Starting phenix.real_space_refine on Thu Mar 5 03:37:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6nyy_0552/03_2026/6nyy_0552.cif Found real_map, /net/cci-nas-00/data/ceres_data/6nyy_0552/03_2026/6nyy_0552.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6nyy_0552/03_2026/6nyy_0552.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6nyy_0552/03_2026/6nyy_0552.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6nyy_0552/03_2026/6nyy_0552.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6nyy_0552/03_2026/6nyy_0552.map" } resolution = 3.0 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= 0.010 sd= 0.024 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: 7 Type Number sf(0) Gaussians Zn 6 6.06 5 P 11 5.49 5 Mg 3 5.21 5 S 60 5.16 5 C 12356 2.51 5 N 3221 2.21 5 O 3569 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19226 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 2038 Classifications: {'peptide': 459} Incomplete info: {'c_alpha_only': 231, 'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 436} Unresolved chain links: 231 Unresolved chain link angles: 707 Unresolved chain link dihedrals: 693 Unresolved non-hydrogen bonds: 1564 Unresolved non-hydrogen angles: 1718 Unresolved non-hydrogen dihedrals: 533 Unresolved non-hydrogen chiralities: 281 Planarities with less than four sites: {'PHE:plan': 14, 'GLU:plan': 13, 'ASP:plan': 15, 'ASN:plan1': 10, 'GLN:plan1': 7, 'TYR:plan': 1, 'ARG:plan': 12, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 352 Chain: "B" Number of atoms: 3786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 3786 Classifications: {'peptide': 487} Link IDs: {'PTRANS': 23, 'TRANS': 463} Chain breaks: 1 Chain: "C" Number of atoms: 3818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3818 Classifications: {'peptide': 491} Link IDs: {'PTRANS': 23, 'TRANS': 467} Chain: "D" Number of atoms: 3818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3818 Classifications: {'peptide': 491} Link IDs: {'PTRANS': 23, 'TRANS': 467} Chain: "E" Number of atoms: 3640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3640 Classifications: {'peptide': 467} Link IDs: {'PTRANS': 21, 'TRANS': 445} Chain breaks: 1 Chain: "F" Number of atoms: 1802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 1802 Classifications: {'peptide': 460} Incomplete info: {'c_alpha_only': 267} Link IDs: {'PTRANS': 22, 'TRANS': 437} Unresolved chain links: 267 Unresolved chain link angles: 815 Unresolved chain link dihedrals: 801 Unresolved non-hydrogen bonds: 1809 Unresolved non-hydrogen angles: 1988 Unresolved non-hydrogen dihedrals: 615 Unresolved non-hydrogen chiralities: 324 Planarities with less than four sites: {'PHE:plan': 15, 'GLU:plan': 17, 'ASP:plan': 16, 'ASN:plan1': 12, 'GLN:plan1': 10, 'TYR:plan': 1, 'ARG:plan': 14, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 421 Chain: "G" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 55 Classifications: {'peptide': 11} Link IDs: {'TRANS': 10} Chain: "H" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 55 Classifications: {'peptide': 11} Link IDs: {'TRANS': 10} Chain: "I" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 45 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Chain: "J" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 40 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' ZN': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.18, per 1000 atoms: 0.27 Number of scatterers: 19226 At special positions: 0 Unit cell: (140.3, 135.7, 100.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 6 29.99 S 60 16.00 P 11 15.00 Mg 3 11.99 O 3569 8.00 N 3221 7.00 C 12356 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.55 Conformation dependent library (CDL) restraints added in 833.6 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 801 " pdb="ZN ZN A 801 " - pdb=" NE2 HIS A 574 " pdb=" ZN B 803 " pdb="ZN ZN B 803 " - pdb=" NE2 HIS B 574 " pdb="ZN ZN B 803 " - pdb=" NE2 HIS B 578 " pdb=" ZN C 802 " pdb="ZN ZN C 802 " - pdb=" NE2 HIS C 578 " pdb="ZN ZN C 802 " - pdb=" NE2 HIS C 574 " pdb=" ZN D 803 " pdb="ZN ZN D 803 " - pdb=" NE2 HIS D 578 " pdb="ZN ZN D 803 " - pdb=" NE2 HIS D 574 " pdb=" ZN E 802 " pdb="ZN ZN E 802 " - pdb=" NE2 HIS E 574 " pdb=" ZN F 801 " pdb="ZN ZN F 801 " - pdb=" NE2 HIS F 574 " pdb="ZN ZN F 801 " - pdb=" NE2 HIS F 578 " 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4420 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 9 sheets defined 43.7% alpha, 3.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 526 through 533 Processing helix chain 'A' and resid 542 through 553 removed outlier: 3.518A pdb=" N GLU A 546 " --> pdb=" O GLN A 542 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLN A 547 " --> pdb=" O LYS A 543 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG A 551 " --> pdb=" O GLN A 547 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL A 552 " --> pdb=" O ALA A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 585 removed outlier: 3.862A pdb=" N THR A 570 " --> pdb=" O GLU A 566 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU A 585 " --> pdb=" O ALA A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 617 through 629 removed outlier: 3.606A pdb=" N ASP A 623 " --> pdb=" O GLU A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 638 Processing helix chain 'A' and resid 646 through 662 removed outlier: 3.753A pdb=" N LYS A 652 " --> pdb=" O ASP A 648 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ALA A 659 " --> pdb=" O GLN A 655 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLN A 660 " --> pdb=" O SER A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 719 removed outlier: 3.604A pdb=" N ILE A 703 " --> pdb=" O ASP A 699 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU A 718 " --> pdb=" O ALA A 714 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 734 Processing helix chain 'A' and resid 737 through 746 Processing helix chain 'B' and resid 306 through 310 removed outlier: 3.688A pdb=" N VAL B 310 " --> pdb=" O PHE B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 329 removed outlier: 3.579A pdb=" N LEU B 327 " --> pdb=" O PHE B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 365 Processing helix chain 'B' and resid 375 through 377 No H-bonds generated for 'chain 'B' and resid 375 through 377' Processing helix chain 'B' and resid 384 through 399 removed outlier: 3.893A pdb=" N VAL B 389 " --> pdb=" O GLY B 385 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N ARG B 390 " --> pdb=" O PRO B 386 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ARG B 397 " --> pdb=" O PHE B 393 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS B 398 " --> pdb=" O ALA B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 412 Processing helix chain 'B' and resid 421 through 440 removed outlier: 4.216A pdb=" N GLN B 427 " --> pdb=" O GLY B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 491 removed outlier: 3.674A pdb=" N SER B 485 " --> pdb=" O LYS B 481 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL B 489 " --> pdb=" O SER B 485 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N HIS B 490 " --> pdb=" O ILE B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 513 Processing helix chain 'B' and resid 517 through 535 removed outlier: 3.508A pdb=" N VAL B 521 " --> pdb=" O SER B 517 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA B 522 " --> pdb=" O GLY B 518 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ALA B 529 " --> pdb=" O CYS B 525 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N HIS B 535 " --> pdb=" O ILE B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 555 removed outlier: 3.732A pdb=" N PHE B 545 " --> pdb=" O ASN B 541 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU B 550 " --> pdb=" O GLU B 546 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE B 553 " --> pdb=" O ILE B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 566 through 585 removed outlier: 3.676A pdb=" N VAL B 571 " --> pdb=" O GLU B 567 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLY B 577 " --> pdb=" O TYR B 573 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N HIS B 578 " --> pdb=" O HIS B 574 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA B 579 " --> pdb=" O GLN B 575 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA B 581 " --> pdb=" O GLY B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 617 through 629 removed outlier: 3.789A pdb=" N ARG B 624 " --> pdb=" O GLN B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 629 through 639 Processing helix chain 'B' and resid 647 through 662 removed outlier: 3.663A pdb=" N LYS B 652 " --> pdb=" O ASP B 648 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ALA B 659 " --> pdb=" O GLN B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 690 through 719 removed outlier: 3.679A pdb=" N ARG B 702 " --> pdb=" O ASP B 698 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLU B 718 " --> pdb=" O ALA B 714 " (cutoff:3.500A) Processing helix chain 'B' and resid 719 through 734 Processing helix chain 'B' and resid 738 through 746 Processing helix chain 'B' and resid 755 through 760 Processing helix chain 'C' and resid 306 through 310 Processing helix chain 'C' and resid 313 through 329 removed outlier: 4.224A pdb=" N GLU C 319 " --> pdb=" O GLU C 315 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE C 320 " --> pdb=" O ALA C 316 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N PHE C 323 " --> pdb=" O GLU C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 335 Processing helix chain 'C' and resid 355 through 365 removed outlier: 3.622A pdb=" N THR C 361 " --> pdb=" O LEU C 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 399 removed outlier: 4.345A pdb=" N ASP C 391 " --> pdb=" O ALA C 387 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU C 395 " --> pdb=" O ASP C 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 412 Processing helix chain 'C' and resid 421 through 439 removed outlier: 3.960A pdb=" N SER C 425 " --> pdb=" O PHE C 421 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N GLU C 426 " --> pdb=" O GLY C 422 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N GLN C 427 " --> pdb=" O GLY C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 459 removed outlier: 3.835A pdb=" N ILE C 458 " --> pdb=" O ARG C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 479 through 491 removed outlier: 3.647A pdb=" N SER C 485 " --> pdb=" O LYS C 481 " (cutoff:3.500A) Processing helix chain 'C' and resid 501 through 512 removed outlier: 3.830A pdb=" N ALA C 506 " --> pdb=" O LYS C 502 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG C 507 " --> pdb=" O ASP C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 533 removed outlier: 3.516A pdb=" N ALA C 528 " --> pdb=" O VAL C 524 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ALA C 529 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing helix chain 'C' and resid 542 through 554 removed outlier: 3.513A pdb=" N GLU C 546 " --> pdb=" O GLN C 542 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLN C 547 " --> pdb=" O LYS C 543 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG C 551 " --> pdb=" O GLN C 547 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL C 552 " --> pdb=" O ALA C 548 " (cutoff:3.500A) Processing helix chain 'C' and resid 567 through 585 removed outlier: 3.709A pdb=" N VAL C 571 " --> pdb=" O GLU C 567 " (cutoff:3.500A) Processing helix chain 'C' and resid 617 through 629 removed outlier: 3.567A pdb=" N LEU C 621 " --> pdb=" O THR C 617 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N MET C 627 " --> pdb=" O ASP C 623 " (cutoff:3.500A) Processing helix chain 'C' and resid 629 through 639 Processing helix chain 'C' and resid 646 through 659 removed outlier: 3.587A pdb=" N LYS C 652 " --> pdb=" O ASP C 648 " (cutoff:3.500A) Processing helix chain 'C' and resid 690 through 714 removed outlier: 3.537A pdb=" N ILE C 703 " --> pdb=" O ASP C 699 " (cutoff:3.500A) Processing helix chain 'C' and resid 719 through 734 removed outlier: 3.579A pdb=" N LEU C 729 " --> pdb=" O LYS C 725 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLU C 732 " --> pdb=" O LEU C 728 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 746 Processing helix chain 'C' and resid 773 through 777 removed outlier: 3.984A pdb=" N LYS C 777 " --> pdb=" O GLU C 774 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 310 Processing helix chain 'D' and resid 313 through 329 removed outlier: 4.059A pdb=" N GLU D 319 " --> pdb=" O GLU D 315 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE D 320 " --> pdb=" O ALA D 316 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N PHE D 323 " --> pdb=" O GLU D 319 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL D 324 " --> pdb=" O ILE D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 329 through 335 removed outlier: 4.027A pdb=" N TYR D 333 " --> pdb=" O ASN D 329 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 365 removed outlier: 3.580A pdb=" N THR D 361 " --> pdb=" O LEU D 357 " (cutoff:3.500A) Processing helix chain 'D' and resid 375 through 377 No H-bonds generated for 'chain 'D' and resid 375 through 377' Processing helix chain 'D' and resid 385 through 399 removed outlier: 3.817A pdb=" N ASP D 391 " --> pdb=" O ALA D 387 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASN D 399 " --> pdb=" O LEU D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 409 through 412 Processing helix chain 'D' and resid 424 through 439 removed outlier: 3.524A pdb=" N GLU D 428 " --> pdb=" O GLN D 424 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR D 430 " --> pdb=" O GLU D 426 " (cutoff:3.500A) Processing helix chain 'D' and resid 479 through 491 removed outlier: 3.770A pdb=" N SER D 485 " --> pdb=" O LYS D 481 " (cutoff:3.500A) Processing helix chain 'D' and resid 501 through 513 removed outlier: 3.515A pdb=" N ALA D 506 " --> pdb=" O LYS D 502 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG D 507 " --> pdb=" O ASP D 503 " (cutoff:3.500A) Processing helix chain 'D' and resid 517 through 535 removed outlier: 3.830A pdb=" N VAL D 521 " --> pdb=" O SER D 517 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA D 522 " --> pdb=" O GLY D 518 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASN D 523 " --> pdb=" O ALA D 519 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA D 529 " --> pdb=" O CYS D 525 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N HIS D 535 " --> pdb=" O ILE D 531 " (cutoff:3.500A) Processing helix chain 'D' and resid 542 through 555 removed outlier: 3.676A pdb=" N ALA D 548 " --> pdb=" O HIS D 544 " (cutoff:3.500A) Processing helix chain 'D' and resid 564 through 585 removed outlier: 3.671A pdb=" N LYS D 569 " --> pdb=" O PRO D 565 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N THR D 570 " --> pdb=" O GLU D 566 " (cutoff:3.500A) Processing helix chain 'D' and resid 617 through 629 removed outlier: 3.787A pdb=" N ARG D 624 " --> pdb=" O GLN D 620 " (cutoff:3.500A) Processing helix chain 'D' and resid 629 through 638 removed outlier: 3.509A pdb=" N GLU D 635 " --> pdb=" O GLY D 631 " (cutoff:3.500A) Processing helix chain 'D' and resid 646 through 662 removed outlier: 3.625A pdb=" N LYS D 652 " --> pdb=" O ASP D 648 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL D 653 " --> pdb=" O ASP D 649 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLN D 660 " --> pdb=" O SER D 656 " (cutoff:3.500A) Processing helix chain 'D' and resid 690 through 714 removed outlier: 3.548A pdb=" N ALA D 694 " --> pdb=" O SER D 690 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG D 702 " --> pdb=" O ASP D 698 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS D 710 " --> pdb=" O ASN D 706 " (cutoff:3.500A) Processing helix chain 'D' and resid 719 through 733 removed outlier: 3.581A pdb=" N LEU D 729 " --> pdb=" O LYS D 725 " (cutoff:3.500A) Processing helix chain 'D' and resid 738 through 746 removed outlier: 3.502A pdb=" N LEU D 744 " --> pdb=" O ASP D 740 " (cutoff:3.500A) Processing helix chain 'D' and resid 755 through 761 removed outlier: 3.505A pdb=" N GLU D 761 " --> pdb=" O GLU D 757 " (cutoff:3.500A) Processing helix chain 'D' and resid 773 through 777 removed outlier: 3.722A pdb=" N LYS D 777 " --> pdb=" O GLU D 774 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 310 removed outlier: 3.501A pdb=" N VAL E 310 " --> pdb=" O PHE E 307 " (cutoff:3.500A) Processing helix chain 'E' and resid 313 through 329 removed outlier: 3.779A pdb=" N LEU E 318 " --> pdb=" O GLU E 314 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N GLU E 319 " --> pdb=" O GLU E 315 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE E 320 " --> pdb=" O ALA E 316 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLU E 322 " --> pdb=" O LEU E 318 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N PHE E 323 " --> pdb=" O GLU E 319 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL E 324 " --> pdb=" O ILE E 320 " (cutoff:3.500A) Processing helix chain 'E' and resid 329 through 335 removed outlier: 4.172A pdb=" N TYR E 333 " --> pdb=" O ASN E 329 " (cutoff:3.500A) Processing helix chain 'E' and resid 353 through 366 removed outlier: 3.545A pdb=" N THR E 361 " --> pdb=" O LEU E 357 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ALA E 365 " --> pdb=" O THR E 361 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 399 removed outlier: 3.670A pdb=" N ASP E 391 " --> pdb=" O ALA E 387 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN E 399 " --> pdb=" O LEU E 395 " (cutoff:3.500A) Processing helix chain 'E' and resid 409 through 412 Processing helix chain 'E' and resid 424 through 439 removed outlier: 3.512A pdb=" N GLU E 428 " --> pdb=" O GLN E 424 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N MET E 438 " --> pdb=" O LEU E 434 " (cutoff:3.500A) Processing helix chain 'E' and resid 455 through 459 removed outlier: 3.701A pdb=" N ILE E 458 " --> pdb=" O ARG E 455 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU E 459 " --> pdb=" O PRO E 456 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 455 through 459' Processing helix chain 'E' and resid 479 through 492 removed outlier: 3.917A pdb=" N SER E 485 " --> pdb=" O LYS E 481 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ARG E 492 " --> pdb=" O LYS E 488 " (cutoff:3.500A) Processing helix chain 'E' and resid 501 through 510 removed outlier: 4.001A pdb=" N ARG E 507 " --> pdb=" O ASP E 503 " (cutoff:3.500A) Processing helix chain 'E' and resid 517 through 535 removed outlier: 3.545A pdb=" N ASN E 526 " --> pdb=" O ALA E 522 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ALA E 529 " --> pdb=" O CYS E 525 " (cutoff:3.500A) Processing helix chain 'E' and resid 541 through 554 removed outlier: 3.680A pdb=" N ILE E 549 " --> pdb=" O PHE E 545 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLU E 550 " --> pdb=" O GLU E 546 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG E 551 " --> pdb=" O GLN E 547 " (cutoff:3.500A) Processing helix chain 'E' and resid 564 through 585 removed outlier: 3.848A pdb=" N THR E 570 " --> pdb=" O GLU E 566 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY E 577 " --> pdb=" O TYR E 573 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N HIS E 578 " --> pdb=" O HIS E 574 " (cutoff:3.500A) Processing helix chain 'E' and resid 618 through 629 removed outlier: 4.072A pdb=" N ARG E 624 " --> pdb=" O GLN E 620 " (cutoff:3.500A) Processing helix chain 'E' and resid 629 through 638 removed outlier: 4.105A pdb=" N GLU E 635 " --> pdb=" O GLY E 631 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU E 636 " --> pdb=" O ARG E 632 " (cutoff:3.500A) Processing helix chain 'E' and resid 644 through 646 No H-bonds generated for 'chain 'E' and resid 644 through 646' Processing helix chain 'E' and resid 647 through 662 removed outlier: 3.777A pdb=" N LYS E 652 " --> pdb=" O ASP E 648 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N VAL E 653 " --> pdb=" O ASP E 649 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N GLN E 660 " --> pdb=" O SER E 656 " (cutoff:3.500A) Processing helix chain 'E' and resid 690 through 717 removed outlier: 3.665A pdb=" N ILE E 703 " --> pdb=" O ASP E 699 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG E 711 " --> pdb=" O ASP E 707 " (cutoff:3.500A) Processing helix chain 'E' and resid 719 through 731 removed outlier: 3.545A pdb=" N LEU E 728 " --> pdb=" O GLU E 724 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LEU E 729 " --> pdb=" O LYS E 725 " (cutoff:3.500A) Processing helix chain 'E' and resid 737 through 746 removed outlier: 3.577A pdb=" N GLU E 743 " --> pdb=" O ASN E 739 " (cutoff:3.500A) Processing helix chain 'F' and resid 564 through 582 removed outlier: 3.548A pdb=" N LYS F 569 " --> pdb=" O PRO F 565 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR F 570 " --> pdb=" O GLU F 566 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY F 577 " --> pdb=" O TYR F 573 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N HIS F 578 " --> pdb=" O HIS F 574 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA F 579 " --> pdb=" O GLN F 575 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL F 580 " --> pdb=" O ALA F 576 " (cutoff:3.500A) Processing helix chain 'F' and resid 617 through 629 removed outlier: 3.580A pdb=" N LEU F 622 " --> pdb=" O LYS F 618 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ARG F 624 " --> pdb=" O GLN F 620 " (cutoff:3.500A) Processing helix chain 'F' and resid 629 through 639 removed outlier: 3.533A pdb=" N VAL F 633 " --> pdb=" O LEU F 629 " (cutoff:3.500A) Processing helix chain 'F' and resid 646 through 660 Processing helix chain 'F' and resid 690 through 717 removed outlier: 3.816A pdb=" N ILE F 703 " --> pdb=" O ASP F 699 " (cutoff:3.500A) Processing helix chain 'F' and resid 719 through 734 removed outlier: 3.513A pdb=" N GLU F 724 " --> pdb=" O LYS F 720 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LEU F 729 " --> pdb=" O LYS F 725 " (cutoff:3.500A) Processing helix chain 'F' and resid 737 through 746 Processing sheet with id=AA1, first strand: chain 'A' and resid 591 through 595 Processing sheet with id=AA2, first strand: chain 'B' and resid 297 through 299 removed outlier: 3.910A pdb=" N LYS B 297 " --> pdb=" O THR B 371 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N THR B 371 " --> pdb=" O LYS B 297 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N PHE B 369 " --> pdb=" O LEU B 299 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ILE B 370 " --> pdb=" O PHE B 405 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N ASP B 407 " --> pdb=" O ILE B 370 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N VAL B 372 " --> pdb=" O ASP B 407 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N LEU B 404 " --> pdb=" O LEU B 450 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N GLY B 452 " --> pdb=" O LEU B 404 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ILE B 406 " --> pdb=" O GLY B 452 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 605 through 608 Processing sheet with id=AA4, first strand: chain 'C' and resid 297 through 298 removed outlier: 3.550A pdb=" N LYS C 297 " --> pdb=" O THR C 371 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ILE C 370 " --> pdb=" O PHE C 405 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N ASP C 407 " --> pdb=" O ILE C 370 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL C 372 " --> pdb=" O ASP C 407 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG C 471 " --> pdb=" O GLY C 343 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 602 through 605 removed outlier: 6.152A pdb=" N ALA I 6 " --> pdb=" O LEU C 603 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 297 through 298 removed outlier: 3.690A pdb=" N LYS D 297 " --> pdb=" O THR D 371 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR D 371 " --> pdb=" O LYS D 297 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ALA D 344 " --> pdb=" O ALA D 451 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N THR D 453 " --> pdb=" O ALA D 344 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N LEU D 346 " --> pdb=" O THR D 453 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 735 through 736 removed outlier: 3.650A pdb=" N ALA J 4 " --> pdb=" O ALA D 606 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 369 through 373 removed outlier: 6.150A pdb=" N ILE E 370 " --> pdb=" O PHE E 405 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N ASP E 407 " --> pdb=" O ILE E 370 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N VAL E 372 " --> pdb=" O ASP E 407 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N LEU E 404 " --> pdb=" O LEU E 450 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N GLY E 452 " --> pdb=" O LEU E 404 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ILE E 406 " --> pdb=" O GLY E 452 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 594 through 595 799 hydrogen bonds defined for protein. 2340 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.99 Time building geometry restraints manager: 2.18 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: 6239 1.34 - 1.46: 3718 1.46 - 1.58: 8963 1.58 - 1.70: 9 1.70 - 1.82: 102 Bond restraints: 19031 Sorted by residual: bond pdb=" O3A ANP B 801 " pdb=" PB ANP B 801 " ideal model delta sigma weight residual 1.700 1.546 0.154 2.00e-02 2.50e+03 5.90e+01 bond pdb=" O3A ANP D 801 " pdb=" PB ANP D 801 " ideal model delta sigma weight residual 1.700 1.548 0.152 2.00e-02 2.50e+03 5.81e+01 bond pdb=" O3A ANP C 803 " pdb=" PB ANP C 803 " ideal model delta sigma weight residual 1.700 1.552 0.148 2.00e-02 2.50e+03 5.48e+01 bond pdb=" N3B ANP D 801 " pdb=" PG ANP D 801 " ideal model delta sigma weight residual 1.795 1.681 0.114 2.00e-02 2.50e+03 3.26e+01 bond pdb=" N3B ANP C 803 " pdb=" PG ANP C 803 " ideal model delta sigma weight residual 1.795 1.681 0.114 2.00e-02 2.50e+03 3.26e+01 ... (remaining 19026 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.81: 25532 3.81 - 7.62: 156 7.62 - 11.43: 26 11.43 - 15.24: 0 15.24 - 19.05: 3 Bond angle restraints: 25717 Sorted by residual: angle pdb=" N LEU F 563 " pdb=" CA LEU F 563 " pdb=" C LEU F 563 " ideal model delta sigma weight residual 108.79 119.17 -10.38 1.53e+00 4.27e-01 4.60e+01 angle pdb=" PB ANP C 803 " pdb=" N3B ANP C 803 " pdb=" PG ANP C 803 " ideal model delta sigma weight residual 126.95 107.90 19.05 3.00e+00 1.11e-01 4.03e+01 angle pdb=" PB ANP B 801 " pdb=" N3B ANP B 801 " pdb=" PG ANP B 801 " ideal model delta sigma weight residual 126.95 109.10 17.85 3.00e+00 1.11e-01 3.54e+01 angle pdb=" PB ANP D 801 " pdb=" N3B ANP D 801 " pdb=" PG ANP D 801 " ideal model delta sigma weight residual 126.95 109.67 17.28 3.00e+00 1.11e-01 3.32e+01 angle pdb=" N GLY A 554 " pdb=" CA GLY A 554 " pdb=" C GLY A 554 " ideal model delta sigma weight residual 112.77 119.12 -6.35 1.28e+00 6.10e-01 2.46e+01 ... (remaining 25712 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.48: 11589 34.48 - 68.95: 82 68.95 - 103.43: 17 103.43 - 137.91: 4 137.91 - 172.38: 3 Dihedral angle restraints: 11695 sinusoidal: 4829 harmonic: 6866 Sorted by residual: dihedral pdb=" C5' ADP E 801 " pdb=" O5' ADP E 801 " pdb=" PA ADP E 801 " pdb=" O2A ADP E 801 " ideal model delta sinusoidal sigma weight residual -60.00 112.39 -172.38 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" O2A ADP E 801 " pdb=" O3A ADP E 801 " pdb=" PA ADP E 801 " pdb=" PB ADP E 801 " ideal model delta sinusoidal sigma weight residual -60.00 66.09 -126.09 1 2.00e+01 2.50e-03 3.81e+01 dihedral pdb=" O1B ADP E 801 " pdb=" O3A ADP E 801 " pdb=" PB ADP E 801 " pdb=" PA ADP E 801 " ideal model delta sinusoidal sigma weight residual -60.00 59.48 -119.49 1 2.00e+01 2.50e-03 3.58e+01 ... (remaining 11692 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 2468 0.069 - 0.138: 407 0.138 - 0.207: 30 0.207 - 0.276: 7 0.276 - 0.345: 3 Chirality restraints: 2915 Sorted by residual: chirality pdb=" CB ILE B 449 " pdb=" CA ILE B 449 " pdb=" CG1 ILE B 449 " pdb=" CG2 ILE B 449 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.35 2.00e-01 2.50e+01 2.98e+00 chirality pdb=" C3' ANP D 801 " pdb=" C2' ANP D 801 " pdb=" C4' ANP D 801 " pdb=" O3' ANP D 801 " both_signs ideal model delta sigma weight residual False -2.36 -2.65 0.29 2.00e-01 2.50e+01 2.16e+00 chirality pdb=" C3' ANP C 803 " pdb=" C2' ANP C 803 " pdb=" C4' ANP C 803 " pdb=" O3' ANP C 803 " both_signs ideal model delta sigma weight residual False -2.36 -2.65 0.29 2.00e-01 2.50e+01 2.11e+00 ... (remaining 2912 not shown) Planarity restraints: 3334 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 552 " 0.028 2.00e-02 2.50e+03 5.61e-02 3.15e+01 pdb=" C VAL A 552 " -0.097 2.00e-02 2.50e+03 pdb=" O VAL A 552 " 0.037 2.00e-02 2.50e+03 pdb=" N ILE A 553 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 523 " 0.016 2.00e-02 2.50e+03 3.14e-02 9.87e+00 pdb=" CG ASN C 523 " -0.054 2.00e-02 2.50e+03 pdb=" OD1 ASN C 523 " 0.020 2.00e-02 2.50e+03 pdb=" ND2 ASN C 523 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY B 385 " -0.046 5.00e-02 4.00e+02 6.91e-02 7.64e+00 pdb=" N PRO B 386 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO B 386 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 386 " -0.038 5.00e-02 4.00e+02 ... (remaining 3331 not shown) Histogram of nonbonded interaction distances: 1.26 - 1.99: 9 1.99 - 2.72: 946 2.72 - 3.45: 25283 3.45 - 4.17: 44904 4.17 - 4.90: 79384 Nonbonded interactions: 150526 Sorted by model distance: nonbonded pdb=" OD1 ASN A 526 " pdb=" N LYS B 339 " model vdw 1.264 3.120 nonbonded pdb=" ND2 ASN A 526 " pdb=" O LYS B 339 " model vdw 1.540 3.120 nonbonded pdb=" NH1 ARG E 534 " pdb=" CA GLU F 322 " model vdw 1.765 2.840 nonbonded pdb=" ND2 ASN A 526 " pdb=" CB LYS B 339 " model vdw 1.878 3.520 nonbonded pdb=" OG1 THR E 560 " pdb=" CA GLU F 314 " model vdw 1.905 3.470 ... (remaining 150521 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' and (resid 291 through 525 or (resid 528 through 529 and (name CA )) \ or (resid 532 through 533 and (name CA )) or (resid 548 and (name CA )) or (resi \ d 554 through 555 and (name CA )) or resid 562 through 596 or resid 605 through \ 753)) selection = (chain 'B' and ((resid 291 through 417 and (name CA )) or (resid 424 through 525 \ and (name CA )) or (resid 528 through 529 and (name CA )) or (resid 532 through \ 533 and (name CA )) or (resid 548 and (name CA )) or (resid 554 through 555 and \ (name CA )) or resid 562 through 596 or resid 605 through 752 or (resid 753 and \ (name N or name CA or name C or name O or name CB )))) selection = (chain 'C' and ((resid 291 through 417 and (name CA )) or (resid 424 through 525 \ and (name CA )) or (resid 528 through 529 and (name CA )) or (resid 532 through \ 533 and (name CA )) or (resid 548 and (name CA )) or (resid 554 through 555 and \ (name CA )) or resid 562 through 596 or resid 605 through 752 or (resid 753 and \ (name N or name CA or name C or name O or name CB )))) selection = (chain 'D' and ((resid 291 through 417 and (name CA )) or (resid 424 through 525 \ and (name CA )) or (resid 528 through 529 and (name CA )) or (resid 532 through \ 533 and (name CA )) or (resid 548 and (name CA )) or (resid 554 through 555 and \ (name CA )) or resid 562 through 596 or resid 605 through 752 or (resid 753 and \ (name N or name CA or name C or name O or name CB )))) selection = (chain 'E' and ((resid 291 through 417 and (name CA )) or (resid 424 through 525 \ and (name CA )) or (resid 528 through 529 and (name CA )) or (resid 532 through \ 533 and (name CA )) or (resid 548 and (name CA )) or (resid 554 through 555 and \ (name CA )) or resid 562 through 752 or (resid 753 and (name N or name CA or na \ me C or name O or name CB )))) selection = (chain 'F' and (resid 291 through 525 or resid 528 through 529 or resid 532 thro \ ugh 533 or resid 548 or resid 554 through 555 or resid 562 through 596 or resid \ 605 through 752 or (resid 753 and (name N or name CA or name C or name O or name \ CB )))) } ncs_group { reference = chain 'G' selection = chain 'H' } ncs_group { reference = (chain 'I' and resid 2 through 9) selection = chain 'J' } 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: 0.100 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: 0.020 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 19.950 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6249 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 : 0.009 0.478 19044 Z= 0.485 Angle : 0.899 19.046 25717 Z= 0.461 Chirality : 0.052 0.345 2915 Planarity : 0.007 0.069 3334 Dihedral : 10.823 172.382 7275 Min Nonbonded Distance : 1.264 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 0.05 % Allowed : 1.68 % Favored : 98.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -5.40 (0.12), residues: 2372 helix: -4.34 (0.06), residues: 1246 sheet: -1.97 (0.37), residues: 149 loop : -2.51 (0.17), residues: 977 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 465 TYR 0.020 0.002 TYR E 584 PHE 0.041 0.004 PHE E 750 TRP 0.019 0.003 TRP C 583 HIS 0.011 0.002 HIS E 578 Details of bonding type rmsd covalent geometry : bond 0.00728 (19031) covalent geometry : angle 0.89925 (25717) hydrogen bonds : bond 0.31768 ( 799) hydrogen bonds : angle 10.42684 ( 2340) metal coordination : bond 0.14665 ( 10) Misc. bond : bond 0.27608 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 527 residues out of total 2375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 526 time to evaluate : 0.584 Fit side-chains TARDY: cannot create tardy model for: "MET A 321 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 380 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 438 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET F 321 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 380 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 438 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 575 GLN cc_start: 0.8496 (mm-40) cc_final: 0.8150 (mm-40) REVERT: A 593 LYS cc_start: 0.6676 (ttmt) cc_final: 0.6274 (mtpp) REVERT: A 652 LYS cc_start: 0.7842 (mttt) cc_final: 0.7582 (mtmt) REVERT: A 683 MET cc_start: 0.3221 (tpp) cc_final: 0.0465 (pmm) REVERT: A 687 LYS cc_start: 0.7500 (mmtp) cc_final: 0.7287 (mmtm) REVERT: A 700 GLU cc_start: 0.7139 (mm-30) cc_final: 0.6867 (mm-30) REVERT: A 733 LYS cc_start: 0.7475 (mtpt) cc_final: 0.6680 (tptp) REVERT: A 744 LEU cc_start: 0.7480 (tp) cc_final: 0.7231 (tp) REVERT: B 428 GLU cc_start: 0.6344 (tt0) cc_final: 0.6119 (mm-30) REVERT: B 465 ARG cc_start: 0.5940 (mtt-85) cc_final: 0.5676 (tpt170) REVERT: B 503 ASP cc_start: 0.7522 (m-30) cc_final: 0.7319 (m-30) REVERT: B 520 ASP cc_start: 0.7113 (m-30) cc_final: 0.6800 (m-30) REVERT: B 722 ASP cc_start: 0.7543 (m-30) cc_final: 0.7316 (m-30) REVERT: C 520 ASP cc_start: 0.7207 (m-30) cc_final: 0.7000 (m-30) REVERT: C 569 LYS cc_start: 0.8526 (tttt) cc_final: 0.8198 (ttmt) REVERT: C 666 MET cc_start: 0.7234 (mmt) cc_final: 0.6965 (mmt) REVERT: C 672 GLN cc_start: 0.7309 (mm-40) cc_final: 0.6988 (mp10) REVERT: C 673 ILE cc_start: 0.8324 (mt) cc_final: 0.8069 (tt) REVERT: C 685 LEU cc_start: 0.7221 (OUTLIER) cc_final: 0.6955 (pp) REVERT: C 695 ARG cc_start: 0.7074 (ttp80) cc_final: 0.6746 (ttp-110) REVERT: C 699 ASP cc_start: 0.7352 (m-30) cc_final: 0.7040 (m-30) REVERT: C 711 ARG cc_start: 0.7897 (ttt180) cc_final: 0.7653 (mtp-110) REVERT: C 774 GLU cc_start: 0.7851 (mp0) cc_final: 0.7604 (mp0) REVERT: D 306 LYS cc_start: 0.8330 (mmtt) cc_final: 0.8009 (mmtm) REVERT: D 321 MET cc_start: 0.8365 (mtp) cc_final: 0.7931 (mtm) REVERT: D 395 LEU cc_start: 0.7526 (tp) cc_final: 0.7249 (tt) REVERT: D 404 LEU cc_start: 0.7627 (tt) cc_final: 0.7360 (tp) REVERT: D 424 GLN cc_start: 0.6684 (mt0) cc_final: 0.6232 (mm-40) REVERT: D 500 LEU cc_start: 0.7874 (mt) cc_final: 0.7663 (mt) REVERT: D 504 LYS cc_start: 0.8298 (mttp) cc_final: 0.8061 (mtpm) REVERT: D 544 HIS cc_start: 0.8171 (m170) cc_final: 0.7915 (m170) REVERT: D 547 GLN cc_start: 0.8539 (mt0) cc_final: 0.8264 (mt0) REVERT: D 559 LYS cc_start: 0.8091 (mtpt) cc_final: 0.7742 (mtpt) REVERT: D 561 GLN cc_start: 0.8268 (tt0) cc_final: 0.7982 (tt0) REVERT: D 619 GLU cc_start: 0.7588 (mp0) cc_final: 0.7259 (mp0) REVERT: D 673 ILE cc_start: 0.7877 (mt) cc_final: 0.7475 (pp) REVERT: D 753 LYS cc_start: 0.8691 (mtmt) cc_final: 0.8476 (mtmm) REVERT: E 309 ASP cc_start: 0.7572 (m-30) cc_final: 0.7171 (t0) REVERT: E 321 MET cc_start: 0.7338 (mtm) cc_final: 0.6902 (mtp) REVERT: E 375 SER cc_start: 0.8253 (p) cc_final: 0.7974 (m) REVERT: E 376 GLU cc_start: 0.7808 (mt-10) cc_final: 0.7572 (tt0) REVERT: E 408 GLN cc_start: 0.7715 (mm-40) cc_final: 0.7440 (tp40) REVERT: E 455 ARG cc_start: 0.8251 (mtp180) cc_final: 0.7830 (mmm-85) REVERT: E 543 LYS cc_start: 0.8383 (mmtt) cc_final: 0.8066 (ttpp) REVERT: E 656 SER cc_start: 0.8280 (t) cc_final: 0.8012 (m) REVERT: F 616 TYR cc_start: 0.8050 (m-80) cc_final: 0.7825 (m-80) REVERT: F 627 MET cc_start: 0.7246 (tmm) cc_final: 0.6918 (tmm) REVERT: F 641 ARG cc_start: 0.7043 (mmt-90) cc_final: 0.6775 (ptp-110) outliers start: 1 outliers final: 1 residues processed: 527 average time/residue: 0.7216 time to fit residues: 419.1367 Evaluate side-chains 337 residues out of total 2375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 335 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 391 ASP Chi-restraints excluded: chain C residue 685 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 50.0000 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 50.0000 chunk 248 optimal weight: 50.0000 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 50.0000 chunk 183 optimal weight: 3.9990 chunk 111 optimal weight: 0.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 578 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 672 GLN B 332 GLN B 663 GLN ** B 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 472 GLN C 613 GLN C 647 GLN C 667 ASN C 706 ASN D 433 GLN D 526 ASN D 535 HIS D 575 GLN D 655 GLN E 454 ASN E 542 GLN E 663 GLN F 667 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.161813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.138040 restraints weight = 26598.471| |-----------------------------------------------------------------------------| r_work (start): 0.3687 rms_B_bonded: 2.15 r_work: 0.3570 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3429 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7038 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 19044 Z= 0.221 Angle : 0.695 11.250 25717 Z= 0.355 Chirality : 0.044 0.153 2915 Planarity : 0.006 0.054 3334 Dihedral : 10.688 179.648 2677 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 3.92 % Allowed : 10.89 % Favored : 85.19 % 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: -3.20 (0.15), residues: 2372 helix: -2.03 (0.12), residues: 1267 sheet: -1.52 (0.40), residues: 135 loop : -2.15 (0.18), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 468 TYR 0.019 0.002 TYR C 605 PHE 0.027 0.003 PHE A 750 TRP 0.015 0.002 TRP D 583 HIS 0.009 0.002 HIS C 578 Details of bonding type rmsd covalent geometry : bond 0.00518 (19031) covalent geometry : angle 0.69545 (25717) hydrogen bonds : bond 0.05447 ( 799) hydrogen bonds : angle 5.29565 ( 2340) metal coordination : bond 0.00337 ( 10) Misc. bond : bond 0.00151 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 2375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 352 time to evaluate : 0.660 Fit side-chains TARDY: cannot create tardy model for: "MET A 321 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 380 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 438 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET F 321 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 380 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 438 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 619 GLU cc_start: 0.7423 (OUTLIER) cc_final: 0.7123 (pp20) REVERT: A 683 MET cc_start: 0.3306 (tpp) cc_final: 0.0607 (pmm) REVERT: A 733 LYS cc_start: 0.7736 (mtpt) cc_final: 0.6984 (tptp) REVERT: B 370 ILE cc_start: 0.7665 (OUTLIER) cc_final: 0.7258 (mt) REVERT: B 402 CYS cc_start: 0.7844 (p) cc_final: 0.7424 (p) REVERT: B 404 LEU cc_start: 0.8204 (tt) cc_final: 0.7952 (tp) REVERT: B 427 GLN cc_start: 0.7317 (OUTLIER) cc_final: 0.6760 (tm-30) REVERT: B 428 GLU cc_start: 0.7047 (tt0) cc_final: 0.6709 (mm-30) REVERT: B 458 ILE cc_start: 0.8902 (OUTLIER) cc_final: 0.8633 (pp) REVERT: B 465 ARG cc_start: 0.6252 (mtt-85) cc_final: 0.5950 (tpt170) REVERT: B 471 ARG cc_start: 0.7892 (OUTLIER) cc_final: 0.6892 (mtp180) REVERT: B 619 GLU cc_start: 0.7817 (pm20) cc_final: 0.7607 (mp0) REVERT: B 673 ILE cc_start: 0.8652 (OUTLIER) cc_final: 0.8420 (pp) REVERT: C 398 LYS cc_start: 0.8377 (mttt) cc_final: 0.8133 (mmtm) REVERT: C 408 GLN cc_start: 0.8217 (OUTLIER) cc_final: 0.5932 (mp10) REVERT: C 547 GLN cc_start: 0.8408 (mt0) cc_final: 0.8205 (mt0) REVERT: C 636 GLU cc_start: 0.8122 (tt0) cc_final: 0.7673 (pt0) REVERT: C 672 GLN cc_start: 0.7956 (mm-40) cc_final: 0.7755 (mp10) REVERT: C 695 ARG cc_start: 0.8008 (ttp80) cc_final: 0.7745 (ttp80) REVERT: C 699 ASP cc_start: 0.7732 (m-30) cc_final: 0.7466 (m-30) REVERT: D 424 GLN cc_start: 0.7581 (mt0) cc_final: 0.7268 (mt0) REVERT: D 556 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8100 (tp) REVERT: D 624 ARG cc_start: 0.7919 (ttm-80) cc_final: 0.7571 (mtt-85) REVERT: E 309 ASP cc_start: 0.8031 (m-30) cc_final: 0.7801 (m-30) REVERT: E 315 GLU cc_start: 0.7551 (mm-30) cc_final: 0.7341 (mt-10) REVERT: E 321 MET cc_start: 0.8030 (mtm) cc_final: 0.7610 (mtp) REVERT: E 455 ARG cc_start: 0.8357 (mtp180) cc_final: 0.8093 (mmm-85) REVERT: E 543 LYS cc_start: 0.8250 (mmtt) cc_final: 0.8024 (tptt) REVERT: E 619 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7780 (mp0) REVERT: E 668 GLU cc_start: 0.7277 (OUTLIER) cc_final: 0.6882 (mp0) REVERT: F 589 ASP cc_start: 0.7258 (m-30) cc_final: 0.6587 (t0) REVERT: F 616 TYR cc_start: 0.8615 (m-80) cc_final: 0.8400 (m-80) REVERT: F 627 MET cc_start: 0.8235 (tmm) cc_final: 0.7830 (tmm) REVERT: F 660 GLN cc_start: 0.8318 (tt0) cc_final: 0.8035 (tt0) REVERT: F 666 MET cc_start: 0.8791 (ptp) cc_final: 0.8586 (ptm) outliers start: 77 outliers final: 28 residues processed: 397 average time/residue: 0.6947 time to fit residues: 305.9159 Evaluate side-chains 320 residues out of total 2375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 282 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 567 GLU Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 689 TYR Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain B residue 370 ILE Chi-restraints excluded: chain B residue 427 GLN Chi-restraints excluded: chain B residue 458 ILE Chi-restraints excluded: chain B residue 471 ARG Chi-restraints excluded: chain B residue 504 LYS Chi-restraints excluded: chain B residue 556 LEU Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 673 ILE Chi-restraints excluded: chain B residue 744 LEU Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 371 THR Chi-restraints excluded: chain C residue 391 ASP Chi-restraints excluded: chain C residue 408 GLN Chi-restraints excluded: chain C residue 538 ASP Chi-restraints excluded: chain C residue 539 SER Chi-restraints excluded: chain C residue 541 ASN Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 457 ASP Chi-restraints excluded: chain D residue 499 THR Chi-restraints excluded: chain D residue 507 ARG Chi-restraints excluded: chain D residue 535 HIS Chi-restraints excluded: chain D residue 556 LEU Chi-restraints excluded: chain D residue 669 LYS Chi-restraints excluded: chain D residue 713 VAL Chi-restraints excluded: chain D residue 739 ASN Chi-restraints excluded: chain E residue 335 ASP Chi-restraints excluded: chain E residue 382 VAL Chi-restraints excluded: chain E residue 556 LEU Chi-restraints excluded: chain E residue 619 GLU Chi-restraints excluded: chain E residue 668 GLU Chi-restraints excluded: chain E residue 669 LYS Chi-restraints excluded: chain F residue 705 ILE Chi-restraints excluded: chain F residue 744 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 178 optimal weight: 6.9990 chunk 134 optimal weight: 0.8980 chunk 63 optimal weight: 9.9990 chunk 80 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 chunk 152 optimal weight: 0.9990 chunk 121 optimal weight: 4.9990 chunk 256 optimal weight: 50.0000 chunk 21 optimal weight: 50.0000 chunk 206 optimal weight: 10.0000 chunk 272 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 541 ASN C 613 GLN C 739 ASN D 535 HIS E 663 GLN F 667 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.162361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.138812 restraints weight = 26618.025| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 2.02 r_work: 0.3585 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3446 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7027 moved from start: 0.3035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19044 Z= 0.146 Angle : 0.596 10.878 25717 Z= 0.300 Chirality : 0.041 0.148 2915 Planarity : 0.004 0.048 3334 Dihedral : 9.901 163.078 2675 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 3.05 % Allowed : 15.11 % Favored : 81.83 % 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: -2.04 (0.16), residues: 2372 helix: -0.87 (0.14), residues: 1275 sheet: -1.45 (0.39), residues: 151 loop : -1.88 (0.19), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 534 TYR 0.020 0.001 TYR C 605 PHE 0.018 0.002 PHE A 750 TRP 0.011 0.002 TRP F 583 HIS 0.006 0.001 HIS D 578 Details of bonding type rmsd covalent geometry : bond 0.00343 (19031) covalent geometry : angle 0.59619 (25717) hydrogen bonds : bond 0.04209 ( 799) hydrogen bonds : angle 4.74858 ( 2340) metal coordination : bond 0.00285 ( 10) Misc. bond : bond 0.00116 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 2375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 313 time to evaluate : 0.621 Fit side-chains TARDY: cannot create tardy model for: "MET A 321 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 380 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 438 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET F 321 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 380 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 438 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 619 GLU cc_start: 0.7470 (OUTLIER) cc_final: 0.7110 (pp20) REVERT: A 683 MET cc_start: 0.3274 (tpp) cc_final: 0.0558 (pmm) REVERT: A 733 LYS cc_start: 0.7734 (mtpt) cc_final: 0.7069 (tptp) REVERT: B 370 ILE cc_start: 0.7638 (OUTLIER) cc_final: 0.7329 (mt) REVERT: B 402 CYS cc_start: 0.7750 (p) cc_final: 0.7369 (p) REVERT: B 404 LEU cc_start: 0.8086 (tt) cc_final: 0.7852 (tp) REVERT: B 427 GLN cc_start: 0.7248 (OUTLIER) cc_final: 0.6681 (tm-30) REVERT: B 428 GLU cc_start: 0.6873 (tt0) cc_final: 0.6573 (mm-30) REVERT: B 433 GLN cc_start: 0.7842 (tp40) cc_final: 0.7568 (tm-30) REVERT: B 465 ARG cc_start: 0.6211 (mtt-85) cc_final: 0.5755 (tpt170) REVERT: B 469 PHE cc_start: 0.8580 (m-10) cc_final: 0.8327 (m-10) REVERT: B 501 GLU cc_start: 0.7239 (pt0) cc_final: 0.6895 (pt0) REVERT: B 573 TYR cc_start: 0.7759 (m-10) cc_final: 0.7553 (m-10) REVERT: B 636 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7998 (tp30) REVERT: B 683 MET cc_start: 0.6366 (ptp) cc_final: 0.4779 (pmm) REVERT: C 398 LYS cc_start: 0.8331 (mttt) cc_final: 0.8126 (mmtm) REVERT: C 408 GLN cc_start: 0.8215 (OUTLIER) cc_final: 0.5949 (mp10) REVERT: C 672 GLN cc_start: 0.8009 (mm-40) cc_final: 0.7737 (mp10) REVERT: C 695 ARG cc_start: 0.8008 (ttp80) cc_final: 0.7624 (ttp80) REVERT: C 699 ASP cc_start: 0.7780 (m-30) cc_final: 0.7507 (m-30) REVERT: D 404 LEU cc_start: 0.8199 (tt) cc_final: 0.7967 (tp) REVERT: D 424 GLN cc_start: 0.7576 (mt0) cc_final: 0.7325 (mt0) REVERT: D 573 TYR cc_start: 0.8432 (m-80) cc_final: 0.7828 (m-10) REVERT: D 624 ARG cc_start: 0.8016 (ttm-80) cc_final: 0.7663 (mtt-85) REVERT: D 734 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7104 (mt-10) REVERT: E 309 ASP cc_start: 0.8008 (m-30) cc_final: 0.7796 (m-30) REVERT: E 318 LEU cc_start: 0.8809 (mt) cc_final: 0.8563 (mp) REVERT: E 407 ASP cc_start: 0.7829 (t0) cc_final: 0.7607 (t0) REVERT: E 455 ARG cc_start: 0.8350 (mtp180) cc_final: 0.8041 (mmm-85) REVERT: E 543 LYS cc_start: 0.8340 (mmtt) cc_final: 0.8073 (tmtm) REVERT: E 632 ARG cc_start: 0.8397 (OUTLIER) cc_final: 0.7203 (tpt170) REVERT: F 616 TYR cc_start: 0.8550 (m-80) cc_final: 0.8313 (m-80) REVERT: F 660 GLN cc_start: 0.8319 (tt0) cc_final: 0.8016 (tt0) outliers start: 60 outliers final: 15 residues processed: 352 average time/residue: 0.6715 time to fit residues: 262.9518 Evaluate side-chains 297 residues out of total 2375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 275 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain B residue 370 ILE Chi-restraints excluded: chain B residue 427 GLN Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 636 GLU Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 744 LEU Chi-restraints excluded: chain C residue 408 GLN Chi-restraints excluded: chain C residue 500 LEU Chi-restraints excluded: chain C residue 538 ASP Chi-restraints excluded: chain C residue 539 SER Chi-restraints excluded: chain C residue 541 ASN Chi-restraints excluded: chain D residue 453 THR Chi-restraints excluded: chain D residue 457 ASP Chi-restraints excluded: chain D residue 507 ARG Chi-restraints excluded: chain D residue 535 HIS Chi-restraints excluded: chain D residue 734 GLU Chi-restraints excluded: chain D residue 739 ASN Chi-restraints excluded: chain E residue 335 ASP Chi-restraints excluded: chain E residue 632 ARG Chi-restraints excluded: chain E residue 669 LYS Chi-restraints excluded: chain F residue 562 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 83 optimal weight: 7.9990 chunk 31 optimal weight: 9.9990 chunk 34 optimal weight: 0.0570 chunk 116 optimal weight: 1.9990 chunk 101 optimal weight: 9.9990 chunk 234 optimal weight: 5.9990 chunk 90 optimal weight: 7.9990 chunk 0 optimal weight: 50.0000 chunk 131 optimal weight: 0.4980 chunk 104 optimal weight: 2.9990 chunk 249 optimal weight: 50.0000 overall best weight: 2.3104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 472 GLN ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 325 ASN C 332 GLN D 535 HIS ** D 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 542 GLN E 663 GLN F 667 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.162006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.139040 restraints weight = 26615.129| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 2.04 r_work: 0.3581 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3441 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7028 moved from start: 0.3336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19044 Z= 0.139 Angle : 0.576 11.683 25717 Z= 0.289 Chirality : 0.041 0.151 2915 Planarity : 0.004 0.045 3334 Dihedral : 9.407 164.782 2673 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.16 % Allowed : 15.83 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.37 (0.17), residues: 2372 helix: -0.24 (0.15), residues: 1262 sheet: -1.28 (0.40), residues: 148 loop : -1.66 (0.20), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 624 TYR 0.020 0.001 TYR C 605 PHE 0.017 0.002 PHE A 750 TRP 0.009 0.001 TRP F 583 HIS 0.010 0.002 HIS D 535 Details of bonding type rmsd covalent geometry : bond 0.00328 (19031) covalent geometry : angle 0.57594 (25717) hydrogen bonds : bond 0.03740 ( 799) hydrogen bonds : angle 4.52713 ( 2340) metal coordination : bond 0.00250 ( 10) Misc. bond : bond 0.00112 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 292 time to evaluate : 0.753 Fit side-chains TARDY: cannot create tardy model for: "MET A 321 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 380 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 438 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET F 321 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 380 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 438 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 589 ASP cc_start: 0.7495 (m-30) cc_final: 0.7288 (t0) REVERT: A 683 MET cc_start: 0.3333 (tpp) cc_final: 0.0572 (pmm) REVERT: B 370 ILE cc_start: 0.7597 (OUTLIER) cc_final: 0.7344 (mt) REVERT: B 402 CYS cc_start: 0.7780 (p) cc_final: 0.7406 (p) REVERT: B 404 LEU cc_start: 0.8091 (tt) cc_final: 0.7845 (tp) REVERT: B 427 GLN cc_start: 0.7218 (OUTLIER) cc_final: 0.6623 (tm-30) REVERT: B 428 GLU cc_start: 0.6904 (tt0) cc_final: 0.6549 (mm-30) REVERT: B 433 GLN cc_start: 0.7801 (tp40) cc_final: 0.7556 (tm-30) REVERT: B 458 ILE cc_start: 0.8881 (OUTLIER) cc_final: 0.8530 (pt) REVERT: B 636 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.8020 (mm-30) REVERT: B 641 ARG cc_start: 0.8348 (OUTLIER) cc_final: 0.8110 (mtm180) REVERT: B 683 MET cc_start: 0.6158 (ptp) cc_final: 0.5512 (ttt) REVERT: C 398 LYS cc_start: 0.8289 (mttt) cc_final: 0.8065 (mmtm) REVERT: C 408 GLN cc_start: 0.8217 (OUTLIER) cc_final: 0.5993 (mp10) REVERT: C 611 LYS cc_start: 0.8338 (OUTLIER) cc_final: 0.7812 (mttp) REVERT: C 666 MET cc_start: 0.8363 (mmt) cc_final: 0.6916 (mtt) REVERT: C 672 GLN cc_start: 0.8081 (mm-40) cc_final: 0.7705 (mp10) REVERT: C 695 ARG cc_start: 0.8003 (ttp80) cc_final: 0.7559 (ttp80) REVERT: C 699 ASP cc_start: 0.7771 (m-30) cc_final: 0.7543 (m-30) REVERT: D 404 LEU cc_start: 0.8178 (tt) cc_final: 0.7927 (tp) REVERT: D 507 ARG cc_start: 0.8703 (OUTLIER) cc_final: 0.7999 (mtm-85) REVERT: D 556 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8462 (tp) REVERT: D 573 TYR cc_start: 0.8459 (m-80) cc_final: 0.7972 (m-80) REVERT: D 624 ARG cc_start: 0.7990 (ttm-80) cc_final: 0.7644 (mtt-85) REVERT: D 734 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.7095 (mt-10) REVERT: E 318 LEU cc_start: 0.8837 (mt) cc_final: 0.8613 (mp) REVERT: E 407 ASP cc_start: 0.7832 (t0) cc_final: 0.7620 (t0) REVERT: E 455 ARG cc_start: 0.8365 (mtp180) cc_final: 0.8048 (mmm-85) REVERT: E 530 LEU cc_start: 0.8145 (mp) cc_final: 0.7825 (mp) REVERT: E 543 LYS cc_start: 0.8492 (mmtt) cc_final: 0.8128 (tmtm) REVERT: E 632 ARG cc_start: 0.8522 (OUTLIER) cc_final: 0.7278 (tpt170) REVERT: F 660 GLN cc_start: 0.8355 (tt0) cc_final: 0.8004 (tt0) REVERT: F 732 GLU cc_start: 0.7775 (mm-30) cc_final: 0.7398 (mt-10) outliers start: 62 outliers final: 19 residues processed: 333 average time/residue: 0.6698 time to fit residues: 248.2715 Evaluate side-chains 301 residues out of total 2375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 271 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 567 GLU Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 689 TYR Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 370 ILE Chi-restraints excluded: chain B residue 427 GLN Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain B residue 458 ILE Chi-restraints excluded: chain B residue 556 LEU Chi-restraints excluded: chain B residue 636 GLU Chi-restraints excluded: chain B residue 641 ARG Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 744 LEU Chi-restraints excluded: chain C residue 408 GLN Chi-restraints excluded: chain C residue 538 ASP Chi-restraints excluded: chain C residue 611 LYS Chi-restraints excluded: chain C residue 673 ILE Chi-restraints excluded: chain D residue 453 THR Chi-restraints excluded: chain D residue 457 ASP Chi-restraints excluded: chain D residue 507 ARG Chi-restraints excluded: chain D residue 556 LEU Chi-restraints excluded: chain D residue 669 LYS Chi-restraints excluded: chain D residue 734 GLU Chi-restraints excluded: chain D residue 739 ASN Chi-restraints excluded: chain D residue 772 LEU Chi-restraints excluded: chain E residue 380 MET Chi-restraints excluded: chain E residue 542 GLN Chi-restraints excluded: chain E residue 632 ARG Chi-restraints excluded: chain F residue 562 VAL Chi-restraints excluded: chain F residue 705 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 3 optimal weight: 50.0000 chunk 12 optimal weight: 50.0000 chunk 259 optimal weight: 50.0000 chunk 8 optimal weight: 50.0000 chunk 72 optimal weight: 5.9990 chunk 232 optimal weight: 6.9990 chunk 277 optimal weight: 3.9990 chunk 185 optimal weight: 7.9990 chunk 106 optimal weight: 7.9990 chunk 47 optimal weight: 0.3980 chunk 263 optimal weight: 40.0000 overall best weight: 5.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN ** A 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 541 ASN C 587 HIS C 613 GLN C 663 GLN ** D 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 542 GLN E 663 GLN F 655 GLN F 667 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.158817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.135983 restraints weight = 26629.558| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 1.84 r_work: 0.3529 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3385 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 moved from start: 0.3683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 19044 Z= 0.234 Angle : 0.666 12.123 25717 Z= 0.331 Chirality : 0.045 0.179 2915 Planarity : 0.005 0.073 3334 Dihedral : 9.485 166.532 2673 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 4.17 % Allowed : 15.57 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.32 (0.17), residues: 2372 helix: -0.16 (0.15), residues: 1258 sheet: -1.27 (0.40), residues: 150 loop : -1.69 (0.20), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 534 TYR 0.024 0.002 TYR D 573 PHE 0.024 0.003 PHE D 638 TRP 0.012 0.002 TRP F 583 HIS 0.010 0.002 HIS C 578 Details of bonding type rmsd covalent geometry : bond 0.00566 (19031) covalent geometry : angle 0.66586 (25717) hydrogen bonds : bond 0.04339 ( 799) hydrogen bonds : angle 4.60839 ( 2340) metal coordination : bond 0.00504 ( 10) Misc. bond : bond 0.00452 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 2375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 277 time to evaluate : 0.577 Fit side-chains TARDY: cannot create tardy model for: "MET A 321 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 380 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 438 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET F 321 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 380 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 438 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 589 ASP cc_start: 0.7645 (m-30) cc_final: 0.7348 (t0) REVERT: A 683 MET cc_start: 0.3634 (tpp) cc_final: 0.0674 (pmm) REVERT: B 402 CYS cc_start: 0.7905 (p) cc_final: 0.7491 (p) REVERT: B 404 LEU cc_start: 0.8149 (tt) cc_final: 0.7930 (tp) REVERT: B 427 GLN cc_start: 0.7191 (OUTLIER) cc_final: 0.6675 (tm-30) REVERT: B 428 GLU cc_start: 0.6857 (tt0) cc_final: 0.6530 (mm-30) REVERT: B 433 GLN cc_start: 0.7761 (tp40) cc_final: 0.7485 (tm-30) REVERT: B 458 ILE cc_start: 0.8963 (OUTLIER) cc_final: 0.8583 (pt) REVERT: B 465 ARG cc_start: 0.6091 (mtt-85) cc_final: 0.5625 (mmt180) REVERT: B 641 ARG cc_start: 0.8396 (OUTLIER) cc_final: 0.8165 (mtm180) REVERT: B 683 MET cc_start: 0.6119 (ptp) cc_final: 0.5680 (ttt) REVERT: C 398 LYS cc_start: 0.8319 (mttt) cc_final: 0.8088 (mmtm) REVERT: C 408 GLN cc_start: 0.8250 (OUTLIER) cc_final: 0.6163 (mp10) REVERT: C 611 LYS cc_start: 0.8370 (OUTLIER) cc_final: 0.7853 (mttp) REVERT: C 672 GLN cc_start: 0.8145 (mm-40) cc_final: 0.7843 (mp10) REVERT: C 683 MET cc_start: 0.6198 (ttt) cc_final: 0.5746 (tmm) REVERT: C 695 ARG cc_start: 0.8072 (ttp80) cc_final: 0.7662 (ttp80) REVERT: C 699 ASP cc_start: 0.7760 (m-30) cc_final: 0.7541 (m-30) REVERT: C 777 LYS cc_start: 0.8174 (OUTLIER) cc_final: 0.7776 (mptm) REVERT: D 376 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7738 (tm-30) REVERT: D 559 LYS cc_start: 0.8523 (mttm) cc_final: 0.8245 (mttm) REVERT: D 668 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7370 (mm-30) REVERT: D 673 ILE cc_start: 0.8522 (OUTLIER) cc_final: 0.8273 (pp) REVERT: D 685 LEU cc_start: 0.6865 (OUTLIER) cc_final: 0.6575 (tt) REVERT: D 734 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7175 (mt-10) REVERT: E 318 LEU cc_start: 0.8875 (mt) cc_final: 0.8642 (mp) REVERT: E 415 LYS cc_start: 0.8365 (tttt) cc_final: 0.8081 (ttmm) REVERT: E 543 LYS cc_start: 0.8353 (mmtt) cc_final: 0.7931 (tmtm) REVERT: E 632 ARG cc_start: 0.8624 (OUTLIER) cc_final: 0.8128 (tpt170) REVERT: F 660 GLN cc_start: 0.8445 (tt0) cc_final: 0.8115 (tt0) REVERT: F 668 GLU cc_start: 0.8816 (tt0) cc_final: 0.7889 (pm20) REVERT: F 687 LYS cc_start: 0.7062 (OUTLIER) cc_final: 0.6309 (mmtp) REVERT: F 732 GLU cc_start: 0.7849 (mm-30) cc_final: 0.7409 (mt-10) outliers start: 82 outliers final: 31 residues processed: 327 average time/residue: 0.6790 time to fit residues: 245.8267 Evaluate side-chains 298 residues out of total 2375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 254 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 567 GLU Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 689 TYR Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 427 GLN Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain B residue 458 ILE Chi-restraints excluded: chain B residue 556 LEU Chi-restraints excluded: chain B residue 641 ARG Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 744 LEU Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 408 GLN Chi-restraints excluded: chain C residue 500 LEU Chi-restraints excluded: chain C residue 538 ASP Chi-restraints excluded: chain C residue 539 SER Chi-restraints excluded: chain C residue 562 VAL Chi-restraints excluded: chain C residue 611 LYS Chi-restraints excluded: chain C residue 673 ILE Chi-restraints excluded: chain C residue 687 LYS Chi-restraints excluded: chain C residue 777 LYS Chi-restraints excluded: chain D residue 376 GLU Chi-restraints excluded: chain D residue 435 LEU Chi-restraints excluded: chain D residue 453 THR Chi-restraints excluded: chain D residue 457 ASP Chi-restraints excluded: chain D residue 499 THR Chi-restraints excluded: chain D residue 507 ARG Chi-restraints excluded: chain D residue 541 ASN Chi-restraints excluded: chain D residue 668 GLU Chi-restraints excluded: chain D residue 669 LYS Chi-restraints excluded: chain D residue 673 ILE Chi-restraints excluded: chain D residue 685 LEU Chi-restraints excluded: chain D residue 734 GLU Chi-restraints excluded: chain D residue 739 ASN Chi-restraints excluded: chain D residue 772 LEU Chi-restraints excluded: chain E residue 335 ASP Chi-restraints excluded: chain E residue 485 SER Chi-restraints excluded: chain E residue 553 ILE Chi-restraints excluded: chain E residue 632 ARG Chi-restraints excluded: chain E residue 736 LEU Chi-restraints excluded: chain F residue 648 ASP Chi-restraints excluded: chain F residue 687 LYS Chi-restraints excluded: chain F residue 705 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 63 optimal weight: 0.4980 chunk 111 optimal weight: 0.5980 chunk 268 optimal weight: 30.0000 chunk 136 optimal weight: 10.0000 chunk 175 optimal weight: 0.9980 chunk 239 optimal weight: 50.0000 chunk 80 optimal weight: 7.9990 chunk 249 optimal weight: 50.0000 chunk 158 optimal weight: 0.7980 chunk 207 optimal weight: 4.9990 chunk 152 optimal weight: 3.9990 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN C 663 GLN C 667 ASN ** D 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 442 ASN E 542 GLN E 613 GLN E 663 GLN E 667 ASN F 667 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.162211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.138599 restraints weight = 26443.336| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 2.06 r_work: 0.3580 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3439 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7018 moved from start: 0.3854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19044 Z= 0.113 Angle : 0.561 12.176 25717 Z= 0.279 Chirality : 0.041 0.151 2915 Planarity : 0.004 0.055 3334 Dihedral : 9.063 172.959 2673 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.70 % Allowed : 17.71 % Favored : 79.59 % 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: -0.73 (0.18), residues: 2372 helix: 0.37 (0.15), residues: 1257 sheet: -1.17 (0.40), residues: 150 loop : -1.45 (0.20), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 551 TYR 0.020 0.001 TYR C 605 PHE 0.014 0.001 PHE D 638 TRP 0.008 0.001 TRP F 583 HIS 0.003 0.001 HIS D 578 Details of bonding type rmsd covalent geometry : bond 0.00265 (19031) covalent geometry : angle 0.56097 (25717) hydrogen bonds : bond 0.03334 ( 799) hydrogen bonds : angle 4.34048 ( 2340) metal coordination : bond 0.00115 ( 10) Misc. bond : bond 0.00075 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 2375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 293 time to evaluate : 0.747 Fit side-chains TARDY: cannot create tardy model for: "MET A 321 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 380 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 438 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET F 321 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 380 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 438 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 683 MET cc_start: 0.3588 (tpp) cc_final: 0.0652 (pmm) REVERT: A 698 ASP cc_start: 0.8292 (m-30) cc_final: 0.8090 (m-30) REVERT: B 402 CYS cc_start: 0.8005 (p) cc_final: 0.7708 (p) REVERT: B 427 GLN cc_start: 0.7159 (OUTLIER) cc_final: 0.6539 (tm-30) REVERT: B 428 GLU cc_start: 0.6848 (tt0) cc_final: 0.6481 (mm-30) REVERT: B 433 GLN cc_start: 0.7664 (tp40) cc_final: 0.7445 (tm-30) REVERT: B 465 ARG cc_start: 0.5991 (mtt-85) cc_final: 0.5509 (tpt170) REVERT: B 469 PHE cc_start: 0.8336 (m-10) cc_final: 0.8005 (m-10) REVERT: B 501 GLU cc_start: 0.7079 (pm20) cc_final: 0.6812 (pm20) REVERT: B 504 LYS cc_start: 0.7650 (mtpt) cc_final: 0.7346 (mtpt) REVERT: B 636 GLU cc_start: 0.8358 (tt0) cc_final: 0.8087 (mm-30) REVERT: B 641 ARG cc_start: 0.8282 (OUTLIER) cc_final: 0.8050 (mtm180) REVERT: B 651 ARG cc_start: 0.7966 (ttm170) cc_final: 0.7707 (mtt90) REVERT: B 683 MET cc_start: 0.6199 (ptp) cc_final: 0.5671 (ttt) REVERT: C 325 ASN cc_start: 0.8457 (t0) cc_final: 0.8231 (OUTLIER) REVERT: C 408 GLN cc_start: 0.8167 (OUTLIER) cc_final: 0.7870 (mp10) REVERT: C 611 LYS cc_start: 0.8336 (OUTLIER) cc_final: 0.7826 (mttp) REVERT: C 672 GLN cc_start: 0.8059 (mm-40) cc_final: 0.7763 (mp10) REVERT: C 683 MET cc_start: 0.6127 (ttt) cc_final: 0.5728 (tmm) REVERT: C 695 ARG cc_start: 0.8003 (ttp80) cc_final: 0.7536 (ttp80) REVERT: C 699 ASP cc_start: 0.7693 (m-30) cc_final: 0.7474 (m-30) REVERT: C 777 LYS cc_start: 0.8151 (OUTLIER) cc_final: 0.7651 (mptm) REVERT: D 404 LEU cc_start: 0.8099 (tt) cc_final: 0.7858 (tp) REVERT: D 624 ARG cc_start: 0.7975 (ttm-80) cc_final: 0.7609 (mtt-85) REVERT: D 668 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7656 (mt-10) REVERT: D 673 ILE cc_start: 0.8509 (OUTLIER) cc_final: 0.8231 (pp) REVERT: D 685 LEU cc_start: 0.7006 (OUTLIER) cc_final: 0.6661 (tt) REVERT: D 734 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.7069 (mt-10) REVERT: E 318 LEU cc_start: 0.8807 (mt) cc_final: 0.8573 (mp) REVERT: E 415 LYS cc_start: 0.8362 (tttt) cc_final: 0.8062 (ttmm) REVERT: E 543 LYS cc_start: 0.8545 (mmtt) cc_final: 0.8136 (tptt) REVERT: E 632 ARG cc_start: 0.8592 (OUTLIER) cc_final: 0.6838 (tpt170) REVERT: F 660 GLN cc_start: 0.8342 (tt0) cc_final: 0.7953 (tt0) REVERT: F 732 GLU cc_start: 0.7800 (mm-30) cc_final: 0.7397 (mt-10) outliers start: 53 outliers final: 21 residues processed: 323 average time/residue: 0.6568 time to fit residues: 235.9340 Evaluate side-chains 301 residues out of total 2375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 271 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 427 GLN Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain B residue 641 ARG Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 744 LEU Chi-restraints excluded: chain C residue 391 ASP Chi-restraints excluded: chain C residue 408 GLN Chi-restraints excluded: chain C residue 538 ASP Chi-restraints excluded: chain C residue 539 SER Chi-restraints excluded: chain C residue 541 ASN Chi-restraints excluded: chain C residue 611 LYS Chi-restraints excluded: chain C residue 777 LYS Chi-restraints excluded: chain D residue 453 THR Chi-restraints excluded: chain D residue 457 ASP Chi-restraints excluded: chain D residue 668 GLU Chi-restraints excluded: chain D residue 669 LYS Chi-restraints excluded: chain D residue 673 ILE Chi-restraints excluded: chain D residue 685 LEU Chi-restraints excluded: chain D residue 734 GLU Chi-restraints excluded: chain D residue 739 ASN Chi-restraints excluded: chain E residue 335 ASP Chi-restraints excluded: chain E residue 632 ARG Chi-restraints excluded: chain E residue 669 LYS Chi-restraints excluded: chain E residue 676 ASP Chi-restraints excluded: chain E residue 729 LEU Chi-restraints excluded: chain F residue 648 ASP Chi-restraints excluded: chain F residue 656 SER Chi-restraints excluded: chain F residue 705 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 177 optimal weight: 7.9990 chunk 47 optimal weight: 8.9990 chunk 260 optimal weight: 50.0000 chunk 101 optimal weight: 10.0000 chunk 249 optimal weight: 50.0000 chunk 281 optimal weight: 9.9990 chunk 83 optimal weight: 9.9990 chunk 184 optimal weight: 1.9990 chunk 59 optimal weight: 10.0000 chunk 22 optimal weight: 50.0000 chunk 148 optimal weight: 6.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 433 GLN ** B 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 325 ASN C 613 GLN ** C 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 366 ASN E 424 GLN E 663 GLN F 655 GLN F 667 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.156614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.133757 restraints weight = 26929.002| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 1.89 r_work: 0.3491 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3345 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7139 moved from start: 0.4126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.063 19044 Z= 0.316 Angle : 0.752 13.572 25717 Z= 0.370 Chirality : 0.049 0.174 2915 Planarity : 0.005 0.063 3334 Dihedral : 9.513 174.654 2673 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 3.51 % Allowed : 17.76 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.19 (0.17), residues: 2372 helix: -0.08 (0.14), residues: 1262 sheet: -1.10 (0.40), residues: 152 loop : -1.61 (0.20), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 468 TYR 0.035 0.003 TYR D 573 PHE 0.031 0.003 PHE C 393 TRP 0.010 0.002 TRP F 583 HIS 0.012 0.002 HIS C 578 Details of bonding type rmsd covalent geometry : bond 0.00772 (19031) covalent geometry : angle 0.75231 (25717) hydrogen bonds : bond 0.04724 ( 799) hydrogen bonds : angle 4.67232 ( 2340) metal coordination : bond 0.00732 ( 10) Misc. bond : bond 0.00264 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 2375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 279 time to evaluate : 0.522 Fit side-chains TARDY: cannot create tardy model for: "MET A 321 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 380 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 438 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET F 321 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 380 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 438 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 683 MET cc_start: 0.3854 (tpp) cc_final: 0.0856 (pmm) REVERT: A 741 MET cc_start: 0.7455 (mmt) cc_final: 0.7123 (mmp) REVERT: B 402 CYS cc_start: 0.7944 (p) cc_final: 0.7454 (p) REVERT: B 427 GLN cc_start: 0.7134 (OUTLIER) cc_final: 0.6582 (tm-30) REVERT: B 428 GLU cc_start: 0.6827 (tt0) cc_final: 0.6553 (mm-30) REVERT: B 433 GLN cc_start: 0.7854 (tp-100) cc_final: 0.7552 (tm-30) REVERT: B 458 ILE cc_start: 0.9016 (OUTLIER) cc_final: 0.8423 (pt) REVERT: B 465 ARG cc_start: 0.6121 (mtt-85) cc_final: 0.5604 (mmt180) REVERT: B 471 ARG cc_start: 0.8120 (OUTLIER) cc_final: 0.7046 (mtp180) REVERT: B 641 ARG cc_start: 0.8408 (OUTLIER) cc_final: 0.8197 (mtm-85) REVERT: B 683 MET cc_start: 0.6213 (ptp) cc_final: 0.5620 (ttt) REVERT: C 404 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8197 (pt) REVERT: C 408 GLN cc_start: 0.8275 (OUTLIER) cc_final: 0.6162 (mp10) REVERT: C 500 LEU cc_start: 0.7878 (OUTLIER) cc_final: 0.7480 (tp) REVERT: C 611 LYS cc_start: 0.8417 (OUTLIER) cc_final: 0.7910 (mttp) REVERT: C 672 GLN cc_start: 0.8172 (mm-40) cc_final: 0.7903 (mp10) REVERT: C 683 MET cc_start: 0.6353 (ttt) cc_final: 0.5962 (tmm) REVERT: C 695 ARG cc_start: 0.8181 (ttp80) cc_final: 0.7794 (ttp80) REVERT: C 699 ASP cc_start: 0.7851 (m-30) cc_final: 0.7606 (m-30) REVERT: C 777 LYS cc_start: 0.8191 (OUTLIER) cc_final: 0.7754 (mptm) REVERT: D 376 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7744 (tm-30) REVERT: D 668 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7719 (mt-10) REVERT: D 673 ILE cc_start: 0.8508 (OUTLIER) cc_final: 0.8265 (pp) REVERT: D 685 LEU cc_start: 0.7415 (OUTLIER) cc_final: 0.7075 (tt) REVERT: D 734 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7192 (mt-10) REVERT: D 753 LYS cc_start: 0.8908 (OUTLIER) cc_final: 0.8301 (mtmm) REVERT: E 318 LEU cc_start: 0.8861 (mt) cc_final: 0.8626 (mp) REVERT: E 543 LYS cc_start: 0.8602 (mmtt) cc_final: 0.8168 (tmtm) REVERT: E 632 ARG cc_start: 0.8641 (OUTLIER) cc_final: 0.8101 (tpt170) REVERT: E 668 GLU cc_start: 0.7358 (OUTLIER) cc_final: 0.7140 (mp0) REVERT: F 660 GLN cc_start: 0.8489 (tt0) cc_final: 0.8190 (tt0) REVERT: F 732 GLU cc_start: 0.7778 (mm-30) cc_final: 0.7382 (mt-10) REVERT: F 744 LEU cc_start: 0.7365 (OUTLIER) cc_final: 0.6700 (mp) outliers start: 69 outliers final: 30 residues processed: 319 average time/residue: 0.6355 time to fit residues: 225.3780 Evaluate side-chains 313 residues out of total 2375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 265 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 567 GLU Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 427 GLN Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain B residue 458 ILE Chi-restraints excluded: chain B residue 471 ARG Chi-restraints excluded: chain B residue 556 LEU Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain B residue 641 ARG Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 408 GLN Chi-restraints excluded: chain C residue 500 LEU Chi-restraints excluded: chain C residue 538 ASP Chi-restraints excluded: chain C residue 539 SER Chi-restraints excluded: chain C residue 541 ASN Chi-restraints excluded: chain C residue 562 VAL Chi-restraints excluded: chain C residue 611 LYS Chi-restraints excluded: chain C residue 687 LYS Chi-restraints excluded: chain C residue 777 LYS Chi-restraints excluded: chain D residue 376 GLU Chi-restraints excluded: chain D residue 435 LEU Chi-restraints excluded: chain D residue 453 THR Chi-restraints excluded: chain D residue 475 ILE Chi-restraints excluded: chain D residue 499 THR Chi-restraints excluded: chain D residue 541 ASN Chi-restraints excluded: chain D residue 668 GLU Chi-restraints excluded: chain D residue 669 LYS Chi-restraints excluded: chain D residue 673 ILE Chi-restraints excluded: chain D residue 685 LEU Chi-restraints excluded: chain D residue 713 VAL Chi-restraints excluded: chain D residue 734 GLU Chi-restraints excluded: chain D residue 739 ASN Chi-restraints excluded: chain D residue 753 LYS Chi-restraints excluded: chain D residue 772 LEU Chi-restraints excluded: chain E residue 382 VAL Chi-restraints excluded: chain E residue 485 SER Chi-restraints excluded: chain E residue 553 ILE Chi-restraints excluded: chain E residue 632 ARG Chi-restraints excluded: chain E residue 668 GLU Chi-restraints excluded: chain E residue 729 LEU Chi-restraints excluded: chain E residue 736 LEU Chi-restraints excluded: chain F residue 648 ASP Chi-restraints excluded: chain F residue 656 SER Chi-restraints excluded: chain F residue 705 ILE Chi-restraints excluded: chain F residue 740 ASP Chi-restraints excluded: chain F residue 744 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 97 optimal weight: 0.4980 chunk 130 optimal weight: 1.9990 chunk 152 optimal weight: 3.9990 chunk 106 optimal weight: 4.9990 chunk 254 optimal weight: 50.0000 chunk 194 optimal weight: 5.9990 chunk 63 optimal weight: 10.0000 chunk 93 optimal weight: 0.0370 chunk 212 optimal weight: 4.9990 chunk 176 optimal weight: 0.9990 chunk 1 optimal weight: 50.0000 overall best weight: 1.5064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN ** C 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 663 GLN F 667 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.160904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.137456 restraints weight = 26687.267| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 2.13 r_work: 0.3553 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3409 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7038 moved from start: 0.4209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19044 Z= 0.119 Angle : 0.582 13.971 25717 Z= 0.289 Chirality : 0.041 0.165 2915 Planarity : 0.004 0.052 3334 Dihedral : 8.962 175.919 2673 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.49 % Allowed : 19.54 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.17), residues: 2372 helix: 0.51 (0.15), residues: 1253 sheet: -1.04 (0.41), residues: 150 loop : -1.42 (0.20), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 624 TYR 0.020 0.001 TYR C 605 PHE 0.013 0.001 PHE E 675 TRP 0.009 0.001 TRP D 583 HIS 0.004 0.001 HIS C 578 Details of bonding type rmsd covalent geometry : bond 0.00280 (19031) covalent geometry : angle 0.58191 (25717) hydrogen bonds : bond 0.03400 ( 799) hydrogen bonds : angle 4.40754 ( 2340) metal coordination : bond 0.00118 ( 10) Misc. bond : bond 0.00072 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 283 time to evaluate : 0.675 Fit side-chains TARDY: cannot create tardy model for: "MET A 321 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 380 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 438 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET F 321 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 380 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 438 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 683 MET cc_start: 0.3500 (tpp) cc_final: 0.0608 (pmm) REVERT: A 741 MET cc_start: 0.7429 (mmt) cc_final: 0.7092 (mmp) REVERT: B 402 CYS cc_start: 0.7955 (p) cc_final: 0.7682 (p) REVERT: B 427 GLN cc_start: 0.7006 (OUTLIER) cc_final: 0.6468 (tm-30) REVERT: B 428 GLU cc_start: 0.6825 (tt0) cc_final: 0.6492 (mm-30) REVERT: B 433 GLN cc_start: 0.7735 (tp-100) cc_final: 0.7441 (tm-30) REVERT: B 458 ILE cc_start: 0.8825 (OUTLIER) cc_final: 0.8418 (pt) REVERT: B 465 ARG cc_start: 0.6083 (mtt-85) cc_final: 0.5512 (mmt180) REVERT: B 471 ARG cc_start: 0.8027 (OUTLIER) cc_final: 0.6978 (mtp180) REVERT: B 683 MET cc_start: 0.6151 (ptp) cc_final: 0.5665 (ttt) REVERT: C 611 LYS cc_start: 0.8380 (OUTLIER) cc_final: 0.7881 (mttp) REVERT: C 624 ARG cc_start: 0.7763 (ttm-80) cc_final: 0.6912 (mpt180) REVERT: C 666 MET cc_start: 0.8294 (mmt) cc_final: 0.7781 (mtt) REVERT: C 672 GLN cc_start: 0.7998 (mm-40) cc_final: 0.7700 (mp10) REVERT: C 683 MET cc_start: 0.6388 (ttt) cc_final: 0.5994 (tmm) REVERT: C 695 ARG cc_start: 0.8081 (ttp80) cc_final: 0.7578 (ttp80) REVERT: C 699 ASP cc_start: 0.7792 (m-30) cc_final: 0.7541 (m-30) REVERT: D 376 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7620 (tm-30) REVERT: D 624 ARG cc_start: 0.7967 (ttm-80) cc_final: 0.7622 (mtt-85) REVERT: D 668 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7664 (mt-10) REVERT: D 673 ILE cc_start: 0.8486 (OUTLIER) cc_final: 0.8252 (pp) REVERT: D 685 LEU cc_start: 0.7049 (OUTLIER) cc_final: 0.6699 (tt) REVERT: D 734 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.7100 (mt-10) REVERT: E 318 LEU cc_start: 0.8771 (mt) cc_final: 0.8533 (mp) REVERT: E 331 LYS cc_start: 0.8239 (pmtt) cc_final: 0.7871 (tttp) REVERT: E 415 LYS cc_start: 0.8359 (tttt) cc_final: 0.8062 (ttmm) REVERT: E 543 LYS cc_start: 0.8545 (mmtt) cc_final: 0.8082 (tptt) REVERT: E 632 ARG cc_start: 0.8622 (OUTLIER) cc_final: 0.7048 (tpt170) REVERT: F 660 GLN cc_start: 0.8380 (tt0) cc_final: 0.7939 (tt0) REVERT: F 666 MET cc_start: 0.8597 (OUTLIER) cc_final: 0.8179 (ptm) REVERT: F 732 GLU cc_start: 0.7741 (mm-30) cc_final: 0.7344 (mt-10) outliers start: 49 outliers final: 18 residues processed: 312 average time/residue: 0.6399 time to fit residues: 222.4294 Evaluate side-chains 294 residues out of total 2375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 265 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain B residue 427 GLN Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain B residue 458 ILE Chi-restraints excluded: chain B residue 471 ARG Chi-restraints excluded: chain B residue 556 LEU Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 410 ASP Chi-restraints excluded: chain C residue 538 ASP Chi-restraints excluded: chain C residue 539 SER Chi-restraints excluded: chain C residue 541 ASN Chi-restraints excluded: chain C residue 611 LYS Chi-restraints excluded: chain C residue 687 LYS Chi-restraints excluded: chain D residue 376 GLU Chi-restraints excluded: chain D residue 453 THR Chi-restraints excluded: chain D residue 668 GLU Chi-restraints excluded: chain D residue 669 LYS Chi-restraints excluded: chain D residue 673 ILE Chi-restraints excluded: chain D residue 685 LEU Chi-restraints excluded: chain D residue 734 GLU Chi-restraints excluded: chain D residue 739 ASN Chi-restraints excluded: chain D residue 767 ASP Chi-restraints excluded: chain E residue 553 ILE Chi-restraints excluded: chain E residue 632 ARG Chi-restraints excluded: chain E residue 676 ASP Chi-restraints excluded: chain F residue 648 ASP Chi-restraints excluded: chain F residue 666 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 50 optimal weight: 0.9980 chunk 80 optimal weight: 7.9990 chunk 74 optimal weight: 0.9990 chunk 249 optimal weight: 50.0000 chunk 157 optimal weight: 8.9990 chunk 284 optimal weight: 20.0000 chunk 36 optimal weight: 0.9980 chunk 187 optimal weight: 0.9990 chunk 188 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 429 ASN ** D 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 663 GLN F 667 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.161672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.138242 restraints weight = 26588.161| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 2.07 r_work: 0.3563 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3420 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7027 moved from start: 0.4277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19044 Z= 0.121 Angle : 0.585 14.455 25717 Z= 0.288 Chirality : 0.041 0.145 2915 Planarity : 0.004 0.052 3334 Dihedral : 8.717 170.489 2673 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.04 % Allowed : 20.61 % Favored : 77.35 % 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: -0.31 (0.18), residues: 2372 helix: 0.74 (0.15), residues: 1257 sheet: -0.78 (0.43), residues: 140 loop : -1.34 (0.20), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 624 TYR 0.022 0.001 TYR C 605 PHE 0.044 0.002 PHE B 469 TRP 0.008 0.001 TRP A 583 HIS 0.004 0.001 HIS D 578 Details of bonding type rmsd covalent geometry : bond 0.00285 (19031) covalent geometry : angle 0.58507 (25717) hydrogen bonds : bond 0.03342 ( 799) hydrogen bonds : angle 4.31643 ( 2340) metal coordination : bond 0.00160 ( 10) Misc. bond : bond 0.00084 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 270 time to evaluate : 0.674 Fit side-chains TARDY: cannot create tardy model for: "MET A 321 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 380 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 438 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET F 321 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 380 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 438 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 683 MET cc_start: 0.3477 (tpp) cc_final: 0.0644 (pmm) REVERT: A 741 MET cc_start: 0.7529 (mmt) cc_final: 0.7178 (mmp) REVERT: B 402 CYS cc_start: 0.7912 (p) cc_final: 0.7649 (p) REVERT: B 427 GLN cc_start: 0.7016 (OUTLIER) cc_final: 0.6442 (tm-30) REVERT: B 428 GLU cc_start: 0.6746 (tt0) cc_final: 0.6419 (mm-30) REVERT: B 433 GLN cc_start: 0.7681 (tp-100) cc_final: 0.7433 (tm-30) REVERT: B 458 ILE cc_start: 0.8830 (OUTLIER) cc_final: 0.8437 (pt) REVERT: B 465 ARG cc_start: 0.6031 (mtt-85) cc_final: 0.5459 (mmt180) REVERT: B 471 ARG cc_start: 0.8033 (OUTLIER) cc_final: 0.6982 (mtp180) REVERT: B 641 ARG cc_start: 0.8273 (OUTLIER) cc_final: 0.8048 (mtm180) REVERT: B 683 MET cc_start: 0.6131 (ptp) cc_final: 0.5642 (ttt) REVERT: C 611 LYS cc_start: 0.8357 (OUTLIER) cc_final: 0.7875 (mttp) REVERT: C 624 ARG cc_start: 0.7624 (ttm-80) cc_final: 0.6883 (mpt180) REVERT: C 672 GLN cc_start: 0.8052 (mm-40) cc_final: 0.7760 (mp10) REVERT: C 683 MET cc_start: 0.6326 (ttt) cc_final: 0.5994 (tmm) REVERT: C 695 ARG cc_start: 0.8051 (ttp80) cc_final: 0.7566 (ttp80) REVERT: C 699 ASP cc_start: 0.7711 (m-30) cc_final: 0.7459 (m-30) REVERT: D 376 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7508 (tm-30) REVERT: D 624 ARG cc_start: 0.7936 (ttm-80) cc_final: 0.7594 (mtt-85) REVERT: D 668 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7584 (mt-10) REVERT: D 673 ILE cc_start: 0.8496 (OUTLIER) cc_final: 0.8257 (pp) REVERT: D 685 LEU cc_start: 0.7075 (OUTLIER) cc_final: 0.6785 (tt) REVERT: D 734 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.7039 (mt-10) REVERT: E 318 LEU cc_start: 0.8737 (mt) cc_final: 0.8473 (mp) REVERT: E 415 LYS cc_start: 0.8377 (tttt) cc_final: 0.8062 (ttmm) REVERT: E 523 ASN cc_start: 0.6798 (m110) cc_final: 0.6472 (m110) REVERT: E 543 LYS cc_start: 0.8553 (mmtt) cc_final: 0.8094 (tptt) REVERT: E 632 ARG cc_start: 0.8638 (OUTLIER) cc_final: 0.7164 (tpt170) REVERT: F 660 GLN cc_start: 0.8376 (tt0) cc_final: 0.7947 (tt0) REVERT: F 666 MET cc_start: 0.8593 (OUTLIER) cc_final: 0.8168 (ptm) REVERT: F 732 GLU cc_start: 0.7729 (mm-30) cc_final: 0.7360 (mt-10) outliers start: 40 outliers final: 18 residues processed: 294 average time/residue: 0.6548 time to fit residues: 213.8295 Evaluate side-chains 296 residues out of total 2375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 266 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain B residue 427 GLN Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain B residue 458 ILE Chi-restraints excluded: chain B residue 471 ARG Chi-restraints excluded: chain B residue 556 LEU Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain B residue 641 ARG Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain C residue 329 ASN Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 538 ASP Chi-restraints excluded: chain C residue 539 SER Chi-restraints excluded: chain C residue 541 ASN Chi-restraints excluded: chain C residue 611 LYS Chi-restraints excluded: chain C residue 687 LYS Chi-restraints excluded: chain D residue 376 GLU Chi-restraints excluded: chain D residue 453 THR Chi-restraints excluded: chain D residue 668 GLU Chi-restraints excluded: chain D residue 669 LYS Chi-restraints excluded: chain D residue 673 ILE Chi-restraints excluded: chain D residue 685 LEU Chi-restraints excluded: chain D residue 734 GLU Chi-restraints excluded: chain D residue 739 ASN Chi-restraints excluded: chain E residue 485 SER Chi-restraints excluded: chain E residue 553 ILE Chi-restraints excluded: chain E residue 632 ARG Chi-restraints excluded: chain F residue 648 ASP Chi-restraints excluded: chain F residue 666 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 102 optimal weight: 0.9990 chunk 64 optimal weight: 10.0000 chunk 171 optimal weight: 10.0000 chunk 18 optimal weight: 50.0000 chunk 146 optimal weight: 0.0010 chunk 9 optimal weight: 50.0000 chunk 211 optimal weight: 7.9990 chunk 116 optimal weight: 6.9990 chunk 256 optimal weight: 50.0000 chunk 219 optimal weight: 6.9990 chunk 31 optimal weight: 20.0000 overall best weight: 4.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 663 GLN F 667 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.158992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.135767 restraints weight = 26755.008| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 1.99 r_work: 0.3526 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3383 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7079 moved from start: 0.4382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 19044 Z= 0.217 Angle : 0.663 14.599 25717 Z= 0.326 Chirality : 0.045 0.153 2915 Planarity : 0.005 0.054 3334 Dihedral : 8.629 169.694 2673 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 2.14 % Allowed : 20.81 % Favored : 77.05 % 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 (0.17), residues: 2372 helix: 0.58 (0.15), residues: 1253 sheet: -0.94 (0.41), residues: 153 loop : -1.42 (0.20), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG E 483 TYR 0.033 0.002 TYR D 605 PHE 0.047 0.002 PHE B 469 TRP 0.009 0.002 TRP F 583 HIS 0.007 0.002 HIS C 578 Details of bonding type rmsd covalent geometry : bond 0.00533 (19031) covalent geometry : angle 0.66259 (25717) hydrogen bonds : bond 0.04020 ( 799) hydrogen bonds : angle 4.46858 ( 2340) metal coordination : bond 0.00471 ( 10) Misc. bond : bond 0.00236 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 264 time to evaluate : 0.756 Fit side-chains TARDY: cannot create tardy model for: "MET A 321 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 380 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 438 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET F 321 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 380 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 438 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 683 MET cc_start: 0.3446 (tpp) cc_final: 0.0771 (pmm) REVERT: A 741 MET cc_start: 0.7585 (mmt) cc_final: 0.7313 (mmp) REVERT: B 402 CYS cc_start: 0.8045 (p) cc_final: 0.7751 (p) REVERT: B 427 GLN cc_start: 0.7049 (OUTLIER) cc_final: 0.6501 (tm-30) REVERT: B 428 GLU cc_start: 0.6743 (tt0) cc_final: 0.6459 (mm-30) REVERT: B 433 GLN cc_start: 0.7693 (tp-100) cc_final: 0.7464 (tm-30) REVERT: B 458 ILE cc_start: 0.8837 (OUTLIER) cc_final: 0.8446 (pt) REVERT: B 465 ARG cc_start: 0.6118 (mtt-85) cc_final: 0.5482 (mmt180) REVERT: B 641 ARG cc_start: 0.8351 (OUTLIER) cc_final: 0.8068 (mtm180) REVERT: B 683 MET cc_start: 0.6180 (ptp) cc_final: 0.5687 (ttt) REVERT: C 611 LYS cc_start: 0.8398 (OUTLIER) cc_final: 0.7902 (mttp) REVERT: C 672 GLN cc_start: 0.8088 (mm-40) cc_final: 0.7756 (mp10) REVERT: C 695 ARG cc_start: 0.8097 (ttp80) cc_final: 0.7659 (ttp80) REVERT: C 699 ASP cc_start: 0.7764 (m-30) cc_final: 0.7512 (m-30) REVERT: D 376 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7701 (tm-30) REVERT: D 624 ARG cc_start: 0.7959 (ttm-80) cc_final: 0.7621 (mtt-85) REVERT: D 668 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7619 (mt-10) REVERT: D 673 ILE cc_start: 0.8523 (OUTLIER) cc_final: 0.8272 (pp) REVERT: D 734 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.7104 (mt-10) REVERT: E 318 LEU cc_start: 0.8746 (mt) cc_final: 0.8478 (mp) REVERT: E 331 LYS cc_start: 0.8236 (pmtt) cc_final: 0.7887 (tttp) REVERT: E 415 LYS cc_start: 0.8378 (tttt) cc_final: 0.8067 (ttmm) REVERT: E 523 ASN cc_start: 0.6681 (m110) cc_final: 0.6329 (m110) REVERT: E 543 LYS cc_start: 0.8517 (mmtt) cc_final: 0.8144 (tmtm) REVERT: E 632 ARG cc_start: 0.8646 (OUTLIER) cc_final: 0.7885 (tpt170) REVERT: F 660 GLN cc_start: 0.8399 (tt0) cc_final: 0.8026 (tt0) REVERT: F 732 GLU cc_start: 0.7774 (mm-30) cc_final: 0.7411 (mt-10) outliers start: 42 outliers final: 22 residues processed: 289 average time/residue: 0.6655 time to fit residues: 214.6193 Evaluate side-chains 293 residues out of total 2375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 262 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain B residue 427 GLN Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain B residue 458 ILE Chi-restraints excluded: chain B residue 556 LEU Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain B residue 641 ARG Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 538 ASP Chi-restraints excluded: chain C residue 539 SER Chi-restraints excluded: chain C residue 541 ASN Chi-restraints excluded: chain C residue 562 VAL Chi-restraints excluded: chain C residue 611 LYS Chi-restraints excluded: chain C residue 687 LYS Chi-restraints excluded: chain D residue 376 GLU Chi-restraints excluded: chain D residue 453 THR Chi-restraints excluded: chain D residue 457 ASP Chi-restraints excluded: chain D residue 541 ASN Chi-restraints excluded: chain D residue 668 GLU Chi-restraints excluded: chain D residue 669 LYS Chi-restraints excluded: chain D residue 673 ILE Chi-restraints excluded: chain D residue 734 GLU Chi-restraints excluded: chain D residue 739 ASN Chi-restraints excluded: chain E residue 320 ILE Chi-restraints excluded: chain E residue 335 ASP Chi-restraints excluded: chain E residue 485 SER Chi-restraints excluded: chain E residue 632 ARG Chi-restraints excluded: chain E residue 676 ASP Chi-restraints excluded: chain F residue 648 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 219 optimal weight: 7.9990 chunk 188 optimal weight: 2.9990 chunk 112 optimal weight: 0.9990 chunk 92 optimal weight: 10.0000 chunk 205 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 275 optimal weight: 0.0370 chunk 130 optimal weight: 9.9990 chunk 245 optimal weight: 50.0000 chunk 46 optimal weight: 9.9990 chunk 104 optimal weight: 0.0470 overall best weight: 1.4162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 575 GLN ** B 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 663 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 667 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.161067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.137717 restraints weight = 26581.368| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 2.04 r_work: 0.3557 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3414 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7029 moved from start: 0.4436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19044 Z= 0.121 Angle : 0.593 14.558 25717 Z= 0.293 Chirality : 0.041 0.152 2915 Planarity : 0.004 0.057 3334 Dihedral : 8.265 163.400 2673 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.73 % Allowed : 21.37 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.22 (0.18), residues: 2372 helix: 0.83 (0.15), residues: 1256 sheet: -0.70 (0.43), residues: 136 loop : -1.34 (0.20), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG E 483 TYR 0.026 0.001 TYR D 605 PHE 0.036 0.002 PHE B 469 TRP 0.008 0.001 TRP A 583 HIS 0.005 0.001 HIS C 578 Details of bonding type rmsd covalent geometry : bond 0.00285 (19031) covalent geometry : angle 0.59289 (25717) hydrogen bonds : bond 0.03408 ( 799) hydrogen bonds : angle 4.36908 ( 2340) metal coordination : bond 0.00148 ( 10) Misc. bond : bond 0.00150 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6812.47 seconds wall clock time: 117 minutes 5.52 seconds (7025.52 seconds total)