Starting phenix.real_space_refine on Sun Oct 25 01:07:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9yej_72852/10_2026/9yej_72852.cif Found real_map, /net/cci-nas-00/data/ceres_data/9yej_72852/10_2026/9yej_72852.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9yej_72852/10_2026/9yej_72852.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9yej_72852/10_2026/9yej_72852.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9yej_72852/10_2026/9yej_72852.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9yej_72852/10_2026/9yej_72852.map" } resolution = 3.3 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= 0.001 sd= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 86 5.16 5 C 9364 2.51 5 N 2443 2.21 5 O 2793 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14686 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 699, 5755 Classifications: {'peptide': 699} Link IDs: {'PTRANS': 34, 'TRANS': 664} Chain: "B" Number of atoms: 1539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1539 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 13, 'TRANS': 185} Chain: "C" Number of atoms: 5755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 699, 5755 Classifications: {'peptide': 699} Link IDs: {'PTRANS': 34, 'TRANS': 664} Chain: "D" Number of atoms: 1539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1539 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 13, 'TRANS': 185} Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" 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 Time building chain proxies: 3.42, per 1000 atoms: 0.23 Number of scatterers: 14686 At special positions: 0 Unit cell: (143, 111, 141, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 86 16.00 O 2793 8.00 N 2443 7.00 C 9364 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.04 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS B 415 " - pdb=" SG CYS B 587 " distance=2.03 Simple disulfide: pdb=" SG CYS B 433 " - pdb=" SG CYS B 486 " distance=2.03 Simple disulfide: pdb=" SG CYS B 511 " - pdb=" SG CYS B 532 " distance=2.03 Simple disulfide: pdb=" SG CYS C 133 " - pdb=" SG CYS C 141 " distance=2.04 Simple disulfide: pdb=" SG CYS C 344 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 530 " - pdb=" SG CYS C 542 " distance=2.03 Simple disulfide: pdb=" SG CYS D 415 " - pdb=" SG CYS D 587 " distance=2.03 Simple disulfide: pdb=" SG CYS D 433 " - pdb=" SG CYS D 486 " distance=2.03 Simple disulfide: pdb=" SG CYS D 511 " - pdb=" SG CYS D 532 " 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 NAG-ASN " NAG A 901 " - " ASN A 53 " " NAG A 902 " - " ASN A 216 " " NAG A 903 " - " ASN A 322 " " NAG C 901 " - " ASN C 53 " " NAG C 902 " - " ASN C 216 " " NAG C 903 " - " ASN C 322 " " NAG C 904 " - " ASN C 690 " Time building additional restraints: 1.19 Conformation dependent library (CDL) restraints added in 639.6 milliseconds 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3412 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 11 sheets defined 48.8% alpha, 8.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 3.542A pdb=" N GLU A 30 " --> pdb=" O LYS A 26 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LYS A 31 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N TYR A 34 " --> pdb=" O GLU A 30 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLU A 35 " --> pdb=" O LYS A 31 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLN A 42 " --> pdb=" O GLU A 38 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASN A 43 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 81 removed outlier: 3.727A pdb=" N MET A 62 " --> pdb=" O ASN A 58 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ASN A 63 " --> pdb=" O ILE A 59 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ILE A 64 " --> pdb=" O GLN A 60 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LYS A 68 " --> pdb=" O ILE A 64 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TRP A 69 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LYS A 81 " --> pdb=" O SER A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 97 Processing helix chain 'A' and resid 109 through 129 removed outlier: 3.803A pdb=" N GLU A 114 " --> pdb=" O ALA A 110 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARG A 115 " --> pdb=" O ASP A 111 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU A 116 " --> pdb=" O LYS A 112 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASN A 117 " --> pdb=" O ARG A 113 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYR A 127 " --> pdb=" O MET A 123 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER A 128 " --> pdb=" O SER A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 155 Processing helix chain 'A' and resid 157 through 172 removed outlier: 3.661A pdb=" N ALA A 164 " --> pdb=" O GLU A 160 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG A 169 " --> pdb=" O TRP A 165 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL A 172 " --> pdb=" O TRP A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 175 No H-bonds generated for 'chain 'A' and resid 173 through 175' Processing helix chain 'A' and resid 176 through 193 removed outlier: 4.090A pdb=" N GLU A 181 " --> pdb=" O ARG A 177 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N GLU A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N TYR A 183 " --> pdb=" O LEU A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 220 through 231 removed outlier: 3.848A pdb=" N GLU A 224 " --> pdb=" O ASN A 220 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N THR A 231 " --> pdb=" O GLU A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 249 removed outlier: 3.519A pdb=" N MET A 249 " --> pdb=" O ARG A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 282 Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 305 through 317 Processing helix chain 'A' and resid 324 through 331 removed outlier: 4.214A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLN A 329 " --> pdb=" O GLU A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 375 removed outlier: 3.690A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 383 Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 400 through 412 removed outlier: 3.646A pdb=" N VAL A 404 " --> pdb=" O PHE A 400 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLY A 405 " --> pdb=" O HIS A 401 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLU A 406 " --> pdb=" O GLU A 402 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ILE A 407 " --> pdb=" O ALA A 403 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 421 removed outlier: 3.570A pdb=" N ASN A 420 " --> pdb=" O ASN A 416 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE A 421 " --> pdb=" O HIS A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 444 removed outlier: 3.860A pdb=" N ASN A 437 " --> pdb=" O GLU A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 465 removed outlier: 3.662A pdb=" N THR A 453 " --> pdb=" O THR A 449 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS A 465 " --> pdb=" O TRP A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 482 removed outlier: 3.554A pdb=" N ARG A 482 " --> pdb=" O TRP A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 503 Processing helix chain 'A' and resid 505 through 509 removed outlier: 3.828A pdb=" N ASP A 509 " --> pdb=" O VAL A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 533 removed outlier: 3.575A pdb=" N GLN A 531 " --> pdb=" O GLU A 527 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ILE A 532 " --> pdb=" O ALA A 528 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA A 533 " --> pdb=" O LEU A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 Processing helix chain 'A' and resid 548 through 559 removed outlier: 3.539A pdb=" N HIS A 555 " --> pdb=" O GLY A 551 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER A 559 " --> pdb=" O HIS A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 572 Processing helix chain 'A' and resid 581 through 588 removed outlier: 3.675A pdb=" N LEU A 585 " --> pdb=" O VAL A 581 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASN A 586 " --> pdb=" O ARG A 582 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TYR A 587 " --> pdb=" O PRO A 583 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N PHE A 588 " --> pdb=" O LEU A 584 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 581 through 588' Processing helix chain 'A' and resid 588 through 599 removed outlier: 4.124A pdb=" N GLU A 597 " --> pdb=" O THR A 593 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N GLN A 598 " --> pdb=" O TRP A 594 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ASN A 599 " --> pdb=" O LEU A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 631 removed outlier: 4.021A pdb=" N GLU A 630 " --> pdb=" O SER A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 659 Processing helix chain 'A' and resid 666 through 668 No H-bonds generated for 'chain 'A' and resid 666 through 668' Processing helix chain 'A' and resid 696 through 707 removed outlier: 3.525A pdb=" N VAL A 700 " --> pdb=" O PRO A 696 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 398 Processing helix chain 'B' and resid 418 through 424 Processing helix chain 'B' and resid 438 through 442 Processing helix chain 'B' and resid 461 through 465 removed outlier: 3.777A pdb=" N LEU B 464 " --> pdb=" O SER B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 476 Processing helix chain 'B' and resid 534 through 538 removed outlier: 4.130A pdb=" N SER B 538 " --> pdb=" O LEU B 535 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 53 removed outlier: 3.540A pdb=" N GLU C 30 " --> pdb=" O LYS C 26 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LYS C 31 " --> pdb=" O THR C 27 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N TYR C 34 " --> pdb=" O GLU C 30 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLU C 35 " --> pdb=" O LYS C 31 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLN C 42 " --> pdb=" O GLU C 38 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASN C 43 " --> pdb=" O LEU C 39 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 81 removed outlier: 3.758A pdb=" N MET C 62 " --> pdb=" O ASN C 58 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ASN C 63 " --> pdb=" O ILE C 59 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ILE C 64 " --> pdb=" O GLN C 60 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LYS C 68 " --> pdb=" O ILE C 64 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N TRP C 69 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LYS C 81 " --> pdb=" O SER C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 109 through 129 removed outlier: 3.802A pdb=" N GLU C 114 " --> pdb=" O ALA C 110 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ARG C 115 " --> pdb=" O ASP C 111 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU C 116 " --> pdb=" O LYS C 112 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ASN C 117 " --> pdb=" O ARG C 113 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TYR C 127 " --> pdb=" O MET C 123 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER C 128 " --> pdb=" O SER C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 155 Processing helix chain 'C' and resid 157 through 172 removed outlier: 3.658A pdb=" N ALA C 164 " --> pdb=" O GLU C 160 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG C 169 " --> pdb=" O TRP C 165 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU C 171 " --> pdb=" O GLY C 167 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL C 172 " --> pdb=" O TRP C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 175 No H-bonds generated for 'chain 'C' and resid 173 through 175' Processing helix chain 'C' and resid 176 through 193 removed outlier: 4.087A pdb=" N GLU C 181 " --> pdb=" O ARG C 177 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N GLU C 182 " --> pdb=" O PRO C 178 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N TYR C 183 " --> pdb=" O LEU C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 205 Processing helix chain 'C' and resid 206 through 208 No H-bonds generated for 'chain 'C' and resid 206 through 208' Processing helix chain 'C' and resid 220 through 231 removed outlier: 3.845A pdb=" N GLU C 224 " --> pdb=" O ASN C 220 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N THR C 231 " --> pdb=" O GLU C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 249 removed outlier: 3.519A pdb=" N MET C 249 " --> pdb=" O ARG C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 282 Processing helix chain 'C' and resid 293 through 300 Processing helix chain 'C' and resid 305 through 317 Processing helix chain 'C' and resid 324 through 331 removed outlier: 4.086A pdb=" N TRP C 328 " --> pdb=" O THR C 324 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLN C 329 " --> pdb=" O GLU C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 375 removed outlier: 3.706A pdb=" N HIS C 373 " --> pdb=" O PHE C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 376 through 383 Processing helix chain 'C' and resid 389 through 393 Processing helix chain 'C' and resid 400 through 412 removed outlier: 3.647A pdb=" N VAL C 404 " --> pdb=" O PHE C 400 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLY C 405 " --> pdb=" O HIS C 401 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU C 406 " --> pdb=" O GLU C 402 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ILE C 407 " --> pdb=" O ALA C 403 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N MET C 408 " --> pdb=" O VAL C 404 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N SER C 409 " --> pdb=" O GLY C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 421 removed outlier: 3.570A pdb=" N ASN C 420 " --> pdb=" O ASN C 416 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE C 421 " --> pdb=" O HIS C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 444 removed outlier: 3.858A pdb=" N ASN C 437 " --> pdb=" O GLU C 433 " (cutoff:3.500A) Processing helix chain 'C' and resid 449 through 465 removed outlier: 3.676A pdb=" N THR C 453 " --> pdb=" O THR C 449 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS C 465 " --> pdb=" O TRP C 461 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 482 removed outlier: 3.542A pdb=" N ARG C 482 " --> pdb=" O TRP C 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 503 Processing helix chain 'C' and resid 505 through 509 removed outlier: 3.826A pdb=" N ASP C 509 " --> pdb=" O VAL C 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 533 removed outlier: 3.575A pdb=" N GLN C 531 " --> pdb=" O GLU C 527 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ILE C 532 " --> pdb=" O ALA C 528 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA C 533 " --> pdb=" O LEU C 529 " (cutoff:3.500A) Processing helix chain 'C' and resid 538 through 542 Processing helix chain 'C' and resid 548 through 559 removed outlier: 3.544A pdb=" N HIS C 555 " --> pdb=" O GLY C 551 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N MET C 557 " --> pdb=" O LYS C 553 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER C 559 " --> pdb=" O HIS C 555 " (cutoff:3.500A) Processing helix chain 'C' and resid 565 through 572 Processing helix chain 'C' and resid 581 through 588 removed outlier: 3.675A pdb=" N LEU C 585 " --> pdb=" O VAL C 581 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASN C 586 " --> pdb=" O ARG C 582 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TYR C 587 " --> pdb=" O PRO C 583 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N PHE C 588 " --> pdb=" O LEU C 584 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 581 through 588' Processing helix chain 'C' and resid 588 through 599 removed outlier: 4.124A pdb=" N GLU C 597 " --> pdb=" O THR C 593 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N GLN C 598 " --> pdb=" O TRP C 594 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ASN C 599 " --> pdb=" O LEU C 595 " (cutoff:3.500A) Processing helix chain 'C' and resid 626 through 631 removed outlier: 3.826A pdb=" N GLU C 630 " --> pdb=" O SER C 626 " (cutoff:3.500A) Processing helix chain 'C' and resid 636 through 659 Processing helix chain 'C' and resid 666 through 668 No H-bonds generated for 'chain 'C' and resid 666 through 668' Processing helix chain 'C' and resid 696 through 707 Processing helix chain 'D' and resid 394 through 398 Processing helix chain 'D' and resid 418 through 424 Processing helix chain 'D' and resid 438 through 442 Processing helix chain 'D' and resid 461 through 465 removed outlier: 3.806A pdb=" N LEU D 464 " --> pdb=" O SER D 461 " (cutoff:3.500A) Processing helix chain 'D' and resid 470 through 475 Processing helix chain 'D' and resid 534 through 538 removed outlier: 4.129A pdb=" N SER D 538 " --> pdb=" O LEU D 535 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.372A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 347 through 350 Processing sheet with id=AA3, first strand: chain 'A' and resid 618 through 621 Processing sheet with id=AA4, first strand: chain 'B' and resid 408 through 412 removed outlier: 4.313A pdb=" N LYS B 408 " --> pdb=" O TYR B 453 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N TYR B 453 " --> pdb=" O LYS B 408 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N THR B 485 " --> pdb=" O HIS B 434 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU B 489 " --> pdb=" O GLU B 430 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLU B 430 " --> pdb=" O LEU B 489 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 518 through 521 removed outlier: 6.635A pdb=" N THR B 559 " --> pdb=" O THR B 509 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N CYS B 511 " --> pdb=" O VAL B 557 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N VAL B 557 " --> pdb=" O CYS B 511 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N LYS B 513 " --> pdb=" O TYR B 555 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N TYR B 555 " --> pdb=" O LYS B 513 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLY B 560 " --> pdb=" O GLN B 545 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLN B 545 " --> pdb=" O GLY B 560 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 131 through 133 Processing sheet with id=AA7, first strand: chain 'C' and resid 262 through 263 removed outlier: 6.371A pdb=" N LEU C 262 " --> pdb=" O VAL C 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 347 through 350 Processing sheet with id=AA9, first strand: chain 'C' and resid 618 through 621 removed outlier: 7.082A pdb=" N SER C 680 " --> pdb=" O LEU C 675 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N LEU C 675 " --> pdb=" O SER C 680 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N ASN C 682 " --> pdb=" O SER C 673 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 408 through 412 removed outlier: 4.310A pdb=" N LYS D 408 " --> pdb=" O TYR D 453 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N TYR D 453 " --> pdb=" O LYS D 408 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR D 485 " --> pdb=" O HIS D 434 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU D 489 " --> pdb=" O GLU D 430 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLU D 430 " --> pdb=" O LEU D 489 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 518 through 521 removed outlier: 6.618A pdb=" N THR D 559 " --> pdb=" O THR D 509 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N CYS D 511 " --> pdb=" O VAL D 557 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N VAL D 557 " --> pdb=" O CYS D 511 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N LYS D 513 " --> pdb=" O TYR D 555 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N TYR D 555 " --> pdb=" O LYS D 513 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLY D 560 " --> pdb=" O GLN D 545 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLN D 545 " --> pdb=" O GLY D 560 " (cutoff:3.500A) 531 hydrogen bonds defined for protein. 1479 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: 1.94 Time building geometry restraints manager: 1.66 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: 4707 1.34 - 1.46: 3721 1.46 - 1.58: 6522 1.58 - 1.70: 0 1.70 - 1.82: 140 Bond restraints: 15090 Sorted by residual: bond pdb=" C5 NAG C 902 " pdb=" O5 NAG C 902 " ideal model delta sigma weight residual 1.413 1.439 -0.026 2.00e-02 2.50e+03 1.74e+00 bond pdb=" C5 NAG A 902 " pdb=" O5 NAG A 902 " ideal model delta sigma weight residual 1.413 1.438 -0.025 2.00e-02 2.50e+03 1.60e+00 bond pdb=" CA ASP B 392 " pdb=" CB ASP B 392 " ideal model delta sigma weight residual 1.524 1.541 -0.017 1.37e-02 5.33e+03 1.52e+00 bond pdb=" CA ASP D 392 " pdb=" CB ASP D 392 " ideal model delta sigma weight residual 1.524 1.540 -0.016 1.37e-02 5.33e+03 1.39e+00 bond pdb=" CB ASP D 480 " pdb=" CG ASP D 480 " ideal model delta sigma weight residual 1.516 1.545 -0.029 2.50e-02 1.60e+03 1.37e+00 ... (remaining 15085 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 20192 1.98 - 3.95: 240 3.95 - 5.93: 37 5.93 - 7.90: 12 7.90 - 9.88: 8 Bond angle restraints: 20489 Sorted by residual: angle pdb=" N ARG C 518 " pdb=" CA ARG C 518 " pdb=" C ARG C 518 " ideal model delta sigma weight residual 114.62 109.25 5.37 1.14e+00 7.69e-01 2.22e+01 angle pdb=" N ARG A 518 " pdb=" CA ARG A 518 " pdb=" C ARG A 518 " ideal model delta sigma weight residual 114.62 109.26 5.36 1.14e+00 7.69e-01 2.21e+01 angle pdb=" C LEU A 144 " pdb=" N GLU A 145 " pdb=" CA GLU A 145 " ideal model delta sigma weight residual 121.80 131.68 -9.88 2.44e+00 1.68e-01 1.64e+01 angle pdb=" C LEU C 144 " pdb=" N GLU C 145 " pdb=" CA GLU C 145 " ideal model delta sigma weight residual 121.80 131.53 -9.73 2.44e+00 1.68e-01 1.59e+01 angle pdb=" CB MET C 557 " pdb=" CG MET C 557 " pdb=" SD MET C 557 " ideal model delta sigma weight residual 112.70 121.40 -8.70 3.00e+00 1.11e-01 8.42e+00 ... (remaining 20484 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.66: 7751 16.66 - 33.33: 1003 33.33 - 49.99: 263 49.99 - 66.65: 60 66.65 - 83.32: 18 Dihedral angle restraints: 9095 sinusoidal: 3791 harmonic: 5304 Sorted by residual: dihedral pdb=" CB CYS C 133 " pdb=" SG CYS C 133 " pdb=" SG CYS C 141 " pdb=" CB CYS C 141 " ideal model delta sinusoidal sigma weight residual -86.00 -127.66 41.66 1 1.00e+01 1.00e-02 2.43e+01 dihedral pdb=" CA CYS A 141 " pdb=" C CYS A 141 " pdb=" N LEU A 142 " pdb=" CA LEU A 142 " ideal model delta harmonic sigma weight residual -180.00 -156.78 -23.22 0 5.00e+00 4.00e-02 2.16e+01 dihedral pdb=" CA CYS C 141 " pdb=" C CYS C 141 " pdb=" N LEU C 142 " pdb=" CA LEU C 142 " ideal model delta harmonic sigma weight residual -180.00 -162.01 -17.99 0 5.00e+00 4.00e-02 1.29e+01 ... (remaining 9092 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.262: 2166 0.262 - 0.523: 0 0.523 - 0.785: 0 0.785 - 1.046: 0 1.046 - 1.308: 1 Chirality restraints: 2167 Sorted by residual: chirality pdb=" C1 NAG A 902 " pdb=" ND2 ASN A 216 " pdb=" C2 NAG A 902 " pdb=" O5 NAG A 902 " both_signs ideal model delta sigma weight residual False -2.40 -1.09 -1.31 2.00e-01 2.50e+01 4.28e+01 chirality pdb=" C1 NAG C 901 " pdb=" ND2 ASN C 53 " pdb=" C2 NAG C 901 " pdb=" O5 NAG C 901 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" C1 NAG C 903 " pdb=" ND2 ASN C 322 " pdb=" C2 NAG C 903 " pdb=" O5 NAG C 903 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-01 2.50e+01 1.52e+00 ... (remaining 2164 not shown) Planarity restraints: 2654 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 902 " 0.150 2.00e-02 2.50e+03 1.24e-01 1.92e+02 pdb=" C7 NAG A 902 " -0.044 2.00e-02 2.50e+03 pdb=" C8 NAG A 902 " 0.112 2.00e-02 2.50e+03 pdb=" N2 NAG A 902 " -0.198 2.00e-02 2.50e+03 pdb=" O7 NAG A 902 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 902 " -0.040 2.00e-02 2.50e+03 3.29e-02 1.35e+01 pdb=" C7 NAG C 902 " 0.012 2.00e-02 2.50e+03 pdb=" C8 NAG C 902 " -0.031 2.00e-02 2.50e+03 pdb=" N2 NAG C 902 " 0.052 2.00e-02 2.50e+03 pdb=" O7 NAG C 902 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP C 674 " -0.010 2.00e-02 2.50e+03 2.07e-02 4.30e+00 pdb=" C ASP C 674 " 0.036 2.00e-02 2.50e+03 pdb=" O ASP C 674 " -0.014 2.00e-02 2.50e+03 pdb=" N LEU C 675 " -0.012 2.00e-02 2.50e+03 ... (remaining 2651 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 293 2.68 - 3.24: 13968 3.24 - 3.79: 21759 3.79 - 4.35: 27200 4.35 - 4.90: 46205 Nonbonded interactions: 109425 Sorted by model distance: nonbonded pdb=" O PHE C 327 " pdb=" OG SER C 331 " model vdw 2.131 3.040 nonbonded pdb=" O PHE A 327 " pdb=" OG SER A 331 " model vdw 2.143 3.040 nonbonded pdb=" OG1 THR A 55 " pdb=" OD1 ASN A 58 " model vdw 2.149 3.040 nonbonded pdb=" OD1 ASP A 494 " pdb=" OG1 THR A 496 " model vdw 2.210 3.040 nonbonded pdb=" OD1 ASP C 494 " pdb=" OG1 THR C 496 " model vdw 2.210 3.040 ... (remaining 109420 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 'A' selection = (chain 'C' and resid 20 through 903) } ncs_group { reference = chain 'B' selection = chain 'D' } 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: 5.060 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 13.520 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6944 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 : 0.002 0.029 15109 Z= 0.118 Angle : 0.583 9.880 20534 Z= 0.298 Chirality : 0.050 1.308 2167 Planarity : 0.004 0.124 2647 Dihedral : 16.040 83.316 5647 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.21 % Favored : 93.68 % Rotamer: Outliers : 1.82 % Allowed : 20.00 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.37 (0.20), residues: 1788 helix: 1.01 (0.21), residues: 742 sheet: 1.09 (0.45), residues: 130 loop : -1.58 (0.19), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 340 TYR 0.007 0.001 TYR C 385 PHE 0.012 0.001 PHE C 683 TRP 0.011 0.001 TRP C 163 HIS 0.002 0.000 HIS A 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.12 (15090) covalent geometry : angle 0.56888 / 0.30 (20489) SS BOND : bond 0.00294 / 0.16 ( 12) SS BOND : angle 1.04514 / 0.61 ( 24) hydrogen bonds : bond 0.16353 / 10.91 ( 531) hydrogen bonds : angle 4.77633 / 3.54 ( 1479) link_NAG-ASN : bond 0.00850 / 0.39 ( 7) link_NAG-ASN : angle 3.91923 / 2.72 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 575 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 546 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.7214 (tp30) cc_final: 0.7011 (mm-30) REVERT: A 57 GLU cc_start: 0.7628 (pm20) cc_final: 0.7242 (pm20) REVERT: A 88 ILE cc_start: 0.6594 (mm) cc_final: 0.6242 (mm) REVERT: A 94 LYS cc_start: 0.7618 (ttpp) cc_final: 0.7303 (ttmt) REVERT: A 102 GLN cc_start: 0.5793 (mp10) cc_final: 0.5465 (mp10) REVERT: A 105 SER cc_start: 0.8294 (t) cc_final: 0.7569 (m) REVERT: A 197 GLU cc_start: 0.7527 (mp0) cc_final: 0.6642 (mp0) REVERT: A 218 SER cc_start: 0.7389 (m) cc_final: 0.7182 (t) REVERT: A 224 GLU cc_start: 0.6422 (mt-10) cc_final: 0.6220 (mt-10) REVERT: A 254 SER cc_start: 0.8080 (m) cc_final: 0.7855 (p) REVERT: A 305 ARG cc_start: 0.7334 (mtp85) cc_final: 0.7081 (ttm170) REVERT: A 332 MET cc_start: 0.7162 (ttm) cc_final: 0.6952 (ttm) REVERT: A 398 GLU cc_start: 0.7823 (pt0) cc_final: 0.7478 (pt0) REVERT: A 430 GLU cc_start: 0.8096 (tt0) cc_final: 0.7872 (tt0) REVERT: A 467 GLU cc_start: 0.7073 (tm-30) cc_final: 0.6681 (tm-30) REVERT: A 471 GLU cc_start: 0.6786 (mp0) cc_final: 0.6439 (mp0) REVERT: A 489 GLU cc_start: 0.7525 (pt0) cc_final: 0.7123 (pm20) REVERT: A 494 ASP cc_start: 0.6792 (p0) cc_final: 0.6557 (p0) REVERT: A 527 GLU cc_start: 0.7478 (tm-30) cc_final: 0.7123 (tp30) REVERT: A 562 ARG cc_start: 0.7274 (mtt-85) cc_final: 0.6942 (mtt-85) REVERT: A 600 ARG cc_start: 0.7950 (tpp-160) cc_final: 0.7283 (mmp80) REVERT: A 607 ASN cc_start: 0.7686 (t0) cc_final: 0.7296 (t0) REVERT: A 609 ASP cc_start: 0.7074 (m-30) cc_final: 0.6417 (m-30) REVERT: A 693 ASP cc_start: 0.6491 (m-30) cc_final: 0.6005 (m-30) REVERT: A 694 ILE cc_start: 0.7121 (pt) cc_final: 0.6804 (pt) REVERT: A 708 ARG cc_start: 0.7563 (ttt90) cc_final: 0.7251 (tpp80) REVERT: A 711 ILE cc_start: 0.7319 (mm) cc_final: 0.7049 (mm) REVERT: A 718 ASP cc_start: 0.6553 (m-30) cc_final: 0.6159 (t0) REVERT: B 431 PHE cc_start: 0.6447 (m-80) cc_final: 0.6110 (m-80) REVERT: B 517 TYR cc_start: 0.7682 (m-80) cc_final: 0.7209 (m-80) REVERT: B 524 ASN cc_start: 0.6653 (m-40) cc_final: 0.6321 (m110) REVERT: B 535 LEU cc_start: 0.7802 (tp) cc_final: 0.7476 (tp) REVERT: B 555 TYR cc_start: 0.7602 (p90) cc_final: 0.7253 (p90) REVERT: C 74 GLU cc_start: 0.7184 (mm-30) cc_final: 0.6792 (tp30) REVERT: C 88 ILE cc_start: 0.6697 (mm) cc_final: 0.6193 (mm) REVERT: C 89 GLN cc_start: 0.6249 (mm110) cc_final: 0.5972 (mm-40) REVERT: C 94 LYS cc_start: 0.7474 (ttpp) cc_final: 0.7025 (ttpt) REVERT: C 102 GLN cc_start: 0.5752 (mp10) cc_final: 0.5449 (mp10) REVERT: C 140 GLU cc_start: 0.5873 (tt0) cc_final: 0.5298 (tt0) REVERT: C 153 GLU cc_start: 0.6168 (tm-30) cc_final: 0.5643 (pp20) REVERT: C 155 SER cc_start: 0.6942 (m) cc_final: 0.6438 (p) REVERT: C 156 LYS cc_start: 0.7546 (ptpp) cc_final: 0.7185 (ptmm) REVERT: C 174 LYS cc_start: 0.7580 (mtmt) cc_final: 0.7334 (mtmt) REVERT: C 197 GLU cc_start: 0.7737 (mp0) cc_final: 0.7515 (mm-30) REVERT: C 254 SER cc_start: 0.7985 (m) cc_final: 0.7711 (p) REVERT: C 257 SER cc_start: 0.8081 (t) cc_final: 0.7512 (p) REVERT: C 398 GLU cc_start: 0.7710 (pt0) cc_final: 0.7361 (pt0) REVERT: C 467 GLU cc_start: 0.6940 (tm-30) cc_final: 0.6738 (tp30) REVERT: C 489 GLU cc_start: 0.7468 (pt0) cc_final: 0.7003 (pm20) REVERT: C 518 ARG cc_start: 0.7480 (tmm-80) cc_final: 0.7261 (ttp80) REVERT: C 527 GLU cc_start: 0.7609 (tm-30) cc_final: 0.7025 (tp30) REVERT: C 607 ASN cc_start: 0.7498 (t0) cc_final: 0.7024 (t0) REVERT: C 609 ASP cc_start: 0.6455 (m-30) cc_final: 0.5662 (m-30) REVERT: C 619 LYS cc_start: 0.7123 (tttm) cc_final: 0.6883 (tttm) REVERT: C 661 GLN cc_start: 0.6398 (tt0) cc_final: 0.5931 (mt0) REVERT: C 668 LYS cc_start: 0.7470 (ptmm) cc_final: 0.7245 (mtmm) REVERT: C 693 ASP cc_start: 0.6120 (m-30) cc_final: 0.5743 (m-30) REVERT: C 694 ILE cc_start: 0.7136 (pt) cc_final: 0.6730 (pt) REVERT: C 705 ARG cc_start: 0.7052 (ttp80) cc_final: 0.6507 (ttp-110) REVERT: C 708 ARG cc_start: 0.7459 (ttt90) cc_final: 0.7140 (tpp80) REVERT: C 711 ILE cc_start: 0.7336 (mm) cc_final: 0.6860 (mt) REVERT: D 474 LYS cc_start: 0.7559 (mtpp) cc_final: 0.7306 (mttt) REVERT: D 477 TYR cc_start: 0.7706 (t80) cc_final: 0.7440 (t80) REVERT: D 479 GLN cc_start: 0.7991 (tt0) cc_final: 0.7627 (tt0) REVERT: D 569 LEU cc_start: 0.7325 (tp) cc_final: 0.6892 (tp) outliers start: 29 outliers final: 10 residues processed: 565 average time/residue: 0.1159 time to fit residues: 96.7530 Evaluate side-chains 472 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 462 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 341 LYS Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 637 ASP Chi-restraints excluded: chain B residue 396 MET Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain D residue 396 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 149] chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.0470 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.4980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 0.3980 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 63 ASN C 175 GLN ** C 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.123502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.105154 restraints weight = 23534.634| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 2.51 r_work: 0.3228 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15109 Z= 0.138 Angle : 0.599 9.730 20534 Z= 0.304 Chirality : 0.043 0.262 2167 Planarity : 0.004 0.047 2647 Dihedral : 5.356 46.847 2141 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.93 % Favored : 93.85 % Rotamer: Outliers : 4.28 % Allowed : 21.38 % Favored : 74.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.51 (0.20), residues: 1788 helix: 0.97 (0.21), residues: 738 sheet: 0.80 (0.44), residues: 144 loop : -1.72 (0.18), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 572 TYR 0.014 0.001 TYR B 505 PHE 0.017 0.001 PHE D 431 TRP 0.013 0.001 TRP A 163 HIS 0.006 0.001 HIS C 535 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (15090) covalent geometry : angle 0.59355 / 0.30 (20489) SS BOND : bond 0.00254 / 0.15 ( 12) SS BOND : angle 1.07425 / 0.72 ( 24) hydrogen bonds : bond 0.05050 / 3.25 ( 531) hydrogen bonds : angle 3.99872 / 2.91 ( 1479) link_NAG-ASN : bond 0.00585 / 0.25 ( 7) link_NAG-ASN : angle 2.44802 / 1.63 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 472 time to evaluate : 0.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ASN cc_start: 0.7776 (m110) cc_final: 0.6937 (m-40) REVERT: A 94 LYS cc_start: 0.8471 (ttpp) cc_final: 0.8211 (ttmt) REVERT: A 102 GLN cc_start: 0.7136 (mp10) cc_final: 0.6931 (mp10) REVERT: A 105 SER cc_start: 0.8757 (t) cc_final: 0.8416 (p) REVERT: A 107 VAL cc_start: 0.8768 (m) cc_final: 0.8487 (p) REVERT: A 163 TRP cc_start: 0.8129 (p-90) cc_final: 0.7559 (p-90) REVERT: A 197 GLU cc_start: 0.7709 (mp0) cc_final: 0.7448 (mm-30) REVERT: A 254 SER cc_start: 0.8508 (m) cc_final: 0.8305 (p) REVERT: A 368 ASP cc_start: 0.7826 (OUTLIER) cc_final: 0.7289 (m-30) REVERT: A 376 MET cc_start: 0.8626 (tpp) cc_final: 0.8054 (mtt) REVERT: A 467 GLU cc_start: 0.7651 (tm-30) cc_final: 0.7275 (tp30) REVERT: A 479 GLU cc_start: 0.7706 (tp30) cc_final: 0.7133 (tp30) REVERT: A 482 ARG cc_start: 0.8644 (ttp-170) cc_final: 0.8315 (ttm170) REVERT: A 489 GLU cc_start: 0.7542 (pt0) cc_final: 0.7282 (pm20) REVERT: A 527 GLU cc_start: 0.8176 (tm-30) cc_final: 0.7810 (tp30) REVERT: A 601 ASN cc_start: 0.8384 (p0) cc_final: 0.7938 (p0) REVERT: A 607 ASN cc_start: 0.8134 (t0) cc_final: 0.7287 (t0) REVERT: A 609 ASP cc_start: 0.7724 (m-30) cc_final: 0.7362 (m-30) REVERT: A 640 MET cc_start: 0.6951 (mmm) cc_final: 0.6583 (mmm) REVERT: A 693 ASP cc_start: 0.7318 (m-30) cc_final: 0.7053 (m-30) REVERT: A 694 ILE cc_start: 0.8055 (pt) cc_final: 0.7759 (pt) REVERT: A 711 ILE cc_start: 0.8380 (mm) cc_final: 0.8117 (mt) REVERT: B 517 TYR cc_start: 0.8622 (m-80) cc_final: 0.8101 (m-80) REVERT: B 555 TYR cc_start: 0.8479 (p90) cc_final: 0.8205 (p90) REVERT: C 58 ASN cc_start: 0.7842 (m110) cc_final: 0.7204 (m-40) REVERT: C 74 GLU cc_start: 0.7764 (mm-30) cc_final: 0.7537 (tp30) REVERT: C 85 LEU cc_start: 0.7856 (tt) cc_final: 0.7541 (tp) REVERT: C 88 ILE cc_start: 0.7616 (mm) cc_final: 0.7253 (mm) REVERT: C 94 LYS cc_start: 0.8368 (ttpp) cc_final: 0.8073 (ttpt) REVERT: C 102 GLN cc_start: 0.7038 (mp10) cc_final: 0.6816 (mp10) REVERT: C 105 SER cc_start: 0.8845 (t) cc_final: 0.8629 (t) REVERT: C 140 GLU cc_start: 0.7621 (tt0) cc_final: 0.7029 (tt0) REVERT: C 149 ASP cc_start: 0.6967 (t0) cc_final: 0.6714 (t0) REVERT: C 155 SER cc_start: 0.8248 (m) cc_final: 0.8042 (t) REVERT: C 163 TRP cc_start: 0.8317 (p-90) cc_final: 0.7649 (p-90) REVERT: C 171 GLU cc_start: 0.7034 (mp0) cc_final: 0.6753 (mp0) REVERT: C 254 SER cc_start: 0.8406 (m) cc_final: 0.8118 (p) REVERT: C 257 SER cc_start: 0.8607 (t) cc_final: 0.8221 (p) REVERT: C 282 MET cc_start: 0.8226 (ptp) cc_final: 0.7963 (ptp) REVERT: C 368 ASP cc_start: 0.7724 (m-30) cc_final: 0.7178 (m-30) REVERT: C 410 LEU cc_start: 0.8336 (tt) cc_final: 0.8069 (tt) REVERT: C 489 GLU cc_start: 0.7499 (pt0) cc_final: 0.7246 (pm20) REVERT: C 527 GLU cc_start: 0.8333 (tm-30) cc_final: 0.7935 (tp30) REVERT: C 534 LYS cc_start: 0.8185 (mmmm) cc_final: 0.7816 (mmmm) REVERT: C 601 ASN cc_start: 0.8403 (p0) cc_final: 0.8093 (p0) REVERT: C 607 ASN cc_start: 0.8028 (t0) cc_final: 0.7719 (t0) REVERT: C 609 ASP cc_start: 0.7448 (m-30) cc_final: 0.6723 (m-30) REVERT: C 619 LYS cc_start: 0.7806 (tttm) cc_final: 0.7580 (tttm) REVERT: C 691 MET cc_start: 0.8153 (OUTLIER) cc_final: 0.7939 (mtp) REVERT: C 694 ILE cc_start: 0.8141 (pt) cc_final: 0.7794 (pt) REVERT: C 705 ARG cc_start: 0.8328 (ttp80) cc_final: 0.7930 (ttp-110) REVERT: C 711 ILE cc_start: 0.8403 (mm) cc_final: 0.8151 (mt) REVERT: D 555 TYR cc_start: 0.8374 (p90) cc_final: 0.7909 (p90) REVERT: D 569 LEU cc_start: 0.8412 (tp) cc_final: 0.8113 (tp) outliers start: 68 outliers final: 35 residues processed: 513 average time/residue: 0.1085 time to fit residues: 83.6494 Evaluate side-chains 501 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 464 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 341 LYS Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 663 ILE Chi-restraints excluded: chain A residue 684 ILE Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain B residue 482 SER Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 79 HIS Chi-restraints excluded: chain C residue 123 MET Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 401 HIS Chi-restraints excluded: chain C residue 455 MET Chi-restraints excluded: chain C residue 544 ILE Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 579 MET Chi-restraints excluded: chain C residue 684 ILE Chi-restraints excluded: chain C residue 691 MET Chi-restraints excluded: chain D residue 428 VAL Chi-restraints excluded: chain D residue 459 SER Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain D residue 556 LEU Chi-restraints excluded: chain D residue 574 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: [133, 48, 60, 98, 43, 33, 101, 9, 12, 144, 103] chunk 133 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 98 optimal weight: 0.7980 chunk 43 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 12 optimal weight: 0.0470 chunk 144 optimal weight: 0.0040 chunk 103 optimal weight: 0.3980 overall best weight: 0.3890 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 374 HIS A 661 GLN B 434 HIS B 476 ASN C 374 HIS D 434 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.123442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.105220 restraints weight = 23791.920| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 2.54 r_work: 0.3223 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15109 Z= 0.122 Angle : 0.579 10.147 20534 Z= 0.294 Chirality : 0.043 0.263 2167 Planarity : 0.004 0.041 2647 Dihedral : 5.081 41.910 2129 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.10 % Favored : 93.68 % Rotamer: Outliers : 3.71 % Allowed : 22.70 % Favored : 73.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.58 (0.20), residues: 1788 helix: 0.88 (0.20), residues: 754 sheet: 1.15 (0.46), residues: 134 loop : -1.82 (0.18), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 514 TYR 0.019 0.001 TYR B 505 PHE 0.019 0.001 PHE B 431 TRP 0.014 0.001 TRP A 163 HIS 0.004 0.001 HIS C 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (15090) covalent geometry : angle 0.57367 / 0.29 (20489) SS BOND : bond 0.00128 / 0.09 ( 12) SS BOND : angle 1.01847 / 0.68 ( 24) hydrogen bonds : bond 0.04475 / 2.87 ( 531) hydrogen bonds : angle 3.90963 / 2.82 ( 1479) link_NAG-ASN : bond 0.00548 / 0.25 ( 7) link_NAG-ASN : angle 2.37325 / 1.58 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 459 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ASN cc_start: 0.7878 (m110) cc_final: 0.7365 (m-40) REVERT: A 88 ILE cc_start: 0.7849 (mm) cc_final: 0.7589 (mm) REVERT: A 94 LYS cc_start: 0.8474 (ttpp) cc_final: 0.8228 (ttmt) REVERT: A 105 SER cc_start: 0.8799 (t) cc_final: 0.8459 (p) REVERT: A 107 VAL cc_start: 0.8774 (m) cc_final: 0.8493 (p) REVERT: A 163 TRP cc_start: 0.8129 (p-90) cc_final: 0.7609 (p-90) REVERT: A 171 GLU cc_start: 0.7199 (mp0) cc_final: 0.6495 (mp0) REVERT: A 197 GLU cc_start: 0.7665 (mp0) cc_final: 0.7463 (mm-30) REVERT: A 224 GLU cc_start: 0.6886 (mt-10) cc_final: 0.6679 (mt-10) REVERT: A 254 SER cc_start: 0.8496 (m) cc_final: 0.8265 (p) REVERT: A 292 ASP cc_start: 0.7804 (t70) cc_final: 0.7582 (t70) REVERT: A 368 ASP cc_start: 0.7798 (OUTLIER) cc_final: 0.7262 (m-30) REVERT: A 376 MET cc_start: 0.8572 (tpp) cc_final: 0.8020 (mtt) REVERT: A 400 PHE cc_start: 0.8603 (OUTLIER) cc_final: 0.7759 (t80) REVERT: A 474 MET cc_start: 0.7509 (mmp) cc_final: 0.7300 (mmp) REVERT: A 479 GLU cc_start: 0.7709 (tp30) cc_final: 0.7077 (tp30) REVERT: A 482 ARG cc_start: 0.8687 (ttp-170) cc_final: 0.8316 (ttm170) REVERT: A 487 VAL cc_start: 0.8425 (m) cc_final: 0.8194 (t) REVERT: A 489 GLU cc_start: 0.7548 (pt0) cc_final: 0.7316 (pm20) REVERT: A 499 ASP cc_start: 0.8277 (m-30) cc_final: 0.8061 (m-30) REVERT: A 527 GLU cc_start: 0.8209 (tm-30) cc_final: 0.7835 (tp30) REVERT: A 556 GLU cc_start: 0.8060 (tp30) cc_final: 0.7692 (tp30) REVERT: A 601 ASN cc_start: 0.8371 (p0) cc_final: 0.7932 (p0) REVERT: A 607 ASN cc_start: 0.8139 (t0) cc_final: 0.7503 (t0) REVERT: A 609 ASP cc_start: 0.7726 (m-30) cc_final: 0.7391 (m-30) REVERT: A 617 SER cc_start: 0.8689 (t) cc_final: 0.8469 (p) REVERT: A 661 GLN cc_start: 0.6917 (mt0) cc_final: 0.6708 (mp10) REVERT: A 693 ASP cc_start: 0.7311 (m-30) cc_final: 0.7054 (m-30) REVERT: A 694 ILE cc_start: 0.8073 (pt) cc_final: 0.7788 (pt) REVERT: A 702 GLU cc_start: 0.7595 (tp30) cc_final: 0.7304 (tp30) REVERT: A 705 ARG cc_start: 0.8383 (ttp80) cc_final: 0.7921 (ttp-110) REVERT: A 708 ARG cc_start: 0.8244 (tpp80) cc_final: 0.7950 (tpp-160) REVERT: A 711 ILE cc_start: 0.8425 (mm) cc_final: 0.8137 (mt) REVERT: B 412 PHE cc_start: 0.6394 (m-10) cc_final: 0.6000 (m-10) REVERT: B 417 TYR cc_start: 0.5746 (OUTLIER) cc_final: 0.5521 (m-10) REVERT: B 474 LYS cc_start: 0.8516 (OUTLIER) cc_final: 0.8101 (tttm) REVERT: B 517 TYR cc_start: 0.8603 (m-80) cc_final: 0.8069 (m-80) REVERT: B 555 TYR cc_start: 0.8501 (p90) cc_final: 0.8255 (p90) REVERT: C 58 ASN cc_start: 0.7924 (m110) cc_final: 0.7244 (m-40) REVERT: C 79 HIS cc_start: 0.8080 (OUTLIER) cc_final: 0.7872 (t-170) REVERT: C 85 LEU cc_start: 0.7828 (OUTLIER) cc_final: 0.7497 (tp) REVERT: C 88 ILE cc_start: 0.7687 (mm) cc_final: 0.7458 (mm) REVERT: C 94 LYS cc_start: 0.8423 (ttpp) cc_final: 0.8137 (ttpt) REVERT: C 102 GLN cc_start: 0.7044 (mp10) cc_final: 0.6712 (mp10) REVERT: C 105 SER cc_start: 0.8870 (t) cc_final: 0.8656 (t) REVERT: C 140 GLU cc_start: 0.7630 (tt0) cc_final: 0.7035 (tt0) REVERT: C 149 ASP cc_start: 0.6937 (t0) cc_final: 0.6705 (t0) REVERT: C 163 TRP cc_start: 0.8314 (p-90) cc_final: 0.7690 (p-90) REVERT: C 171 GLU cc_start: 0.7025 (mp0) cc_final: 0.6586 (mp0) REVERT: C 189 GLU cc_start: 0.7455 (tp30) cc_final: 0.7153 (tt0) REVERT: C 213 ASP cc_start: 0.7655 (t0) cc_final: 0.7395 (t0) REVERT: C 254 SER cc_start: 0.8395 (m) cc_final: 0.8111 (p) REVERT: C 257 SER cc_start: 0.8584 (t) cc_final: 0.8196 (p) REVERT: C 368 ASP cc_start: 0.7684 (m-30) cc_final: 0.7170 (m-30) REVERT: C 400 PHE cc_start: 0.8644 (OUTLIER) cc_final: 0.7710 (t80) REVERT: C 410 LEU cc_start: 0.8332 (tt) cc_final: 0.8057 (tt) REVERT: C 487 VAL cc_start: 0.8467 (m) cc_final: 0.8188 (t) REVERT: C 489 GLU cc_start: 0.7498 (pt0) cc_final: 0.7245 (pm20) REVERT: C 527 GLU cc_start: 0.8312 (tm-30) cc_final: 0.7951 (tp30) REVERT: C 556 GLU cc_start: 0.8137 (tp30) cc_final: 0.7911 (tp30) REVERT: C 601 ASN cc_start: 0.8428 (p0) cc_final: 0.8133 (p0) REVERT: C 607 ASN cc_start: 0.8059 (t0) cc_final: 0.7765 (t0) REVERT: C 609 ASP cc_start: 0.7487 (m-30) cc_final: 0.6774 (m-30) REVERT: C 619 LYS cc_start: 0.7876 (tttm) cc_final: 0.7516 (tttm) REVERT: C 621 ARG cc_start: 0.7587 (ttm170) cc_final: 0.7112 (ttm170) REVERT: C 661 GLN cc_start: 0.7103 (mt0) cc_final: 0.6708 (mp10) REVERT: C 705 ARG cc_start: 0.8286 (ttp80) cc_final: 0.7955 (ttp-110) REVERT: C 708 ARG cc_start: 0.8085 (OUTLIER) cc_final: 0.7846 (tpp-160) REVERT: C 711 ILE cc_start: 0.8416 (mm) cc_final: 0.8176 (mt) REVERT: D 412 PHE cc_start: 0.6223 (m-10) cc_final: 0.6016 (m-10) REVERT: D 474 LYS cc_start: 0.8587 (mttt) cc_final: 0.8218 (mtpt) REVERT: D 555 TYR cc_start: 0.8363 (p90) cc_final: 0.8003 (p90) REVERT: D 569 LEU cc_start: 0.8449 (tp) cc_final: 0.8174 (tp) outliers start: 59 outliers final: 35 residues processed: 489 average time/residue: 0.1105 time to fit residues: 80.7439 Evaluate side-chains 494 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 451 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 341 LYS Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 663 ILE Chi-restraints excluded: chain A residue 684 ILE Chi-restraints excluded: chain B residue 417 TYR Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 474 LYS Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 556 LEU Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 79 HIS Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 123 MET Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 400 PHE Chi-restraints excluded: chain C residue 401 HIS Chi-restraints excluded: chain C residue 421 ILE Chi-restraints excluded: chain C residue 455 MET Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 579 MET Chi-restraints excluded: chain C residue 684 ILE Chi-restraints excluded: chain C residue 708 ARG Chi-restraints excluded: chain D residue 428 VAL Chi-restraints excluded: chain D residue 461 SER Chi-restraints excluded: chain D residue 556 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: [166, 124, 116, 171, 167, 35, 120, 78, 54, 113, 155] chunk 166 optimal weight: 1.9990 chunk 124 optimal weight: 0.9980 chunk 116 optimal weight: 0.8980 chunk 171 optimal weight: 1.9990 chunk 167 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 120 optimal weight: 0.7980 chunk 78 optimal weight: 0.0270 chunk 54 optimal weight: 0.7980 chunk 113 optimal weight: 0.4980 chunk 155 optimal weight: 0.5980 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 476 ASN D 550 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.122028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.103866 restraints weight = 23610.610| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 2.53 r_work: 0.3203 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15109 Z= 0.136 Angle : 0.580 9.938 20534 Z= 0.295 Chirality : 0.043 0.282 2167 Planarity : 0.004 0.044 2647 Dihedral : 5.091 43.270 2129 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.10 % Favored : 93.68 % Rotamer: Outliers : 3.65 % Allowed : 23.65 % Favored : 72.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.64 (0.20), residues: 1788 helix: 0.76 (0.20), residues: 760 sheet: 1.35 (0.50), residues: 114 loop : -1.77 (0.18), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 572 TYR 0.018 0.001 TYR C 654 PHE 0.015 0.002 PHE C 683 TRP 0.015 0.001 TRP C 163 HIS 0.004 0.001 HIS C 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (15090) covalent geometry : angle 0.57496 / 0.29 (20489) SS BOND : bond 0.00408 / 0.19 ( 12) SS BOND : angle 1.05657 / 0.67 ( 24) hydrogen bonds : bond 0.04991 / 3.22 ( 531) hydrogen bonds : angle 3.83817 / 2.75 ( 1479) link_NAG-ASN : bond 0.00518 / 0.24 ( 7) link_NAG-ASN : angle 2.35563 / 1.55 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 459 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ASN cc_start: 0.7992 (m110) cc_final: 0.7429 (m-40) REVERT: A 61 LYS cc_start: 0.8025 (OUTLIER) cc_final: 0.7637 (mppt) REVERT: A 88 ILE cc_start: 0.7940 (mm) cc_final: 0.7710 (mm) REVERT: A 94 LYS cc_start: 0.8602 (ttpp) cc_final: 0.8365 (ttmt) REVERT: A 105 SER cc_start: 0.8840 (t) cc_final: 0.8501 (p) REVERT: A 107 VAL cc_start: 0.8839 (m) cc_final: 0.8591 (p) REVERT: A 163 TRP cc_start: 0.8386 (p-90) cc_final: 0.8022 (p-90) REVERT: A 171 GLU cc_start: 0.7472 (mp0) cc_final: 0.6757 (mp0) REVERT: A 197 GLU cc_start: 0.7832 (mp0) cc_final: 0.7532 (mm-30) REVERT: A 213 ASP cc_start: 0.7777 (t0) cc_final: 0.7497 (t0) REVERT: A 254 SER cc_start: 0.8483 (m) cc_final: 0.8244 (p) REVERT: A 316 VAL cc_start: 0.8884 (OUTLIER) cc_final: 0.8667 (t) REVERT: A 368 ASP cc_start: 0.8011 (OUTLIER) cc_final: 0.7501 (m-30) REVERT: A 376 MET cc_start: 0.8785 (tpp) cc_final: 0.8403 (mtt) REVERT: A 479 GLU cc_start: 0.8151 (tp30) cc_final: 0.7468 (tp30) REVERT: A 482 ARG cc_start: 0.8839 (ttp-170) cc_final: 0.8510 (ttm170) REVERT: A 487 VAL cc_start: 0.8547 (m) cc_final: 0.8325 (t) REVERT: A 489 GLU cc_start: 0.7797 (pt0) cc_final: 0.7462 (pm20) REVERT: A 495 GLU cc_start: 0.7887 (mm-30) cc_final: 0.7544 (mm-30) REVERT: A 527 GLU cc_start: 0.8529 (tm-30) cc_final: 0.8058 (tm-30) REVERT: A 556 GLU cc_start: 0.8361 (tp30) cc_final: 0.7864 (tp30) REVERT: A 601 ASN cc_start: 0.8586 (p0) cc_final: 0.8176 (p0) REVERT: A 607 ASN cc_start: 0.8333 (t0) cc_final: 0.8115 (t0) REVERT: A 609 ASP cc_start: 0.7962 (m-30) cc_final: 0.7578 (m-30) REVERT: A 617 SER cc_start: 0.8788 (t) cc_final: 0.8565 (p) REVERT: A 661 GLN cc_start: 0.7061 (mt0) cc_final: 0.6704 (mp10) REVERT: A 691 MET cc_start: 0.8731 (mtp) cc_final: 0.8518 (mtp) REVERT: A 693 ASP cc_start: 0.7592 (m-30) cc_final: 0.7310 (m-30) REVERT: A 694 ILE cc_start: 0.8154 (pt) cc_final: 0.7869 (pt) REVERT: A 708 ARG cc_start: 0.8433 (tpp80) cc_final: 0.8123 (tpp-160) REVERT: A 711 ILE cc_start: 0.8627 (mm) cc_final: 0.8395 (mt) REVERT: B 412 PHE cc_start: 0.6605 (m-10) cc_final: 0.6001 (m-10) REVERT: B 474 LYS cc_start: 0.8648 (OUTLIER) cc_final: 0.8247 (tttm) REVERT: B 500 THR cc_start: 0.8370 (m) cc_final: 0.7908 (p) REVERT: B 517 TYR cc_start: 0.8745 (m-80) cc_final: 0.8220 (m-80) REVERT: C 58 ASN cc_start: 0.8054 (m110) cc_final: 0.7354 (m-40) REVERT: C 62 MET cc_start: 0.7839 (mmm) cc_final: 0.7529 (mtp) REVERT: C 79 HIS cc_start: 0.8300 (OUTLIER) cc_final: 0.8040 (t-170) REVERT: C 85 LEU cc_start: 0.7954 (OUTLIER) cc_final: 0.7595 (tp) REVERT: C 94 LYS cc_start: 0.8569 (ttpp) cc_final: 0.8318 (ttpt) REVERT: C 102 GLN cc_start: 0.7352 (mp10) cc_final: 0.6994 (mp10) REVERT: C 105 SER cc_start: 0.8908 (t) cc_final: 0.8703 (t) REVERT: C 140 GLU cc_start: 0.7796 (tt0) cc_final: 0.7177 (tt0) REVERT: C 149 ASP cc_start: 0.7281 (t0) cc_final: 0.7014 (t0) REVERT: C 163 TRP cc_start: 0.8540 (p-90) cc_final: 0.8235 (p-90) REVERT: C 171 GLU cc_start: 0.7339 (mp0) cc_final: 0.6805 (mp0) REVERT: C 189 GLU cc_start: 0.7583 (tp30) cc_final: 0.7235 (tt0) REVERT: C 198 ASP cc_start: 0.7017 (OUTLIER) cc_final: 0.6730 (p0) REVERT: C 213 ASP cc_start: 0.7793 (t0) cc_final: 0.7446 (t0) REVERT: C 254 SER cc_start: 0.8391 (m) cc_final: 0.8093 (p) REVERT: C 257 SER cc_start: 0.8684 (t) cc_final: 0.8315 (p) REVERT: C 325 GLU cc_start: 0.7726 (mt-10) cc_final: 0.7275 (mp0) REVERT: C 376 MET cc_start: 0.8622 (tpp) cc_final: 0.8165 (mtt) REVERT: C 410 LEU cc_start: 0.8370 (tt) cc_final: 0.8080 (tt) REVERT: C 455 MET cc_start: 0.8207 (OUTLIER) cc_final: 0.7830 (tmm) REVERT: C 483 ASP cc_start: 0.8354 (t0) cc_final: 0.8104 (t0) REVERT: C 487 VAL cc_start: 0.8575 (m) cc_final: 0.8304 (t) REVERT: C 489 GLU cc_start: 0.7785 (pt0) cc_final: 0.7515 (pm20) REVERT: C 527 GLU cc_start: 0.8675 (tm-30) cc_final: 0.8189 (tp30) REVERT: C 556 GLU cc_start: 0.8484 (tp30) cc_final: 0.8277 (tp30) REVERT: C 562 ARG cc_start: 0.8622 (mtt90) cc_final: 0.8342 (mtt90) REVERT: C 601 ASN cc_start: 0.8549 (p0) cc_final: 0.8253 (p0) REVERT: C 607 ASN cc_start: 0.8259 (t0) cc_final: 0.7618 (t0) REVERT: C 609 ASP cc_start: 0.7788 (m-30) cc_final: 0.7192 (m-30) REVERT: C 619 LYS cc_start: 0.8083 (tttm) cc_final: 0.7854 (tttm) REVERT: C 621 ARG cc_start: 0.8034 (ttm170) cc_final: 0.7556 (ttm170) REVERT: C 661 GLN cc_start: 0.7260 (mt0) cc_final: 0.6765 (mp10) REVERT: C 689 GLU cc_start: 0.6819 (tm-30) cc_final: 0.6590 (tm-30) REVERT: C 708 ARG cc_start: 0.8317 (tpp80) cc_final: 0.7980 (tpp-160) REVERT: C 711 ILE cc_start: 0.8655 (mm) cc_final: 0.8398 (mt) REVERT: D 412 PHE cc_start: 0.6481 (m-80) cc_final: 0.6104 (m-10) REVERT: D 474 LYS cc_start: 0.8786 (mttt) cc_final: 0.8457 (mtpt) REVERT: D 505 TYR cc_start: 0.7221 (m-10) cc_final: 0.6995 (m-10) REVERT: D 550 GLN cc_start: 0.8178 (tp40) cc_final: 0.7970 (tp-100) REVERT: D 555 TYR cc_start: 0.8475 (p90) cc_final: 0.8262 (p90) outliers start: 58 outliers final: 39 residues processed: 492 average time/residue: 0.1149 time to fit residues: 83.9217 Evaluate side-chains 493 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 446 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 61 LYS Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 341 LYS Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 684 ILE Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 461 SER Chi-restraints excluded: chain B residue 474 LYS Chi-restraints excluded: chain B residue 482 SER Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 556 LEU Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 79 HIS Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 123 MET Chi-restraints excluded: chain C residue 133 CYS Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 401 HIS Chi-restraints excluded: chain C residue 421 ILE Chi-restraints excluded: chain C residue 455 MET Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 579 MET Chi-restraints excluded: chain C residue 684 ILE Chi-restraints excluded: chain D residue 428 VAL Chi-restraints excluded: chain D residue 461 SER Chi-restraints excluded: chain D residue 488 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: [15, 3, 137, 7, 54, 69, 125, 85, 155, 147, 148] chunk 15 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 137 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 chunk 54 optimal weight: 0.0970 chunk 69 optimal weight: 3.9990 chunk 125 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 155 optimal weight: 0.3980 chunk 147 optimal weight: 0.9980 chunk 148 optimal weight: 2.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 136 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.121427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.103363 restraints weight = 23656.179| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 2.54 r_work: 0.3189 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.2991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15109 Z= 0.146 Angle : 0.599 9.974 20534 Z= 0.302 Chirality : 0.044 0.355 2167 Planarity : 0.004 0.045 2647 Dihedral : 5.120 40.820 2129 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.15 % Favored : 93.62 % Rotamer: Outliers : 4.47 % Allowed : 23.14 % Favored : 72.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.71 (0.19), residues: 1788 helix: 0.75 (0.20), residues: 760 sheet: 1.29 (0.49), residues: 114 loop : -1.85 (0.18), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 572 TYR 0.018 0.001 TYR C 654 PHE 0.015 0.002 PHE C 683 TRP 0.016 0.001 TRP A 163 HIS 0.005 0.001 HIS C 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 (15090) covalent geometry : angle 0.58754 / 0.30 (20489) SS BOND : bond 0.00674 / 0.26 ( 12) SS BOND : angle 1.15274 / 0.77 ( 24) hydrogen bonds : bond 0.05216 / 3.37 ( 531) hydrogen bonds : angle 3.93261 / 2.81 ( 1479) link_NAG-ASN : bond 0.00583 / 0.28 ( 7) link_NAG-ASN : angle 3.47833 / 2.10 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 467 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ASN cc_start: 0.8051 (m110) cc_final: 0.7367 (m-40) REVERT: A 88 ILE cc_start: 0.8037 (mm) cc_final: 0.7817 (mm) REVERT: A 94 LYS cc_start: 0.8627 (ttpp) cc_final: 0.8390 (ttmt) REVERT: A 105 SER cc_start: 0.8851 (t) cc_final: 0.8502 (p) REVERT: A 107 VAL cc_start: 0.8851 (m) cc_final: 0.8606 (p) REVERT: A 163 TRP cc_start: 0.8419 (p-90) cc_final: 0.8128 (p-90) REVERT: A 189 GLU cc_start: 0.7939 (tp30) cc_final: 0.7714 (tp30) REVERT: A 197 GLU cc_start: 0.7745 (mp0) cc_final: 0.7544 (mm-30) REVERT: A 213 ASP cc_start: 0.7803 (t0) cc_final: 0.7490 (t0) REVERT: A 224 GLU cc_start: 0.6983 (mt-10) cc_final: 0.6731 (mp0) REVERT: A 254 SER cc_start: 0.8490 (m) cc_final: 0.8242 (p) REVERT: A 316 VAL cc_start: 0.8880 (OUTLIER) cc_final: 0.8670 (t) REVERT: A 366 MET cc_start: 0.7297 (ttp) cc_final: 0.6972 (ttt) REVERT: A 368 ASP cc_start: 0.8009 (OUTLIER) cc_final: 0.7533 (m-30) REVERT: A 376 MET cc_start: 0.8806 (tpp) cc_final: 0.8502 (mtt) REVERT: A 479 GLU cc_start: 0.8140 (tp30) cc_final: 0.7441 (tp30) REVERT: A 482 ARG cc_start: 0.8839 (ttp-170) cc_final: 0.8514 (ttm170) REVERT: A 487 VAL cc_start: 0.8584 (m) cc_final: 0.8337 (t) REVERT: A 489 GLU cc_start: 0.7796 (pt0) cc_final: 0.7521 (pm20) REVERT: A 495 GLU cc_start: 0.7866 (mm-30) cc_final: 0.7550 (mm-30) REVERT: A 527 GLU cc_start: 0.8518 (tm-30) cc_final: 0.8025 (tm-30) REVERT: A 556 GLU cc_start: 0.8354 (tp30) cc_final: 0.8047 (tp30) REVERT: A 601 ASN cc_start: 0.8532 (p0) cc_final: 0.8121 (p0) REVERT: A 607 ASN cc_start: 0.8369 (t0) cc_final: 0.8130 (t0) REVERT: A 609 ASP cc_start: 0.7964 (m-30) cc_final: 0.7571 (m-30) REVERT: A 691 MET cc_start: 0.8748 (mtp) cc_final: 0.8536 (mtp) REVERT: A 693 ASP cc_start: 0.7573 (m-30) cc_final: 0.7292 (m-30) REVERT: A 694 ILE cc_start: 0.8155 (pt) cc_final: 0.7871 (pt) REVERT: B 412 PHE cc_start: 0.6665 (m-10) cc_final: 0.6008 (m-10) REVERT: B 417 TYR cc_start: 0.5728 (OUTLIER) cc_final: 0.5411 (m-10) REVERT: B 474 LYS cc_start: 0.8618 (tttt) cc_final: 0.8314 (tttm) REVERT: B 500 THR cc_start: 0.8376 (m) cc_final: 0.7953 (p) REVERT: B 517 TYR cc_start: 0.8735 (m-80) cc_final: 0.8190 (m-80) REVERT: B 562 VAL cc_start: 0.9021 (p) cc_final: 0.8762 (m) REVERT: C 58 ASN cc_start: 0.8098 (m110) cc_final: 0.7387 (m-40) REVERT: C 62 MET cc_start: 0.7880 (mmm) cc_final: 0.7628 (mtp) REVERT: C 79 HIS cc_start: 0.8306 (OUTLIER) cc_final: 0.8049 (t-170) REVERT: C 85 LEU cc_start: 0.8016 (OUTLIER) cc_final: 0.7598 (tp) REVERT: C 94 LYS cc_start: 0.8531 (ttpp) cc_final: 0.8222 (ttpt) REVERT: C 98 ARG cc_start: 0.7941 (ttm-80) cc_final: 0.7655 (ttm-80) REVERT: C 140 GLU cc_start: 0.7924 (tt0) cc_final: 0.7319 (tt0) REVERT: C 149 ASP cc_start: 0.7399 (t0) cc_final: 0.7147 (t0) REVERT: C 163 TRP cc_start: 0.8561 (p-90) cc_final: 0.8328 (p-90) REVERT: C 171 GLU cc_start: 0.7394 (mp0) cc_final: 0.6882 (mp0) REVERT: C 189 GLU cc_start: 0.7604 (tp30) cc_final: 0.7339 (tt0) REVERT: C 197 GLU cc_start: 0.7708 (mm-30) cc_final: 0.7429 (mp0) REVERT: C 198 ASP cc_start: 0.6878 (OUTLIER) cc_final: 0.6602 (p0) REVERT: C 213 ASP cc_start: 0.7830 (t0) cc_final: 0.7481 (t0) REVERT: C 254 SER cc_start: 0.8376 (m) cc_final: 0.8075 (p) REVERT: C 257 SER cc_start: 0.8667 (t) cc_final: 0.8339 (p) REVERT: C 376 MET cc_start: 0.8619 (tpp) cc_final: 0.8248 (mtt) REVERT: C 410 LEU cc_start: 0.8342 (tt) cc_final: 0.8051 (tp) REVERT: C 455 MET cc_start: 0.8162 (OUTLIER) cc_final: 0.7819 (tmm) REVERT: C 483 ASP cc_start: 0.8354 (t0) cc_final: 0.8122 (t0) REVERT: C 487 VAL cc_start: 0.8594 (m) cc_final: 0.8324 (t) REVERT: C 489 GLU cc_start: 0.7767 (pt0) cc_final: 0.7506 (pm20) REVERT: C 527 GLU cc_start: 0.8682 (tm-30) cc_final: 0.8193 (tp30) REVERT: C 556 GLU cc_start: 0.8460 (tp30) cc_final: 0.8224 (tp30) REVERT: C 562 ARG cc_start: 0.8638 (mtt90) cc_final: 0.8372 (mtt90) REVERT: C 601 ASN cc_start: 0.8588 (p0) cc_final: 0.8296 (p0) REVERT: C 607 ASN cc_start: 0.8256 (t0) cc_final: 0.7637 (t0) REVERT: C 609 ASP cc_start: 0.7846 (m-30) cc_final: 0.7250 (m-30) REVERT: C 621 ARG cc_start: 0.8141 (ttm170) cc_final: 0.7681 (ttm170) REVERT: C 654 TYR cc_start: 0.8319 (t80) cc_final: 0.8044 (t80) REVERT: C 661 GLN cc_start: 0.7343 (mt0) cc_final: 0.6832 (mp10) REVERT: C 678 ARG cc_start: 0.7360 (mpp80) cc_final: 0.7058 (mpp80) REVERT: C 689 GLU cc_start: 0.6919 (tm-30) cc_final: 0.6659 (tm-30) REVERT: C 705 ARG cc_start: 0.8694 (ttm110) cc_final: 0.8289 (ttp-110) REVERT: D 412 PHE cc_start: 0.6596 (m-80) cc_final: 0.6068 (m-10) REVERT: D 417 TYR cc_start: 0.5385 (OUTLIER) cc_final: 0.5011 (m-10) REVERT: D 474 LYS cc_start: 0.8756 (mttt) cc_final: 0.8420 (mmmt) REVERT: D 551 LEU cc_start: 0.7779 (tp) cc_final: 0.7562 (tp) REVERT: D 562 VAL cc_start: 0.8923 (p) cc_final: 0.8698 (m) outliers start: 71 outliers final: 52 residues processed: 504 average time/residue: 0.1094 time to fit residues: 82.0965 Evaluate side-chains 516 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 456 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 61 LYS Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 341 LYS Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 375 GLU Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 684 ILE Chi-restraints excluded: chain B residue 396 MET Chi-restraints excluded: chain B residue 405 TYR Chi-restraints excluded: chain B residue 417 TYR Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 461 SER Chi-restraints excluded: chain B residue 482 SER Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 556 LEU Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 79 HIS Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 123 MET Chi-restraints excluded: chain C residue 131 LYS Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 401 HIS Chi-restraints excluded: chain C residue 421 ILE Chi-restraints excluded: chain C residue 455 MET Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 579 MET Chi-restraints excluded: chain C residue 684 ILE Chi-restraints excluded: chain D residue 405 TYR Chi-restraints excluded: chain D residue 417 TYR Chi-restraints excluded: chain D residue 428 VAL Chi-restraints excluded: chain D residue 461 SER Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 558 THR Chi-restraints excluded: chain D residue 574 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: [10, 30, 7, 156, 135, 91, 121, 132, 175, 123, 15] chunk 10 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 156 optimal weight: 1.9990 chunk 135 optimal weight: 0.0040 chunk 91 optimal weight: 0.6980 chunk 121 optimal weight: 1.9990 chunk 132 optimal weight: 0.0770 chunk 175 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 15 optimal weight: 0.0870 overall best weight: 0.3730 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 79 HIS D 435 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.122723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.104728 restraints weight = 23415.028| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 2.52 r_work: 0.3214 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15109 Z= 0.115 Angle : 0.602 11.337 20534 Z= 0.301 Chirality : 0.043 0.345 2167 Planarity : 0.004 0.044 2647 Dihedral : 5.222 49.464 2129 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.15 % Favored : 93.62 % Rotamer: Outliers : 3.96 % Allowed : 23.77 % Favored : 72.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.67 (0.19), residues: 1788 helix: 0.78 (0.20), residues: 760 sheet: 1.41 (0.48), residues: 114 loop : -1.85 (0.18), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 705 TYR 0.016 0.001 TYR C 654 PHE 0.014 0.001 PHE C 683 TRP 0.017 0.001 TRP A 163 HIS 0.011 0.001 HIS D 434 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 (15090) covalent geometry : angle 0.58381 / 0.30 (20489) SS BOND : bond 0.00257 / 0.16 ( 12) SS BOND : angle 1.06246 / 0.69 ( 24) hydrogen bonds : bond 0.04496 / 2.91 ( 531) hydrogen bonds : angle 3.92086 / 2.80 ( 1479) link_NAG-ASN : bond 0.00934 / 0.47 ( 7) link_NAG-ASN : angle 4.56252 / 2.69 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 452 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ASN cc_start: 0.8006 (m110) cc_final: 0.7476 (m-40) REVERT: A 61 LYS cc_start: 0.7946 (OUTLIER) cc_final: 0.7733 (mtmm) REVERT: A 88 ILE cc_start: 0.8006 (mm) cc_final: 0.7798 (mm) REVERT: A 94 LYS cc_start: 0.8491 (ttpp) cc_final: 0.8238 (ttmt) REVERT: A 105 SER cc_start: 0.8798 (t) cc_final: 0.8454 (p) REVERT: A 107 VAL cc_start: 0.8838 (m) cc_final: 0.8577 (p) REVERT: A 163 TRP cc_start: 0.8156 (p-90) cc_final: 0.7777 (p-90) REVERT: A 224 GLU cc_start: 0.6722 (mt-10) cc_final: 0.6462 (mp0) REVERT: A 254 SER cc_start: 0.8442 (m) cc_final: 0.8218 (p) REVERT: A 292 ASP cc_start: 0.7801 (t70) cc_final: 0.7589 (t70) REVERT: A 316 VAL cc_start: 0.8791 (OUTLIER) cc_final: 0.8561 (t) REVERT: A 366 MET cc_start: 0.7063 (ttp) cc_final: 0.6853 (ttt) REVERT: A 368 ASP cc_start: 0.7750 (m-30) cc_final: 0.7290 (m-30) REVERT: A 376 MET cc_start: 0.8576 (tpp) cc_final: 0.8261 (mtt) REVERT: A 433 GLU cc_start: 0.7847 (mm-30) cc_final: 0.7639 (tp30) REVERT: A 479 GLU cc_start: 0.7732 (tp30) cc_final: 0.7066 (tp30) REVERT: A 482 ARG cc_start: 0.8739 (ttp-170) cc_final: 0.8344 (ttm170) REVERT: A 487 VAL cc_start: 0.8514 (m) cc_final: 0.8255 (t) REVERT: A 489 GLU cc_start: 0.7459 (pt0) cc_final: 0.7247 (pm20) REVERT: A 495 GLU cc_start: 0.7706 (mm-30) cc_final: 0.7405 (mm-30) REVERT: A 527 GLU cc_start: 0.8206 (tm-30) cc_final: 0.7696 (tm-30) REVERT: A 534 LYS cc_start: 0.8379 (mmmt) cc_final: 0.8021 (mmmm) REVERT: A 556 GLU cc_start: 0.8062 (tp30) cc_final: 0.7770 (tp30) REVERT: A 601 ASN cc_start: 0.8536 (p0) cc_final: 0.8132 (p0) REVERT: A 607 ASN cc_start: 0.8194 (t0) cc_final: 0.7965 (t0) REVERT: A 609 ASP cc_start: 0.7772 (m-30) cc_final: 0.7445 (m-30) REVERT: A 661 GLN cc_start: 0.7027 (mt0) cc_final: 0.6706 (mp10) REVERT: A 691 MET cc_start: 0.8627 (mtp) cc_final: 0.8413 (mtp) REVERT: A 693 ASP cc_start: 0.7375 (m-30) cc_final: 0.7107 (m-30) REVERT: A 694 ILE cc_start: 0.8066 (pt) cc_final: 0.7789 (pt) REVERT: B 412 PHE cc_start: 0.6280 (m-80) cc_final: 0.5752 (m-10) REVERT: B 417 TYR cc_start: 0.5490 (OUTLIER) cc_final: 0.5235 (m-10) REVERT: B 474 LYS cc_start: 0.8364 (tttt) cc_final: 0.8009 (tttm) REVERT: B 500 THR cc_start: 0.8281 (m) cc_final: 0.7862 (p) REVERT: B 517 TYR cc_start: 0.8579 (m-80) cc_final: 0.8024 (m-80) REVERT: B 562 VAL cc_start: 0.9002 (p) cc_final: 0.8734 (m) REVERT: B 571 MET cc_start: 0.7574 (mmm) cc_final: 0.7287 (mmm) REVERT: C 58 ASN cc_start: 0.8024 (m110) cc_final: 0.7376 (m-40) REVERT: C 62 MET cc_start: 0.7671 (mmm) cc_final: 0.7456 (mtp) REVERT: C 85 LEU cc_start: 0.7927 (OUTLIER) cc_final: 0.7666 (tt) REVERT: C 94 LYS cc_start: 0.8440 (ttpp) cc_final: 0.8177 (ttpt) REVERT: C 102 GLN cc_start: 0.7172 (mp10) cc_final: 0.6845 (mp10) REVERT: C 140 GLU cc_start: 0.7729 (tt0) cc_final: 0.7118 (tt0) REVERT: C 149 ASP cc_start: 0.7214 (t0) cc_final: 0.6949 (t0) REVERT: C 163 TRP cc_start: 0.8324 (p-90) cc_final: 0.8030 (p-90) REVERT: C 171 GLU cc_start: 0.7176 (mp0) cc_final: 0.6634 (mp0) REVERT: C 174 LYS cc_start: 0.8815 (mtmt) cc_final: 0.8482 (mttt) REVERT: C 189 GLU cc_start: 0.7433 (tp30) cc_final: 0.7230 (tt0) REVERT: C 198 ASP cc_start: 0.6550 (p0) cc_final: 0.6281 (p0) REVERT: C 213 ASP cc_start: 0.7714 (t0) cc_final: 0.7440 (t0) REVERT: C 254 SER cc_start: 0.8325 (m) cc_final: 0.8034 (p) REVERT: C 257 SER cc_start: 0.8560 (t) cc_final: 0.8183 (p) REVERT: C 323 MET cc_start: 0.8200 (mmm) cc_final: 0.7919 (tpp) REVERT: C 376 MET cc_start: 0.8384 (tpp) cc_final: 0.7795 (mtt) REVERT: C 410 LEU cc_start: 0.8280 (tt) cc_final: 0.7975 (tp) REVERT: C 455 MET cc_start: 0.7830 (OUTLIER) cc_final: 0.7504 (tmm) REVERT: C 483 ASP cc_start: 0.8117 (t0) cc_final: 0.7875 (t0) REVERT: C 487 VAL cc_start: 0.8514 (m) cc_final: 0.8236 (t) REVERT: C 527 GLU cc_start: 0.8348 (tm-30) cc_final: 0.7872 (tp30) REVERT: C 556 GLU cc_start: 0.8131 (tp30) cc_final: 0.7875 (tp30) REVERT: C 601 ASN cc_start: 0.8497 (p0) cc_final: 0.8191 (p0) REVERT: C 607 ASN cc_start: 0.8144 (t0) cc_final: 0.7494 (t0) REVERT: C 609 ASP cc_start: 0.7517 (m-30) cc_final: 0.6975 (m-30) REVERT: C 621 ARG cc_start: 0.7864 (ttm170) cc_final: 0.7429 (ttm170) REVERT: C 654 TYR cc_start: 0.8181 (t80) cc_final: 0.7931 (t80) REVERT: C 689 GLU cc_start: 0.6837 (tm-30) cc_final: 0.6578 (tm-30) REVERT: C 705 ARG cc_start: 0.8348 (ttm110) cc_final: 0.7935 (ttp-110) REVERT: D 412 PHE cc_start: 0.6299 (m-80) cc_final: 0.5708 (m-10) REVERT: D 474 LYS cc_start: 0.8567 (mttt) cc_final: 0.8206 (mmmt) REVERT: D 562 VAL cc_start: 0.8907 (p) cc_final: 0.8683 (m) REVERT: D 571 MET cc_start: 0.7710 (mmm) cc_final: 0.7442 (mmm) outliers start: 63 outliers final: 49 residues processed: 491 average time/residue: 0.1150 time to fit residues: 83.8604 Evaluate side-chains 503 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 449 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 61 LYS Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 341 LYS Chi-restraints excluded: chain A residue 354 HIS Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 375 GLU Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 684 ILE Chi-restraints excluded: chain B residue 405 TYR Chi-restraints excluded: chain B residue 417 TYR Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 461 SER Chi-restraints excluded: chain B residue 482 SER Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 556 LEU Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 123 MET Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 225 ASP Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 401 HIS Chi-restraints excluded: chain C residue 455 MET Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 579 MET Chi-restraints excluded: chain C residue 684 ILE Chi-restraints excluded: chain D residue 405 TYR Chi-restraints excluded: chain D residue 417 TYR Chi-restraints excluded: chain D residue 428 VAL Chi-restraints excluded: chain D residue 461 SER Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain D residue 503 SER Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 556 LEU Chi-restraints excluded: chain D residue 574 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: [41, 8, 148, 40, 2, 110, 0, 45, 130, 18, 66] chunk 41 optimal weight: 0.0040 chunk 8 optimal weight: 0.4980 chunk 148 optimal weight: 0.7980 chunk 40 optimal weight: 0.0000 chunk 2 optimal weight: 0.8980 chunk 110 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 130 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 overall best weight: 0.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 79 HIS C 79 HIS C 661 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.122903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.104949 restraints weight = 23407.285| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 2.52 r_work: 0.3216 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.3227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15109 Z= 0.118 Angle : 0.616 10.068 20534 Z= 0.305 Chirality : 0.043 0.356 2167 Planarity : 0.004 0.044 2647 Dihedral : 5.263 48.986 2127 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.10 % Favored : 93.68 % Rotamer: Outliers : 4.03 % Allowed : 23.84 % Favored : 72.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.66 (0.19), residues: 1788 helix: 0.81 (0.20), residues: 760 sheet: 1.46 (0.49), residues: 114 loop : -1.87 (0.17), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 710 TYR 0.014 0.001 TYR C 654 PHE 0.026 0.001 PHE B 573 TRP 0.016 0.001 TRP A 163 HIS 0.006 0.001 HIS D 434 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (15090) covalent geometry : angle 0.60007 / 0.30 (20489) SS BOND : bond 0.00261 / 0.15 ( 12) SS BOND : angle 1.09557 / 0.69 ( 24) hydrogen bonds : bond 0.04385 / 2.83 ( 531) hydrogen bonds : angle 3.90204 / 2.79 ( 1479) link_NAG-ASN : bond 0.01615 / 0.82 ( 7) link_NAG-ASN : angle 4.32575 / 2.37 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 455 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ASN cc_start: 0.8046 (m110) cc_final: 0.7367 (m-40) REVERT: A 88 ILE cc_start: 0.7987 (mm) cc_final: 0.7753 (mm) REVERT: A 94 LYS cc_start: 0.8646 (ttpp) cc_final: 0.8415 (ttmt) REVERT: A 105 SER cc_start: 0.8832 (t) cc_final: 0.8552 (p) REVERT: A 107 VAL cc_start: 0.8883 (m) cc_final: 0.8643 (p) REVERT: A 163 TRP cc_start: 0.8299 (p-90) cc_final: 0.7935 (p-90) REVERT: A 224 GLU cc_start: 0.6953 (mt-10) cc_final: 0.6707 (mp0) REVERT: A 254 SER cc_start: 0.8449 (m) cc_final: 0.8231 (p) REVERT: A 292 ASP cc_start: 0.7926 (t70) cc_final: 0.7710 (t70) REVERT: A 316 VAL cc_start: 0.8827 (OUTLIER) cc_final: 0.8601 (t) REVERT: A 368 ASP cc_start: 0.7982 (OUTLIER) cc_final: 0.7507 (m-30) REVERT: A 376 MET cc_start: 0.8782 (tpp) cc_final: 0.8542 (mtt) REVERT: A 433 GLU cc_start: 0.8144 (mm-30) cc_final: 0.7917 (tp30) REVERT: A 479 GLU cc_start: 0.8117 (tp30) cc_final: 0.7454 (tp30) REVERT: A 482 ARG cc_start: 0.8842 (ttp-170) cc_final: 0.8464 (ttp-170) REVERT: A 487 VAL cc_start: 0.8587 (m) cc_final: 0.8329 (t) REVERT: A 489 GLU cc_start: 0.7732 (pt0) cc_final: 0.7527 (pm20) REVERT: A 495 GLU cc_start: 0.7854 (mm-30) cc_final: 0.7517 (mm-30) REVERT: A 527 GLU cc_start: 0.8523 (tm-30) cc_final: 0.8029 (tm-30) REVERT: A 534 LYS cc_start: 0.8451 (mmmt) cc_final: 0.8101 (mmmm) REVERT: A 556 GLU cc_start: 0.8327 (tp30) cc_final: 0.7898 (tp30) REVERT: A 601 ASN cc_start: 0.8604 (p0) cc_final: 0.8212 (p0) REVERT: A 607 ASN cc_start: 0.8352 (t0) cc_final: 0.8123 (t0) REVERT: A 609 ASP cc_start: 0.8035 (m-30) cc_final: 0.7656 (m-30) REVERT: A 661 GLN cc_start: 0.7101 (mt0) cc_final: 0.6721 (mp10) REVERT: A 690 ASN cc_start: 0.7492 (t0) cc_final: 0.7015 (t0) REVERT: A 691 MET cc_start: 0.8759 (mtp) cc_final: 0.8485 (mtp) REVERT: A 693 ASP cc_start: 0.7585 (m-30) cc_final: 0.7295 (m-30) REVERT: A 694 ILE cc_start: 0.8149 (pt) cc_final: 0.7890 (pt) REVERT: A 708 ARG cc_start: 0.8421 (tpp80) cc_final: 0.8096 (tpp-160) REVERT: B 412 PHE cc_start: 0.6535 (m-80) cc_final: 0.6010 (m-10) REVERT: B 474 LYS cc_start: 0.8539 (tttt) cc_final: 0.8206 (tttm) REVERT: B 500 THR cc_start: 0.8337 (m) cc_final: 0.7920 (p) REVERT: B 517 TYR cc_start: 0.8697 (m-80) cc_final: 0.8150 (m-80) REVERT: B 562 VAL cc_start: 0.9013 (p) cc_final: 0.8761 (m) REVERT: B 571 MET cc_start: 0.8018 (mmm) cc_final: 0.7737 (mmm) REVERT: C 58 ASN cc_start: 0.8079 (m110) cc_final: 0.7393 (m-40) REVERT: C 85 LEU cc_start: 0.8011 (OUTLIER) cc_final: 0.7734 (tt) REVERT: C 94 LYS cc_start: 0.8538 (ttpp) cc_final: 0.8292 (ttpt) REVERT: C 102 GLN cc_start: 0.7390 (mp10) cc_final: 0.7052 (mp10) REVERT: C 140 GLU cc_start: 0.7772 (tt0) cc_final: 0.7096 (tt0) REVERT: C 163 TRP cc_start: 0.8454 (p-90) cc_final: 0.8177 (p-90) REVERT: C 171 GLU cc_start: 0.7416 (mp0) cc_final: 0.6885 (mp0) REVERT: C 174 LYS cc_start: 0.8847 (mtmt) cc_final: 0.8528 (mttt) REVERT: C 189 GLU cc_start: 0.7613 (tp30) cc_final: 0.7308 (tt0) REVERT: C 198 ASP cc_start: 0.6643 (p0) cc_final: 0.6360 (p0) REVERT: C 213 ASP cc_start: 0.7842 (t0) cc_final: 0.7556 (t0) REVERT: C 254 SER cc_start: 0.8388 (m) cc_final: 0.8100 (p) REVERT: C 257 SER cc_start: 0.8626 (t) cc_final: 0.8288 (p) REVERT: C 323 MET cc_start: 0.8196 (mmm) cc_final: 0.7938 (tpp) REVERT: C 324 THR cc_start: 0.8135 (m) cc_final: 0.7830 (t) REVERT: C 354 HIS cc_start: 0.8893 (OUTLIER) cc_final: 0.8615 (m-70) REVERT: C 376 MET cc_start: 0.8599 (tpp) cc_final: 0.8127 (mtt) REVERT: C 410 LEU cc_start: 0.8318 (tt) cc_final: 0.8017 (tt) REVERT: C 455 MET cc_start: 0.8070 (OUTLIER) cc_final: 0.7752 (tmm) REVERT: C 483 ASP cc_start: 0.8351 (t0) cc_final: 0.8118 (t0) REVERT: C 487 VAL cc_start: 0.8576 (m) cc_final: 0.8303 (t) REVERT: C 527 GLU cc_start: 0.8664 (tm-30) cc_final: 0.8181 (tp30) REVERT: C 556 GLU cc_start: 0.8441 (tp30) cc_final: 0.8183 (tp30) REVERT: C 601 ASN cc_start: 0.8585 (p0) cc_final: 0.8286 (p0) REVERT: C 607 ASN cc_start: 0.8277 (t0) cc_final: 0.7671 (t0) REVERT: C 609 ASP cc_start: 0.7755 (m-30) cc_final: 0.7158 (m-30) REVERT: C 621 ARG cc_start: 0.8139 (ttm170) cc_final: 0.7847 (ttm170) REVERT: C 652 ARG cc_start: 0.8566 (OUTLIER) cc_final: 0.8292 (ttm170) REVERT: C 654 TYR cc_start: 0.8279 (t80) cc_final: 0.7993 (t80) REVERT: C 661 GLN cc_start: 0.7470 (mt0) cc_final: 0.6932 (mp10) REVERT: C 680 SER cc_start: 0.8688 (p) cc_final: 0.8420 (t) REVERT: C 689 GLU cc_start: 0.7027 (tm-30) cc_final: 0.6770 (tm-30) REVERT: C 705 ARG cc_start: 0.8646 (ttm110) cc_final: 0.8248 (ttp-110) REVERT: D 412 PHE cc_start: 0.6529 (m-80) cc_final: 0.5835 (m-10) REVERT: D 474 LYS cc_start: 0.8734 (mttt) cc_final: 0.8484 (tttm) REVERT: D 562 VAL cc_start: 0.8942 (p) cc_final: 0.8718 (m) outliers start: 64 outliers final: 49 residues processed: 493 average time/residue: 0.1149 time to fit residues: 84.0232 Evaluate side-chains 501 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 446 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 61 LYS Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 341 LYS Chi-restraints excluded: chain A residue 354 HIS Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 684 ILE Chi-restraints excluded: chain B residue 405 TYR Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 461 SER Chi-restraints excluded: chain B residue 482 SER Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 556 LEU Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 123 MET Chi-restraints excluded: chain C residue 131 LYS Chi-restraints excluded: chain C residue 225 ASP Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain C residue 354 HIS Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 401 HIS Chi-restraints excluded: chain C residue 455 MET Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 579 MET Chi-restraints excluded: chain C residue 652 ARG Chi-restraints excluded: chain C residue 684 ILE Chi-restraints excluded: chain D residue 405 TYR Chi-restraints excluded: chain D residue 417 TYR Chi-restraints excluded: chain D residue 428 VAL Chi-restraints excluded: chain D residue 459 SER Chi-restraints excluded: chain D residue 461 SER Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 546 SER Chi-restraints excluded: chain D residue 556 LEU Chi-restraints excluded: chain D residue 574 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: [137, 77, 86, 18, 112, 71, 147, 136, 53, 58, 144] chunk 137 optimal weight: 0.0060 chunk 77 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 18 optimal weight: 0.2980 chunk 112 optimal weight: 0.5980 chunk 71 optimal weight: 0.6980 chunk 147 optimal weight: 1.9990 chunk 136 optimal weight: 0.0970 chunk 53 optimal weight: 0.5980 chunk 58 optimal weight: 0.1980 chunk 144 optimal weight: 0.0870 overall best weight: 0.1372 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 79 HIS A 136 ASN C 79 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.128439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.110512 restraints weight = 23487.674| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 2.46 r_work: 0.3265 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.3282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 15109 Z= 0.106 Angle : 0.609 10.499 20534 Z= 0.298 Chirality : 0.042 0.236 2167 Planarity : 0.004 0.039 2647 Dihedral : 5.122 49.253 2127 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.87 % Favored : 94.02 % Rotamer: Outliers : 3.27 % Allowed : 24.91 % Favored : 71.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.56 (0.19), residues: 1788 helix: 0.89 (0.20), residues: 748 sheet: 1.33 (0.45), residues: 134 loop : -1.82 (0.18), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 705 TYR 0.015 0.001 TYR C 654 PHE 0.010 0.001 PHE B 431 TRP 0.017 0.001 TRP C 163 HIS 0.006 0.000 HIS D 434 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.10 (15090) covalent geometry : angle 0.59206 / 0.29 (20489) SS BOND : bond 0.00297 / 0.16 ( 12) SS BOND : angle 1.15028 / 0.69 ( 24) hydrogen bonds : bond 0.03310 / 2.14 ( 531) hydrogen bonds : angle 3.87327 / 2.75 ( 1479) link_NAG-ASN : bond 0.02007 / 1.03 ( 7) link_NAG-ASN : angle 4.42112 / 2.50 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 453 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ASN cc_start: 0.7998 (m110) cc_final: 0.7501 (m-40) REVERT: A 61 LYS cc_start: 0.7971 (OUTLIER) cc_final: 0.7679 (mtmm) REVERT: A 105 SER cc_start: 0.8916 (t) cc_final: 0.8545 (p) REVERT: A 107 VAL cc_start: 0.8898 (m) cc_final: 0.8649 (p) REVERT: A 163 TRP cc_start: 0.8187 (p-90) cc_final: 0.7781 (p-90) REVERT: A 224 GLU cc_start: 0.6916 (mt-10) cc_final: 0.6671 (mp0) REVERT: A 254 SER cc_start: 0.8463 (m) cc_final: 0.8108 (p) REVERT: A 298 VAL cc_start: 0.8346 (OUTLIER) cc_final: 0.8133 (p) REVERT: A 316 VAL cc_start: 0.8855 (OUTLIER) cc_final: 0.8596 (t) REVERT: A 368 ASP cc_start: 0.7933 (OUTLIER) cc_final: 0.7460 (m-30) REVERT: A 376 MET cc_start: 0.8806 (tpp) cc_final: 0.8273 (ttm) REVERT: A 479 GLU cc_start: 0.8175 (tp30) cc_final: 0.7538 (tp30) REVERT: A 487 VAL cc_start: 0.8603 (m) cc_final: 0.8402 (t) REVERT: A 495 GLU cc_start: 0.7811 (mm-30) cc_final: 0.7489 (mm-30) REVERT: A 527 GLU cc_start: 0.8560 (tm-30) cc_final: 0.7964 (tm-30) REVERT: A 534 LYS cc_start: 0.8482 (mmmt) cc_final: 0.8175 (mmmm) REVERT: A 556 GLU cc_start: 0.8274 (tp30) cc_final: 0.7901 (tp30) REVERT: A 601 ASN cc_start: 0.8556 (p0) cc_final: 0.8166 (p0) REVERT: A 607 ASN cc_start: 0.8282 (t0) cc_final: 0.7751 (t0) REVERT: A 609 ASP cc_start: 0.7869 (m-30) cc_final: 0.7551 (m-30) REVERT: A 661 GLN cc_start: 0.7039 (mt0) cc_final: 0.6721 (mp10) REVERT: A 690 ASN cc_start: 0.7589 (t0) cc_final: 0.7095 (t0) REVERT: A 691 MET cc_start: 0.8714 (mtp) cc_final: 0.8452 (mtp) REVERT: A 693 ASP cc_start: 0.7574 (m-30) cc_final: 0.7343 (m-30) REVERT: A 694 ILE cc_start: 0.8206 (pt) cc_final: 0.7956 (pt) REVERT: B 412 PHE cc_start: 0.6443 (m-80) cc_final: 0.5990 (m-10) REVERT: B 472 ILE cc_start: 0.8658 (mm) cc_final: 0.8438 (mt) REVERT: B 474 LYS cc_start: 0.8583 (OUTLIER) cc_final: 0.8285 (tttm) REVERT: B 517 TYR cc_start: 0.8699 (m-80) cc_final: 0.8183 (m-80) REVERT: B 562 VAL cc_start: 0.9045 (p) cc_final: 0.8785 (m) REVERT: B 571 MET cc_start: 0.7889 (mmm) cc_final: 0.7651 (mmm) REVERT: C 58 ASN cc_start: 0.7959 (m110) cc_final: 0.7268 (m-40) REVERT: C 76 GLU cc_start: 0.8111 (mm-30) cc_final: 0.7836 (mm-30) REVERT: C 94 LYS cc_start: 0.8637 (ttpp) cc_final: 0.8368 (ttpt) REVERT: C 102 GLN cc_start: 0.7353 (mp10) cc_final: 0.7028 (mp10) REVERT: C 140 GLU cc_start: 0.7776 (tt0) cc_final: 0.7136 (tt0) REVERT: C 149 ASP cc_start: 0.7378 (t0) cc_final: 0.7033 (t0) REVERT: C 163 TRP cc_start: 0.8357 (p-90) cc_final: 0.7979 (p-90) REVERT: C 171 GLU cc_start: 0.7421 (mp0) cc_final: 0.6897 (mp0) REVERT: C 174 LYS cc_start: 0.8830 (mtmt) cc_final: 0.8625 (mttt) REVERT: C 198 ASP cc_start: 0.6530 (p0) cc_final: 0.6249 (p0) REVERT: C 213 ASP cc_start: 0.7839 (t0) cc_final: 0.7502 (t0) REVERT: C 254 SER cc_start: 0.8416 (m) cc_final: 0.8147 (p) REVERT: C 257 SER cc_start: 0.8540 (t) cc_final: 0.8227 (p) REVERT: C 324 THR cc_start: 0.7925 (m) cc_final: 0.7673 (t) REVERT: C 376 MET cc_start: 0.8550 (tpp) cc_final: 0.8109 (mtt) REVERT: C 410 LEU cc_start: 0.8408 (tt) cc_final: 0.8115 (tt) REVERT: C 435 ASP cc_start: 0.7757 (p0) cc_final: 0.7531 (p0) REVERT: C 483 ASP cc_start: 0.8358 (t0) cc_final: 0.8128 (t0) REVERT: C 527 GLU cc_start: 0.8679 (tm-30) cc_final: 0.8231 (tp30) REVERT: C 556 GLU cc_start: 0.8424 (tp30) cc_final: 0.8215 (tp30) REVERT: C 601 ASN cc_start: 0.8533 (p0) cc_final: 0.8222 (p0) REVERT: C 607 ASN cc_start: 0.8200 (t0) cc_final: 0.7450 (t0) REVERT: C 609 ASP cc_start: 0.7747 (m-30) cc_final: 0.7174 (m-30) REVERT: C 661 GLN cc_start: 0.7407 (mt0) cc_final: 0.6805 (mp10) REVERT: C 680 SER cc_start: 0.8698 (p) cc_final: 0.8473 (t) REVERT: C 689 GLU cc_start: 0.6911 (tm-30) cc_final: 0.6675 (tm-30) REVERT: C 705 ARG cc_start: 0.8588 (ttm110) cc_final: 0.8217 (ttp-110) REVERT: D 412 PHE cc_start: 0.6406 (m-80) cc_final: 0.5735 (m-10) REVERT: D 474 LYS cc_start: 0.8692 (mttt) cc_final: 0.8476 (tttm) REVERT: D 562 VAL cc_start: 0.8977 (p) cc_final: 0.8733 (m) outliers start: 52 outliers final: 43 residues processed: 483 average time/residue: 0.1143 time to fit residues: 82.2579 Evaluate side-chains 496 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 448 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 61 LYS Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 102 GLN Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 341 LYS Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 657 LYS Chi-restraints excluded: chain A residue 684 ILE Chi-restraints excluded: chain B residue 405 TYR Chi-restraints excluded: chain B residue 417 TYR Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 474 LYS Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 123 MET Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 225 ASP Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 401 HIS Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 684 ILE Chi-restraints excluded: chain D residue 405 TYR Chi-restraints excluded: chain D residue 417 TYR Chi-restraints excluded: chain D residue 428 VAL Chi-restraints excluded: chain D residue 461 SER Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 546 SER Chi-restraints excluded: chain D residue 556 LEU Chi-restraints excluded: chain D residue 574 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: [102, 99, 89, 58, 47, 113, 112, 56, 169, 166, 59] chunk 102 optimal weight: 0.8980 chunk 99 optimal weight: 0.9990 chunk 89 optimal weight: 0.6980 chunk 58 optimal weight: 0.0770 chunk 47 optimal weight: 0.0970 chunk 113 optimal weight: 0.0970 chunk 112 optimal weight: 0.0370 chunk 56 optimal weight: 0.0070 chunk 169 optimal weight: 1.9990 chunk 166 optimal weight: 0.1980 chunk 59 optimal weight: 0.6980 overall best weight: 0.0630 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 79 HIS A 136 ASN ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 79 HIS D 435 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.126757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.108519 restraints weight = 23715.601| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 2.56 r_work: 0.3271 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.3389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 15109 Z= 0.106 Angle : 0.604 11.209 20534 Z= 0.296 Chirality : 0.042 0.305 2167 Planarity : 0.004 0.038 2647 Dihedral : 4.874 45.554 2127 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.82 % Favored : 94.07 % Rotamer: Outliers : 3.08 % Allowed : 25.85 % Favored : 71.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.52 (0.19), residues: 1788 helix: 0.90 (0.20), residues: 754 sheet: 1.32 (0.45), residues: 134 loop : -1.78 (0.17), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 705 TYR 0.015 0.001 TYR C 654 PHE 0.025 0.001 PHE B 573 TRP 0.016 0.001 TRP C 163 HIS 0.008 0.000 HIS D 434 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.11 (15090) covalent geometry : angle 0.59280 / 0.29 (20489) SS BOND : bond 0.00278 / 0.15 ( 12) SS BOND : angle 1.14071 / 0.69 ( 24) hydrogen bonds : bond 0.02989 / 1.92 ( 531) hydrogen bonds : angle 3.82952 / 2.72 ( 1479) link_NAG-ASN : bond 0.00862 / 0.42 ( 7) link_NAG-ASN : angle 3.52373 / 1.99 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 439 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ASN cc_start: 0.7891 (m110) cc_final: 0.7435 (m-40) REVERT: A 61 LYS cc_start: 0.7918 (OUTLIER) cc_final: 0.7642 (mtmm) REVERT: A 105 SER cc_start: 0.8870 (t) cc_final: 0.8470 (p) REVERT: A 107 VAL cc_start: 0.8880 (m) cc_final: 0.8614 (p) REVERT: A 163 TRP cc_start: 0.7887 (p-90) cc_final: 0.7462 (p-90) REVERT: A 213 ASP cc_start: 0.7615 (t0) cc_final: 0.7375 (t0) REVERT: A 224 GLU cc_start: 0.6697 (mt-10) cc_final: 0.6431 (mp0) REVERT: A 254 SER cc_start: 0.8399 (m) cc_final: 0.8052 (p) REVERT: A 316 VAL cc_start: 0.8707 (OUTLIER) cc_final: 0.8469 (t) REVERT: A 368 ASP cc_start: 0.7704 (OUTLIER) cc_final: 0.7306 (m-30) REVERT: A 376 MET cc_start: 0.8563 (tpp) cc_final: 0.8080 (mtt) REVERT: A 433 GLU cc_start: 0.7917 (mm-30) cc_final: 0.7679 (mm-30) REVERT: A 479 GLU cc_start: 0.7724 (tp30) cc_final: 0.7109 (tp30) REVERT: A 487 VAL cc_start: 0.8470 (m) cc_final: 0.8227 (t) REVERT: A 495 GLU cc_start: 0.7663 (mm-30) cc_final: 0.7365 (mm-30) REVERT: A 527 GLU cc_start: 0.8213 (tm-30) cc_final: 0.7922 (tm-30) REVERT: A 534 LYS cc_start: 0.8359 (mmmt) cc_final: 0.8037 (mmmm) REVERT: A 556 GLU cc_start: 0.8045 (tp30) cc_final: 0.7648 (tp30) REVERT: A 607 ASN cc_start: 0.8130 (t0) cc_final: 0.7499 (t0) REVERT: A 609 ASP cc_start: 0.7576 (m-30) cc_final: 0.7278 (m-30) REVERT: A 661 GLN cc_start: 0.7020 (mt0) cc_final: 0.6787 (mp10) REVERT: A 678 ARG cc_start: 0.7289 (mpp80) cc_final: 0.6993 (mtm-85) REVERT: A 690 ASN cc_start: 0.7463 (t0) cc_final: 0.6922 (t0) REVERT: A 691 MET cc_start: 0.8601 (mtp) cc_final: 0.8374 (mtp) REVERT: A 693 ASP cc_start: 0.7356 (m-30) cc_final: 0.7103 (m-30) REVERT: A 694 ILE cc_start: 0.8034 (pt) cc_final: 0.7775 (pt) REVERT: B 412 PHE cc_start: 0.6227 (m-80) cc_final: 0.5797 (m-10) REVERT: B 474 LYS cc_start: 0.8353 (OUTLIER) cc_final: 0.7998 (tttm) REVERT: B 517 TYR cc_start: 0.8545 (m-80) cc_final: 0.8020 (m-80) REVERT: B 562 VAL cc_start: 0.9022 (p) cc_final: 0.8746 (m) REVERT: B 568 ASN cc_start: 0.8481 (m-40) cc_final: 0.8263 (m-40) REVERT: B 571 MET cc_start: 0.7516 (mmm) cc_final: 0.7230 (mmm) REVERT: C 58 ASN cc_start: 0.7859 (m110) cc_final: 0.7174 (m-40) REVERT: C 94 LYS cc_start: 0.8450 (ttpp) cc_final: 0.8141 (ttpt) REVERT: C 98 ARG cc_start: 0.7513 (ttm-80) cc_final: 0.7233 (ttm-80) REVERT: C 102 GLN cc_start: 0.7061 (mp10) cc_final: 0.6762 (mp10) REVERT: C 140 GLU cc_start: 0.7541 (tt0) cc_final: 0.6887 (tt0) REVERT: C 149 ASP cc_start: 0.6982 (t0) cc_final: 0.6231 (t0) REVERT: C 153 GLU cc_start: 0.7253 (tp30) cc_final: 0.6659 (mp0) REVERT: C 163 TRP cc_start: 0.8090 (p-90) cc_final: 0.7763 (p-90) REVERT: C 171 GLU cc_start: 0.7143 (mp0) cc_final: 0.6607 (mp0) REVERT: C 174 LYS cc_start: 0.8688 (mtmt) cc_final: 0.8476 (mttt) REVERT: C 189 GLU cc_start: 0.7419 (tp30) cc_final: 0.7150 (tt0) REVERT: C 198 ASP cc_start: 0.6220 (p0) cc_final: 0.5936 (p0) REVERT: C 213 ASP cc_start: 0.7699 (t0) cc_final: 0.7396 (t0) REVERT: C 254 SER cc_start: 0.8376 (m) cc_final: 0.8103 (p) REVERT: C 257 SER cc_start: 0.8467 (t) cc_final: 0.8118 (p) REVERT: C 324 THR cc_start: 0.7808 (m) cc_final: 0.7462 (t) REVERT: C 376 MET cc_start: 0.8326 (tpp) cc_final: 0.7735 (mtt) REVERT: C 410 LEU cc_start: 0.8279 (tt) cc_final: 0.8004 (tt) REVERT: C 435 ASP cc_start: 0.7404 (p0) cc_final: 0.7179 (p0) REVERT: C 483 ASP cc_start: 0.8134 (t0) cc_final: 0.7865 (t0) REVERT: C 527 GLU cc_start: 0.8340 (tm-30) cc_final: 0.8079 (tm-30) REVERT: C 556 GLU cc_start: 0.8194 (tp30) cc_final: 0.7884 (tp30) REVERT: C 601 ASN cc_start: 0.8483 (p0) cc_final: 0.8171 (p0) REVERT: C 607 ASN cc_start: 0.8088 (t0) cc_final: 0.7209 (t0) REVERT: C 609 ASP cc_start: 0.7449 (m-30) cc_final: 0.6870 (m-30) REVERT: C 661 GLN cc_start: 0.7314 (mt0) cc_final: 0.6712 (mp10) REVERT: C 680 SER cc_start: 0.8634 (p) cc_final: 0.8370 (t) REVERT: C 689 GLU cc_start: 0.6787 (tm-30) cc_final: 0.6555 (tm-30) REVERT: C 705 ARG cc_start: 0.8283 (ttm110) cc_final: 0.7872 (ttp-110) REVERT: D 412 PHE cc_start: 0.6157 (m-80) cc_final: 0.5427 (m-10) REVERT: D 474 LYS cc_start: 0.8516 (mttt) cc_final: 0.8233 (mmmt) REVERT: D 540 PHE cc_start: 0.8941 (m-80) cc_final: 0.8733 (m-80) REVERT: D 562 VAL cc_start: 0.8937 (p) cc_final: 0.8685 (m) outliers start: 49 outliers final: 35 residues processed: 466 average time/residue: 0.1091 time to fit residues: 76.0666 Evaluate side-chains 476 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 437 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 61 LYS Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 341 LYS Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 657 LYS Chi-restraints excluded: chain A residue 684 ILE Chi-restraints excluded: chain B residue 405 TYR Chi-restraints excluded: chain B residue 417 TYR Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain B residue 474 LYS Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 123 MET Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 401 HIS Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 684 ILE Chi-restraints excluded: chain D residue 405 TYR Chi-restraints excluded: chain D residue 417 TYR Chi-restraints excluded: chain D residue 428 VAL Chi-restraints excluded: chain D residue 481 PHE Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 556 LEU Chi-restraints excluded: chain D residue 574 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: [103, 23, 0, 53, 160, 42, 138, 13, 173, 156, 125] chunk 103 optimal weight: 0.6980 chunk 23 optimal weight: 0.0870 chunk 0 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 160 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 138 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 173 optimal weight: 0.9980 chunk 156 optimal weight: 1.9990 chunk 125 optimal weight: 0.8980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 79 HIS A 89 GLN A 139 GLN ** C 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 79 HIS C 175 GLN D 435 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.122389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.104245 restraints weight = 23429.791| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.54 r_work: 0.3206 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.3540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15109 Z= 0.160 Angle : 0.645 10.512 20534 Z= 0.325 Chirality : 0.045 0.410 2167 Planarity : 0.004 0.047 2647 Dihedral : 5.061 48.360 2127 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.32 % Favored : 93.57 % Rotamer: Outliers : 2.64 % Allowed : 26.16 % Favored : 71.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.55 (0.20), residues: 1788 helix: 1.03 (0.21), residues: 750 sheet: 1.39 (0.49), residues: 114 loop : -1.88 (0.17), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 708 TYR 0.021 0.002 TYR A 641 PHE 0.017 0.002 PHE B 454 TRP 0.011 0.001 TRP A 163 HIS 0.008 0.001 HIS D 434 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 (15090) covalent geometry : angle 0.63396 / 0.32 (20489) SS BOND : bond 0.00336 / 0.17 ( 12) SS BOND : angle 1.28017 / 0.80 ( 24) hydrogen bonds : bond 0.05091 / 3.29 ( 531) hydrogen bonds : angle 3.89567 / 2.76 ( 1479) link_NAG-ASN : bond 0.00927 / 0.46 ( 7) link_NAG-ASN : angle 3.49859 / 1.95 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 445 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ASN cc_start: 0.8073 (m110) cc_final: 0.7428 (m-40) REVERT: A 105 SER cc_start: 0.8943 (t) cc_final: 0.8629 (t) REVERT: A 107 VAL cc_start: 0.8897 (m) cc_final: 0.8656 (p) REVERT: A 113 ARG cc_start: 0.8145 (ttp80) cc_final: 0.7821 (tpp80) REVERT: A 163 TRP cc_start: 0.8378 (p-90) cc_final: 0.8170 (p-90) REVERT: A 213 ASP cc_start: 0.7760 (t0) cc_final: 0.7491 (t0) REVERT: A 224 GLU cc_start: 0.6954 (mt-10) cc_final: 0.6707 (mp0) REVERT: A 254 SER cc_start: 0.8460 (m) cc_final: 0.8102 (p) REVERT: A 316 VAL cc_start: 0.8869 (OUTLIER) cc_final: 0.8632 (t) REVERT: A 325 GLU cc_start: 0.8208 (pm20) cc_final: 0.7989 (pm20) REVERT: A 368 ASP cc_start: 0.8006 (m-30) cc_final: 0.7577 (m-30) REVERT: A 376 MET cc_start: 0.8766 (tpp) cc_final: 0.8513 (ttm) REVERT: A 433 GLU cc_start: 0.8272 (mm-30) cc_final: 0.7782 (tp30) REVERT: A 479 GLU cc_start: 0.8125 (tp30) cc_final: 0.7527 (tp30) REVERT: A 487 VAL cc_start: 0.8603 (m) cc_final: 0.8366 (t) REVERT: A 495 GLU cc_start: 0.7827 (mm-30) cc_final: 0.7544 (mm-30) REVERT: A 527 GLU cc_start: 0.8493 (tm-30) cc_final: 0.8226 (tm-30) REVERT: A 534 LYS cc_start: 0.8447 (mmmt) cc_final: 0.8086 (mmmm) REVERT: A 556 GLU cc_start: 0.8347 (tp30) cc_final: 0.7952 (tp30) REVERT: A 607 ASN cc_start: 0.8350 (t0) cc_final: 0.7798 (t0) REVERT: A 609 ASP cc_start: 0.7877 (m-30) cc_final: 0.7540 (m-30) REVERT: A 661 GLN cc_start: 0.7230 (mt0) cc_final: 0.6848 (mp10) REVERT: A 678 ARG cc_start: 0.7504 (mpp80) cc_final: 0.7164 (mtm-85) REVERT: A 690 ASN cc_start: 0.7452 (t0) cc_final: 0.6959 (t0) REVERT: A 691 MET cc_start: 0.8737 (mtp) cc_final: 0.8508 (mtp) REVERT: A 693 ASP cc_start: 0.7612 (m-30) cc_final: 0.7322 (m-30) REVERT: A 694 ILE cc_start: 0.8144 (pt) cc_final: 0.7863 (pt) REVERT: A 708 ARG cc_start: 0.8406 (tpp-160) cc_final: 0.8168 (tpp-160) REVERT: B 412 PHE cc_start: 0.6501 (m-80) cc_final: 0.6057 (m-10) REVERT: B 474 LYS cc_start: 0.8544 (OUTLIER) cc_final: 0.8212 (tttm) REVERT: B 517 TYR cc_start: 0.8735 (m-80) cc_final: 0.8274 (m-80) REVERT: B 562 VAL cc_start: 0.9025 (p) cc_final: 0.8790 (m) REVERT: C 58 ASN cc_start: 0.8104 (m110) cc_final: 0.7398 (m-40) REVERT: C 76 GLU cc_start: 0.8186 (mm-30) cc_final: 0.7921 (mm-30) REVERT: C 94 LYS cc_start: 0.8598 (ttpp) cc_final: 0.8320 (ttpt) REVERT: C 102 GLN cc_start: 0.7470 (mp10) cc_final: 0.7244 (mp10) REVERT: C 140 GLU cc_start: 0.7716 (tt0) cc_final: 0.7075 (tt0) REVERT: C 149 ASP cc_start: 0.7317 (t0) cc_final: 0.6562 (t0) REVERT: C 153 GLU cc_start: 0.7496 (tp30) cc_final: 0.6856 (mp0) REVERT: C 171 GLU cc_start: 0.7419 (mp0) cc_final: 0.6876 (mp0) REVERT: C 174 LYS cc_start: 0.8794 (mtmt) cc_final: 0.8505 (mttt) REVERT: C 189 GLU cc_start: 0.7628 (tp30) cc_final: 0.7321 (tt0) REVERT: C 213 ASP cc_start: 0.7825 (t0) cc_final: 0.7495 (t0) REVERT: C 257 SER cc_start: 0.8589 (t) cc_final: 0.8265 (p) REVERT: C 324 THR cc_start: 0.8186 (m) cc_final: 0.7887 (t) REVERT: C 376 MET cc_start: 0.8627 (tpp) cc_final: 0.8164 (mtt) REVERT: C 410 LEU cc_start: 0.8334 (tt) cc_final: 0.8034 (tt) REVERT: C 483 ASP cc_start: 0.8374 (t0) cc_final: 0.8132 (t0) REVERT: C 527 GLU cc_start: 0.8641 (tm-30) cc_final: 0.8408 (tm-30) REVERT: C 556 GLU cc_start: 0.8475 (tp30) cc_final: 0.8200 (tp30) REVERT: C 562 ARG cc_start: 0.8606 (mtt90) cc_final: 0.8376 (mtt90) REVERT: C 601 ASN cc_start: 0.8584 (p0) cc_final: 0.8277 (p0) REVERT: C 607 ASN cc_start: 0.8247 (t0) cc_final: 0.7521 (t0) REVERT: C 609 ASP cc_start: 0.7819 (m-30) cc_final: 0.7213 (m-30) REVERT: C 661 GLN cc_start: 0.7555 (mt0) cc_final: 0.6885 (mp10) REVERT: C 680 SER cc_start: 0.8782 (p) cc_final: 0.8548 (t) REVERT: C 689 GLU cc_start: 0.7019 (tm-30) cc_final: 0.6742 (tm-30) REVERT: C 705 ARG cc_start: 0.8612 (ttm110) cc_final: 0.8199 (ttp-110) REVERT: D 412 PHE cc_start: 0.6358 (m-80) cc_final: 0.5712 (m-10) REVERT: D 474 LYS cc_start: 0.8718 (mttt) cc_final: 0.8474 (tttm) REVERT: D 488 VAL cc_start: 0.8480 (OUTLIER) cc_final: 0.8078 (m) REVERT: D 562 VAL cc_start: 0.8970 (p) cc_final: 0.8749 (m) REVERT: D 571 MET cc_start: 0.8162 (mmm) cc_final: 0.7855 (mmm) outliers start: 42 outliers final: 31 residues processed: 470 average time/residue: 0.1122 time to fit residues: 78.2671 Evaluate side-chains 474 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 440 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 61 LYS Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 341 LYS Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 684 ILE Chi-restraints excluded: chain B residue 405 TYR Chi-restraints excluded: chain B residue 474 LYS Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 123 MET Chi-restraints excluded: chain C residue 354 HIS Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 401 HIS Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 579 MET Chi-restraints excluded: chain C residue 684 ILE Chi-restraints excluded: chain D residue 417 TYR Chi-restraints excluded: chain D residue 428 VAL Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 574 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: [0, 25, 33, 85, 128, 82, 152, 23, 144, 132, 77] chunk 0 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 128 optimal weight: 0.6980 chunk 82 optimal weight: 0.9990 chunk 152 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 144 optimal weight: 0.1980 chunk 132 optimal weight: 0.5980 chunk 77 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 79 HIS C 60 GLN C 79 HIS C 535 HIS D 435 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.122499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.104330 restraints weight = 23304.501| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 2.54 r_work: 0.3207 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.3646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15109 Z= 0.142 Angle : 0.649 10.894 20534 Z= 0.326 Chirality : 0.045 0.407 2167 Planarity : 0.004 0.048 2647 Dihedral : 5.164 49.829 2127 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.21 % Favored : 93.68 % Rotamer: Outliers : 2.58 % Allowed : 26.42 % Favored : 71.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.67 (0.19), residues: 1788 helix: 0.91 (0.20), residues: 758 sheet: 1.17 (0.49), residues: 114 loop : -1.94 (0.17), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 705 TYR 0.016 0.001 TYR C 202 PHE 0.016 0.001 PHE B 454 TRP 0.029 0.001 TRP C 163 HIS 0.008 0.001 HIS D 434 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 (15090) covalent geometry : angle 0.63958 / 0.32 (20489) SS BOND : bond 0.00330 / 0.18 ( 12) SS BOND : angle 1.31932 / 0.91 ( 24) hydrogen bonds : bond 0.04861 / 3.15 ( 531) hydrogen bonds : angle 3.91989 / 2.78 ( 1479) link_NAG-ASN : bond 0.00839 / 0.42 ( 7) link_NAG-ASN : angle 3.36988 / 1.87 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3686.81 seconds wall clock time: 63 minutes 43.91 seconds (3823.91 seconds total)