Starting phenix.real_space_refine on Sun Feb 18 05:44:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8epl_28529/02_2024/8epl_28529_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8epl_28529/02_2024/8epl_28529.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8epl_28529/02_2024/8epl_28529_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8epl_28529/02_2024/8epl_28529_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8epl_28529/02_2024/8epl_28529_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8epl_28529/02_2024/8epl_28529.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8epl_28529/02_2024/8epl_28529.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8epl_28529/02_2024/8epl_28529_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8epl_28529/02_2024/8epl_28529_updated.pdb" } resolution = 3.1 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= 0.006 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: 6 Type Number sf(0) Gaussians Ca 2 9.91 5 P 5 5.49 5 S 117 5.16 5 C 13552 2.51 5 N 3441 2.21 5 O 3836 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 114": "OE1" <-> "OE2" Residue "A TYR 585": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 715": "OD1" <-> "OD2" Residue "A PHE 1197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1200": "OE1" <-> "OE2" Residue "A TYR 1296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1337": "OE1" <-> "OE2" Residue "A GLU 1428": "OE1" <-> "OE2" Residue "A TYR 1499": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1761": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 152": "OD1" <-> "OD2" Residue "C PHE 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 366": "OE1" <-> "OE2" Residue "C ASP 379": "OD1" <-> "OD2" Residue "C ASP 569": "OD1" <-> "OD2" Residue "C GLU 597": "OE1" <-> "OE2" Residue "C PHE 686": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 719": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 780": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 892": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 984": "OD1" <-> "OD2" Residue "C GLU 1035": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 20953 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 10316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1274, 10316 Classifications: {'peptide': 1274} Link IDs: {'PTRANS': 37, 'TRANS': 1236} Chain breaks: 7 Chain: "B" Number of atoms: 2575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2575 Classifications: {'peptide': 324} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 304} Chain: "C" Number of atoms: 7570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 948, 7570 Classifications: {'peptide': 948} Link IDs: {'PCIS': 2, 'PTRANS': 38, 'TRANS': 907} Chain breaks: 5 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 281 Unusual residues: {' CA': 1, '3PE': 2, 'CLR': 5, 'PT5': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 31 Chain: "C" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 43 Unusual residues: {' CA': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 11.37, per 1000 atoms: 0.54 Number of scatterers: 20953 At special positions: 0 Unit cell: (168.214, 180.468, 186.038, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 2 19.99 S 117 16.00 P 5 15.00 O 3836 8.00 N 3441 7.00 C 13552 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 251 " - pdb=" SG CYS A 273 " distance=2.03 Simple disulfide: pdb=" SG CYS A 268 " - pdb=" SG CYS A 279 " distance=2.03 Simple disulfide: pdb=" SG CYS A1318 " - pdb=" SG CYS A1329 " distance=2.03 Simple disulfide: pdb=" SG CYS A1678 " - pdb=" SG CYS A1694 " distance=2.03 Simple disulfide: pdb=" SG CYS C 303 " - pdb=" SG CYS C1044 " distance=2.03 Simple disulfide: pdb=" SG CYS C 404 " - pdb=" SG CYS C1071 " distance=2.03 Simple disulfide: pdb=" SG CYS C 667 " - pdb=" SG CYS C 697 " distance=2.03 Simple disulfide: pdb=" SG CYS C 904 " - pdb=" SG CYS C 974 " distance=2.03 Simple disulfide: pdb=" SG CYS C 996 " - pdb=" SG CYS C1026 " distance=2.03 Simple disulfide: pdb=" SG CYS C 999 " - pdb=" SG CYS C1024 " distance=2.03 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=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " NAG F 3 " " NAG F 3 " - " NAG F 4 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG C1201 " - " ASN C 92 " " NAG C1202 " - " ASN C 781 " " NAG D 1 " - " ASN C 184 " " NAG E 1 " - " ASN C 348 " " NAG F 1 " - " ASN C 468 " " NAG G 1 " - " ASN C 613 " " NAG H 1 " - " ASN C 895 " Time building additional restraints: 8.61 Conformation dependent library (CDL) restraints added in 4.1 seconds 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4818 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 94 helices and 16 sheets defined 48.2% alpha, 7.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.30 Creating SS restraints... Processing helix chain 'A' and resid 91 through 108 Processing helix chain 'A' and resid 119 through 143 removed outlier: 3.625A pdb=" N LYS A 126 " --> pdb=" O ARG A 122 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N THR A 127 " --> pdb=" O ARG A 123 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N GLU A 128 " --> pdb=" O LEU A 124 " (cutoff:3.500A) Proline residue: A 129 - end of helix removed outlier: 3.528A pdb=" N LYS A 142 " --> pdb=" O GLU A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 177 removed outlier: 3.838A pdb=" N MET A 163 " --> pdb=" O GLY A 159 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ASP A 164 " --> pdb=" O TRP A 160 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR A 175 " --> pdb=" O GLY A 171 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY A 177 " --> pdb=" O LEU A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 203 Proline residue: A 197 - end of helix Processing helix chain 'A' and resid 205 through 218 Processing helix chain 'A' and resid 221 through 240 Processing helix chain 'A' and resid 295 through 306 Processing helix chain 'A' and resid 311 through 322 removed outlier: 3.504A pdb=" N ASP A 320 " --> pdb=" O TYR A 316 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA A 321 " --> pdb=" O ASN A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 338 removed outlier: 3.685A pdb=" N PHE A 331 " --> pdb=" O TRP A 328 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N ILE A 332 " --> pdb=" O LEU A 329 " (cutoff:3.500A) Proline residue: A 333 - end of helix removed outlier: 3.858A pdb=" N ILE A 337 " --> pdb=" O LEU A 334 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLY A 338 " --> pdb=" O ILE A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 359 removed outlier: 4.001A pdb=" N GLU A 359 " --> pdb=" O ALA A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 397 removed outlier: 3.583A pdb=" N GLY A 382 " --> pdb=" O ARG A 378 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N TYR A 383 " --> pdb=" O GLU A 379 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA A 385 " --> pdb=" O ASN A 381 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N TRP A 386 " --> pdb=" O GLY A 382 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE A 387 " --> pdb=" O TYR A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 474 No H-bonds generated for 'chain 'A' and resid 472 through 474' Processing helix chain 'A' and resid 476 through 495 removed outlier: 3.660A pdb=" N VAL A 486 " --> pdb=" O VAL A 482 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE A 495 " --> pdb=" O ALA A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 525 removed outlier: 3.504A pdb=" N HIS A 506 " --> pdb=" O GLN A 502 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE A 513 " --> pdb=" O TYR A 509 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU A 525 " --> pdb=" O LEU A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 560 removed outlier: 3.812A pdb=" N GLY A 546 " --> pdb=" O CYS A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 582 removed outlier: 3.630A pdb=" N ILE A 582 " --> pdb=" O ILE A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 598 Processing helix chain 'A' and resid 601 through 625 Processing helix chain 'A' and resid 643 through 655 Processing helix chain 'A' and resid 659 through 668 Processing helix chain 'A' and resid 672 through 675 No H-bonds generated for 'chain 'A' and resid 672 through 675' Processing helix chain 'A' and resid 677 through 727 removed outlier: 3.502A pdb=" N ILE A 681 " --> pdb=" O TRP A 678 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR A 682 " --> pdb=" O SER A 679 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE A 689 " --> pdb=" O LEU A 686 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N TYR A 692 " --> pdb=" O PHE A 689 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N THR A 693 " --> pdb=" O GLY A 690 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N LEU A 694 " --> pdb=" O ASN A 691 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE A 698 " --> pdb=" O LEU A 695 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU A 699 " --> pdb=" O ASN A 696 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ALA A 707 " --> pdb=" O ASP A 704 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ASN A 708 " --> pdb=" O ASN A 705 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLN A 717 " --> pdb=" O LYS A 714 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLU A 718 " --> pdb=" O ASP A 715 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLU A 719 " --> pdb=" O GLU A 716 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N GLU A 720 " --> pdb=" O GLN A 717 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU A 721 " --> pdb=" O GLU A 718 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ALA A 722 " --> pdb=" O GLU A 719 " (cutoff:3.500A) Processing helix chain 'A' and resid 777 through 787 Processing helix chain 'A' and resid 1145 through 1150 Processing helix chain 'A' and resid 1156 through 1171 Processing helix chain 'A' and resid 1181 through 1208 removed outlier: 3.538A pdb=" N VAL A1192 " --> pdb=" O TYR A1188 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N MET A1201 " --> pdb=" O PHE A1197 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ILE A1203 " --> pdb=" O PHE A1199 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N LYS A1204 " --> pdb=" O GLU A1200 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASP A1207 " --> pdb=" O ILE A1203 " (cutoff:3.500A) Processing helix chain 'A' and resid 1222 through 1240 removed outlier: 3.896A pdb=" N LEU A1225 " --> pdb=" O TRP A1222 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASP A1226 " --> pdb=" O ASN A1223 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL A1231 " --> pdb=" O VAL A1228 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLY A1232 " --> pdb=" O VAL A1229 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL A1235 " --> pdb=" O GLY A1232 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LEU A1239 " --> pdb=" O ALA A1236 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ALA A1240 " --> pdb=" O PHE A1237 " (cutoff:3.500A) Processing helix chain 'A' and resid 1252 through 1263 removed outlier: 4.601A pdb=" N LEU A1260 " --> pdb=" O SER A1256 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N ARG A1261 " --> pdb=" O LEU A1257 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N VAL A1262 " --> pdb=" O ARG A1258 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N LEU A1263 " --> pdb=" O VAL A1259 " (cutoff:3.500A) Processing helix chain 'A' and resid 1265 through 1271 removed outlier: 3.553A pdb=" N ILE A1269 " --> pdb=" O LEU A1266 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N LYS A1270 " --> pdb=" O LYS A1267 " (cutoff:3.500A) Processing helix chain 'A' and resid 1273 through 1311 removed outlier: 4.458A pdb=" N ASN A1291 " --> pdb=" O LYS A1287 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N ILE A1292 " --> pdb=" O ASN A1288 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL A1295 " --> pdb=" O ASN A1291 " (cutoff:3.500A) Processing helix chain 'A' and resid 1337 through 1339 No H-bonds generated for 'chain 'A' and resid 1337 through 1339' Processing helix chain 'A' and resid 1358 through 1370 Processing helix chain 'A' and resid 1374 through 1382 Processing helix chain 'A' and resid 1397 through 1409 removed outlier: 3.536A pdb=" N TYR A1403 " --> pdb=" O SER A1400 " (cutoff:3.500A) Processing helix chain 'A' and resid 1414 through 1424 Processing helix chain 'A' and resid 1443 through 1452 removed outlier: 4.664A pdb=" N ILE A1451 " --> pdb=" O ILE A1447 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N SER A1452 " --> pdb=" O ASP A1448 " (cutoff:3.500A) Processing helix chain 'A' and resid 1468 through 1474 removed outlier: 4.171A pdb=" N PHE A1474 " --> pdb=" O ARG A1470 " (cutoff:3.500A) Processing helix chain 'A' and resid 1478 through 1497 removed outlier: 3.600A pdb=" N MET A1497 " --> pdb=" O VAL A1493 " (cutoff:3.500A) Processing helix chain 'A' and resid 1504 through 1531 removed outlier: 3.638A pdb=" N VAL A1529 " --> pdb=" O CYS A1525 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE A1530 " --> pdb=" O VAL A1526 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA A1531 " --> pdb=" O LEU A1527 " (cutoff:3.500A) Processing helix chain 'A' and resid 1534 through 1539 removed outlier: 4.041A pdb=" N PHE A1538 " --> pdb=" O PHE A1534 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N ARG A1539 " --> pdb=" O LEU A1535 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1534 through 1539' Processing helix chain 'A' and resid 1541 through 1559 Processing helix chain 'A' and resid 1573 through 1588 removed outlier: 3.597A pdb=" N LYS A1576 " --> pdb=" O SER A1573 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ALA A1581 " --> pdb=" O PHE A1578 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG A1582 " --> pdb=" O ARG A1579 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU A1583 " --> pdb=" O ALA A1580 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ILE A1584 " --> pdb=" O ALA A1581 " (cutoff:3.500A) Processing helix chain 'A' and resid 1591 through 1604 Processing helix chain 'A' and resid 1610 through 1629 Processing helix chain 'A' and resid 1649 through 1660 Processing helix chain 'A' and resid 1665 through 1671 Processing helix chain 'A' and resid 1699 through 1729 removed outlier: 3.597A pdb=" N PHE A1706 " --> pdb=" O TYR A1702 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP A1724 " --> pdb=" O ALA A1720 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASN A1725 " --> pdb=" O VAL A1721 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N GLU A1727 " --> pdb=" O MET A1723 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N TYR A1728 " --> pdb=" O ASP A1724 " (cutoff:3.500A) Processing helix chain 'A' and resid 1741 through 1751 Processing helix chain 'A' and resid 1767 through 1770 No H-bonds generated for 'chain 'A' and resid 1767 through 1770' Processing helix chain 'A' and resid 1781 through 1788 removed outlier: 4.037A pdb=" N LYS A1784 " --> pdb=" O CYS A1781 " (cutoff:3.500A) Processing helix chain 'A' and resid 1796 through 1798 No H-bonds generated for 'chain 'A' and resid 1796 through 1798' Processing helix chain 'A' and resid 1806 through 1816 Processing helix chain 'A' and resid 1829 through 1839 Processing helix chain 'B' and resid 39 through 54 removed outlier: 3.569A pdb=" N GLU B 53 " --> pdb=" O GLN B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 133 Processing helix chain 'B' and resid 156 through 158 No H-bonds generated for 'chain 'B' and resid 156 through 158' Processing helix chain 'B' and resid 191 through 207 removed outlier: 3.777A pdb=" N ALA B 199 " --> pdb=" O MET B 195 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N LEU B 200 " --> pdb=" O MET B 196 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N PHE B 201 " --> pdb=" O GLN B 197 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASP B 202 " --> pdb=" O LYS B 198 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N PHE B 203 " --> pdb=" O ALA B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 263 removed outlier: 4.558A pdb=" N GLU B 255 " --> pdb=" O GLN B 251 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ARG B 256 " --> pdb=" O SER B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 280 Processing helix chain 'B' and resid 297 through 305 removed outlier: 4.140A pdb=" N GLN B 301 " --> pdb=" O LYS B 298 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG B 302 " --> pdb=" O VAL B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 313 Processing helix chain 'B' and resid 315 through 326 removed outlier: 3.655A pdb=" N ALA B 321 " --> pdb=" O VAL B 317 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N TYR B 322 " --> pdb=" O GLN B 318 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASP B 323 " --> pdb=" O MET B 319 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS B 324 " --> pdb=" O MET B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 332 No H-bonds generated for 'chain 'B' and resid 330 through 332' Processing helix chain 'B' and resid 342 through 360 Processing helix chain 'C' and resid 30 through 52 Processing helix chain 'C' and resid 54 through 64 removed outlier: 3.536A pdb=" N VAL C 58 " --> pdb=" O VAL C 54 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ASP C 59 " --> pdb=" O ASN C 55 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE C 60 " --> pdb=" O GLN C 56 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N TYR C 64 " --> pdb=" O ILE C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 109 Processing helix chain 'C' and resid 177 through 199 removed outlier: 3.547A pdb=" N TRP C 185 " --> pdb=" O ASN C 181 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N SER C 187 " --> pdb=" O LEU C 183 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ALA C 188 " --> pdb=" O ASN C 184 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N LEU C 189 " --> pdb=" O TRP C 185 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ASP C 190 " --> pdb=" O THR C 186 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N GLU C 191 " --> pdb=" O SER C 187 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N VAL C 192 " --> pdb=" O ALA C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 240 No H-bonds generated for 'chain 'C' and resid 238 through 240' Processing helix chain 'C' and resid 242 through 248 removed outlier: 3.725A pdb=" N GLY C 247 " --> pdb=" O TRP C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 264 No H-bonds generated for 'chain 'C' and resid 262 through 264' Processing helix chain 'C' and resid 267 through 282 removed outlier: 3.651A pdb=" N GLU C 281 " --> pdb=" O SER C 277 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N THR C 282 " --> pdb=" O GLU C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 322 removed outlier: 3.539A pdb=" N LYS C 316 " --> pdb=" O VAL C 312 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL C 317 " --> pdb=" O ARG C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 345 Processing helix chain 'C' and resid 370 through 373 No H-bonds generated for 'chain 'C' and resid 370 through 373' Processing helix chain 'C' and resid 397 through 404 removed outlier: 3.748A pdb=" N CYS C 404 " --> pdb=" O GLN C 400 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 4.220A pdb=" N ARG C 420 " --> pdb=" O GLY C 417 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE C 421 " --> pdb=" O ALA C 418 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASN C 422 " --> pdb=" O ILE C 419 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 430 removed outlier: 3.583A pdb=" N LEU C 430 " --> pdb=" O LEU C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 432 through 436 Processing helix chain 'C' and resid 438 through 441 Processing helix chain 'C' and resid 494 through 500 removed outlier: 3.670A pdb=" N LEU C 500 " --> pdb=" O ASP C 496 " (cutoff:3.500A) Processing helix chain 'C' and resid 561 through 564 No H-bonds generated for 'chain 'C' and resid 561 through 564' Processing helix chain 'C' and resid 569 through 580 removed outlier: 3.555A pdb=" N GLU C 573 " --> pdb=" O ASP C 569 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASP C 580 " --> pdb=" O ASN C 576 " (cutoff:3.500A) Processing helix chain 'C' and resid 638 through 647 removed outlier: 3.588A pdb=" N ARG C 643 " --> pdb=" O ILE C 639 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLU C 646 " --> pdb=" O ALA C 642 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N THR C 647 " --> pdb=" O ARG C 643 " (cutoff:3.500A) Processing helix chain 'C' and resid 650 through 652 No H-bonds generated for 'chain 'C' and resid 650 through 652' Processing helix chain 'C' and resid 679 through 689 Processing helix chain 'C' and resid 699 through 718 removed outlier: 3.625A pdb=" N ASP C 708 " --> pdb=" O ARG C 704 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ALA C 709 " --> pdb=" O VAL C 705 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY C 710 " --> pdb=" O LEU C 706 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 748 No H-bonds generated for 'chain 'C' and resid 746 through 748' Processing helix chain 'C' and resid 758 through 760 No H-bonds generated for 'chain 'C' and resid 758 through 760' Processing helix chain 'C' and resid 762 through 769 removed outlier: 3.525A pdb=" N ASP C 769 " --> pdb=" O LYS C 765 " (cutoff:3.500A) Processing helix chain 'C' and resid 818 through 826 removed outlier: 3.510A pdb=" N ASN C 824 " --> pdb=" O SER C 820 " (cutoff:3.500A) Processing helix chain 'C' and resid 875 through 878 No H-bonds generated for 'chain 'C' and resid 875 through 878' Processing helix chain 'C' and resid 880 through 888 Processing helix chain 'C' and resid 1043 through 1046 No H-bonds generated for 'chain 'C' and resid 1043 through 1046' Processing sheet with id= A, first strand: chain 'A' and resid 249 through 251 Processing sheet with id= B, first strand: chain 'A' and resid 1316 through 1318 Processing sheet with id= C, first strand: chain 'A' and resid 1332 through 1335 Processing sheet with id= D, first strand: chain 'B' and resid 171 through 174 removed outlier: 4.150A pdb=" N ALA B 63 " --> pdb=" O VAL B 174 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N ILE B 105 " --> pdb=" O LYS B 96 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 180 through 183 removed outlier: 5.413A pdb=" N ILE B 288 " --> pdb=" O VAL B 181 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N VAL B 183 " --> pdb=" O ILE B 288 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N VAL B 290 " --> pdb=" O VAL B 183 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N VAL B 335 " --> pdb=" O PHE B 291 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'B' and resid 212 through 214 removed outlier: 6.424A pdb=" N LEU B 266 " --> pdb=" O SER B 213 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'C' and resid 68 through 72 Processing sheet with id= H, first strand: chain 'C' and resid 165 through 167 removed outlier: 6.625A pdb=" N VAL C 466 " --> pdb=" O LEU C 485 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N VAL C 487 " --> pdb=" O LEU C 464 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N LEU C 464 " --> pdb=" O VAL C 487 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 409 through 413 removed outlier: 3.706A pdb=" N TYR C 409 " --> pdb=" O VAL C 384 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N LEU C 255 " --> pdb=" O MET C 359 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N PHE C 361 " --> pdb=" O LEU C 255 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N LEU C 257 " --> pdb=" O PHE C 361 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ASN C 290 " --> pdb=" O ILE C 256 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N VAL C 258 " --> pdb=" O ASN C 290 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ALA C 292 " --> pdb=" O VAL C 258 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 459 through 461 Processing sheet with id= K, first strand: chain 'C' and resid 511 through 515 Processing sheet with id= L, first strand: chain 'C' and resid 741 through 743 removed outlier: 6.501A pdb=" N LYS C 815 " --> pdb=" O LYS C 730 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N ARG C 732 " --> pdb=" O GLY C 813 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N GLY C 813 " --> pdb=" O ARG C 732 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N VAL C 734 " --> pdb=" O VAL C 811 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N VAL C 811 " --> pdb=" O VAL C 734 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 774 through 776 removed outlier: 3.582A pdb=" N MET C 793 " --> pdb=" O THR C 776 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 848 through 853 removed outlier: 3.563A pdb=" N VAL C1018 " --> pdb=" O ASP C 849 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N GLU C1019 " --> pdb=" O ILE C1002 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N ILE C1002 " --> pdb=" O GLU C1019 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 892 through 899 removed outlier: 3.888A pdb=" N ASN C 895 " --> pdb=" O GLN C 980 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLN C 980 " --> pdb=" O ASN C 895 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 903 through 905 837 hydrogen bonds defined for protein. 2205 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: 7.41 Time building geometry restraints manager: 9.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3363 1.31 - 1.43: 5757 1.43 - 1.56: 12094 1.56 - 1.69: 17 1.69 - 1.82: 189 Bond restraints: 21420 Sorted by residual: bond pdb=" C1 NAG F 3 " pdb=" O5 NAG F 3 " ideal model delta sigma weight residual 1.406 1.494 -0.088 2.00e-02 2.50e+03 1.91e+01 bond pdb=" C1 NAG H 2 " pdb=" O5 NAG H 2 " ideal model delta sigma weight residual 1.406 1.487 -0.081 2.00e-02 2.50e+03 1.65e+01 bond pdb=" C1 NAG C1202 " pdb=" O5 NAG C1202 " ideal model delta sigma weight residual 1.406 1.475 -0.069 2.00e-02 2.50e+03 1.19e+01 bond pdb=" C9 PT5 A2409 " pdb=" O18 PT5 A2409 " ideal model delta sigma weight residual 1.410 1.464 -0.054 2.00e-02 2.50e+03 7.43e+00 bond pdb=" CA PRO A 89 " pdb=" C PRO A 89 " ideal model delta sigma weight residual 1.517 1.542 -0.025 9.30e-03 1.16e+04 7.15e+00 ... (remaining 21415 not shown) Histogram of bond angle deviations from ideal: 98.85 - 109.69: 2079 109.69 - 120.54: 19011 120.54 - 131.38: 7878 131.38 - 142.23: 40 142.23 - 153.07: 3 Bond angle restraints: 29011 Sorted by residual: angle pdb=" C18 PT5 A2409 " pdb=" C19 PT5 A2409 " pdb=" C20 PT5 A2409 " ideal model delta sigma weight residual 85.86 151.89 -66.03 3.00e+00 1.11e-01 4.84e+02 angle pdb=" N PRO B 330 " pdb=" CA PRO B 330 " pdb=" C PRO B 330 " ideal model delta sigma weight residual 113.75 107.64 6.11 1.49e+00 4.50e-01 1.68e+01 angle pdb=" CA GLN A 373 " pdb=" CB GLN A 373 " pdb=" CG GLN A 373 " ideal model delta sigma weight residual 114.10 120.38 -6.28 2.00e+00 2.50e-01 9.85e+00 angle pdb=" C TRP A 88 " pdb=" N PRO A 89 " pdb=" CA PRO A 89 " ideal model delta sigma weight residual 120.38 117.36 3.02 1.03e+00 9.43e-01 8.62e+00 angle pdb=" N VAL B 73 " pdb=" CA VAL B 73 " pdb=" C VAL B 73 " ideal model delta sigma weight residual 113.39 109.22 4.17 1.47e+00 4.63e-01 8.03e+00 ... (remaining 29006 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.22: 12329 28.22 - 56.43: 821 56.43 - 84.65: 84 84.65 - 112.86: 35 112.86 - 141.08: 6 Dihedral angle restraints: 13275 sinusoidal: 5829 harmonic: 7446 Sorted by residual: dihedral pdb=" CA PHE C 894 " pdb=" C PHE C 894 " pdb=" N ASN C 895 " pdb=" CA ASN C 895 " ideal model delta harmonic sigma weight residual 180.00 151.58 28.42 0 5.00e+00 4.00e-02 3.23e+01 dihedral pdb=" C13 PT5 A2409 " pdb=" C10 PT5 A2409 " pdb=" C12 PT5 A2409 " pdb=" O16 PT5 A2409 " ideal model delta sinusoidal sigma weight residual 133.87 -85.05 -141.08 1 3.00e+01 1.11e-03 1.90e+01 dihedral pdb=" C21 PT5 A2409 " pdb=" C22 PT5 A2409 " pdb=" C23 PT5 A2409 " pdb=" C24 PT5 A2409 " ideal model delta sinusoidal sigma weight residual -14.04 125.83 -139.87 1 3.00e+01 1.11e-03 1.88e+01 ... (remaining 13272 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.121: 3269 0.121 - 0.242: 18 0.242 - 0.363: 3 0.363 - 0.483: 0 0.483 - 0.604: 1 Chirality restraints: 3291 Sorted by residual: chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN C 895 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.80 -0.60 2.00e-01 2.50e+01 9.13e+00 chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN C 348 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN C 184 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.08e+00 ... (remaining 3288 not shown) Planarity restraints: 3636 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR C 744 " 0.063 5.00e-02 4.00e+02 9.48e-02 1.44e+01 pdb=" N PRO C 745 " -0.164 5.00e-02 4.00e+02 pdb=" CA PRO C 745 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO C 745 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS C 649 " -0.058 5.00e-02 4.00e+02 8.85e-02 1.25e+01 pdb=" N PRO C 650 " 0.153 5.00e-02 4.00e+02 pdb=" CA PRO C 650 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO C 650 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A1737 " 0.036 5.00e-02 4.00e+02 5.48e-02 4.81e+00 pdb=" N PRO A1738 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO A1738 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A1738 " 0.031 5.00e-02 4.00e+02 ... (remaining 3633 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1991 2.74 - 3.28: 20849 3.28 - 3.82: 33744 3.82 - 4.36: 39889 4.36 - 4.90: 68567 Nonbonded interactions: 165040 Sorted by model distance: nonbonded pdb=" O4 NAG E 2 " pdb=" O7 NAG E 2 " model vdw 2.205 2.440 nonbonded pdb=" O GLN C 717 " pdb=" OG SER C 721 " model vdw 2.206 2.440 nonbonded pdb=" OH TYR C 450 " pdb=" OG1 THR C 461 " model vdw 2.218 2.440 nonbonded pdb=" OG SER C 673 " pdb=" OE2 GLU C 678 " model vdw 2.234 2.440 nonbonded pdb=" OD1 ASN C 468 " pdb=" N2 NAG F 1 " model vdw 2.243 2.520 ... (remaining 165035 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'G' selection = chain 'H' } 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: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.120 Check model and map are aligned: 0.310 Set scattering table: 0.210 Process input model: 60.190 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.130 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7043 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 : 0.003 0.088 21420 Z= 0.208 Angle : 0.651 66.029 29011 Z= 0.297 Chirality : 0.042 0.604 3291 Planarity : 0.004 0.095 3629 Dihedral : 18.441 141.077 8427 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.57 % Favored : 95.35 % Rotamer: Outliers : 0.27 % Allowed : 18.51 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.52 (0.17), residues: 2516 helix: 0.55 (0.15), residues: 1175 sheet: -0.32 (0.32), residues: 274 loop : -1.33 (0.19), residues: 1067 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A1472 HIS 0.003 0.001 HIS A 266 PHE 0.013 0.001 PHE C 149 TYR 0.011 0.001 TYR A1537 ARG 0.003 0.000 ARG A 384 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 249 time to evaluate : 2.482 Fit side-chains revert: symmetry clash REVERT: A 1200 GLU cc_start: 0.7497 (pt0) cc_final: 0.7197 (pt0) REVERT: A 1519 MET cc_start: 0.6399 (mmm) cc_final: 0.6131 (mmm) REVERT: A 1801 MET cc_start: 0.0597 (mmt) cc_final: -0.0016 (mmt) REVERT: B 260 LEU cc_start: 0.4373 (tp) cc_final: 0.3880 (mt) outliers start: 6 outliers final: 1 residues processed: 251 average time/residue: 0.2994 time to fit residues: 122.0067 Evaluate side-chains 238 residues out of total 2247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 237 time to evaluate : 2.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 213 optimal weight: 1.9990 chunk 191 optimal weight: 0.0870 chunk 106 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 129 optimal weight: 9.9990 chunk 102 optimal weight: 1.9990 chunk 198 optimal weight: 0.9980 chunk 76 optimal weight: 8.9990 chunk 120 optimal weight: 0.2980 chunk 147 optimal weight: 4.9990 chunk 229 optimal weight: 2.9990 overall best weight: 1.0762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 HIS ** C 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 595 GLN C 718 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7044 moved from start: 0.0643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 21420 Z= 0.182 Angle : 0.539 9.403 29011 Z= 0.267 Chirality : 0.043 0.466 3291 Planarity : 0.004 0.068 3629 Dihedral : 12.747 132.648 3506 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 2.05 % Allowed : 18.02 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.25 (0.17), residues: 2516 helix: 0.87 (0.15), residues: 1188 sheet: -0.22 (0.31), residues: 280 loop : -1.35 (0.19), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 88 HIS 0.004 0.001 HIS B 348 PHE 0.012 0.001 PHE C 513 TYR 0.013 0.001 TYR A 479 ARG 0.005 0.000 ARG B 358 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 256 time to evaluate : 2.481 Fit side-chains revert: symmetry clash REVERT: A 523 MET cc_start: 0.6046 (tpt) cc_final: 0.4196 (tmm) REVERT: A 1200 GLU cc_start: 0.7550 (pt0) cc_final: 0.7294 (pt0) REVERT: A 1472 TRP cc_start: 0.6920 (t60) cc_final: 0.6578 (t60) REVERT: A 1519 MET cc_start: 0.6522 (mmm) cc_final: 0.6187 (mmm) REVERT: A 1850 MET cc_start: 0.3082 (tpt) cc_final: 0.1691 (mtt) REVERT: B 124 LEU cc_start: 0.3415 (OUTLIER) cc_final: 0.3146 (mp) REVERT: C 320 ASP cc_start: 0.8610 (m-30) cc_final: 0.8313 (m-30) REVERT: C 772 ASN cc_start: 0.8003 (p0) cc_final: 0.7674 (p0) outliers start: 46 outliers final: 24 residues processed: 286 average time/residue: 0.2956 time to fit residues: 138.0696 Evaluate side-chains 264 residues out of total 2247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 239 time to evaluate : 2.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 1161 LEU Chi-restraints excluded: chain A residue 1321 SER Chi-restraints excluded: chain A residue 1324 ASP Chi-restraints excluded: chain A residue 1541 THR Chi-restraints excluded: chain A residue 1592 THR Chi-restraints excluded: chain A residue 1809 LEU Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 140 ASN Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain C residue 43 ASP Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 439 ASP Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain C residue 590 THR Chi-restraints excluded: chain C residue 817 ASP Chi-restraints excluded: chain C residue 850 CYS Chi-restraints excluded: chain C residue 851 VAL Chi-restraints excluded: chain C residue 1037 THR Chi-restraints excluded: chain C residue 1059 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 127 optimal weight: 7.9990 chunk 71 optimal weight: 0.9980 chunk 191 optimal weight: 1.9990 chunk 156 optimal weight: 7.9990 chunk 63 optimal weight: 2.9990 chunk 230 optimal weight: 3.9990 chunk 248 optimal weight: 0.9980 chunk 204 optimal weight: 1.9990 chunk 228 optimal weight: 5.9990 chunk 78 optimal weight: 0.6980 chunk 184 optimal weight: 5.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 472 GLN C 595 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7052 moved from start: 0.0901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21420 Z= 0.198 Angle : 0.524 9.418 29011 Z= 0.258 Chirality : 0.043 0.460 3291 Planarity : 0.004 0.057 3629 Dihedral : 11.455 130.260 3504 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 2.80 % Allowed : 18.29 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.19 (0.17), residues: 2516 helix: 0.96 (0.15), residues: 1190 sheet: -0.23 (0.31), residues: 280 loop : -1.36 (0.19), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 185 HIS 0.003 0.001 HIS A 266 PHE 0.020 0.001 PHE A 553 TYR 0.014 0.001 TYR C 719 ARG 0.004 0.000 ARG A1693 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 259 time to evaluate : 2.333 Fit side-chains REVERT: A 512 GLU cc_start: 0.7141 (mm-30) cc_final: 0.6889 (mm-30) REVERT: A 1519 MET cc_start: 0.6432 (mmm) cc_final: 0.6060 (mmm) REVERT: A 1850 MET cc_start: 0.3203 (tpt) cc_final: 0.1877 (mtt) REVERT: B 300 LEU cc_start: 0.5768 (OUTLIER) cc_final: 0.5121 (tp) REVERT: C 198 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.7260 (mp0) REVERT: C 320 ASP cc_start: 0.8647 (m-30) cc_final: 0.8338 (m-30) REVERT: C 772 ASN cc_start: 0.8094 (p0) cc_final: 0.7705 (p0) REVERT: C 978 GLN cc_start: 0.8781 (mt0) cc_final: 0.8444 (mt0) outliers start: 63 outliers final: 44 residues processed: 305 average time/residue: 0.3073 time to fit residues: 154.9798 Evaluate side-chains 292 residues out of total 2247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 246 time to evaluate : 2.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 633 ASP Chi-restraints excluded: chain A residue 1161 LEU Chi-restraints excluded: chain A residue 1178 THR Chi-restraints excluded: chain A residue 1321 SER Chi-restraints excluded: chain A residue 1324 ASP Chi-restraints excluded: chain A residue 1384 VAL Chi-restraints excluded: chain A residue 1541 THR Chi-restraints excluded: chain A residue 1549 THR Chi-restraints excluded: chain A residue 1583 LEU Chi-restraints excluded: chain A residue 1592 THR Chi-restraints excluded: chain A residue 1607 LEU Chi-restraints excluded: chain A residue 1617 LEU Chi-restraints excluded: chain A residue 1809 LEU Chi-restraints excluded: chain A residue 1839 THR Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 140 ASN Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 312 MET Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain C residue 43 ASP Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 439 ASP Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain C residue 590 THR Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain C residue 817 ASP Chi-restraints excluded: chain C residue 826 THR Chi-restraints excluded: chain C residue 849 ASP Chi-restraints excluded: chain C residue 850 CYS Chi-restraints excluded: chain C residue 979 THR Chi-restraints excluded: chain C residue 1037 THR Chi-restraints excluded: chain C residue 1045 ASP Chi-restraints excluded: chain C residue 1059 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 227 optimal weight: 0.9990 chunk 173 optimal weight: 1.9990 chunk 119 optimal weight: 40.0000 chunk 25 optimal weight: 0.5980 chunk 109 optimal weight: 6.9990 chunk 154 optimal weight: 5.9990 chunk 230 optimal weight: 0.9980 chunk 244 optimal weight: 0.7980 chunk 120 optimal weight: 2.9990 chunk 218 optimal weight: 6.9990 chunk 65 optimal weight: 0.0670 overall best weight: 0.6920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 595 GLN C1042 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7024 moved from start: 0.1102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 21420 Z= 0.143 Angle : 0.492 9.425 29011 Z= 0.241 Chirality : 0.041 0.436 3291 Planarity : 0.004 0.056 3629 Dihedral : 10.755 127.348 3504 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 2.76 % Allowed : 18.78 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.01 (0.17), residues: 2516 helix: 1.14 (0.15), residues: 1188 sheet: -0.10 (0.32), residues: 272 loop : -1.32 (0.19), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 185 HIS 0.004 0.000 HIS A 266 PHE 0.026 0.001 PHE A 553 TYR 0.015 0.001 TYR B 190 ARG 0.003 0.000 ARG C 114 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 270 time to evaluate : 2.416 Fit side-chains REVERT: A 142 LYS cc_start: 0.7265 (mtmt) cc_final: 0.6937 (mttp) REVERT: A 230 PHE cc_start: 0.8551 (t80) cc_final: 0.8252 (t80) REVERT: A 512 GLU cc_start: 0.7267 (mm-30) cc_final: 0.6976 (mm-30) REVERT: A 523 MET cc_start: 0.5772 (tpt) cc_final: 0.4367 (tmm) REVERT: A 557 TRP cc_start: 0.6303 (t-100) cc_final: 0.5887 (t60) REVERT: A 1200 GLU cc_start: 0.7254 (OUTLIER) cc_final: 0.6699 (pt0) REVERT: A 1497 MET cc_start: 0.9012 (ttm) cc_final: 0.8792 (ttm) REVERT: A 1519 MET cc_start: 0.6337 (mmm) cc_final: 0.5901 (mmm) REVERT: A 1604 PHE cc_start: 0.8892 (OUTLIER) cc_final: 0.8418 (m-80) REVERT: A 1850 MET cc_start: 0.3288 (tpt) cc_final: 0.1973 (mtt) REVERT: C 198 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7223 (mp0) REVERT: C 309 GLN cc_start: 0.9165 (OUTLIER) cc_final: 0.8411 (tt0) REVERT: C 320 ASP cc_start: 0.8568 (m-30) cc_final: 0.8255 (m-30) REVERT: C 772 ASN cc_start: 0.8083 (p0) cc_final: 0.7684 (p0) REVERT: C 865 ASP cc_start: 0.6973 (OUTLIER) cc_final: 0.6267 (t0) REVERT: C 978 GLN cc_start: 0.8768 (mt0) cc_final: 0.8416 (mt0) outliers start: 62 outliers final: 43 residues processed: 318 average time/residue: 0.2965 time to fit residues: 154.6142 Evaluate side-chains 306 residues out of total 2247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 258 time to evaluate : 2.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 492 CYS Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 633 ASP Chi-restraints excluded: chain A residue 1161 LEU Chi-restraints excluded: chain A residue 1200 GLU Chi-restraints excluded: chain A residue 1321 SER Chi-restraints excluded: chain A residue 1384 VAL Chi-restraints excluded: chain A residue 1541 THR Chi-restraints excluded: chain A residue 1592 THR Chi-restraints excluded: chain A residue 1604 PHE Chi-restraints excluded: chain A residue 1607 LEU Chi-restraints excluded: chain A residue 1809 LEU Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 140 ASN Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 312 MET Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain C residue 43 ASP Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 309 GLN Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 439 ASP Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain C residue 590 THR Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 817 ASP Chi-restraints excluded: chain C residue 849 ASP Chi-restraints excluded: chain C residue 850 CYS Chi-restraints excluded: chain C residue 851 VAL Chi-restraints excluded: chain C residue 865 ASP Chi-restraints excluded: chain C residue 979 THR Chi-restraints excluded: chain C residue 1037 THR Chi-restraints excluded: chain C residue 1045 ASP Chi-restraints excluded: chain C residue 1059 CYS Chi-restraints excluded: chain C residue 1064 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 203 optimal weight: 0.0980 chunk 138 optimal weight: 20.0000 chunk 3 optimal weight: 7.9990 chunk 182 optimal weight: 3.9990 chunk 100 optimal weight: 0.9990 chunk 208 optimal weight: 0.0270 chunk 169 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 124 optimal weight: 10.0000 chunk 219 optimal weight: 7.9990 chunk 61 optimal weight: 3.9990 overall best weight: 1.6244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 591 ASN A 788 HIS C 55 ASN C 595 GLN C1033 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7064 moved from start: 0.1209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21420 Z= 0.225 Angle : 0.532 9.708 29011 Z= 0.261 Chirality : 0.043 0.453 3291 Planarity : 0.004 0.059 3629 Dihedral : 10.534 127.780 3504 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 3.52 % Allowed : 18.51 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.13 (0.17), residues: 2516 helix: 1.04 (0.15), residues: 1194 sheet: -0.20 (0.31), residues: 273 loop : -1.38 (0.19), residues: 1049 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 243 HIS 0.003 0.001 HIS A 151 PHE 0.027 0.001 PHE A 553 TYR 0.015 0.001 TYR C 719 ARG 0.002 0.000 ARG C 114 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 265 time to evaluate : 2.528 Fit side-chains revert: symmetry clash REVERT: A 142 LYS cc_start: 0.7324 (mtmt) cc_final: 0.6965 (mttp) REVERT: A 172 ILE cc_start: 0.6996 (OUTLIER) cc_final: 0.6710 (mm) REVERT: A 504 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.7778 (tt) REVERT: A 512 GLU cc_start: 0.7244 (mm-30) cc_final: 0.6985 (mm-30) REVERT: A 523 MET cc_start: 0.5972 (tpt) cc_final: 0.4531 (tmm) REVERT: A 1497 MET cc_start: 0.9062 (ttm) cc_final: 0.8839 (ttm) REVERT: A 1519 MET cc_start: 0.6389 (mmm) cc_final: 0.5928 (mmm) REVERT: A 1693 ARG cc_start: 0.7678 (mmt90) cc_final: 0.7299 (mmm160) REVERT: A 1850 MET cc_start: 0.3303 (tpt) cc_final: 0.1991 (mtt) REVERT: C 309 GLN cc_start: 0.9230 (OUTLIER) cc_final: 0.8544 (tt0) REVERT: C 320 ASP cc_start: 0.8602 (m-30) cc_final: 0.8290 (m-30) REVERT: C 772 ASN cc_start: 0.8086 (p0) cc_final: 0.7703 (p0) REVERT: C 978 GLN cc_start: 0.8813 (mt0) cc_final: 0.8399 (mt0) outliers start: 79 outliers final: 61 residues processed: 325 average time/residue: 0.2904 time to fit residues: 153.5977 Evaluate side-chains 327 residues out of total 2247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 263 time to evaluate : 2.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 492 CYS Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 633 ASP Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 718 GLU Chi-restraints excluded: chain A residue 1149 ILE Chi-restraints excluded: chain A residue 1161 LEU Chi-restraints excluded: chain A residue 1178 THR Chi-restraints excluded: chain A residue 1200 GLU Chi-restraints excluded: chain A residue 1321 SER Chi-restraints excluded: chain A residue 1324 ASP Chi-restraints excluded: chain A residue 1384 VAL Chi-restraints excluded: chain A residue 1505 THR Chi-restraints excluded: chain A residue 1535 LEU Chi-restraints excluded: chain A residue 1541 THR Chi-restraints excluded: chain A residue 1549 THR Chi-restraints excluded: chain A residue 1583 LEU Chi-restraints excluded: chain A residue 1592 THR Chi-restraints excluded: chain A residue 1607 LEU Chi-restraints excluded: chain A residue 1617 LEU Chi-restraints excluded: chain A residue 1809 LEU Chi-restraints excluded: chain A residue 1817 LEU Chi-restraints excluded: chain A residue 1839 THR Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 140 ASN Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain C residue 43 ASP Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 309 GLN Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 439 ASP Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain C residue 590 THR Chi-restraints excluded: chain C residue 668 ASN Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 741 THR Chi-restraints excluded: chain C residue 817 ASP Chi-restraints excluded: chain C residue 826 THR Chi-restraints excluded: chain C residue 849 ASP Chi-restraints excluded: chain C residue 850 CYS Chi-restraints excluded: chain C residue 851 VAL Chi-restraints excluded: chain C residue 979 THR Chi-restraints excluded: chain C residue 1037 THR Chi-restraints excluded: chain C residue 1045 ASP Chi-restraints excluded: chain C residue 1059 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 82 optimal weight: 0.8980 chunk 220 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 chunk 143 optimal weight: 0.8980 chunk 60 optimal weight: 5.9990 chunk 244 optimal weight: 0.7980 chunk 203 optimal weight: 3.9990 chunk 113 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 chunk 128 optimal weight: 5.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 595 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7041 moved from start: 0.1316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 21420 Z= 0.156 Angle : 0.494 9.819 29011 Z= 0.242 Chirality : 0.041 0.443 3291 Planarity : 0.004 0.059 3629 Dihedral : 10.211 126.745 3504 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.98 % Allowed : 19.27 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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 (0.17), residues: 2516 helix: 1.12 (0.15), residues: 1199 sheet: -0.14 (0.31), residues: 276 loop : -1.37 (0.19), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 185 HIS 0.004 0.001 HIS A 266 PHE 0.013 0.001 PHE C 513 TYR 0.014 0.001 TYR C 719 ARG 0.003 0.000 ARG C 114 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 271 time to evaluate : 2.298 Fit side-chains revert: symmetry clash REVERT: A 142 LYS cc_start: 0.7471 (mtmt) cc_final: 0.7114 (mttp) REVERT: A 504 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.7778 (tt) REVERT: A 512 GLU cc_start: 0.7231 (mm-30) cc_final: 0.7000 (mm-30) REVERT: A 523 MET cc_start: 0.5918 (tpt) cc_final: 0.4514 (tmm) REVERT: A 1200 GLU cc_start: 0.7135 (OUTLIER) cc_final: 0.6827 (pt0) REVERT: A 1519 MET cc_start: 0.6298 (mmm) cc_final: 0.5906 (mmm) REVERT: A 1604 PHE cc_start: 0.8909 (OUTLIER) cc_final: 0.8417 (m-80) REVERT: A 1693 ARG cc_start: 0.7576 (mmt90) cc_final: 0.7173 (mmm160) REVERT: A 1850 MET cc_start: 0.3296 (tpt) cc_final: 0.1978 (mtt) REVERT: C 309 GLN cc_start: 0.9227 (OUTLIER) cc_final: 0.8499 (tt0) REVERT: C 320 ASP cc_start: 0.8600 (m-30) cc_final: 0.8294 (m-30) REVERT: C 772 ASN cc_start: 0.8065 (p0) cc_final: 0.7648 (p0) REVERT: C 978 GLN cc_start: 0.8810 (mt0) cc_final: 0.8401 (mt0) outliers start: 67 outliers final: 51 residues processed: 325 average time/residue: 0.2973 time to fit residues: 156.3869 Evaluate side-chains 313 residues out of total 2247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 258 time to evaluate : 2.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 492 CYS Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 633 ASP Chi-restraints excluded: chain A residue 718 GLU Chi-restraints excluded: chain A residue 1161 LEU Chi-restraints excluded: chain A residue 1200 GLU Chi-restraints excluded: chain A residue 1321 SER Chi-restraints excluded: chain A residue 1384 VAL Chi-restraints excluded: chain A residue 1505 THR Chi-restraints excluded: chain A residue 1535 LEU Chi-restraints excluded: chain A residue 1541 THR Chi-restraints excluded: chain A residue 1592 THR Chi-restraints excluded: chain A residue 1604 PHE Chi-restraints excluded: chain A residue 1607 LEU Chi-restraints excluded: chain A residue 1817 LEU Chi-restraints excluded: chain A residue 1839 THR Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 140 ASN Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain C residue 43 ASP Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 309 GLN Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 439 ASP Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain C residue 601 ASP Chi-restraints excluded: chain C residue 668 ASN Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 817 ASP Chi-restraints excluded: chain C residue 849 ASP Chi-restraints excluded: chain C residue 850 CYS Chi-restraints excluded: chain C residue 851 VAL Chi-restraints excluded: chain C residue 979 THR Chi-restraints excluded: chain C residue 1037 THR Chi-restraints excluded: chain C residue 1045 ASP Chi-restraints excluded: chain C residue 1059 CYS Chi-restraints excluded: chain C residue 1064 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 236 optimal weight: 8.9990 chunk 27 optimal weight: 4.9990 chunk 139 optimal weight: 0.0270 chunk 178 optimal weight: 0.0060 chunk 138 optimal weight: 3.9990 chunk 206 optimal weight: 1.9990 chunk 136 optimal weight: 3.9990 chunk 243 optimal weight: 0.0980 chunk 152 optimal weight: 5.9990 chunk 148 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 overall best weight: 1.0258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 595 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7046 moved from start: 0.1392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 21420 Z= 0.167 Angle : 0.500 10.081 29011 Z= 0.245 Chirality : 0.042 0.455 3291 Planarity : 0.004 0.088 3629 Dihedral : 10.022 126.105 3504 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 3.12 % Allowed : 19.58 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.03 (0.17), residues: 2516 helix: 1.15 (0.15), residues: 1199 sheet: -0.20 (0.31), residues: 276 loop : -1.36 (0.19), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 185 HIS 0.004 0.001 HIS A 266 PHE 0.012 0.001 PHE A1708 TYR 0.015 0.001 TYR C 719 ARG 0.002 0.000 ARG C 114 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 269 time to evaluate : 2.438 Fit side-chains revert: symmetry clash REVERT: A 142 LYS cc_start: 0.7599 (mtmt) cc_final: 0.7220 (mttp) REVERT: A 504 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.7798 (tt) REVERT: A 512 GLU cc_start: 0.7320 (mm-30) cc_final: 0.7098 (mm-30) REVERT: A 523 MET cc_start: 0.6086 (tpt) cc_final: 0.4721 (tmm) REVERT: A 1200 GLU cc_start: 0.7144 (OUTLIER) cc_final: 0.6849 (pt0) REVERT: A 1519 MET cc_start: 0.6378 (mmm) cc_final: 0.6040 (mmm) REVERT: A 1604 PHE cc_start: 0.8915 (OUTLIER) cc_final: 0.8485 (m-80) REVERT: A 1693 ARG cc_start: 0.7584 (mmt90) cc_final: 0.7185 (mmm160) REVERT: A 1850 MET cc_start: 0.3299 (tpt) cc_final: 0.1976 (mtt) REVERT: B 319 MET cc_start: 0.3859 (ppp) cc_final: 0.3652 (ppp) REVERT: C 199 GLU cc_start: 0.7178 (OUTLIER) cc_final: 0.6895 (tm-30) REVERT: C 309 GLN cc_start: 0.9232 (OUTLIER) cc_final: 0.8521 (tt0) REVERT: C 320 ASP cc_start: 0.8597 (m-30) cc_final: 0.8293 (m-30) REVERT: C 469 ILE cc_start: 0.8711 (OUTLIER) cc_final: 0.8484 (pt) REVERT: C 772 ASN cc_start: 0.8080 (p0) cc_final: 0.7713 (p0) REVERT: C 978 GLN cc_start: 0.8826 (mt0) cc_final: 0.8395 (mt0) outliers start: 70 outliers final: 56 residues processed: 324 average time/residue: 0.2995 time to fit residues: 156.9316 Evaluate side-chains 325 residues out of total 2247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 263 time to evaluate : 2.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 492 CYS Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 633 ASP Chi-restraints excluded: chain A residue 718 GLU Chi-restraints excluded: chain A residue 1149 ILE Chi-restraints excluded: chain A residue 1161 LEU Chi-restraints excluded: chain A residue 1178 THR Chi-restraints excluded: chain A residue 1200 GLU Chi-restraints excluded: chain A residue 1321 SER Chi-restraints excluded: chain A residue 1324 ASP Chi-restraints excluded: chain A residue 1384 VAL Chi-restraints excluded: chain A residue 1505 THR Chi-restraints excluded: chain A residue 1535 LEU Chi-restraints excluded: chain A residue 1541 THR Chi-restraints excluded: chain A residue 1549 THR Chi-restraints excluded: chain A residue 1592 THR Chi-restraints excluded: chain A residue 1604 PHE Chi-restraints excluded: chain A residue 1607 LEU Chi-restraints excluded: chain A residue 1617 LEU Chi-restraints excluded: chain A residue 1817 LEU Chi-restraints excluded: chain A residue 1839 THR Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 140 ASN Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain C residue 43 ASP Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 199 GLU Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 309 GLN Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 439 ASP Chi-restraints excluded: chain C residue 469 ILE Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain C residue 590 THR Chi-restraints excluded: chain C residue 601 ASP Chi-restraints excluded: chain C residue 668 ASN Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 741 THR Chi-restraints excluded: chain C residue 817 ASP Chi-restraints excluded: chain C residue 849 ASP Chi-restraints excluded: chain C residue 850 CYS Chi-restraints excluded: chain C residue 851 VAL Chi-restraints excluded: chain C residue 979 THR Chi-restraints excluded: chain C residue 1037 THR Chi-restraints excluded: chain C residue 1045 ASP Chi-restraints excluded: chain C residue 1064 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 150 optimal weight: 9.9990 chunk 97 optimal weight: 8.9990 chunk 145 optimal weight: 7.9990 chunk 73 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 155 optimal weight: 8.9990 chunk 166 optimal weight: 3.9990 chunk 120 optimal weight: 4.9990 chunk 22 optimal weight: 0.9980 chunk 191 optimal weight: 1.9990 chunk 221 optimal weight: 4.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 GLN C 595 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7093 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 21420 Z= 0.284 Angle : 0.569 10.452 29011 Z= 0.280 Chirality : 0.044 0.463 3291 Planarity : 0.004 0.077 3629 Dihedral : 10.172 127.626 3504 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 3.65 % Allowed : 19.40 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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 (0.17), residues: 2516 helix: 0.94 (0.15), residues: 1198 sheet: -0.33 (0.31), residues: 277 loop : -1.44 (0.19), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1472 HIS 0.004 0.001 HIS A 151 PHE 0.015 0.002 PHE A1410 TYR 0.017 0.002 TYR A1355 ARG 0.003 0.000 ARG C1029 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 274 time to evaluate : 2.486 Fit side-chains revert: symmetry clash REVERT: A 142 LYS cc_start: 0.7538 (mtmt) cc_final: 0.7203 (mttp) REVERT: A 172 ILE cc_start: 0.7098 (OUTLIER) cc_final: 0.6790 (mm) REVERT: A 504 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.7765 (tt) REVERT: A 512 GLU cc_start: 0.7208 (mm-30) cc_final: 0.6970 (mm-30) REVERT: A 523 MET cc_start: 0.5875 (tpt) cc_final: 0.5500 (tpt) REVERT: A 1519 MET cc_start: 0.6357 (mmm) cc_final: 0.5884 (mmm) REVERT: A 1693 ARG cc_start: 0.7647 (mmt90) cc_final: 0.7249 (mmm160) REVERT: A 1697 ASP cc_start: 0.8670 (OUTLIER) cc_final: 0.8152 (t0) REVERT: A 1850 MET cc_start: 0.3192 (tpt) cc_final: 0.2789 (mmm) REVERT: C 309 GLN cc_start: 0.9292 (OUTLIER) cc_final: 0.8697 (tt0) REVERT: C 320 ASP cc_start: 0.8615 (m-30) cc_final: 0.8311 (m-30) REVERT: C 469 ILE cc_start: 0.8770 (OUTLIER) cc_final: 0.8563 (pt) REVERT: C 978 GLN cc_start: 0.8834 (mt0) cc_final: 0.8405 (mt0) outliers start: 82 outliers final: 64 residues processed: 335 average time/residue: 0.3038 time to fit residues: 163.3445 Evaluate side-chains 331 residues out of total 2247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 262 time to evaluate : 2.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 492 CYS Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 633 ASP Chi-restraints excluded: chain A residue 704 ASP Chi-restraints excluded: chain A residue 718 GLU Chi-restraints excluded: chain A residue 1149 ILE Chi-restraints excluded: chain A residue 1161 LEU Chi-restraints excluded: chain A residue 1178 THR Chi-restraints excluded: chain A residue 1200 GLU Chi-restraints excluded: chain A residue 1223 ASN Chi-restraints excluded: chain A residue 1321 SER Chi-restraints excluded: chain A residue 1324 ASP Chi-restraints excluded: chain A residue 1384 VAL Chi-restraints excluded: chain A residue 1505 THR Chi-restraints excluded: chain A residue 1535 LEU Chi-restraints excluded: chain A residue 1541 THR Chi-restraints excluded: chain A residue 1549 THR Chi-restraints excluded: chain A residue 1561 ASP Chi-restraints excluded: chain A residue 1583 LEU Chi-restraints excluded: chain A residue 1592 THR Chi-restraints excluded: chain A residue 1607 LEU Chi-restraints excluded: chain A residue 1617 LEU Chi-restraints excluded: chain A residue 1697 ASP Chi-restraints excluded: chain A residue 1817 LEU Chi-restraints excluded: chain A residue 1839 THR Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 140 ASN Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain C residue 43 ASP Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 246 GLN Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 309 GLN Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 439 ASP Chi-restraints excluded: chain C residue 469 ILE Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain C residue 590 THR Chi-restraints excluded: chain C residue 601 ASP Chi-restraints excluded: chain C residue 668 ASN Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 741 THR Chi-restraints excluded: chain C residue 817 ASP Chi-restraints excluded: chain C residue 849 ASP Chi-restraints excluded: chain C residue 850 CYS Chi-restraints excluded: chain C residue 851 VAL Chi-restraints excluded: chain C residue 979 THR Chi-restraints excluded: chain C residue 1037 THR Chi-restraints excluded: chain C residue 1045 ASP Chi-restraints excluded: chain C residue 1059 CYS Chi-restraints excluded: chain C residue 1064 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 233 optimal weight: 5.9990 chunk 213 optimal weight: 0.7980 chunk 227 optimal weight: 0.9980 chunk 136 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 178 optimal weight: 0.3980 chunk 69 optimal weight: 1.9990 chunk 205 optimal weight: 2.9990 chunk 214 optimal weight: 0.5980 chunk 226 optimal weight: 7.9990 chunk 149 optimal weight: 9.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 374 ASN C 595 GLN C 652 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7055 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21420 Z= 0.164 Angle : 0.520 10.112 29011 Z= 0.256 Chirality : 0.042 0.448 3291 Planarity : 0.004 0.073 3629 Dihedral : 9.888 126.200 3504 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.98 % Allowed : 20.12 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.07 (0.17), residues: 2516 helix: 1.11 (0.15), residues: 1198 sheet: -0.22 (0.31), residues: 276 loop : -1.37 (0.19), residues: 1042 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 185 HIS 0.004 0.001 HIS A 266 PHE 0.013 0.001 PHE C 513 TYR 0.017 0.001 TYR C 719 ARG 0.005 0.000 ARG C 843 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 271 time to evaluate : 2.661 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 142 LYS cc_start: 0.7618 (mtmt) cc_final: 0.7266 (mttp) REVERT: A 377 GLU cc_start: 0.8130 (tp30) cc_final: 0.7772 (mm-30) REVERT: A 504 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.7801 (tt) REVERT: A 512 GLU cc_start: 0.7262 (mm-30) cc_final: 0.7030 (mm-30) REVERT: A 523 MET cc_start: 0.6008 (tpt) cc_final: 0.4798 (tmm) REVERT: A 725 GLN cc_start: 0.5781 (mm110) cc_final: 0.5361 (tm-30) REVERT: A 1200 GLU cc_start: 0.7179 (OUTLIER) cc_final: 0.6837 (pt0) REVERT: A 1519 MET cc_start: 0.6315 (mmm) cc_final: 0.5911 (mmm) REVERT: A 1693 ARG cc_start: 0.7604 (mmt90) cc_final: 0.7190 (mmm160) REVERT: A 1850 MET cc_start: 0.3176 (tpt) cc_final: 0.2773 (mmm) REVERT: C 309 GLN cc_start: 0.9264 (OUTLIER) cc_final: 0.8624 (tt0) REVERT: C 320 ASP cc_start: 0.8608 (m-30) cc_final: 0.8305 (m-30) REVERT: C 772 ASN cc_start: 0.8090 (p0) cc_final: 0.7680 (p0) REVERT: C 978 GLN cc_start: 0.8822 (mt0) cc_final: 0.8419 (mt0) outliers start: 67 outliers final: 59 residues processed: 322 average time/residue: 0.3067 time to fit residues: 159.2428 Evaluate side-chains 326 residues out of total 2247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 264 time to evaluate : 2.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 492 CYS Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 633 ASP Chi-restraints excluded: chain A residue 718 GLU Chi-restraints excluded: chain A residue 1149 ILE Chi-restraints excluded: chain A residue 1161 LEU Chi-restraints excluded: chain A residue 1178 THR Chi-restraints excluded: chain A residue 1200 GLU Chi-restraints excluded: chain A residue 1223 ASN Chi-restraints excluded: chain A residue 1321 SER Chi-restraints excluded: chain A residue 1324 ASP Chi-restraints excluded: chain A residue 1384 VAL Chi-restraints excluded: chain A residue 1535 LEU Chi-restraints excluded: chain A residue 1541 THR Chi-restraints excluded: chain A residue 1549 THR Chi-restraints excluded: chain A residue 1592 THR Chi-restraints excluded: chain A residue 1607 LEU Chi-restraints excluded: chain A residue 1617 LEU Chi-restraints excluded: chain A residue 1817 LEU Chi-restraints excluded: chain A residue 1839 THR Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 140 ASN Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain C residue 43 ASP Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 246 GLN Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 309 GLN Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 439 ASP Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain C residue 590 THR Chi-restraints excluded: chain C residue 601 ASP Chi-restraints excluded: chain C residue 652 ASN Chi-restraints excluded: chain C residue 655 GLU Chi-restraints excluded: chain C residue 668 ASN Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 741 THR Chi-restraints excluded: chain C residue 817 ASP Chi-restraints excluded: chain C residue 849 ASP Chi-restraints excluded: chain C residue 850 CYS Chi-restraints excluded: chain C residue 851 VAL Chi-restraints excluded: chain C residue 979 THR Chi-restraints excluded: chain C residue 1037 THR Chi-restraints excluded: chain C residue 1045 ASP Chi-restraints excluded: chain C residue 1059 CYS Chi-restraints excluded: chain C residue 1064 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 240 optimal weight: 5.9990 chunk 146 optimal weight: 0.0980 chunk 113 optimal weight: 0.8980 chunk 167 optimal weight: 4.9990 chunk 252 optimal weight: 6.9990 chunk 231 optimal weight: 3.9990 chunk 200 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 155 optimal weight: 1.9990 chunk 123 optimal weight: 6.9990 chunk 159 optimal weight: 0.0770 overall best weight: 0.8142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1536 ASN C 595 GLN C 844 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7048 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 21420 Z= 0.158 Angle : 0.519 9.765 29011 Z= 0.255 Chirality : 0.041 0.445 3291 Planarity : 0.004 0.069 3629 Dihedral : 9.745 125.296 3504 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 2.85 % Allowed : 20.47 % Favored : 76.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.01 (0.17), residues: 2516 helix: 1.20 (0.15), residues: 1199 sheet: -0.19 (0.31), residues: 276 loop : -1.36 (0.19), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 185 HIS 0.004 0.001 HIS A 266 PHE 0.012 0.001 PHE C 513 TYR 0.018 0.001 TYR C 719 ARG 0.007 0.000 ARG A 384 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 272 time to evaluate : 2.488 Fit side-chains revert: symmetry clash REVERT: A 136 CYS cc_start: 0.7005 (m) cc_final: 0.6710 (m) REVERT: A 142 LYS cc_start: 0.7659 (mtmt) cc_final: 0.7308 (mttp) REVERT: A 377 GLU cc_start: 0.8117 (tp30) cc_final: 0.7772 (mm-30) REVERT: A 504 LEU cc_start: 0.8375 (OUTLIER) cc_final: 0.7820 (tt) REVERT: A 512 GLU cc_start: 0.7301 (mm-30) cc_final: 0.7079 (mm-30) REVERT: A 523 MET cc_start: 0.5984 (tpt) cc_final: 0.4699 (tmm) REVERT: A 725 GLN cc_start: 0.5805 (mm110) cc_final: 0.5403 (tm-30) REVERT: A 1519 MET cc_start: 0.6358 (mmm) cc_final: 0.5968 (mmm) REVERT: A 1604 PHE cc_start: 0.8943 (OUTLIER) cc_final: 0.8473 (m-80) REVERT: A 1764 MET cc_start: 0.1246 (tpp) cc_final: 0.0921 (ptp) REVERT: A 1817 LEU cc_start: 0.2360 (OUTLIER) cc_final: 0.2118 (pp) REVERT: A 1850 MET cc_start: 0.3101 (tpt) cc_final: 0.2708 (mmm) REVERT: C 309 GLN cc_start: 0.9261 (OUTLIER) cc_final: 0.8610 (tt0) REVERT: C 320 ASP cc_start: 0.8572 (m-30) cc_final: 0.8258 (m-30) REVERT: C 772 ASN cc_start: 0.8105 (p0) cc_final: 0.7615 (p0) REVERT: C 978 GLN cc_start: 0.8810 (mt0) cc_final: 0.8401 (mt0) outliers start: 64 outliers final: 54 residues processed: 321 average time/residue: 0.3006 time to fit residues: 155.2067 Evaluate side-chains 322 residues out of total 2247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 264 time to evaluate : 2.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 492 CYS Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 633 ASP Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 718 GLU Chi-restraints excluded: chain A residue 1161 LEU Chi-restraints excluded: chain A residue 1178 THR Chi-restraints excluded: chain A residue 1200 GLU Chi-restraints excluded: chain A residue 1321 SER Chi-restraints excluded: chain A residue 1324 ASP Chi-restraints excluded: chain A residue 1384 VAL Chi-restraints excluded: chain A residue 1505 THR Chi-restraints excluded: chain A residue 1535 LEU Chi-restraints excluded: chain A residue 1541 THR Chi-restraints excluded: chain A residue 1549 THR Chi-restraints excluded: chain A residue 1592 THR Chi-restraints excluded: chain A residue 1604 PHE Chi-restraints excluded: chain A residue 1607 LEU Chi-restraints excluded: chain A residue 1617 LEU Chi-restraints excluded: chain A residue 1817 LEU Chi-restraints excluded: chain A residue 1839 THR Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 140 ASN Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain C residue 43 ASP Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 246 GLN Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 309 GLN Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 439 ASP Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain C residue 601 ASP Chi-restraints excluded: chain C residue 668 ASN Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 741 THR Chi-restraints excluded: chain C residue 817 ASP Chi-restraints excluded: chain C residue 850 CYS Chi-restraints excluded: chain C residue 851 VAL Chi-restraints excluded: chain C residue 979 THR Chi-restraints excluded: chain C residue 1037 THR Chi-restraints excluded: chain C residue 1045 ASP Chi-restraints excluded: chain C residue 1059 CYS Chi-restraints excluded: chain C residue 1064 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 213 optimal weight: 0.0470 chunk 61 optimal weight: 0.0980 chunk 185 optimal weight: 0.5980 chunk 29 optimal weight: 3.9990 chunk 55 optimal weight: 9.9990 chunk 201 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 206 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 176 optimal weight: 0.8980 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 591 ASN C 595 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.200944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 94)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.145905 restraints weight = 24815.901| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 1.72 r_work: 0.3224 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 21420 Z= 0.128 Angle : 0.495 9.440 29011 Z= 0.242 Chirality : 0.041 0.436 3291 Planarity : 0.004 0.067 3629 Dihedral : 9.357 123.546 3504 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.09 % Allowed : 21.18 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.17 (0.17), residues: 2516 helix: 1.35 (0.15), residues: 1202 sheet: -0.13 (0.31), residues: 276 loop : -1.32 (0.19), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 185 HIS 0.004 0.000 HIS A 266 PHE 0.013 0.001 PHE C 513 TYR 0.017 0.001 TYR C 719 ARG 0.007 0.000 ARG A 384 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5195.91 seconds wall clock time: 94 minutes 49.51 seconds (5689.51 seconds total)