pdb=" N ILE A1316 " pdb=" C ILE A1316 " pdb=" CB ILE A1316 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CA ILE A 839 " pdb=" N ILE A 839 " pdb=" C ILE A 839 " pdb=" CB ILE A 839 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.21 2.00e-01 2.50e+01 1.13e+00 ... (remaining 1521 not shown) Planarity restraints: 1640 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 558 " 0.020 2.00e-02 2.50e+03 1.34e-02 3.13e+00 pdb=" CG PHE A 558 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 PHE A 558 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE A 558 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE A 558 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 558 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE A 558 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 553 " 0.011 2.00e-02 2.50e+03 7.16e-03 1.28e+00 pdb=" CG TRP A 553 " -0.019 2.00e-02 2.50e+03 pdb=" CD1 TRP A 553 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 TRP A 553 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 553 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 553 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 553 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 553 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 553 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 553 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A1125 " -0.013 2.00e-02 2.50e+03 7.94e-03 1.26e+00 pdb=" CG TYR A1125 " 0.018 2.00e-02 2.50e+03 pdb=" CD1 TYR A1125 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR A1125 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A1125 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A1125 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR A1125 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR A1125 " -0.003 2.00e-02 2.50e+03 ... (remaining 1637 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 1055 2.80 - 3.33: 9937 3.33 - 3.85: 13547 3.85 - 4.38: 18465 4.38 - 4.90: 30113 Nonbonded interactions: 73117 Sorted by model distance: nonbonded pdb=" OE2 GLU A1203 " pdb=" OH TYR B 10 " model vdw 2.278 2.440 nonbonded pdb=" OG1 THR A 378 " pdb=" OE1 GLU A1203 " model vdw 2.417 2.440 nonbonded pdb=" O THR A 552 " pdb=" OG1 THR A 556 " model vdw 2.457 2.440 nonbonded pdb=" O SER B 15 " pdb=" C THR B 16 " model vdw 2.498 3.270 nonbonded pdb=" OG1 THR A1370 " pdb=" OG1 THR A1447 " model vdw 2.519 2.440 ... (remaining 73112 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.830 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: 0.000 Extract box with map and model: 7.840 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 30.060 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6460 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 : 0.014 0.057 9687 Z= 0.895 Angle : 1.820 10.754 13136 Z= 1.395 Chirality : 0.087 0.223 1524 Planarity : 0.003 0.015 1640 Dihedral : 12.695 78.943 3525 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 1.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 0.10 % Allowed : 1.82 % Favored : 98.09 % 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: -2.97 (0.20), residues: 1188 helix: -1.63 (0.15), residues: 719 sheet: -0.85 (0.57), residues: 77 loop : -2.57 (0.26), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 553 HIS 0.007 0.002 HIS A 386 PHE 0.027 0.002 PHE A 558 TYR 0.018 0.002 TYR A1125 ARG 0.005 0.001 ARG A1165 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 221 time to evaluate : 1.060 Fit side-chains REVERT: A 239 THR cc_start: 0.7804 (m) cc_final: 0.7536 (p) REVERT: A 240 ASP cc_start: 0.6114 (m-30) cc_final: 0.5508 (m-30) REVERT: A 246 LYS cc_start: 0.7414 (mttt) cc_final: 0.6576 (tppt) REVERT: A 247 GLU cc_start: 0.7549 (mm-30) cc_final: 0.7267 (pm20) REVERT: A 251 GLU cc_start: 0.7595 (mt-10) cc_final: 0.7322 (pt0) REVERT: A 344 GLU cc_start: 0.6014 (mt-10) cc_final: 0.5615 (tt0) REVERT: A 356 LYS cc_start: 0.6995 (mttt) cc_final: 0.6527 (mmtt) REVERT: A 357 LYS cc_start: 0.7868 (mttt) cc_final: 0.7294 (mmtm) REVERT: A 444 ILE cc_start: 0.8361 (tt) cc_final: 0.7788 (pt) REVERT: A 485 MET cc_start: 0.5349 (ttp) cc_final: 0.5007 (mmt) REVERT: A 496 LYS cc_start: 0.7138 (mmtt) cc_final: 0.6765 (mtmt) REVERT: A 503 LYS cc_start: 0.6579 (tttm) cc_final: 0.6185 (ptmt) REVERT: A 534 GLU cc_start: 0.7467 (tt0) cc_final: 0.7106 (mt-10) REVERT: A 617 ARG cc_start: 0.6637 (ttp80) cc_final: 0.6015 (ttm110) REVERT: A 652 THR cc_start: 0.7704 (p) cc_final: 0.7487 (p) REVERT: A 685 SER cc_start: 0.8391 (t) cc_final: 0.8184 (m) REVERT: A 695 MET cc_start: 0.8381 (mtp) cc_final: 0.8106 (mtm) REVERT: A 699 GLU cc_start: 0.7327 (mt-10) cc_final: 0.6948 (pp20) REVERT: A 738 LYS cc_start: 0.7715 (tttp) cc_final: 0.7457 (mmmt) REVERT: A 751 GLU cc_start: 0.7437 (tp30) cc_final: 0.7165 (mt-10) REVERT: A 758 ARG cc_start: 0.7384 (ptt180) cc_final: 0.7047 (mtm-85) REVERT: A 764 LYS cc_start: 0.7570 (tptt) cc_final: 0.7247 (mtpp) REVERT: A 783 TYR cc_start: 0.7672 (t80) cc_final: 0.7385 (t80) REVERT: A 784 CYS cc_start: 0.8381 (t) cc_final: 0.8026 (m) REVERT: A 804 LYS cc_start: 0.7899 (mttt) cc_final: 0.7690 (mttm) REVERT: A 808 GLU cc_start: 0.8119 (tt0) cc_final: 0.7725 (tm-30) REVERT: A 814 LYS cc_start: 0.8661 (mtpp) cc_final: 0.8416 (mtpp) REVERT: A 864 GLU cc_start: 0.7667 (mt-10) cc_final: 0.7449 (mm-30) REVERT: A 971 LEU cc_start: 0.6895 (mp) cc_final: 0.6695 (mm) REVERT: A 972 PHE cc_start: 0.7227 (t80) cc_final: 0.6901 (t80) REVERT: A 1080 ASP cc_start: 0.7113 (t70) cc_final: 0.6839 (m-30) REVERT: A 1098 PHE cc_start: 0.7837 (m-80) cc_final: 0.7593 (m-80) REVERT: A 1113 MET cc_start: 0.7015 (mtp) cc_final: 0.6283 (mmm) REVERT: A 1133 VAL cc_start: 0.7723 (t) cc_final: 0.7317 (m) REVERT: A 1176 GLN cc_start: 0.6669 (tp40) cc_final: 0.5954 (mt0) REVERT: A 1252 GLU cc_start: 0.6422 (tp30) cc_final: 0.5831 (mt-10) REVERT: A 1310 LYS cc_start: 0.6439 (tttp) cc_final: 0.6158 (tptt) REVERT: A 1343 LYS cc_start: 0.6628 (mttm) cc_final: 0.6316 (mmtm) REVERT: A 1368 LYS cc_start: 0.8129 (mmtp) cc_final: 0.7453 (mmmt) REVERT: A 1377 VAL cc_start: 0.6954 (m) cc_final: 0.6691 (p) REVERT: A 1385 MET cc_start: 0.6371 (tmm) cc_final: 0.5344 (mmp) REVERT: A 1498 VAL cc_start: 0.6292 (t) cc_final: 0.5949 (p) REVERT: A 1505 GLN cc_start: 0.6907 (mm110) cc_final: 0.6698 (mp10) outliers start: 1 outliers final: 0 residues processed: 222 average time/residue: 0.2799 time to fit residues: 81.4659 Evaluate side-chains 142 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 100 optimal weight: 0.9980 chunk 90 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 93 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 56 optimal weight: 0.7980 chunk 69 optimal weight: 0.8980 chunk 108 optimal weight: 6.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 ASN A 480 ASN A 597 ASN A 622 HIS ** A 805 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1474 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6467 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9687 Z= 0.229 Angle : 0.560 9.196 13136 Z= 0.295 Chirality : 0.040 0.148 1524 Planarity : 0.004 0.032 1640 Dihedral : 4.563 46.348 1293 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.34 % Allowed : 7.94 % Favored : 90.72 % 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: -0.69 (0.23), residues: 1188 helix: 0.35 (0.18), residues: 752 sheet: -0.35 (0.54), residues: 79 loop : -2.16 (0.30), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 998 HIS 0.004 0.001 HIS A 985 PHE 0.015 0.001 PHE A 558 TYR 0.019 0.002 TYR A1032 ARG 0.007 0.001 ARG A 233 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 146 time to evaluate : 1.118 Fit side-chains REVERT: A 239 THR cc_start: 0.7587 (m) cc_final: 0.7203 (p) REVERT: A 246 LYS cc_start: 0.7389 (mttt) cc_final: 0.6822 (tppt) REVERT: A 251 GLU cc_start: 0.7364 (mt-10) cc_final: 0.7059 (pt0) REVERT: A 356 LYS cc_start: 0.6694 (mttt) cc_final: 0.6473 (mmtm) REVERT: A 357 LYS cc_start: 0.7657 (mttt) cc_final: 0.7420 (mmtm) REVERT: A 444 ILE cc_start: 0.8488 (tt) cc_final: 0.7917 (pt) REVERT: A 496 LYS cc_start: 0.7046 (mmtt) cc_final: 0.6636 (mtmt) REVERT: A 503 LYS cc_start: 0.6405 (tttm) cc_final: 0.6058 (ptmt) REVERT: A 534 GLU cc_start: 0.7097 (tt0) cc_final: 0.6672 (mt-10) REVERT: A 617 ARG cc_start: 0.6459 (ttp80) cc_final: 0.6066 (ttm110) REVERT: A 647 LYS cc_start: 0.6805 (mttt) cc_final: 0.6495 (mtmm) REVERT: A 699 GLU cc_start: 0.7071 (mt-10) cc_final: 0.6558 (pt0) REVERT: A 738 LYS cc_start: 0.7519 (tttp) cc_final: 0.7281 (mmmt) REVERT: A 751 GLU cc_start: 0.7337 (tp30) cc_final: 0.7038 (mm-30) REVERT: A 758 ARG cc_start: 0.7427 (ptt180) cc_final: 0.7066 (mtm-85) REVERT: A 764 LYS cc_start: 0.7221 (tptt) cc_final: 0.6778 (mtpp) REVERT: A 784 CYS cc_start: 0.8127 (t) cc_final: 0.7624 (t) REVERT: A 808 GLU cc_start: 0.7910 (tt0) cc_final: 0.7588 (tm-30) REVERT: A 1080 ASP cc_start: 0.7154 (t70) cc_final: 0.6759 (m-30) REVERT: A 1113 MET cc_start: 0.6899 (mtp) cc_final: 0.6306 (mmm) REVERT: A 1133 VAL cc_start: 0.7629 (t) cc_final: 0.7424 (m) REVERT: A 1176 GLN cc_start: 0.6031 (tp40) cc_final: 0.5400 (mt0) REVERT: A 1235 TYR cc_start: 0.7325 (OUTLIER) cc_final: 0.6447 (m-80) REVERT: A 1310 LYS cc_start: 0.6331 (tttp) cc_final: 0.6067 (tptp) REVERT: A 1368 LYS cc_start: 0.8060 (mmtp) cc_final: 0.6875 (tmtt) REVERT: A 1385 MET cc_start: 0.6217 (tmm) cc_final: 0.5325 (mmp) REVERT: A 1498 VAL cc_start: 0.6412 (t) cc_final: 0.6189 (p) REVERT: A 1505 GLN cc_start: 0.6916 (mm110) cc_final: 0.6588 (mp10) REVERT: B 2 PHE cc_start: 0.4876 (OUTLIER) cc_final: 0.4398 (m-80) REVERT: B 11 GLU cc_start: 0.8170 (mp0) cc_final: 0.7822 (mt-10) outliers start: 14 outliers final: 7 residues processed: 158 average time/residue: 0.2513 time to fit residues: 53.5292 Evaluate side-chains 133 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 124 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 701 HIS Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 1105 ILE Chi-restraints excluded: chain A residue 1144 SER Chi-restraints excluded: chain A residue 1235 TYR Chi-restraints excluded: chain A residue 1257 ILE Chi-restraints excluded: chain B residue 2 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 60 optimal weight: 4.9990 chunk 33 optimal weight: 0.6980 chunk 89 optimal weight: 1.9990 chunk 73 optimal weight: 0.5980 chunk 29 optimal weight: 3.9990 chunk 108 optimal weight: 7.9990 chunk 116 optimal weight: 9.9990 chunk 96 optimal weight: 0.9990 chunk 107 optimal weight: 7.9990 chunk 36 optimal weight: 1.9990 chunk 86 optimal weight: 0.5980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 ASN A 805 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6492 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9687 Z= 0.222 Angle : 0.507 6.888 13136 Z= 0.266 Chirality : 0.040 0.147 1524 Planarity : 0.004 0.043 1640 Dihedral : 4.382 49.294 1293 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.20 % Allowed : 9.28 % Favored : 88.52 % 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: -0.16 (0.24), residues: 1188 helix: 0.78 (0.19), residues: 762 sheet: -0.32 (0.53), residues: 80 loop : -1.99 (0.31), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 8 HIS 0.004 0.001 HIS A1048 PHE 0.016 0.001 PHE A 558 TYR 0.012 0.001 TYR A1032 ARG 0.004 0.001 ARG A 233 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 136 time to evaluate : 1.019 Fit side-chains REVERT: A 228 MET cc_start: 0.6951 (mmt) cc_final: 0.6512 (mmt) REVERT: A 239 THR cc_start: 0.7612 (m) cc_final: 0.7269 (p) REVERT: A 246 LYS cc_start: 0.7476 (mttt) cc_final: 0.6857 (tptt) REVERT: A 251 GLU cc_start: 0.7571 (mt-10) cc_final: 0.7247 (pt0) REVERT: A 356 LYS cc_start: 0.6816 (mttt) cc_final: 0.6526 (mmtt) REVERT: A 357 LYS cc_start: 0.7695 (mttt) cc_final: 0.7431 (mmtm) REVERT: A 496 LYS cc_start: 0.7038 (mmtt) cc_final: 0.6638 (mtmt) REVERT: A 503 LYS cc_start: 0.6366 (tttm) cc_final: 0.6055 (ptmt) REVERT: A 534 GLU cc_start: 0.6926 (tt0) cc_final: 0.6495 (mt-10) REVERT: A 617 ARG cc_start: 0.6929 (ttp80) cc_final: 0.6282 (ttm110) REVERT: A 647 LYS cc_start: 0.6832 (mttt) cc_final: 0.6614 (mtmm) REVERT: A 699 GLU cc_start: 0.7067 (mt-10) cc_final: 0.6632 (pt0) REVERT: A 731 GLN cc_start: 0.7526 (tt0) cc_final: 0.7203 (pm20) REVERT: A 738 LYS cc_start: 0.7503 (tttp) cc_final: 0.7253 (mmmt) REVERT: A 751 GLU cc_start: 0.7383 (tp30) cc_final: 0.7075 (mm-30) REVERT: A 758 ARG cc_start: 0.7447 (ptt180) cc_final: 0.7005 (mtm-85) REVERT: A 764 LYS cc_start: 0.7591 (tptt) cc_final: 0.7199 (mtpp) REVERT: A 808 GLU cc_start: 0.7896 (tt0) cc_final: 0.7575 (tm-30) REVERT: A 819 ASN cc_start: 0.7453 (m-40) cc_final: 0.7106 (t0) REVERT: A 827 HIS cc_start: 0.7030 (t70) cc_final: 0.6707 (t-90) REVERT: A 1080 ASP cc_start: 0.7200 (t70) cc_final: 0.6915 (m-30) REVERT: A 1113 MET cc_start: 0.7010 (mtp) cc_final: 0.6407 (mmm) REVERT: A 1133 VAL cc_start: 0.7818 (t) cc_final: 0.7582 (m) REVERT: A 1176 GLN cc_start: 0.6232 (tp40) cc_final: 0.5700 (mt0) REVERT: A 1235 TYR cc_start: 0.7426 (OUTLIER) cc_final: 0.6491 (m-80) REVERT: A 1368 LYS cc_start: 0.7965 (mmtp) cc_final: 0.6789 (tmtt) REVERT: A 1385 MET cc_start: 0.6176 (tmm) cc_final: 0.5331 (mmp) REVERT: A 1492 ASP cc_start: 0.6851 (t0) cc_final: 0.6348 (p0) REVERT: A 1505 GLN cc_start: 0.6470 (mm110) cc_final: 0.6168 (mm-40) REVERT: B 11 GLU cc_start: 0.8283 (mp0) cc_final: 0.8003 (mp0) outliers start: 23 outliers final: 15 residues processed: 153 average time/residue: 0.2563 time to fit residues: 53.8383 Evaluate side-chains 139 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 123 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 563 SER Chi-restraints excluded: chain A residue 652 THR Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 701 HIS Chi-restraints excluded: chain A residue 826 THR Chi-restraints excluded: chain A residue 847 SER Chi-restraints excluded: chain A residue 1001 ASP Chi-restraints excluded: chain A residue 1032 TYR Chi-restraints excluded: chain A residue 1041 ILE Chi-restraints excluded: chain A residue 1209 ILE Chi-restraints excluded: chain A residue 1235 TYR Chi-restraints excluded: chain A residue 1257 ILE Chi-restraints excluded: chain A residue 1377 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 106 optimal weight: 0.1980 chunk 81 optimal weight: 0.6980 chunk 56 optimal weight: 0.0040 chunk 11 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 chunk 115 optimal weight: 0.0270 chunk 102 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 95 optimal weight: 9.9990 overall best weight: 0.3650 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1474 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6454 moved from start: 0.3179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9687 Z= 0.140 Angle : 0.455 6.082 13136 Z= 0.237 Chirality : 0.037 0.135 1524 Planarity : 0.003 0.041 1640 Dihedral : 4.127 47.842 1293 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.63 % Allowed : 11.10 % Favored : 87.27 % 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: 0.26 (0.24), residues: 1188 helix: 1.14 (0.19), residues: 758 sheet: 0.05 (0.56), residues: 79 loop : -1.95 (0.30), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1197 HIS 0.004 0.001 HIS A 805 PHE 0.013 0.001 PHE A 558 TYR 0.012 0.001 TYR A1032 ARG 0.006 0.000 ARG A 233 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 144 time to evaluate : 1.101 Fit side-chains revert: symmetry clash REVERT: A 239 THR cc_start: 0.7547 (m) cc_final: 0.7223 (p) REVERT: A 246 LYS cc_start: 0.7462 (mttt) cc_final: 0.6787 (tptt) REVERT: A 251 GLU cc_start: 0.7548 (mt-10) cc_final: 0.7235 (pt0) REVERT: A 356 LYS cc_start: 0.6777 (mttt) cc_final: 0.6491 (mmtt) REVERT: A 357 LYS cc_start: 0.7662 (mttt) cc_final: 0.7424 (mmtm) REVERT: A 496 LYS cc_start: 0.7113 (mmtt) cc_final: 0.6718 (mtmt) REVERT: A 503 LYS cc_start: 0.6369 (tttm) cc_final: 0.6085 (ptmt) REVERT: A 534 GLU cc_start: 0.6776 (tt0) cc_final: 0.6383 (mt-10) REVERT: A 617 ARG cc_start: 0.6743 (ttp80) cc_final: 0.6015 (ttm110) REVERT: A 647 LYS cc_start: 0.6837 (mttt) cc_final: 0.6616 (mtmm) REVERT: A 656 ASN cc_start: 0.7126 (t0) cc_final: 0.6784 (t0) REVERT: A 699 GLU cc_start: 0.6994 (mt-10) cc_final: 0.6559 (pt0) REVERT: A 731 GLN cc_start: 0.7430 (tt0) cc_final: 0.7081 (pm20) REVERT: A 738 LYS cc_start: 0.7490 (tttp) cc_final: 0.7252 (mmmt) REVERT: A 751 GLU cc_start: 0.7374 (tp30) cc_final: 0.7054 (mm-30) REVERT: A 758 ARG cc_start: 0.7532 (ptt180) cc_final: 0.7071 (mtm-85) REVERT: A 764 LYS cc_start: 0.7495 (tptt) cc_final: 0.7039 (mtpp) REVERT: A 804 LYS cc_start: 0.7323 (mmtp) cc_final: 0.7062 (mmtp) REVERT: A 808 GLU cc_start: 0.7873 (tt0) cc_final: 0.7542 (tm-30) REVERT: A 827 HIS cc_start: 0.7026 (t70) cc_final: 0.6772 (t-90) REVERT: A 1080 ASP cc_start: 0.7347 (t70) cc_final: 0.6898 (m-30) REVERT: A 1113 MET cc_start: 0.6837 (mtp) cc_final: 0.6269 (mmm) REVERT: A 1176 GLN cc_start: 0.6285 (tp40) cc_final: 0.5864 (mt0) REVERT: A 1368 LYS cc_start: 0.7970 (mmtp) cc_final: 0.6774 (tmtt) REVERT: A 1385 MET cc_start: 0.6172 (tmm) cc_final: 0.5287 (mmp) REVERT: A 1454 GLU cc_start: 0.3874 (tt0) cc_final: 0.3470 (pt0) REVERT: A 1492 ASP cc_start: 0.6841 (t0) cc_final: 0.6491 (p0) REVERT: A 1505 GLN cc_start: 0.6427 (mm110) cc_final: 0.6155 (mm-40) REVERT: B 11 GLU cc_start: 0.8296 (mp0) cc_final: 0.7978 (mp0) outliers start: 17 outliers final: 11 residues processed: 153 average time/residue: 0.2661 time to fit residues: 55.0582 Evaluate side-chains 140 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 129 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 563 SER Chi-restraints excluded: chain A residue 652 THR Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 847 SER Chi-restraints excluded: chain A residue 1032 TYR Chi-restraints excluded: chain A residue 1235 TYR Chi-restraints excluded: chain A residue 1257 ILE Chi-restraints excluded: chain A residue 1377 VAL Chi-restraints excluded: chain B residue 5 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 65 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 chunk 85 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 98 optimal weight: 6.9990 chunk 79 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 103 optimal weight: 7.9990 chunk 29 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 ASN A1474 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6550 moved from start: 0.3467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 9687 Z= 0.425 Angle : 0.614 7.159 13136 Z= 0.320 Chirality : 0.044 0.155 1524 Planarity : 0.004 0.049 1640 Dihedral : 4.610 49.739 1293 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.06 % Allowed : 11.39 % Favored : 85.55 % 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: -0.23 (0.24), residues: 1188 helix: 0.66 (0.19), residues: 744 sheet: -0.15 (0.53), residues: 86 loop : -1.82 (0.30), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 716 HIS 0.007 0.002 HIS A1048 PHE 0.019 0.002 PHE A 365 TYR 0.020 0.002 TYR A1032 ARG 0.007 0.001 ARG A 633 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 133 time to evaluate : 1.031 Fit side-chains REVERT: A 246 LYS cc_start: 0.7541 (mttt) cc_final: 0.7023 (tptt) REVERT: A 251 GLU cc_start: 0.7647 (mt-10) cc_final: 0.7016 (tp30) REVERT: A 356 LYS cc_start: 0.7090 (mttt) cc_final: 0.6739 (mmtt) REVERT: A 357 LYS cc_start: 0.7894 (mttt) cc_final: 0.7613 (mmtm) REVERT: A 496 LYS cc_start: 0.6972 (mmtt) cc_final: 0.6606 (mtmt) REVERT: A 503 LYS cc_start: 0.6516 (tttm) cc_final: 0.6213 (ptmt) REVERT: A 534 GLU cc_start: 0.6925 (tt0) cc_final: 0.6508 (mt-10) REVERT: A 617 ARG cc_start: 0.6919 (ttp80) cc_final: 0.6239 (ttm110) REVERT: A 647 LYS cc_start: 0.6783 (mttt) cc_final: 0.6549 (mtmm) REVERT: A 699 GLU cc_start: 0.7139 (mt-10) cc_final: 0.6655 (pt0) REVERT: A 731 GLN cc_start: 0.7308 (tt0) cc_final: 0.6852 (pm20) REVERT: A 738 LYS cc_start: 0.7406 (tttp) cc_final: 0.7154 (mmmt) REVERT: A 751 GLU cc_start: 0.7302 (tp30) cc_final: 0.6905 (mt-10) REVERT: A 758 ARG cc_start: 0.7288 (ptt180) cc_final: 0.6724 (mtm-85) REVERT: A 764 LYS cc_start: 0.7369 (tptt) cc_final: 0.6936 (mtpp) REVERT: A 827 HIS cc_start: 0.7140 (t70) cc_final: 0.6858 (t-90) REVERT: A 1080 ASP cc_start: 0.7354 (t70) cc_final: 0.7076 (t0) REVERT: A 1113 MET cc_start: 0.6986 (mtp) cc_final: 0.6319 (mmm) REVERT: A 1176 GLN cc_start: 0.6391 (OUTLIER) cc_final: 0.5678 (mt0) REVERT: A 1235 TYR cc_start: 0.7450 (OUTLIER) cc_final: 0.6745 (m-80) REVERT: A 1306 ASP cc_start: 0.6881 (t0) cc_final: 0.6170 (p0) REVERT: A 1368 LYS cc_start: 0.8013 (mmtp) cc_final: 0.6785 (tmtt) REVERT: A 1385 MET cc_start: 0.6216 (tmm) cc_final: 0.5340 (mmp) REVERT: A 1491 MET cc_start: 0.7394 (tpp) cc_final: 0.7173 (tpp) REVERT: A 1492 ASP cc_start: 0.6726 (t0) cc_final: 0.6307 (p0) REVERT: A 1505 GLN cc_start: 0.5960 (mm110) cc_final: 0.5700 (mm-40) REVERT: B 11 GLU cc_start: 0.8391 (mp0) cc_final: 0.8043 (mp0) outliers start: 32 outliers final: 20 residues processed: 156 average time/residue: 0.2447 time to fit residues: 52.2225 Evaluate side-chains 149 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 127 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 563 SER Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 652 THR Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 701 HIS Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 826 THR Chi-restraints excluded: chain A residue 847 SER Chi-restraints excluded: chain A residue 996 SER Chi-restraints excluded: chain A residue 1032 TYR Chi-restraints excluded: chain A residue 1041 ILE Chi-restraints excluded: chain A residue 1084 SER Chi-restraints excluded: chain A residue 1176 GLN Chi-restraints excluded: chain A residue 1235 TYR Chi-restraints excluded: chain A residue 1257 ILE Chi-restraints excluded: chain A residue 1377 VAL Chi-restraints excluded: chain A residue 1382 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 103 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 chunk 67 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 115 optimal weight: 6.9990 chunk 95 optimal weight: 6.9990 chunk 53 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 60 optimal weight: 5.9990 chunk 111 optimal weight: 0.0060 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 ASN A 819 ASN A1238 GLN A1474 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6505 moved from start: 0.3612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9687 Z= 0.188 Angle : 0.498 9.600 13136 Z= 0.256 Chirality : 0.038 0.145 1524 Planarity : 0.004 0.046 1640 Dihedral : 4.272 47.877 1293 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.78 % Allowed : 13.11 % Favored : 84.11 % 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: 0.04 (0.24), residues: 1188 helix: 0.90 (0.19), residues: 750 sheet: -0.05 (0.56), residues: 80 loop : -1.79 (0.31), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1197 HIS 0.004 0.001 HIS A1048 PHE 0.012 0.001 PHE A 558 TYR 0.014 0.001 TYR A1032 ARG 0.006 0.000 ARG A 233 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 131 time to evaluate : 1.052 Fit side-chains REVERT: A 246 LYS cc_start: 0.7521 (mttt) cc_final: 0.6888 (tppt) REVERT: A 251 GLU cc_start: 0.7608 (mt-10) cc_final: 0.6969 (tp30) REVERT: A 356 LYS cc_start: 0.7096 (mttt) cc_final: 0.6752 (mmtt) REVERT: A 357 LYS cc_start: 0.7743 (mttt) cc_final: 0.7464 (mmtm) REVERT: A 496 LYS cc_start: 0.7040 (mmtt) cc_final: 0.6681 (mtmt) REVERT: A 503 LYS cc_start: 0.6413 (tttm) cc_final: 0.6103 (ptmt) REVERT: A 534 GLU cc_start: 0.6779 (tt0) cc_final: 0.6381 (mt-10) REVERT: A 617 ARG cc_start: 0.6894 (ttp80) cc_final: 0.6219 (ttm110) REVERT: A 647 LYS cc_start: 0.6805 (mttt) cc_final: 0.6590 (mtmm) REVERT: A 656 ASN cc_start: 0.7180 (t0) cc_final: 0.6935 (t0) REVERT: A 699 GLU cc_start: 0.7123 (mt-10) cc_final: 0.6627 (pt0) REVERT: A 731 GLN cc_start: 0.7283 (tt0) cc_final: 0.6591 (pm20) REVERT: A 758 ARG cc_start: 0.7577 (ptt180) cc_final: 0.6966 (mtm-85) REVERT: A 764 LYS cc_start: 0.7375 (tptt) cc_final: 0.6890 (mtpp) REVERT: A 1080 ASP cc_start: 0.7387 (t70) cc_final: 0.6947 (m-30) REVERT: A 1113 MET cc_start: 0.6869 (mtp) cc_final: 0.6261 (mmm) REVERT: A 1176 GLN cc_start: 0.6485 (OUTLIER) cc_final: 0.5834 (mt0) REVERT: A 1235 TYR cc_start: 0.7415 (OUTLIER) cc_final: 0.6434 (m-80) REVERT: A 1306 ASP cc_start: 0.6982 (t0) cc_final: 0.6315 (p0) REVERT: A 1368 LYS cc_start: 0.8001 (mmtp) cc_final: 0.6766 (tmtt) REVERT: A 1385 MET cc_start: 0.6218 (tmm) cc_final: 0.5351 (mmp) REVERT: A 1454 GLU cc_start: 0.4116 (tt0) cc_final: 0.3861 (pt0) REVERT: A 1491 MET cc_start: 0.7250 (tpp) cc_final: 0.7026 (tpp) REVERT: A 1492 ASP cc_start: 0.6802 (t0) cc_final: 0.6461 (p0) REVERT: A 1505 GLN cc_start: 0.5924 (mm110) cc_final: 0.5668 (mm-40) REVERT: B 11 GLU cc_start: 0.8355 (mp0) cc_final: 0.8008 (mp0) outliers start: 29 outliers final: 18 residues processed: 152 average time/residue: 0.2545 time to fit residues: 52.9033 Evaluate side-chains 148 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 128 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 563 SER Chi-restraints excluded: chain A residue 652 THR Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 701 HIS Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 826 THR Chi-restraints excluded: chain A residue 847 SER Chi-restraints excluded: chain A residue 996 SER Chi-restraints excluded: chain A residue 1032 TYR Chi-restraints excluded: chain A residue 1041 ILE Chi-restraints excluded: chain A residue 1144 SER Chi-restraints excluded: chain A residue 1176 GLN Chi-restraints excluded: chain A residue 1235 TYR Chi-restraints excluded: chain A residue 1257 ILE Chi-restraints excluded: chain A residue 1377 VAL Chi-restraints excluded: chain A residue 1382 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 12 optimal weight: 2.9990 chunk 65 optimal weight: 0.0060 chunk 84 optimal weight: 1.9990 chunk 96 optimal weight: 6.9990 chunk 64 optimal weight: 0.7980 chunk 114 optimal weight: 0.3980 chunk 71 optimal weight: 0.1980 chunk 69 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 733 GLN A 819 ASN ** A1311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1474 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6496 moved from start: 0.3772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9687 Z= 0.181 Angle : 0.487 8.828 13136 Z= 0.250 Chirality : 0.039 0.273 1524 Planarity : 0.004 0.044 1640 Dihedral : 4.089 47.049 1293 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.58 % Allowed : 12.92 % Favored : 84.50 % 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: 0.26 (0.25), residues: 1188 helix: 1.08 (0.19), residues: 750 sheet: 0.03 (0.56), residues: 80 loop : -1.71 (0.31), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1197 HIS 0.008 0.001 HIS A1311 PHE 0.013 0.001 PHE A 558 TYR 0.014 0.001 TYR A1032 ARG 0.005 0.000 ARG A 633 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 135 time to evaluate : 1.094 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 240 ASP cc_start: 0.7047 (t70) cc_final: 0.6777 (t0) REVERT: A 246 LYS cc_start: 0.7418 (mttt) cc_final: 0.6749 (tppt) REVERT: A 251 GLU cc_start: 0.7619 (mt-10) cc_final: 0.6947 (tp30) REVERT: A 338 MET cc_start: 0.8119 (tpp) cc_final: 0.7879 (tpp) REVERT: A 356 LYS cc_start: 0.7188 (mttt) cc_final: 0.6824 (mmtt) REVERT: A 357 LYS cc_start: 0.7701 (mttt) cc_final: 0.7434 (mmtm) REVERT: A 496 LYS cc_start: 0.7045 (mmtt) cc_final: 0.6689 (mtmt) REVERT: A 503 LYS cc_start: 0.6468 (tttm) cc_final: 0.6170 (ptmt) REVERT: A 534 GLU cc_start: 0.6713 (tt0) cc_final: 0.6403 (mt-10) REVERT: A 617 ARG cc_start: 0.6917 (ttp80) cc_final: 0.6224 (ttm110) REVERT: A 699 GLU cc_start: 0.7097 (mt-10) cc_final: 0.6625 (pt0) REVERT: A 731 GLN cc_start: 0.7278 (tt0) cc_final: 0.6559 (pm20) REVERT: A 758 ARG cc_start: 0.7578 (ptt180) cc_final: 0.6980 (mtm-85) REVERT: A 764 LYS cc_start: 0.7367 (tptt) cc_final: 0.6863 (mtpp) REVERT: A 1080 ASP cc_start: 0.7431 (t70) cc_final: 0.7001 (m-30) REVERT: A 1113 MET cc_start: 0.6976 (mtp) cc_final: 0.6298 (mmm) REVERT: A 1176 GLN cc_start: 0.6498 (OUTLIER) cc_final: 0.5919 (mt0) REVERT: A 1306 ASP cc_start: 0.6860 (t0) cc_final: 0.6181 (p0) REVERT: A 1368 LYS cc_start: 0.7990 (mmtp) cc_final: 0.6766 (tmtt) REVERT: A 1385 MET cc_start: 0.6237 (tmm) cc_final: 0.5394 (mmp) REVERT: A 1454 GLU cc_start: 0.4068 (tt0) cc_final: 0.3818 (pt0) REVERT: A 1491 MET cc_start: 0.7272 (tpp) cc_final: 0.7036 (tpp) REVERT: A 1492 ASP cc_start: 0.6889 (t0) cc_final: 0.6477 (p0) REVERT: A 1505 GLN cc_start: 0.5972 (mm110) cc_final: 0.5698 (mm-40) REVERT: B 11 GLU cc_start: 0.8348 (mp0) cc_final: 0.8009 (mp0) outliers start: 27 outliers final: 23 residues processed: 153 average time/residue: 0.2659 time to fit residues: 55.7853 Evaluate side-chains 152 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 128 time to evaluate : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 563 SER Chi-restraints excluded: chain A residue 652 THR Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 701 HIS Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 826 THR Chi-restraints excluded: chain A residue 847 SER Chi-restraints excluded: chain A residue 996 SER Chi-restraints excluded: chain A residue 1032 TYR Chi-restraints excluded: chain A residue 1041 ILE Chi-restraints excluded: chain A residue 1144 SER Chi-restraints excluded: chain A residue 1176 GLN Chi-restraints excluded: chain A residue 1209 ILE Chi-restraints excluded: chain A residue 1235 TYR Chi-restraints excluded: chain A residue 1249 MET Chi-restraints excluded: chain A residue 1257 ILE Chi-restraints excluded: chain A residue 1305 LEU Chi-restraints excluded: chain A residue 1377 VAL Chi-restraints excluded: chain A residue 1382 SER Chi-restraints excluded: chain A residue 1403 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 68 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 chunk 22 optimal weight: 0.0980 chunk 72 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 chunk 104 optimal weight: 0.0370 chunk 109 optimal weight: 0.7980 chunk 100 optimal weight: 4.9990 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6477 moved from start: 0.3949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 9687 Z= 0.153 Angle : 0.467 8.551 13136 Z= 0.239 Chirality : 0.038 0.190 1524 Planarity : 0.003 0.043 1640 Dihedral : 3.918 45.839 1293 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.20 % Allowed : 13.01 % Favored : 84.78 % 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: 0.51 (0.25), residues: 1188 helix: 1.32 (0.19), residues: 744 sheet: 0.11 (0.57), residues: 80 loop : -1.68 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1197 HIS 0.007 0.001 HIS A1311 PHE 0.012 0.001 PHE A 558 TYR 0.013 0.001 TYR A1032 ARG 0.004 0.000 ARG A 633 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 136 time to evaluate : 1.174 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 240 ASP cc_start: 0.7307 (t70) cc_final: 0.6989 (t0) REVERT: A 246 LYS cc_start: 0.7393 (mttt) cc_final: 0.6712 (tppt) REVERT: A 251 GLU cc_start: 0.7630 (mt-10) cc_final: 0.6899 (tp30) REVERT: A 338 MET cc_start: 0.8100 (tpp) cc_final: 0.7877 (tpp) REVERT: A 356 LYS cc_start: 0.7166 (mttt) cc_final: 0.6798 (mmtt) REVERT: A 357 LYS cc_start: 0.7706 (mttt) cc_final: 0.7440 (mmtm) REVERT: A 496 LYS cc_start: 0.7078 (mmtt) cc_final: 0.6723 (mtmt) REVERT: A 503 LYS cc_start: 0.6417 (tttm) cc_final: 0.6103 (ptmt) REVERT: A 534 GLU cc_start: 0.6513 (tt0) cc_final: 0.6227 (mt-10) REVERT: A 617 ARG cc_start: 0.6838 (ttp80) cc_final: 0.6155 (ttm110) REVERT: A 699 GLU cc_start: 0.7093 (mt-10) cc_final: 0.6686 (pt0) REVERT: A 731 GLN cc_start: 0.7237 (tt0) cc_final: 0.6660 (pm20) REVERT: A 758 ARG cc_start: 0.7613 (ptt180) cc_final: 0.7001 (mtm-85) REVERT: A 764 LYS cc_start: 0.7452 (tptt) cc_final: 0.6924 (mtpp) REVERT: A 1080 ASP cc_start: 0.7469 (t70) cc_final: 0.7067 (m-30) REVERT: A 1113 MET cc_start: 0.6914 (mtp) cc_final: 0.6327 (mmm) REVERT: A 1176 GLN cc_start: 0.6441 (tp40) cc_final: 0.5947 (mt0) REVERT: A 1306 ASP cc_start: 0.6779 (t0) cc_final: 0.6121 (p0) REVERT: A 1368 LYS cc_start: 0.7980 (mmtp) cc_final: 0.6769 (tmtt) REVERT: A 1385 MET cc_start: 0.6191 (tmm) cc_final: 0.5268 (mmp) REVERT: A 1492 ASP cc_start: 0.6929 (t0) cc_final: 0.6664 (p0) REVERT: A 1505 GLN cc_start: 0.5986 (mm110) cc_final: 0.5716 (mm-40) REVERT: B 11 GLU cc_start: 0.8341 (mp0) cc_final: 0.8015 (mp0) outliers start: 23 outliers final: 18 residues processed: 150 average time/residue: 0.2608 time to fit residues: 53.2261 Evaluate side-chains 145 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 127 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain A residue 652 THR Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 826 THR Chi-restraints excluded: chain A residue 847 SER Chi-restraints excluded: chain A residue 1032 TYR Chi-restraints excluded: chain A residue 1041 ILE Chi-restraints excluded: chain A residue 1209 ILE Chi-restraints excluded: chain A residue 1235 TYR Chi-restraints excluded: chain A residue 1257 ILE Chi-restraints excluded: chain A residue 1305 LEU Chi-restraints excluded: chain A residue 1377 VAL Chi-restraints excluded: chain A residue 1382 SER Chi-restraints excluded: chain A residue 1403 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 106 optimal weight: 0.4980 chunk 109 optimal weight: 1.9990 chunk 64 optimal weight: 0.5980 chunk 46 optimal weight: 0.7980 chunk 83 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 96 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 819 ASN A1311 HIS ** A1474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6489 moved from start: 0.3985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9687 Z= 0.181 Angle : 0.483 8.399 13136 Z= 0.248 Chirality : 0.038 0.186 1524 Planarity : 0.004 0.044 1640 Dihedral : 3.906 45.752 1293 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.30 % Allowed : 13.68 % Favored : 84.02 % 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: 0.55 (0.25), residues: 1188 helix: 1.32 (0.19), residues: 748 sheet: 0.22 (0.57), residues: 80 loop : -1.65 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1197 HIS 0.007 0.001 HIS A1311 PHE 0.012 0.001 PHE A 558 TYR 0.014 0.001 TYR A1032 ARG 0.007 0.000 ARG A 233 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 132 time to evaluate : 1.114 Fit side-chains revert: symmetry clash REVERT: A 240 ASP cc_start: 0.7361 (t70) cc_final: 0.7058 (t0) REVERT: A 246 LYS cc_start: 0.7389 (mttt) cc_final: 0.6719 (tppt) REVERT: A 251 GLU cc_start: 0.7624 (mt-10) cc_final: 0.6907 (tp30) REVERT: A 338 MET cc_start: 0.8070 (tpp) cc_final: 0.7862 (tpp) REVERT: A 356 LYS cc_start: 0.7178 (mttt) cc_final: 0.6808 (mmtt) REVERT: A 357 LYS cc_start: 0.7694 (mttt) cc_final: 0.7437 (mmtm) REVERT: A 496 LYS cc_start: 0.7165 (mmtt) cc_final: 0.6792 (mtmt) REVERT: A 503 LYS cc_start: 0.6480 (tttm) cc_final: 0.6179 (ptmt) REVERT: A 534 GLU cc_start: 0.6473 (tt0) cc_final: 0.6209 (mt-10) REVERT: A 544 TYR cc_start: 0.6153 (m-80) cc_final: 0.5901 (m-10) REVERT: A 617 ARG cc_start: 0.6898 (ttp80) cc_final: 0.6197 (ttm110) REVERT: A 699 GLU cc_start: 0.7045 (mt-10) cc_final: 0.6553 (pt0) REVERT: A 731 GLN cc_start: 0.7205 (tt0) cc_final: 0.6467 (pm20) REVERT: A 751 GLU cc_start: 0.6522 (mm-30) cc_final: 0.5914 (mp0) REVERT: A 758 ARG cc_start: 0.7613 (ptt180) cc_final: 0.7121 (mtm-85) REVERT: A 764 LYS cc_start: 0.7432 (tptt) cc_final: 0.6920 (mtpp) REVERT: A 1080 ASP cc_start: 0.7463 (t70) cc_final: 0.7064 (m-30) REVERT: A 1113 MET cc_start: 0.7124 (mtp) cc_final: 0.6418 (mmm) REVERT: A 1176 GLN cc_start: 0.6443 (tp40) cc_final: 0.5943 (mt0) REVERT: A 1306 ASP cc_start: 0.6820 (t0) cc_final: 0.6149 (p0) REVERT: A 1368 LYS cc_start: 0.7983 (mmtp) cc_final: 0.6770 (tmtt) REVERT: A 1385 MET cc_start: 0.6184 (tmm) cc_final: 0.5271 (mmp) REVERT: A 1492 ASP cc_start: 0.6981 (t0) cc_final: 0.6635 (p0) REVERT: A 1505 GLN cc_start: 0.6041 (mm110) cc_final: 0.5664 (mm-40) REVERT: B 11 GLU cc_start: 0.8336 (mp0) cc_final: 0.7983 (mp0) outliers start: 24 outliers final: 21 residues processed: 147 average time/residue: 0.2440 time to fit residues: 49.7481 Evaluate side-chains 149 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 128 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain A residue 652 THR Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 826 THR Chi-restraints excluded: chain A residue 847 SER Chi-restraints excluded: chain A residue 1032 TYR Chi-restraints excluded: chain A residue 1041 ILE Chi-restraints excluded: chain A residue 1144 SER Chi-restraints excluded: chain A residue 1209 ILE Chi-restraints excluded: chain A residue 1235 TYR Chi-restraints excluded: chain A residue 1249 MET Chi-restraints excluded: chain A residue 1257 ILE Chi-restraints excluded: chain A residue 1305 LEU Chi-restraints excluded: chain A residue 1311 HIS Chi-restraints excluded: chain A residue 1377 VAL Chi-restraints excluded: chain A residue 1382 SER Chi-restraints excluded: chain A residue 1403 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 53 optimal weight: 0.6980 chunk 78 optimal weight: 0.8980 chunk 118 optimal weight: 4.9990 chunk 109 optimal weight: 0.8980 chunk 94 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 57 optimal weight: 6.9990 chunk 74 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1311 HIS ** A1474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6509 moved from start: 0.4006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9687 Z= 0.240 Angle : 0.516 8.667 13136 Z= 0.264 Chirality : 0.039 0.191 1524 Planarity : 0.004 0.044 1640 Dihedral : 4.004 45.935 1293 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.30 % Allowed : 13.97 % Favored : 83.73 % 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: 0.41 (0.25), residues: 1188 helix: 1.18 (0.19), residues: 749 sheet: 0.19 (0.57), residues: 80 loop : -1.64 (0.31), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1197 HIS 0.008 0.001 HIS A1311 PHE 0.013 0.001 PHE A 583 TYR 0.015 0.001 TYR A1032 ARG 0.007 0.000 ARG A 233 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 129 time to evaluate : 1.182 Fit side-chains revert: symmetry clash REVERT: A 240 ASP cc_start: 0.7421 (t70) cc_final: 0.7140 (t0) REVERT: A 246 LYS cc_start: 0.7478 (mttt) cc_final: 0.6835 (tppt) REVERT: A 251 GLU cc_start: 0.7646 (mt-10) cc_final: 0.6926 (tp30) REVERT: A 338 MET cc_start: 0.8079 (tpp) cc_final: 0.7867 (tpp) REVERT: A 356 LYS cc_start: 0.7258 (mttt) cc_final: 0.6956 (mmmt) REVERT: A 357 LYS cc_start: 0.7728 (mttt) cc_final: 0.7484 (mmtm) REVERT: A 496 LYS cc_start: 0.7311 (mmtt) cc_final: 0.6890 (mtmt) REVERT: A 503 LYS cc_start: 0.6487 (tttm) cc_final: 0.6185 (ptmt) REVERT: A 534 GLU cc_start: 0.6490 (tt0) cc_final: 0.6217 (mt-10) REVERT: A 544 TYR cc_start: 0.6167 (m-80) cc_final: 0.5911 (m-10) REVERT: A 617 ARG cc_start: 0.6928 (ttp80) cc_final: 0.6200 (ttm110) REVERT: A 699 GLU cc_start: 0.7044 (mt-10) cc_final: 0.6564 (pt0) REVERT: A 731 GLN cc_start: 0.7170 (tt0) cc_final: 0.6376 (pm20) REVERT: A 751 GLU cc_start: 0.6593 (mm-30) cc_final: 0.5947 (mp0) REVERT: A 758 ARG cc_start: 0.7464 (ptt180) cc_final: 0.6921 (mtm-85) REVERT: A 764 LYS cc_start: 0.7413 (tptt) cc_final: 0.6922 (mtpp) REVERT: A 1080 ASP cc_start: 0.7457 (t70) cc_final: 0.7073 (m-30) REVERT: A 1113 MET cc_start: 0.7075 (mtp) cc_final: 0.6389 (mmm) REVERT: A 1176 GLN cc_start: 0.6482 (OUTLIER) cc_final: 0.5905 (mt0) REVERT: A 1306 ASP cc_start: 0.6832 (t0) cc_final: 0.6123 (p0) REVERT: A 1368 LYS cc_start: 0.7992 (mmtp) cc_final: 0.6800 (tmtt) REVERT: A 1385 MET cc_start: 0.6226 (tmm) cc_final: 0.5317 (mmp) REVERT: A 1492 ASP cc_start: 0.7000 (t0) cc_final: 0.6636 (p0) REVERT: A 1505 GLN cc_start: 0.6061 (mm110) cc_final: 0.5716 (mm-40) REVERT: B 11 GLU cc_start: 0.8343 (mp0) cc_final: 0.7980 (mp0) outliers start: 24 outliers final: 21 residues processed: 144 average time/residue: 0.2425 time to fit residues: 48.3121 Evaluate side-chains 151 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 129 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 563 SER Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain A residue 652 THR Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 826 THR Chi-restraints excluded: chain A residue 847 SER Chi-restraints excluded: chain A residue 996 SER Chi-restraints excluded: chain A residue 1032 TYR Chi-restraints excluded: chain A residue 1041 ILE Chi-restraints excluded: chain A residue 1144 SER Chi-restraints excluded: chain A residue 1176 GLN Chi-restraints excluded: chain A residue 1235 TYR Chi-restraints excluded: chain A residue 1249 MET Chi-restraints excluded: chain A residue 1257 ILE Chi-restraints excluded: chain A residue 1311 HIS Chi-restraints excluded: chain A residue 1377 VAL Chi-restraints excluded: chain A residue 1382 SER Chi-restraints excluded: chain A residue 1403 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 87 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 26 optimal weight: 0.1980 chunk 94 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 97 optimal weight: 8.9990 chunk 11 optimal weight: 0.4980 chunk 17 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 5 optimal weight: 0.0980 chunk 68 optimal weight: 0.7980 overall best weight: 0.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1311 HIS ** A1474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.158441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.120896 restraints weight = 11474.688| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 1.93 r_work: 0.3180 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.4049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 9687 Z= 0.161 Angle : 0.486 8.443 13136 Z= 0.248 Chirality : 0.038 0.179 1524 Planarity : 0.003 0.042 1640 Dihedral : 3.912 45.701 1293 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.20 % Allowed : 14.35 % Favored : 83.44 % 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: 0.59 (0.25), residues: 1188 helix: 1.34 (0.20), residues: 744 sheet: 0.29 (0.57), residues: 80 loop : -1.58 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1197 HIS 0.005 0.001 HIS A1311 PHE 0.013 0.001 PHE A 558 TYR 0.013 0.001 TYR A1032 ARG 0.007 0.000 ARG A 233 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2530.15 seconds wall clock time: 46 minutes 38.82 seconds (2798.82 seconds total)