Starting phenix.real_space_refine on Sun Aug 24 00:09:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8epm_28530/08_2025/8epm_28530.cif Found real_map, /net/cci-nas-00/data/ceres_data/8epm_28530/08_2025/8epm_28530.map 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 { model { file = "/net/cci-nas-00/data/ceres_data/8epm_28530/08_2025/8epm_28530.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8epm_28530/08_2025/8epm_28530.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8epm_28530/08_2025/8epm_28530.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8epm_28530/08_2025/8epm_28530.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 2 9.91 5 S 84 5.16 5 C 9990 2.51 5 N 2519 2.21 5 O 2863 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15458 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 7676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 991, 7676 Classifications: {'peptide': 991} Incomplete info: {'truncation_to_alanine': 75} Link IDs: {'PTRANS': 28, 'TRANS': 962} Chain breaks: 8 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 297 Unresolved non-hydrogen angles: 394 Unresolved non-hydrogen dihedrals: 257 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'ASN:plan1': 5, 'PHE:plan': 13, 'ASP:plan': 4, 'GLU:plan': 2, 'TRP:plan': 3, 'TYR:plan': 3, 'ARG:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 175 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: "B" 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: "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: 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: "F" 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: "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: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} 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: 3.28, per 1000 atoms: 0.21 Number of scatterers: 15458 At special positions: 0 Unit cell: (130.338, 142.592, 149.276, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 2 19.99 S 84 16.00 O 2863 8.00 N 2519 7.00 C 9990 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " NAG E 3 " " NAG E 3 " - " NAG E 4 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " NAG-ASN " NAG B 1 " - " ASN C 184 " " NAG C1201 " - " ASN C 92 " " NAG C1202 " - " ASN C 781 " " NAG D 1 " - " ASN C 348 " " NAG E 1 " - " ASN C 468 " " NAG F 1 " - " ASN C 613 " " NAG G 1 " - " ASN C 895 " Time building additional restraints: 2.91 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 1.2 microseconds 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3648 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 15 sheets defined 54.5% alpha, 10.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 90 through 107 Processing helix chain 'A' and resid 118 through 127 removed outlier: 3.793A pdb=" N ARG A 123 " --> pdb=" O PRO A 119 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR A 127 " --> pdb=" O ARG A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 144 removed outlier: 3.975A pdb=" N PHE A 131 " --> pdb=" O THR A 127 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ILE A 134 " --> pdb=" O TYR A 130 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE A 135 " --> pdb=" O PHE A 131 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA A 139 " --> pdb=" O PHE A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 175 Processing helix chain 'A' and resid 195 through 197 No H-bonds generated for 'chain 'A' and resid 195 through 197' Processing helix chain 'A' and resid 198 through 204 removed outlier: 4.117A pdb=" N SER A 202 " --> pdb=" O LEU A 198 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE A 204 " --> pdb=" O LEU A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 216 removed outlier: 3.622A pdb=" N GLN A 208 " --> pdb=" O ILE A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 241 removed outlier: 3.677A pdb=" N GLN A 223 " --> pdb=" O VAL A 219 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE A 224 " --> pdb=" O PRO A 220 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU A 227 " --> pdb=" O GLN A 223 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU A 228 " --> pdb=" O ILE A 224 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE A 235 " --> pdb=" O ALA A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 307 Processing helix chain 'A' and resid 310 through 323 removed outlier: 3.833A pdb=" N ALA A 321 " --> pdb=" O ASN A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 337 Proline residue: A 333 - end of helix Processing helix chain 'A' and resid 339 through 356 removed outlier: 3.707A pdb=" N GLU A 353 " --> pdb=" O VAL A 349 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS A 356 " --> pdb=" O GLY A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 494 removed outlier: 3.678A pdb=" N LEU A 488 " --> pdb=" O SER A 484 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR A 490 " --> pdb=" O VAL A 486 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALA A 491 " --> pdb=" O ALA A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 526 removed outlier: 3.549A pdb=" N PHE A 513 " --> pdb=" O TYR A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 560 removed outlier: 3.921A pdb=" N ILE A 552 " --> pdb=" O THR A 548 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N PHE A 560 " --> pdb=" O VAL A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 577 removed outlier: 3.586A pdb=" N LEU A 574 " --> pdb=" O LEU A 571 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG A 575 " --> pdb=" O ARG A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 602 Processing helix chain 'A' and resid 603 through 626 Processing helix chain 'A' and resid 642 through 656 Processing helix chain 'A' and resid 658 through 670 removed outlier: 3.577A pdb=" N VAL A 662 " --> pdb=" O ASP A 658 " (cutoff:3.500A) Processing helix chain 'A' and resid 676 through 678 No H-bonds generated for 'chain 'A' and resid 676 through 678' Processing helix chain 'A' and resid 679 through 708 removed outlier: 4.100A pdb=" N PHE A 683 " --> pdb=" O SER A 679 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASN A 696 " --> pdb=" O TYR A 692 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ALA A 707 " --> pdb=" O VAL A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 1156 through 1172 removed outlier: 3.571A pdb=" N ILE A1163 " --> pdb=" O ILE A1159 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA A1171 " --> pdb=" O SER A1167 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA A1172 " --> pdb=" O ILE A1168 " (cutoff:3.500A) Processing helix chain 'A' and resid 1180 through 1208 removed outlier: 4.333A pdb=" N TYR A1188 " --> pdb=" O LYS A1184 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N PHE A1189 " --> pdb=" O VAL A1185 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ILE A1206 " --> pdb=" O VAL A1202 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ASP A1207 " --> pdb=" O ILE A1203 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLN A1208 " --> pdb=" O LYS A1204 " (cutoff:3.500A) Processing helix chain 'A' and resid 1222 through 1241 removed outlier: 3.677A pdb=" N ASN A1241 " --> pdb=" O PHE A1237 " (cutoff:3.500A) Processing helix chain 'A' and resid 1252 through 1259 removed outlier: 3.920A pdb=" N SER A1256 " --> pdb=" O LYS A1252 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N LEU A1257 " --> pdb=" O THR A1253 " (cutoff:3.500A) Processing helix chain 'A' and resid 1260 through 1266 Proline residue: A1265 - end of helix Processing helix chain 'A' and resid 1267 through 1272 removed outlier: 3.728A pdb=" N ARG A1271 " --> pdb=" O LYS A1267 " (cutoff:3.500A) Processing helix chain 'A' and resid 1272 through 1312 removed outlier: 3.720A pdb=" N VAL A1278 " --> pdb=" O LYS A1274 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N ASN A1291 " --> pdb=" O LYS A1287 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N ILE A1292 " --> pdb=" O ASN A1288 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL A1295 " --> pdb=" O ASN A1291 " (cutoff:3.500A) Processing helix chain 'A' and resid 1336 through 1340 removed outlier: 3.553A pdb=" N ASN A1339 " --> pdb=" O HIS A1336 " (cutoff:3.500A) Processing helix chain 'A' and resid 1357 through 1371 Processing helix chain 'A' and resid 1373 through 1383 removed outlier: 3.574A pdb=" N ASP A1383 " --> pdb=" O GLN A1379 " (cutoff:3.500A) Processing helix chain 'A' and resid 1396 through 1398 No H-bonds generated for 'chain 'A' and resid 1396 through 1398' Processing helix chain 'A' and resid 1399 through 1425 removed outlier: 4.094A pdb=" N TYR A1403 " --> pdb=" O MET A1399 " (cutoff:3.500A) Proline residue: A1411 - end of helix removed outlier: 3.922A pdb=" N VAL A1415 " --> pdb=" O PRO A1411 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N ASN A1416 " --> pdb=" O PHE A1412 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL A1419 " --> pdb=" O VAL A1415 " (cutoff:3.500A) Processing helix chain 'A' and resid 1477 through 1496 removed outlier: 3.571A pdb=" N ALA A1489 " --> pdb=" O MET A1485 " (cutoff:3.500A) Processing helix chain 'A' and resid 1503 through 1533 Processing helix chain 'A' and resid 1533 through 1538 removed outlier: 4.376A pdb=" N PHE A1538 " --> pdb=" O PHE A1534 " (cutoff:3.500A) Processing helix chain 'A' and resid 1540 through 1562 removed outlier: 3.863A pdb=" N ASP A1561 " --> pdb=" O ILE A1557 " (cutoff:3.500A) Processing helix chain 'A' and resid 1575 through 1580 removed outlier: 3.936A pdb=" N ARG A1579 " --> pdb=" O LEU A1575 " (cutoff:3.500A) Processing helix chain 'A' and resid 1581 through 1587 removed outlier: 3.732A pdb=" N LYS A1585 " --> pdb=" O ALA A1581 " (cutoff:3.500A) Processing helix chain 'A' and resid 1591 through 1596 Processing helix chain 'A' and resid 1606 through 1609 Processing helix chain 'A' and resid 1610 through 1630 Processing helix chain 'A' and resid 1648 through 1662 Processing helix chain 'A' and resid 1664 through 1672 Processing helix chain 'A' and resid 1698 through 1725 Processing helix chain 'A' and resid 1725 through 1730 Processing helix chain 'C' and resid 29 through 53 Processing helix chain 'C' and resid 53 through 65 removed outlier: 3.624A pdb=" N GLN C 65 " --> pdb=" O TYR C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 110 removed outlier: 3.699A pdb=" N ALA C 110 " --> pdb=" O LYS C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 187 Processing helix chain 'C' and resid 188 through 200 removed outlier: 4.510A pdb=" N VAL C 192 " --> pdb=" O ALA C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 240 Processing helix chain 'C' and resid 241 through 249 removed outlier: 3.681A pdb=" N ALA C 249 " --> pdb=" O ILE C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 261 through 265 Processing helix chain 'C' and resid 266 through 281 removed outlier: 3.621A pdb=" N LYS C 270 " --> pdb=" O GLY C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 323 Processing helix chain 'C' and resid 332 through 344 Processing helix chain 'C' and resid 369 through 376 Processing helix chain 'C' and resid 396 through 406 removed outlier: 4.055A pdb=" N ASN C 406 " --> pdb=" O MET C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 423 removed outlier: 4.457A pdb=" N ARG C 420 " --> pdb=" O ILE C 416 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N ILE C 421 " --> pdb=" O GLY C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 431 removed outlier: 4.168A pdb=" N VAL C 429 " --> pdb=" O GLU C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 438 removed outlier: 3.783A pdb=" N GLY C 438 " --> pdb=" O MET C 434 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 442 removed outlier: 3.521A pdb=" N LYS C 442 " --> pdb=" O ASP C 439 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 439 through 442' Processing helix chain 'C' and resid 494 through 500 removed outlier: 3.506A pdb=" N LEU C 500 " --> pdb=" O ASP C 496 " (cutoff:3.500A) Processing helix chain 'C' and resid 560 through 565 removed outlier: 3.678A pdb=" N GLU C 565 " --> pdb=" O PHE C 561 " (cutoff:3.500A) Processing helix chain 'C' and resid 568 through 581 removed outlier: 3.605A pdb=" N ASP C 580 " --> pdb=" O ASN C 576 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLY C 581 " --> pdb=" O LYS C 577 " (cutoff:3.500A) Processing helix chain 'C' and resid 637 through 646 removed outlier: 3.604A pdb=" N GLN C 641 " --> pdb=" O GLU C 637 " (cutoff:3.500A) Processing helix chain 'C' and resid 647 through 654 Proline residue: C 650 - end of helix removed outlier: 4.481A pdb=" N GLU C 654 " --> pdb=" O ASP C 651 " (cutoff:3.500A) Processing helix chain 'C' and resid 678 through 690 Processing helix chain 'C' and resid 698 through 719 removed outlier: 4.073A pdb=" N ILE C 702 " --> pdb=" O ASN C 698 " (cutoff:3.500A) Processing helix chain 'C' and resid 720 through 723 Processing helix chain 'C' and resid 745 through 752 Processing helix chain 'C' and resid 757 through 760 Processing helix chain 'C' and resid 761 through 770 Processing helix chain 'C' and resid 817 through 827 Processing helix chain 'C' and resid 874 through 878 removed outlier: 3.598A pdb=" N ILE C 878 " --> pdb=" O PHE C 875 " (cutoff:3.500A) Processing helix chain 'C' and resid 879 through 889 Processing sheet with id=AA1, first strand: chain 'A' and resid 249 through 251 removed outlier: 3.794A pdb=" N ALA A 250 " --> pdb=" O LYS A 280 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LYS A 280 " --> pdb=" O ALA A 250 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 1316 through 1318 Processing sheet with id=AA3, first strand: chain 'A' and resid 1332 through 1335 Processing sheet with id=AA4, first strand: chain 'C' and resid 69 through 72 Processing sheet with id=AA5, first strand: chain 'C' and resid 122 through 123 removed outlier: 6.093A pdb=" N VAL C 122 " --> pdb=" O GLN C 143 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 125 through 126 removed outlier: 6.835A pdb=" N TYR C 125 " --> pdb=" O VAL C 166 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 125 through 126 removed outlier: 6.835A pdb=" N TYR C 125 " --> pdb=" O VAL C 166 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 150 through 151 Processing sheet with id=AA9, first strand: chain 'C' and resid 298 through 300 removed outlier: 6.153A pdb=" N ILE C 256 " --> pdb=" O ALA C 292 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N PHE C 294 " --> pdb=" O ILE C 256 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N VAL C 258 " --> pdb=" O PHE C 294 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N VAL C 384 " --> pdb=" O TYR C 409 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N TYR C 411 " --> pdb=" O VAL C 384 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N THR C 386 " --> pdb=" O TYR C 411 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N ILE C 413 " --> pdb=" O THR C 386 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N SER C 388 " --> pdb=" O ILE C 413 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 521 through 523 removed outlier: 6.506A pdb=" N ALA C 514 " --> pdb=" O LEU C 522 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TRP C 609 " --> pdb=" O GLY C 584 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 658 through 659 removed outlier: 3.770A pdb=" N ALA C 731 " --> pdb=" O LYS C 815 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N MET C 793 " --> pdb=" O THR C 776 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 800 through 801 Processing sheet with id=AB4, first strand: chain 'C' and resid 859 through 861 removed outlier: 7.005A pdb=" N ILE C 852 " --> pdb=" O LEU C 860 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU C1019 " --> pdb=" O ILE C1002 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ILE C1002 " --> pdb=" O GLU C1019 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 892 through 899 Processing sheet with id=AB6, first strand: chain 'C' and resid 903 through 904 813 hydrogen bonds defined for protein. 2304 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: 2.90 Time building geometry restraints manager: 1.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4894 1.34 - 1.46: 3662 1.46 - 1.58: 7096 1.58 - 1.70: 1 1.70 - 1.82: 133 Bond restraints: 15786 Sorted by residual: bond pdb=" C1 NAG E 3 " pdb=" O5 NAG E 3 " ideal model delta sigma weight residual 1.406 1.489 -0.083 2.00e-02 2.50e+03 1.73e+01 bond pdb=" C1 NAG G 2 " pdb=" O5 NAG G 2 " ideal model delta sigma weight residual 1.406 1.486 -0.080 2.00e-02 2.50e+03 1.58e+01 bond pdb=" C1 NAG C1202 " pdb=" O5 NAG C1202 " ideal model delta sigma weight residual 1.406 1.477 -0.071 2.00e-02 2.50e+03 1.27e+01 bond pdb=" CB PRO A1680 " pdb=" CG PRO A1680 " ideal model delta sigma weight residual 1.492 1.598 -0.106 5.00e-02 4.00e+02 4.51e+00 bond pdb=" C1 NAG D 1 " pdb=" C2 NAG D 1 " ideal model delta sigma weight residual 1.532 1.565 -0.033 2.00e-02 2.50e+03 2.72e+00 ... (remaining 15781 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.54: 20906 1.54 - 3.08: 410 3.08 - 4.62: 63 4.62 - 6.16: 22 6.16 - 7.70: 9 Bond angle restraints: 21410 Sorted by residual: angle pdb=" N ILE A 579 " pdb=" CA ILE A 579 " pdb=" C ILE A 579 " ideal model delta sigma weight residual 113.20 108.68 4.52 9.60e-01 1.09e+00 2.22e+01 angle pdb=" N GLN A1589 " pdb=" CA GLN A1589 " pdb=" C GLN A1589 " ideal model delta sigma weight residual 111.28 106.36 4.92 1.09e+00 8.42e-01 2.04e+01 angle pdb=" CA PRO A1680 " pdb=" N PRO A1680 " pdb=" CD PRO A1680 " ideal model delta sigma weight residual 112.00 105.96 6.04 1.40e+00 5.10e-01 1.86e+01 angle pdb=" N PRO A1680 " pdb=" CD PRO A1680 " pdb=" CG PRO A1680 " ideal model delta sigma weight residual 103.20 97.32 5.88 1.50e+00 4.44e-01 1.54e+01 angle pdb=" N LYS A1585 " pdb=" CA LYS A1585 " pdb=" C LYS A1585 " ideal model delta sigma weight residual 113.41 108.87 4.54 1.22e+00 6.72e-01 1.38e+01 ... (remaining 21405 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.71: 8777 24.71 - 49.43: 661 49.43 - 74.14: 80 74.14 - 98.85: 36 98.85 - 123.57: 14 Dihedral angle restraints: 9568 sinusoidal: 3919 harmonic: 5649 Sorted by residual: dihedral pdb=" CB CYS A 268 " pdb=" SG CYS A 268 " pdb=" SG CYS A 279 " pdb=" CB CYS A 279 " ideal model delta sinusoidal sigma weight residual -86.00 -139.19 53.19 1 1.00e+01 1.00e-02 3.85e+01 dihedral pdb=" CB CYS C 404 " pdb=" SG CYS C 404 " pdb=" SG CYS C1071 " pdb=" CB CYS C1071 " ideal model delta sinusoidal sigma weight residual 93.00 50.80 42.20 1 1.00e+01 1.00e-02 2.49e+01 dihedral pdb=" CA ASP A 263 " pdb=" C ASP A 263 " pdb=" N PRO A 264 " pdb=" CA PRO A 264 " ideal model delta harmonic sigma weight residual 180.00 157.71 22.29 0 5.00e+00 4.00e-02 1.99e+01 ... (remaining 9565 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 2243 0.067 - 0.134: 219 0.134 - 0.202: 9 0.202 - 0.269: 1 0.269 - 0.336: 3 Chirality restraints: 2475 Sorted by residual: chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN C 348 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.83e+00 chirality pdb=" C4 NAG D 1 " pdb=" C3 NAG D 1 " pdb=" C5 NAG D 1 " pdb=" O4 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.53 -2.23 -0.30 2.00e-01 2.50e+01 2.21e+00 chirality pdb=" C1 NAG B 1 " pdb=" ND2 ASN C 184 " pdb=" C2 NAG B 1 " pdb=" O5 NAG B 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.14e+00 ... (remaining 2472 not shown) Planarity restraints: 2709 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A1679 " -0.053 5.00e-02 4.00e+02 7.66e-02 9.38e+00 pdb=" N PRO A1680 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO A1680 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO A1680 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 263 " -0.041 5.00e-02 4.00e+02 6.21e-02 6.16e+00 pdb=" N PRO A 264 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO A 264 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 264 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP C 674 " -0.010 2.00e-02 2.50e+03 2.10e-02 4.43e+00 pdb=" CG ASP C 674 " 0.036 2.00e-02 2.50e+03 pdb=" OD1 ASP C 674 " -0.013 2.00e-02 2.50e+03 pdb=" OD2 ASP C 674 " -0.013 2.00e-02 2.50e+03 ... (remaining 2706 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1494 2.74 - 3.28: 15429 3.28 - 3.82: 25492 3.82 - 4.36: 29347 4.36 - 4.90: 51372 Nonbonded interactions: 123134 Sorted by model distance: nonbonded pdb=" OH TYR A 479 " pdb=" O ARG A 578 " model vdw 2.203 3.040 nonbonded pdb=" O GLU C 182 " pdb=" OG1 THR C 186 " model vdw 2.212 3.040 nonbonded pdb=" O4 NAG D 2 " pdb=" O7 NAG D 2 " model vdw 2.233 3.040 nonbonded pdb=" O ASP C 285 " pdb=" NE2 GLN C 309 " model vdw 2.268 3.120 nonbonded pdb=" OH TYR C 450 " pdb=" OG1 THR C 461 " model vdw 2.273 3.040 ... (remaining 123129 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'G' } 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: 1.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 14.030 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 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 : 0.004 0.106 15810 Z= 0.165 Angle : 0.569 9.862 21472 Z= 0.290 Chirality : 0.042 0.336 2475 Planarity : 0.003 0.077 2702 Dihedral : 18.036 123.568 5890 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.81 % Favored : 94.08 % Rotamer: Outliers : 0.55 % Allowed : 18.50 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.05 (0.19), residues: 1909 helix: 1.07 (0.17), residues: 948 sheet: -0.21 (0.38), residues: 185 loop : -1.38 (0.22), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 590 TYR 0.015 0.001 TYR A1728 PHE 0.020 0.001 PHE C1003 TRP 0.012 0.001 TRP C 185 HIS 0.002 0.001 HIS A1639 Details of bonding type rmsd covalent geometry : bond 0.00372 (15786) covalent geometry : angle 0.55226 (21410) SS BOND : bond 0.00161 ( 10) SS BOND : angle 1.05700 ( 20) hydrogen bonds : bond 0.19453 ( 793) hydrogen bonds : angle 6.41113 ( 2304) link_BETA1-4 : bond 0.00746 ( 7) link_BETA1-4 : angle 3.32426 ( 21) link_NAG-ASN : bond 0.00572 ( 7) link_NAG-ASN : angle 2.84149 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 205 time to evaluate : 0.451 Fit side-chains outliers start: 9 outliers final: 3 residues processed: 211 average time/residue: 0.1216 time to fit residues: 38.3601 Evaluate side-chains 203 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 200 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1584 ILE Chi-restraints excluded: chain A residue 1586 LEU Chi-restraints excluded: chain C residue 379 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 5.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 344 ASN A 691 ASN A1288 ASN A1491 ASN A1725 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.157449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.121250 restraints weight = 20105.184| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 2.37 r_work: 0.3050 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.0815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15810 Z= 0.149 Angle : 0.589 9.308 21472 Z= 0.292 Chirality : 0.044 0.332 2475 Planarity : 0.004 0.037 2702 Dihedral : 11.700 114.607 2395 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.34 % Favored : 94.60 % Rotamer: Outliers : 2.14 % Allowed : 17.22 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.15 (0.19), residues: 1909 helix: 1.32 (0.17), residues: 967 sheet: -0.22 (0.35), residues: 197 loop : -1.47 (0.22), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1187 TYR 0.011 0.001 TYR C 744 PHE 0.010 0.001 PHE A1426 TRP 0.015 0.001 TRP C 185 HIS 0.003 0.001 HIS A 497 Details of bonding type rmsd covalent geometry : bond 0.00340 (15786) covalent geometry : angle 0.57513 (21410) SS BOND : bond 0.00150 ( 10) SS BOND : angle 1.10586 ( 20) hydrogen bonds : bond 0.04897 ( 793) hydrogen bonds : angle 4.57028 ( 2304) link_BETA1-4 : bond 0.00856 ( 7) link_BETA1-4 : angle 2.79544 ( 21) link_NAG-ASN : bond 0.00714 ( 7) link_NAG-ASN : angle 2.83633 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 219 time to evaluate : 0.678 Fit side-chains revert: symmetry clash REVERT: A 190 ARG cc_start: 0.7106 (ptt90) cc_final: 0.6298 (ptp-170) REVERT: A 293 ASP cc_start: 0.8507 (m-30) cc_final: 0.8286 (m-30) REVERT: A 1335 ASP cc_start: 0.8468 (t70) cc_final: 0.7953 (t0) REVERT: C 309 GLN cc_start: 0.8983 (OUTLIER) cc_final: 0.8132 (tm-30) REVERT: C 675 ASN cc_start: 0.6656 (t0) cc_final: 0.6430 (t0) outliers start: 35 outliers final: 19 residues processed: 243 average time/residue: 0.1124 time to fit residues: 41.3507 Evaluate side-chains 221 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 201 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 604 ILE Chi-restraints excluded: chain A residue 679 SER Chi-restraints excluded: chain A residue 1230 VAL Chi-restraints excluded: chain A residue 1294 ILE Chi-restraints excluded: chain A residue 1584 ILE Chi-restraints excluded: chain A residue 1586 LEU Chi-restraints excluded: chain A residue 1626 MET Chi-restraints excluded: chain A residue 1675 GLU Chi-restraints excluded: chain A residue 1701 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 309 GLN Chi-restraints excluded: chain C residue 585 GLU Chi-restraints excluded: chain C residue 587 THR Chi-restraints excluded: chain C residue 667 CYS Chi-restraints excluded: chain C residue 741 THR Chi-restraints excluded: chain C residue 1032 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 66 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 149 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 96 optimal weight: 3.9990 chunk 105 optimal weight: 0.9980 chunk 138 optimal weight: 0.6980 chunk 127 optimal weight: 4.9990 chunk 94 optimal weight: 8.9990 chunk 151 optimal weight: 0.3980 chunk 184 optimal weight: 6.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1179 ASN A1309 GLN A1395 ASN ** A1416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1725 ASN C 65 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.159277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.122869 restraints weight = 20323.608| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 2.57 r_work: 0.3077 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.1045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15810 Z= 0.115 Angle : 0.550 9.440 21472 Z= 0.271 Chirality : 0.042 0.314 2475 Planarity : 0.003 0.058 2702 Dihedral : 10.902 113.949 2393 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.13 % Favored : 94.81 % Rotamer: Outliers : 2.51 % Allowed : 17.46 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.30 (0.19), residues: 1909 helix: 1.49 (0.17), residues: 966 sheet: -0.30 (0.35), residues: 201 loop : -1.43 (0.22), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C1001 TYR 0.016 0.001 TYR C 744 PHE 0.012 0.001 PHE A 230 TRP 0.016 0.001 TRP C 185 HIS 0.003 0.001 HIS A 266 Details of bonding type rmsd covalent geometry : bond 0.00250 (15786) covalent geometry : angle 0.53691 (21410) SS BOND : bond 0.00486 ( 10) SS BOND : angle 1.15621 ( 20) hydrogen bonds : bond 0.04124 ( 793) hydrogen bonds : angle 4.25827 ( 2304) link_BETA1-4 : bond 0.00825 ( 7) link_BETA1-4 : angle 2.60783 ( 21) link_NAG-ASN : bond 0.00670 ( 7) link_NAG-ASN : angle 2.65634 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 216 time to evaluate : 0.604 Fit side-chains REVERT: A 163 MET cc_start: 0.8337 (ttp) cc_final: 0.7556 (ptm) REVERT: A 293 ASP cc_start: 0.8463 (m-30) cc_final: 0.8169 (m-30) REVERT: A 304 GLN cc_start: 0.9033 (OUTLIER) cc_final: 0.8779 (pp30) REVERT: A 705 ASN cc_start: 0.8357 (OUTLIER) cc_final: 0.7952 (t0) REVERT: A 1335 ASP cc_start: 0.8494 (t70) cc_final: 0.8028 (t0) outliers start: 41 outliers final: 26 residues processed: 250 average time/residue: 0.1083 time to fit residues: 41.6310 Evaluate side-chains 234 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 206 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 304 GLN Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 679 SER Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 705 ASN Chi-restraints excluded: chain A residue 1230 VAL Chi-restraints excluded: chain A residue 1294 ILE Chi-restraints excluded: chain A residue 1584 ILE Chi-restraints excluded: chain A residue 1586 LEU Chi-restraints excluded: chain A residue 1626 MET Chi-restraints excluded: chain A residue 1670 LEU Chi-restraints excluded: chain A residue 1701 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 65 GLN Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 585 GLU Chi-restraints excluded: chain C residue 587 THR Chi-restraints excluded: chain C residue 667 CYS Chi-restraints excluded: chain C residue 741 THR Chi-restraints excluded: chain C residue 1032 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 162 optimal weight: 5.9990 chunk 173 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 111 optimal weight: 0.7980 chunk 74 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 119 optimal weight: 0.6980 chunk 80 optimal weight: 20.0000 chunk 100 optimal weight: 8.9990 chunk 84 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 344 ASN A1725 ASN C 65 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.157597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.121108 restraints weight = 20060.107| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 2.45 r_work: 0.3064 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.1185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15810 Z= 0.139 Angle : 0.563 9.532 21472 Z= 0.276 Chirality : 0.043 0.298 2475 Planarity : 0.003 0.046 2702 Dihedral : 10.486 113.821 2393 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.50 % Favored : 94.45 % Rotamer: Outliers : 3.31 % Allowed : 18.14 % Favored : 78.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.30 (0.19), residues: 1909 helix: 1.54 (0.17), residues: 961 sheet: -0.41 (0.36), residues: 187 loop : -1.43 (0.22), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1187 TYR 0.012 0.001 TYR C 719 PHE 0.014 0.001 PHE C 686 TRP 0.015 0.001 TRP C 185 HIS 0.003 0.001 HIS A 497 Details of bonding type rmsd covalent geometry : bond 0.00325 (15786) covalent geometry : angle 0.55029 (21410) SS BOND : bond 0.00123 ( 10) SS BOND : angle 1.09566 ( 20) hydrogen bonds : bond 0.03985 ( 793) hydrogen bonds : angle 4.15080 ( 2304) link_BETA1-4 : bond 0.00816 ( 7) link_BETA1-4 : angle 2.67412 ( 21) link_NAG-ASN : bond 0.00603 ( 7) link_NAG-ASN : angle 2.70037 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 217 time to evaluate : 0.621 Fit side-chains revert: symmetry clash REVERT: A 163 MET cc_start: 0.8420 (ttp) cc_final: 0.7623 (ptm) REVERT: A 190 ARG cc_start: 0.7190 (ptt90) cc_final: 0.6286 (ptp-170) REVERT: A 293 ASP cc_start: 0.8512 (m-30) cc_final: 0.8226 (m-30) REVERT: A 1193 PHE cc_start: 0.8250 (m-80) cc_final: 0.8012 (m-80) REVERT: A 1335 ASP cc_start: 0.8489 (t70) cc_final: 0.8051 (t0) outliers start: 54 outliers final: 37 residues processed: 259 average time/residue: 0.1147 time to fit residues: 46.1174 Evaluate side-chains 240 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 203 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 679 SER Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 1230 VAL Chi-restraints excluded: chain A residue 1294 ILE Chi-restraints excluded: chain A residue 1584 ILE Chi-restraints excluded: chain A residue 1586 LEU Chi-restraints excluded: chain A residue 1626 MET Chi-restraints excluded: chain A residue 1670 LEU Chi-restraints excluded: chain A residue 1675 GLU Chi-restraints excluded: chain A residue 1701 VAL Chi-restraints excluded: chain A residue 1719 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain C residue 515 ILE Chi-restraints excluded: chain C residue 585 GLU Chi-restraints excluded: chain C residue 587 THR Chi-restraints excluded: chain C residue 667 CYS Chi-restraints excluded: chain C residue 740 ILE Chi-restraints excluded: chain C residue 741 THR Chi-restraints excluded: chain C residue 795 SER Chi-restraints excluded: chain C residue 848 MET Chi-restraints excluded: chain C residue 871 ILE Chi-restraints excluded: chain C residue 979 THR Chi-restraints excluded: chain C residue 1032 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 3 optimal weight: 3.9990 chunk 101 optimal weight: 10.0000 chunk 9 optimal weight: 0.9990 chunk 192 optimal weight: 8.9990 chunk 152 optimal weight: 2.9990 chunk 153 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 78 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1309 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.155132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.117776 restraints weight = 20251.591| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 2.81 r_work: 0.2967 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.1414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 15810 Z= 0.214 Angle : 0.634 9.742 21472 Z= 0.313 Chirality : 0.045 0.308 2475 Planarity : 0.004 0.040 2702 Dihedral : 10.309 114.861 2393 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.66 % Favored : 94.29 % Rotamer: Outliers : 3.92 % Allowed : 18.81 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.08 (0.19), residues: 1909 helix: 1.35 (0.17), residues: 964 sheet: -0.50 (0.36), residues: 189 loop : -1.52 (0.21), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1187 TYR 0.014 0.002 TYR C 217 PHE 0.024 0.002 PHE C1003 TRP 0.014 0.002 TRP C 185 HIS 0.004 0.001 HIS A 266 Details of bonding type rmsd covalent geometry : bond 0.00521 (15786) covalent geometry : angle 0.61903 (21410) SS BOND : bond 0.00370 ( 10) SS BOND : angle 1.36023 ( 20) hydrogen bonds : bond 0.04498 ( 793) hydrogen bonds : angle 4.27573 ( 2304) link_BETA1-4 : bond 0.00818 ( 7) link_BETA1-4 : angle 2.99490 ( 21) link_NAG-ASN : bond 0.00576 ( 7) link_NAG-ASN : angle 3.10703 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 213 time to evaluate : 0.365 Fit side-chains revert: symmetry clash REVERT: A 190 ARG cc_start: 0.7232 (ptt90) cc_final: 0.6476 (ptm160) REVERT: A 287 ASP cc_start: 0.8167 (t0) cc_final: 0.7836 (t0) REVERT: A 1335 ASP cc_start: 0.8348 (t70) cc_final: 0.7948 (t0) REVERT: A 1374 TRP cc_start: 0.9314 (OUTLIER) cc_final: 0.9074 (p-90) REVERT: C 674 ASP cc_start: 0.7605 (t0) cc_final: 0.7359 (t0) REVERT: C 708 ASP cc_start: 0.7925 (m-30) cc_final: 0.7693 (m-30) REVERT: C 799 GLU cc_start: 0.7666 (mp0) cc_final: 0.7440 (mp0) outliers start: 64 outliers final: 50 residues processed: 264 average time/residue: 0.1075 time to fit residues: 44.0192 Evaluate side-chains 256 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 205 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 480 TRP Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 633 ASP Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 1211 ILE Chi-restraints excluded: chain A residue 1230 VAL Chi-restraints excluded: chain A residue 1253 THR Chi-restraints excluded: chain A residue 1294 ILE Chi-restraints excluded: chain A residue 1374 TRP Chi-restraints excluded: chain A residue 1417 ILE Chi-restraints excluded: chain A residue 1505 THR Chi-restraints excluded: chain A residue 1584 ILE Chi-restraints excluded: chain A residue 1586 LEU Chi-restraints excluded: chain A residue 1626 MET Chi-restraints excluded: chain A residue 1648 SER Chi-restraints excluded: chain A residue 1670 LEU Chi-restraints excluded: chain A residue 1675 GLU Chi-restraints excluded: chain A residue 1697 ASP Chi-restraints excluded: chain A residue 1701 VAL Chi-restraints excluded: chain A residue 1719 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 199 GLU Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain C residue 515 ILE Chi-restraints excluded: chain C residue 585 GLU Chi-restraints excluded: chain C residue 587 THR Chi-restraints excluded: chain C residue 625 THR Chi-restraints excluded: chain C residue 667 CYS Chi-restraints excluded: chain C residue 691 THR Chi-restraints excluded: chain C residue 740 ILE Chi-restraints excluded: chain C residue 741 THR Chi-restraints excluded: chain C residue 795 SER Chi-restraints excluded: chain C residue 848 MET Chi-restraints excluded: chain C residue 979 THR Chi-restraints excluded: chain C residue 1032 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 82 optimal weight: 40.0000 chunk 58 optimal weight: 0.9980 chunk 158 optimal weight: 0.9990 chunk 148 optimal weight: 3.9990 chunk 129 optimal weight: 1.9990 chunk 93 optimal weight: 0.9980 chunk 169 optimal weight: 2.9990 chunk 161 optimal weight: 0.9990 chunk 116 optimal weight: 0.9990 chunk 131 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 705 ASN ** A1416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1725 ASN C 65 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.157908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.121505 restraints weight = 20033.013| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 2.37 r_work: 0.3079 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.1475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15810 Z= 0.124 Angle : 0.568 9.569 21472 Z= 0.277 Chirality : 0.042 0.288 2475 Planarity : 0.003 0.039 2702 Dihedral : 9.912 115.701 2393 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.29 % Favored : 94.66 % Rotamer: Outliers : 3.06 % Allowed : 20.10 % Favored : 76.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.26 (0.19), residues: 1909 helix: 1.51 (0.17), residues: 965 sheet: -0.52 (0.36), residues: 189 loop : -1.44 (0.22), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1588 TYR 0.013 0.001 TYR C 744 PHE 0.025 0.001 PHE C1003 TRP 0.020 0.001 TRP C 185 HIS 0.002 0.001 HIS A 266 Details of bonding type rmsd covalent geometry : bond 0.00282 (15786) covalent geometry : angle 0.55358 (21410) SS BOND : bond 0.00155 ( 10) SS BOND : angle 1.06913 ( 20) hydrogen bonds : bond 0.03793 ( 793) hydrogen bonds : angle 4.07791 ( 2304) link_BETA1-4 : bond 0.00794 ( 7) link_BETA1-4 : angle 2.76533 ( 21) link_NAG-ASN : bond 0.00604 ( 7) link_NAG-ASN : angle 2.86297 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 221 time to evaluate : 0.568 Fit side-chains revert: symmetry clash REVERT: A 190 ARG cc_start: 0.7109 (ptt90) cc_final: 0.6331 (ptm160) REVERT: A 199 LYS cc_start: 0.8787 (OUTLIER) cc_final: 0.8217 (ptpp) REVERT: A 278 GLU cc_start: 0.7357 (OUTLIER) cc_final: 0.6644 (pp20) REVERT: A 287 ASP cc_start: 0.8491 (t0) cc_final: 0.8052 (t0) REVERT: A 354 PHE cc_start: 0.6102 (OUTLIER) cc_final: 0.5569 (t80) REVERT: A 485 LEU cc_start: 0.8341 (mp) cc_final: 0.8031 (tt) REVERT: A 648 MET cc_start: 0.9210 (mmp) cc_final: 0.8862 (mmp) REVERT: A 1161 LEU cc_start: 0.8593 (mt) cc_final: 0.8334 (mt) REVERT: A 1201 MET cc_start: 0.6568 (tpt) cc_final: 0.6297 (tpt) REVERT: A 1335 ASP cc_start: 0.8459 (t70) cc_final: 0.8043 (t0) REVERT: C 675 ASN cc_start: 0.6728 (t0) cc_final: 0.6455 (t0) REVERT: C 708 ASP cc_start: 0.8035 (m-30) cc_final: 0.7791 (m-30) REVERT: C 799 GLU cc_start: 0.7993 (mp0) cc_final: 0.7690 (mp0) outliers start: 50 outliers final: 41 residues processed: 259 average time/residue: 0.1077 time to fit residues: 43.0925 Evaluate side-chains 252 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 208 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 199 LYS Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 604 ILE Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 705 ASN Chi-restraints excluded: chain A residue 1230 VAL Chi-restraints excluded: chain A residue 1289 VAL Chi-restraints excluded: chain A residue 1294 ILE Chi-restraints excluded: chain A residue 1417 ILE Chi-restraints excluded: chain A residue 1505 THR Chi-restraints excluded: chain A residue 1584 ILE Chi-restraints excluded: chain A residue 1586 LEU Chi-restraints excluded: chain A residue 1626 MET Chi-restraints excluded: chain A residue 1670 LEU Chi-restraints excluded: chain A residue 1675 GLU Chi-restraints excluded: chain A residue 1697 ASP Chi-restraints excluded: chain A residue 1701 VAL Chi-restraints excluded: chain A residue 1719 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 65 GLN Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain C residue 585 GLU Chi-restraints excluded: chain C residue 587 THR Chi-restraints excluded: chain C residue 625 THR Chi-restraints excluded: chain C residue 667 CYS Chi-restraints excluded: chain C residue 691 THR Chi-restraints excluded: chain C residue 740 ILE Chi-restraints excluded: chain C residue 741 THR Chi-restraints excluded: chain C residue 795 SER Chi-restraints excluded: chain C residue 848 MET Chi-restraints excluded: chain C residue 852 ILE Chi-restraints excluded: chain C residue 979 THR Chi-restraints excluded: chain C residue 1032 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 108 optimal weight: 4.9990 chunk 166 optimal weight: 0.0980 chunk 44 optimal weight: 0.9980 chunk 156 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 100 optimal weight: 8.9990 chunk 140 optimal weight: 0.0980 chunk 46 optimal weight: 0.6980 chunk 77 optimal weight: 6.9990 chunk 40 optimal weight: 4.9990 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 705 ASN ** A1416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 65 GLN C 481 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.158996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.122554 restraints weight = 20029.497| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 2.38 r_work: 0.3058 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 15810 Z= 0.108 Angle : 0.555 9.576 21472 Z= 0.272 Chirality : 0.042 0.309 2475 Planarity : 0.003 0.037 2702 Dihedral : 9.666 115.568 2393 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.34 % Favored : 94.60 % Rotamer: Outliers : 3.31 % Allowed : 19.73 % Favored : 76.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.37 (0.20), residues: 1909 helix: 1.60 (0.17), residues: 966 sheet: -0.51 (0.36), residues: 190 loop : -1.37 (0.22), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1187 TYR 0.010 0.001 TYR C 744 PHE 0.024 0.001 PHE C1003 TRP 0.018 0.001 TRP C 185 HIS 0.002 0.001 HIS A 266 Details of bonding type rmsd covalent geometry : bond 0.00233 (15786) covalent geometry : angle 0.54213 (21410) SS BOND : bond 0.00155 ( 10) SS BOND : angle 0.99557 ( 20) hydrogen bonds : bond 0.03558 ( 793) hydrogen bonds : angle 3.98995 ( 2304) link_BETA1-4 : bond 0.00812 ( 7) link_BETA1-4 : angle 2.68782 ( 21) link_NAG-ASN : bond 0.00610 ( 7) link_NAG-ASN : angle 2.69940 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 220 time to evaluate : 0.398 Fit side-chains revert: symmetry clash REVERT: A 190 ARG cc_start: 0.7086 (ptt90) cc_final: 0.6337 (ptm160) REVERT: A 199 LYS cc_start: 0.8738 (OUTLIER) cc_final: 0.8164 (ptpp) REVERT: A 278 GLU cc_start: 0.7347 (OUTLIER) cc_final: 0.6642 (pp20) REVERT: A 287 ASP cc_start: 0.8519 (t0) cc_final: 0.8056 (t0) REVERT: A 354 PHE cc_start: 0.6152 (OUTLIER) cc_final: 0.5545 (t80) REVERT: A 485 LEU cc_start: 0.8353 (mp) cc_final: 0.8038 (tt) REVERT: A 648 MET cc_start: 0.9209 (mmp) cc_final: 0.8862 (mmp) REVERT: A 1201 MET cc_start: 0.6528 (tpt) cc_final: 0.6266 (tpt) REVERT: A 1335 ASP cc_start: 0.8415 (t70) cc_final: 0.8016 (t0) REVERT: A 1374 TRP cc_start: 0.9307 (OUTLIER) cc_final: 0.8951 (p-90) REVERT: C 708 ASP cc_start: 0.8055 (m-30) cc_final: 0.7815 (m-30) REVERT: C 770 ASN cc_start: 0.8189 (m110) cc_final: 0.7886 (m110) REVERT: C 799 GLU cc_start: 0.7997 (mp0) cc_final: 0.7657 (mp0) REVERT: C 848 MET cc_start: 0.3823 (OUTLIER) cc_final: 0.3261 (ptt) outliers start: 54 outliers final: 43 residues processed: 262 average time/residue: 0.1059 time to fit residues: 42.4199 Evaluate side-chains 260 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 212 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 199 LYS Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 304 GLN Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 604 ILE Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 679 SER Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 705 ASN Chi-restraints excluded: chain A residue 1211 ILE Chi-restraints excluded: chain A residue 1230 VAL Chi-restraints excluded: chain A residue 1289 VAL Chi-restraints excluded: chain A residue 1294 ILE Chi-restraints excluded: chain A residue 1374 TRP Chi-restraints excluded: chain A residue 1417 ILE Chi-restraints excluded: chain A residue 1421 LEU Chi-restraints excluded: chain A residue 1505 THR Chi-restraints excluded: chain A residue 1584 ILE Chi-restraints excluded: chain A residue 1586 LEU Chi-restraints excluded: chain A residue 1626 MET Chi-restraints excluded: chain A residue 1670 LEU Chi-restraints excluded: chain A residue 1675 GLU Chi-restraints excluded: chain A residue 1697 ASP Chi-restraints excluded: chain A residue 1701 VAL Chi-restraints excluded: chain A residue 1719 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain C residue 585 GLU Chi-restraints excluded: chain C residue 587 THR Chi-restraints excluded: chain C residue 667 CYS Chi-restraints excluded: chain C residue 691 THR Chi-restraints excluded: chain C residue 740 ILE Chi-restraints excluded: chain C residue 741 THR Chi-restraints excluded: chain C residue 795 SER Chi-restraints excluded: chain C residue 848 MET Chi-restraints excluded: chain C residue 871 ILE Chi-restraints excluded: chain C residue 979 THR Chi-restraints excluded: chain C residue 1032 ILE Chi-restraints excluded: chain C residue 1037 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 162 optimal weight: 3.9990 chunk 181 optimal weight: 5.9990 chunk 146 optimal weight: 0.8980 chunk 89 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 135 optimal weight: 0.8980 chunk 148 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 chunk 15 optimal weight: 6.9990 chunk 41 optimal weight: 0.5980 chunk 54 optimal weight: 7.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 705 ASN ** A1416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 65 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.159783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.123035 restraints weight = 20065.288| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 2.43 r_work: 0.3131 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15810 Z= 0.114 Angle : 0.558 9.598 21472 Z= 0.273 Chirality : 0.042 0.259 2475 Planarity : 0.003 0.040 2702 Dihedral : 9.497 115.382 2393 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.13 % Favored : 94.81 % Rotamer: Outliers : 3.43 % Allowed : 19.67 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.42 (0.20), residues: 1909 helix: 1.64 (0.17), residues: 964 sheet: -0.40 (0.35), residues: 204 loop : -1.38 (0.23), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1258 TYR 0.009 0.001 TYR C 512 PHE 0.023 0.001 PHE C1003 TRP 0.017 0.001 TRP C 185 HIS 0.002 0.001 HIS A1639 Details of bonding type rmsd covalent geometry : bond 0.00256 (15786) covalent geometry : angle 0.54545 (21410) SS BOND : bond 0.00254 ( 10) SS BOND : angle 1.10495 ( 20) hydrogen bonds : bond 0.03533 ( 793) hydrogen bonds : angle 3.95645 ( 2304) link_BETA1-4 : bond 0.00801 ( 7) link_BETA1-4 : angle 2.70201 ( 21) link_NAG-ASN : bond 0.00597 ( 7) link_NAG-ASN : angle 2.63612 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 213 time to evaluate : 0.361 Fit side-chains revert: symmetry clash REVERT: A 190 ARG cc_start: 0.6987 (ptt90) cc_final: 0.6155 (ptm160) REVERT: A 199 LYS cc_start: 0.8637 (OUTLIER) cc_final: 0.8059 (ptpp) REVERT: A 278 GLU cc_start: 0.7233 (OUTLIER) cc_final: 0.6496 (pp20) REVERT: A 287 ASP cc_start: 0.8464 (t0) cc_final: 0.7972 (t0) REVERT: A 293 ASP cc_start: 0.8505 (m-30) cc_final: 0.8067 (m-30) REVERT: A 354 PHE cc_start: 0.6004 (OUTLIER) cc_final: 0.5278 (t80) REVERT: A 485 LEU cc_start: 0.8236 (mp) cc_final: 0.7903 (tt) REVERT: A 523 MET cc_start: 0.4916 (ttm) cc_final: 0.4203 (ttt) REVERT: A 648 MET cc_start: 0.9233 (mmp) cc_final: 0.8854 (mmp) REVERT: A 1201 MET cc_start: 0.6350 (tpt) cc_final: 0.6117 (tpt) REVERT: A 1335 ASP cc_start: 0.8348 (t70) cc_final: 0.7916 (t0) REVERT: A 1374 TRP cc_start: 0.9300 (OUTLIER) cc_final: 0.8968 (p-90) REVERT: C 708 ASP cc_start: 0.8113 (m-30) cc_final: 0.7861 (m-30) REVERT: C 770 ASN cc_start: 0.8063 (m110) cc_final: 0.7735 (m110) REVERT: C 799 GLU cc_start: 0.7924 (mp0) cc_final: 0.7574 (mp0) REVERT: C 848 MET cc_start: 0.3623 (OUTLIER) cc_final: 0.3091 (ptt) outliers start: 56 outliers final: 44 residues processed: 257 average time/residue: 0.1006 time to fit residues: 39.8537 Evaluate side-chains 261 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 212 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 199 LYS Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 604 ILE Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 679 SER Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 705 ASN Chi-restraints excluded: chain A residue 1211 ILE Chi-restraints excluded: chain A residue 1230 VAL Chi-restraints excluded: chain A residue 1289 VAL Chi-restraints excluded: chain A residue 1294 ILE Chi-restraints excluded: chain A residue 1374 TRP Chi-restraints excluded: chain A residue 1417 ILE Chi-restraints excluded: chain A residue 1421 LEU Chi-restraints excluded: chain A residue 1505 THR Chi-restraints excluded: chain A residue 1584 ILE Chi-restraints excluded: chain A residue 1586 LEU Chi-restraints excluded: chain A residue 1626 MET Chi-restraints excluded: chain A residue 1670 LEU Chi-restraints excluded: chain A residue 1675 GLU Chi-restraints excluded: chain A residue 1697 ASP Chi-restraints excluded: chain A residue 1701 VAL Chi-restraints excluded: chain A residue 1719 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 65 GLN Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain C residue 585 GLU Chi-restraints excluded: chain C residue 587 THR Chi-restraints excluded: chain C residue 667 CYS Chi-restraints excluded: chain C residue 691 THR Chi-restraints excluded: chain C residue 740 ILE Chi-restraints excluded: chain C residue 741 THR Chi-restraints excluded: chain C residue 795 SER Chi-restraints excluded: chain C residue 848 MET Chi-restraints excluded: chain C residue 871 ILE Chi-restraints excluded: chain C residue 979 THR Chi-restraints excluded: chain C residue 1032 ILE Chi-restraints excluded: chain C residue 1037 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 145 optimal weight: 0.0010 chunk 78 optimal weight: 0.9980 chunk 187 optimal weight: 7.9990 chunk 4 optimal weight: 0.9980 chunk 160 optimal weight: 0.7980 chunk 33 optimal weight: 6.9990 chunk 81 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 82 optimal weight: 20.0000 overall best weight: 0.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 705 ASN ** A1416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.159581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.122860 restraints weight = 20021.143| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 2.40 r_work: 0.3121 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15810 Z= 0.122 Angle : 0.563 9.599 21472 Z= 0.277 Chirality : 0.042 0.265 2475 Planarity : 0.003 0.043 2702 Dihedral : 9.396 115.316 2393 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.24 % Favored : 94.71 % Rotamer: Outliers : 3.31 % Allowed : 19.55 % Favored : 77.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.42 (0.20), residues: 1909 helix: 1.64 (0.17), residues: 964 sheet: -0.40 (0.35), residues: 204 loop : -1.37 (0.23), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1258 TYR 0.012 0.001 TYR C 61 PHE 0.023 0.001 PHE C1003 TRP 0.016 0.001 TRP C 185 HIS 0.003 0.001 HIS A 497 Details of bonding type rmsd covalent geometry : bond 0.00277 (15786) covalent geometry : angle 0.55076 (21410) SS BOND : bond 0.00147 ( 10) SS BOND : angle 1.08550 ( 20) hydrogen bonds : bond 0.03553 ( 793) hydrogen bonds : angle 3.94178 ( 2304) link_BETA1-4 : bond 0.00804 ( 7) link_BETA1-4 : angle 2.73451 ( 21) link_NAG-ASN : bond 0.00580 ( 7) link_NAG-ASN : angle 2.60572 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 214 time to evaluate : 0.609 Fit side-chains revert: symmetry clash REVERT: A 190 ARG cc_start: 0.6991 (ptt90) cc_final: 0.6124 (ptp-170) REVERT: A 199 LYS cc_start: 0.8640 (OUTLIER) cc_final: 0.8062 (ptpp) REVERT: A 278 GLU cc_start: 0.7200 (OUTLIER) cc_final: 0.6444 (pp20) REVERT: A 287 ASP cc_start: 0.8483 (t0) cc_final: 0.7949 (t0) REVERT: A 354 PHE cc_start: 0.6089 (OUTLIER) cc_final: 0.5220 (t80) REVERT: A 485 LEU cc_start: 0.8231 (mp) cc_final: 0.7887 (tt) REVERT: A 523 MET cc_start: 0.4832 (ttm) cc_final: 0.4196 (ttt) REVERT: A 648 MET cc_start: 0.9244 (mmp) cc_final: 0.8859 (mmp) REVERT: A 1335 ASP cc_start: 0.8339 (t70) cc_final: 0.7908 (t0) REVERT: A 1374 TRP cc_start: 0.9293 (OUTLIER) cc_final: 0.8951 (p-90) REVERT: C 708 ASP cc_start: 0.8104 (m-30) cc_final: 0.7856 (m-30) REVERT: C 770 ASN cc_start: 0.8073 (m110) cc_final: 0.7746 (m110) REVERT: C 799 GLU cc_start: 0.7918 (mp0) cc_final: 0.7505 (mp0) REVERT: C 848 MET cc_start: 0.3877 (OUTLIER) cc_final: 0.3193 (ptm) outliers start: 54 outliers final: 46 residues processed: 254 average time/residue: 0.1141 time to fit residues: 44.7216 Evaluate side-chains 261 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 210 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 199 LYS Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 304 GLN Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 604 ILE Chi-restraints excluded: chain A residue 633 ASP Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 679 SER Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 705 ASN Chi-restraints excluded: chain A residue 1211 ILE Chi-restraints excluded: chain A residue 1230 VAL Chi-restraints excluded: chain A residue 1289 VAL Chi-restraints excluded: chain A residue 1294 ILE Chi-restraints excluded: chain A residue 1374 TRP Chi-restraints excluded: chain A residue 1417 ILE Chi-restraints excluded: chain A residue 1421 LEU Chi-restraints excluded: chain A residue 1505 THR Chi-restraints excluded: chain A residue 1584 ILE Chi-restraints excluded: chain A residue 1586 LEU Chi-restraints excluded: chain A residue 1626 MET Chi-restraints excluded: chain A residue 1670 LEU Chi-restraints excluded: chain A residue 1675 GLU Chi-restraints excluded: chain A residue 1697 ASP Chi-restraints excluded: chain A residue 1701 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain C residue 585 GLU Chi-restraints excluded: chain C residue 587 THR Chi-restraints excluded: chain C residue 667 CYS Chi-restraints excluded: chain C residue 691 THR Chi-restraints excluded: chain C residue 740 ILE Chi-restraints excluded: chain C residue 741 THR Chi-restraints excluded: chain C residue 795 SER Chi-restraints excluded: chain C residue 848 MET Chi-restraints excluded: chain C residue 852 ILE Chi-restraints excluded: chain C residue 871 ILE Chi-restraints excluded: chain C residue 979 THR Chi-restraints excluded: chain C residue 1032 ILE Chi-restraints excluded: chain C residue 1037 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 169 optimal weight: 0.9980 chunk 134 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 30 optimal weight: 9.9990 chunk 108 optimal weight: 3.9990 chunk 92 optimal weight: 0.9990 chunk 174 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 chunk 186 optimal weight: 6.9990 chunk 58 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 705 ASN ** A1416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 65 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.159274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.122887 restraints weight = 20032.882| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 2.42 r_work: 0.3134 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15810 Z= 0.131 Angle : 0.571 9.631 21472 Z= 0.281 Chirality : 0.043 0.262 2475 Planarity : 0.003 0.044 2702 Dihedral : 9.342 115.125 2393 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.13 % Favored : 94.81 % Rotamer: Outliers : 3.37 % Allowed : 19.73 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (0.20), residues: 1909 helix: 1.62 (0.17), residues: 964 sheet: -0.40 (0.35), residues: 204 loop : -1.37 (0.23), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1187 TYR 0.010 0.001 TYR C 512 PHE 0.022 0.001 PHE C1003 TRP 0.015 0.001 TRP C 185 HIS 0.003 0.001 HIS A 497 Details of bonding type rmsd covalent geometry : bond 0.00304 (15786) covalent geometry : angle 0.55861 (21410) SS BOND : bond 0.00160 ( 10) SS BOND : angle 1.11812 ( 20) hydrogen bonds : bond 0.03619 ( 793) hydrogen bonds : angle 3.95583 ( 2304) link_BETA1-4 : bond 0.00754 ( 7) link_BETA1-4 : angle 2.76751 ( 21) link_NAG-ASN : bond 0.00561 ( 7) link_NAG-ASN : angle 2.60027 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 211 time to evaluate : 0.521 Fit side-chains revert: symmetry clash REVERT: A 190 ARG cc_start: 0.7018 (ptt90) cc_final: 0.6185 (ptm160) REVERT: A 199 LYS cc_start: 0.8669 (OUTLIER) cc_final: 0.8094 (ptpp) REVERT: A 278 GLU cc_start: 0.7198 (OUTLIER) cc_final: 0.6463 (pp20) REVERT: A 287 ASP cc_start: 0.8442 (t0) cc_final: 0.7924 (t0) REVERT: A 354 PHE cc_start: 0.6110 (OUTLIER) cc_final: 0.5188 (t80) REVERT: A 523 MET cc_start: 0.4804 (ttm) cc_final: 0.4475 (ttt) REVERT: A 1335 ASP cc_start: 0.8342 (t70) cc_final: 0.7920 (t0) REVERT: A 1374 TRP cc_start: 0.9303 (OUTLIER) cc_final: 0.9030 (p-90) REVERT: C 708 ASP cc_start: 0.8117 (m-30) cc_final: 0.7862 (m-30) REVERT: C 770 ASN cc_start: 0.8114 (m110) cc_final: 0.7799 (m110) REVERT: C 799 GLU cc_start: 0.7899 (mp0) cc_final: 0.7550 (mp0) REVERT: C 848 MET cc_start: 0.3915 (OUTLIER) cc_final: 0.3239 (ptm) outliers start: 55 outliers final: 46 residues processed: 254 average time/residue: 0.0999 time to fit residues: 38.4899 Evaluate side-chains 261 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 210 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 199 LYS Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 304 GLN Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 633 ASP Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 679 SER Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 705 ASN Chi-restraints excluded: chain A residue 1211 ILE Chi-restraints excluded: chain A residue 1230 VAL Chi-restraints excluded: chain A residue 1289 VAL Chi-restraints excluded: chain A residue 1294 ILE Chi-restraints excluded: chain A residue 1374 TRP Chi-restraints excluded: chain A residue 1421 LEU Chi-restraints excluded: chain A residue 1505 THR Chi-restraints excluded: chain A residue 1584 ILE Chi-restraints excluded: chain A residue 1586 LEU Chi-restraints excluded: chain A residue 1626 MET Chi-restraints excluded: chain A residue 1648 SER Chi-restraints excluded: chain A residue 1670 LEU Chi-restraints excluded: chain A residue 1675 GLU Chi-restraints excluded: chain A residue 1697 ASP Chi-restraints excluded: chain A residue 1701 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 65 GLN Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain C residue 585 GLU Chi-restraints excluded: chain C residue 587 THR Chi-restraints excluded: chain C residue 667 CYS Chi-restraints excluded: chain C residue 691 THR Chi-restraints excluded: chain C residue 740 ILE Chi-restraints excluded: chain C residue 741 THR Chi-restraints excluded: chain C residue 795 SER Chi-restraints excluded: chain C residue 848 MET Chi-restraints excluded: chain C residue 852 ILE Chi-restraints excluded: chain C residue 979 THR Chi-restraints excluded: chain C residue 1032 ILE Chi-restraints excluded: chain C residue 1037 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 70 optimal weight: 0.9980 chunk 115 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 52 optimal weight: 0.3980 chunk 22 optimal weight: 0.9980 chunk 89 optimal weight: 4.9990 chunk 165 optimal weight: 0.9980 chunk 112 optimal weight: 0.5980 chunk 7 optimal weight: 4.9990 chunk 180 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1416 ASN C 65 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.160081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.123427 restraints weight = 19957.488| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 2.42 r_work: 0.3116 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15810 Z= 0.115 Angle : 0.566 9.959 21472 Z= 0.279 Chirality : 0.042 0.262 2475 Planarity : 0.003 0.050 2702 Dihedral : 9.280 115.218 2393 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.19 % Favored : 94.76 % Rotamer: Outliers : 3.00 % Allowed : 20.10 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.44 (0.20), residues: 1909 helix: 1.65 (0.17), residues: 964 sheet: -0.39 (0.35), residues: 204 loop : -1.35 (0.23), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1187 TYR 0.009 0.001 TYR C 512 PHE 0.022 0.001 PHE C1003 TRP 0.018 0.001 TRP C 185 HIS 0.002 0.001 HIS A1639 Details of bonding type rmsd covalent geometry : bond 0.00257 (15786) covalent geometry : angle 0.55370 (21410) SS BOND : bond 0.00152 ( 10) SS BOND : angle 1.02938 ( 20) hydrogen bonds : bond 0.03526 ( 793) hydrogen bonds : angle 3.94168 ( 2304) link_BETA1-4 : bond 0.00790 ( 7) link_BETA1-4 : angle 2.73491 ( 21) link_NAG-ASN : bond 0.00574 ( 7) link_NAG-ASN : angle 2.54448 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4289.48 seconds wall clock time: 73 minutes 57.95 seconds (4437.95 seconds total)