Starting phenix.real_space_refine on Mon Jun 16 16:57:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6nyy_0552/06_2025/6nyy_0552.cif Found real_map, /net/cci-nas-00/data/ceres_data/6nyy_0552/06_2025/6nyy_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6nyy_0552/06_2025/6nyy_0552.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6nyy_0552/06_2025/6nyy_0552.map" model { file = "/net/cci-nas-00/data/ceres_data/6nyy_0552/06_2025/6nyy_0552.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6nyy_0552/06_2025/6nyy_0552.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.010 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 7, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 10, 'ASP:plan': 15, 'PHE:plan': 14, 'GLU:plan': 13, 'ARG:plan': 12} 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: {'GLN:plan1': 10, 'HIS:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 12, 'ASP:plan': 16, 'PHE:plan': 15, 'GLU:plan': 17, 'ARG:plan': 14} 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: 13.23, per 1000 atoms: 0.69 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: 4.37 Conformation dependent library (CDL) restraints added in 2.4 seconds 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: 1.76 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: 5.80 Time building geometry restraints manager: 5.26 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: 0.360 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: 0.070 Extract box with map and model: 0.830 Check model and map are aligned: 0.140 Set scattering table: 0.190 Process input model: 48.440 Find NCS groups from input model: 1.430 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.540 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.019 0.003 TRP C 583 HIS 0.011 0.002 HIS E 578 PHE 0.041 0.004 PHE E 750 TYR 0.020 0.002 TYR E 584 ARG 0.014 0.001 ARG C 465 Details of bonding type rmsd hydrogen bonds : bond 0.31768 ( 799) hydrogen bonds : angle 10.42684 ( 2340) metal coordination : bond 0.14665 ( 10) covalent geometry : bond 0.00728 (19031) covalent geometry : angle 0.89925 (25717) 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 : 2.288 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: 0.8149 (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: 0.7583 (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: 0.6120 (mm-30) REVERT: B 465 ARG cc_start: 0.5940 (mtt-85) cc_final: 0.5686 (mmt180) REVERT: B 503 ASP cc_start: 0.7522 (m-30) cc_final: 0.7318 (m-30) REVERT: B 520 ASP cc_start: 0.7113 (m-30) cc_final: 0.6801 (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: 0.6999 (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: 0.6964 (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: 0.7652 (mtp-110) REVERT: C 774 GLU cc_start: 0.7851 (mp0) cc_final: 0.7603 (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: 0.7626 (tt) cc_final: 0.7360 (tp) REVERT: D 424 GLN cc_start: 0.6684 (mt0) cc_final: 0.6233 (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: 0.7172 (t0) REVERT: E 321 MET cc_start: 0.7339 (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: 0.6919 (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: 1.6546 time to fit residues: 963.5193 Evaluate side-chains 336 residues out of total 2375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 334 time to evaluate : 2.479 ------------------------------------------------------------------------------- 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 240 optimal weight: 100.0000 chunk 216 optimal weight: 0.9990 chunk 119 optimal weight: 0.8980 chunk 73 optimal weight: 0.9990 chunk 145 optimal weight: 1.9990 chunk 115 optimal weight: 10.0000 chunk 223 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 135 optimal weight: 8.9990 chunk 166 optimal weight: 10.0000 chunk 258 optimal weight: 50.0000 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 578 HIS A 672 GLN B 332 GLN ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 663 GLN C 472 GLN C 647 GLN ** C 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 706 ASN D 433 GLN D 526 ASN D 535 HIS D 575 GLN D 655 GLN E 454 ASN E 663 GLN F 667 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.165740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.142205 restraints weight = 26481.942| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 2.01 r_work: 0.3639 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3504 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6975 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19044 Z= 0.136 Angle : 0.617 10.900 25717 Z= 0.320 Chirality : 0.041 0.148 2915 Planarity : 0.005 0.051 3334 Dihedral : 10.713 173.067 2677 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.05 % Allowed : 11.15 % Favored : 85.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.06 (0.15), residues: 2372 helix: -1.93 (0.12), residues: 1255 sheet: -1.45 (0.41), residues: 134 loop : -2.06 (0.18), residues: 983 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP F 583 HIS 0.006 0.001 HIS C 578 PHE 0.020 0.002 PHE E 638 TYR 0.019 0.001 TYR C 605 ARG 0.008 0.001 ARG C 624 Details of bonding type rmsd hydrogen bonds : bond 0.05331 ( 799) hydrogen bonds : angle 5.27741 ( 2340) metal coordination : bond 0.00574 ( 10) covalent geometry : bond 0.00287 (19031) covalent geometry : angle 0.61715 (25717) Misc. bond : bond 0.00275 ( 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 428 residues out of total 2375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 368 time to evaluate : 2.168 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 575 GLN cc_start: 0.8410 (mm-40) cc_final: 0.8210 (mm110) REVERT: A 619 GLU cc_start: 0.7327 (OUTLIER) cc_final: 0.7048 (pp20) REVERT: A 683 MET cc_start: 0.3077 (tpp) cc_final: 0.0526 (pmm) REVERT: B 402 CYS cc_start: 0.7718 (p) cc_final: 0.7392 (p) REVERT: B 404 LEU cc_start: 0.7958 (tt) cc_final: 0.7757 (tp) REVERT: B 427 GLN cc_start: 0.7341 (OUTLIER) cc_final: 0.6945 (tm130) REVERT: B 465 ARG cc_start: 0.6302 (mtt-85) cc_final: 0.6029 (mmt180) REVERT: B 673 ILE cc_start: 0.8592 (OUTLIER) cc_final: 0.8384 (pp) REVERT: C 328 LYS cc_start: 0.8676 (ttmm) cc_final: 0.8149 (mmmm) REVERT: C 504 LYS cc_start: 0.8746 (mttt) cc_final: 0.8517 (mtpp) REVERT: C 541 ASN cc_start: 0.8170 (OUTLIER) cc_final: 0.7932 (p0) REVERT: C 547 GLN cc_start: 0.8336 (mt0) cc_final: 0.8123 (mt0) REVERT: C 636 GLU cc_start: 0.8009 (tt0) cc_final: 0.7569 (pt0) REVERT: C 695 ARG cc_start: 0.8067 (ttp80) cc_final: 0.7769 (ttp80) REVERT: C 699 ASP cc_start: 0.7653 (m-30) cc_final: 0.7397 (m-30) REVERT: D 424 GLN cc_start: 0.7602 (mt0) cc_final: 0.7201 (mt0) REVERT: D 500 LEU cc_start: 0.8040 (mt) cc_final: 0.7775 (mt) REVERT: D 547 GLN cc_start: 0.8421 (mt0) cc_final: 0.8150 (mt0) REVERT: D 624 ARG cc_start: 0.7870 (ttm-80) cc_final: 0.7538 (mtt-85) REVERT: D 706 ASN cc_start: 0.7927 (t0) cc_final: 0.7710 (t0) REVERT: E 309 ASP cc_start: 0.7956 (m-30) cc_final: 0.7606 (t0) REVERT: E 318 LEU cc_start: 0.8897 (tp) cc_final: 0.8572 (mp) REVERT: E 543 LYS cc_start: 0.8272 (mmtt) cc_final: 0.8065 (tmtm) REVERT: E 668 GLU cc_start: 0.7211 (OUTLIER) cc_final: 0.6864 (mp0) REVERT: F 589 ASP cc_start: 0.7197 (m-30) cc_final: 0.6752 (t0) REVERT: F 627 MET cc_start: 0.8204 (tmm) cc_final: 0.7921 (tmm) REVERT: F 660 GLN cc_start: 0.8191 (tt0) cc_final: 0.7895 (tt0) outliers start: 60 outliers final: 18 residues processed: 405 average time/residue: 1.4673 time to fit residues: 660.3585 Evaluate side-chains 314 residues out of total 2375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 291 time to evaluate : 2.119 ------------------------------------------------------------------------------- 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 B residue 427 GLN Chi-restraints excluded: chain B residue 504 LYS Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 641 ARG 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 345 ILE Chi-restraints excluded: chain C residue 371 THR Chi-restraints excluded: chain C residue 391 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 D residue 457 ASP Chi-restraints excluded: chain D residue 535 HIS Chi-restraints excluded: chain D residue 739 ASN Chi-restraints excluded: chain E residue 335 ASP Chi-restraints excluded: chain E residue 668 GLU 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 250 optimal weight: 50.0000 chunk 241 optimal weight: 50.0000 chunk 21 optimal weight: 50.0000 chunk 201 optimal weight: 3.9990 chunk 96 optimal weight: 0.9990 chunk 58 optimal weight: 8.9990 chunk 275 optimal weight: 8.9990 chunk 85 optimal weight: 0.9990 chunk 276 optimal weight: 1.9990 chunk 144 optimal weight: 9.9990 chunk 91 optimal weight: 30.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 607 GLN ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 663 GLN ** C 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 541 ASN ** E 663 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 655 GLN F 667 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.162035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.138484 restraints weight = 26326.483| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 1.86 r_work: 0.3587 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3447 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7033 moved from start: 0.3005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 19044 Z= 0.180 Angle : 0.628 11.388 25717 Z= 0.315 Chirality : 0.043 0.189 2915 Planarity : 0.005 0.048 3334 Dihedral : 9.867 162.848 2675 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 3.26 % Allowed : 15.22 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.16), residues: 2372 helix: -0.82 (0.14), residues: 1273 sheet: -1.38 (0.39), residues: 150 loop : -1.86 (0.19), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 583 HIS 0.010 0.002 HIS D 535 PHE 0.024 0.002 PHE A 750 TYR 0.020 0.002 TYR C 605 ARG 0.007 0.001 ARG D 534 Details of bonding type rmsd hydrogen bonds : bond 0.04436 ( 799) hydrogen bonds : angle 4.73758 ( 2340) metal coordination : bond 0.00457 ( 10) covalent geometry : bond 0.00432 (19031) covalent geometry : angle 0.62783 (25717) Misc. bond : bond 0.00170 ( 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 380 residues out of total 2375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 316 time to evaluate : 2.311 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: 0.3157 (tpp) cc_final: 0.0493 (pmm) REVERT: A 733 LYS cc_start: 0.7842 (mtpt) cc_final: 0.7051 (tptp) REVERT: B 370 ILE cc_start: 0.7619 (OUTLIER) cc_final: 0.7401 (tt) REVERT: B 402 CYS cc_start: 0.7711 (p) cc_final: 0.7343 (p) REVERT: B 404 LEU cc_start: 0.8137 (tt) cc_final: 0.7889 (tp) REVERT: B 427 GLN cc_start: 0.7140 (OUTLIER) cc_final: 0.6806 (tm-30) REVERT: B 433 GLN cc_start: 0.7828 (tp40) cc_final: 0.7516 (tm-30) REVERT: B 458 ILE cc_start: 0.8991 (OUTLIER) cc_final: 0.8583 (pt) REVERT: B 465 ARG cc_start: 0.6148 (mtt-85) cc_final: 0.5918 (tpt170) REVERT: B 469 PHE cc_start: 0.8553 (m-10) cc_final: 0.8292 (m-10) REVERT: B 501 GLU cc_start: 0.7330 (pt0) cc_final: 0.6966 (pt0) REVERT: B 636 GLU cc_start: 0.8205 (tt0) cc_final: 0.7903 (mm-30) REVERT: B 673 ILE cc_start: 0.8652 (OUTLIER) cc_final: 0.8447 (pp) REVERT: B 683 MET cc_start: 0.6257 (ptp) cc_final: 0.4698 (pmm) REVERT: B 724 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7416 (tm-30) REVERT: C 332 GLN cc_start: 0.7823 (mt0) cc_final: 0.7616 (pt0) REVERT: C 408 GLN cc_start: 0.8246 (OUTLIER) cc_final: 0.5913 (mp10) REVERT: C 472 GLN cc_start: 0.8470 (OUTLIER) cc_final: 0.8106 (mt0) REVERT: C 547 GLN cc_start: 0.8352 (mt0) cc_final: 0.8146 (mt0) REVERT: C 611 LYS cc_start: 0.8295 (OUTLIER) cc_final: 0.7763 (mttp) REVERT: C 666 MET cc_start: 0.8370 (mmt) cc_final: 0.7100 (mtt) REVERT: C 695 ARG cc_start: 0.7981 (ttp80) cc_final: 0.7603 (ttp80) REVERT: C 699 ASP cc_start: 0.7736 (m-30) cc_final: 0.7463 (m-30) REVERT: D 404 LEU cc_start: 0.8214 (tt) cc_final: 0.8004 (tp) REVERT: D 424 GLN cc_start: 0.7579 (mt0) cc_final: 0.7322 (mt0) REVERT: D 543 LYS cc_start: 0.8814 (mttt) cc_final: 0.8476 (mtmm) REVERT: D 547 GLN cc_start: 0.8410 (mt0) cc_final: 0.8177 (mt0) REVERT: D 556 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8227 (tp) REVERT: D 557 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.8077 (tm-30) REVERT: D 734 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.7123 (mt-10) REVERT: E 309 ASP cc_start: 0.8070 (m-30) cc_final: 0.7843 (m-30) REVERT: E 321 MET cc_start: 0.8052 (mtm) cc_final: 0.7709 (mtp) REVERT: E 543 LYS cc_start: 0.8433 (mmtt) cc_final: 0.8080 (tptt) REVERT: E 619 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7734 (mp0) REVERT: F 568 LYS cc_start: 0.7061 (OUTLIER) cc_final: 0.6812 (mmtt) REVERT: F 619 GLU cc_start: 0.7715 (mp0) cc_final: 0.7503 (mp0) REVERT: F 627 MET cc_start: 0.8248 (tmm) cc_final: 0.7852 (tmm) REVERT: F 660 GLN cc_start: 0.8361 (tt0) cc_final: 0.7966 (tt0) REVERT: F 666 MET cc_start: 0.8789 (ptp) cc_final: 0.8527 (ptm) REVERT: F 724 GLU cc_start: 0.7361 (tt0) cc_final: 0.7140 (tt0) REVERT: F 732 GLU cc_start: 0.7634 (mm-30) cc_final: 0.7298 (mt-10) outliers start: 64 outliers final: 27 residues processed: 355 average time/residue: 1.4931 time to fit residues: 589.8171 Evaluate side-chains 321 residues out of total 2375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 281 time to evaluate : 2.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 689 TYR 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 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 724 GLU Chi-restraints excluded: chain B residue 744 LEU Chi-restraints excluded: chain C residue 329 ASN Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 408 GLN Chi-restraints excluded: chain C residue 472 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 611 LYS Chi-restraints excluded: chain C residue 668 GLU Chi-restraints excluded: chain C residue 673 ILE Chi-restraints excluded: chain C residue 687 LYS 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 556 LEU Chi-restraints excluded: chain D residue 557 GLU Chi-restraints excluded: chain D residue 669 LYS 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 E residue 335 ASP Chi-restraints excluded: chain E residue 380 MET Chi-restraints excluded: chain E residue 382 VAL Chi-restraints excluded: chain E residue 619 GLU Chi-restraints excluded: chain F residue 562 VAL Chi-restraints excluded: chain F residue 568 LYS Chi-restraints excluded: chain F residue 705 ILE Chi-restraints excluded: chain F residue 728 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 1 optimal weight: 50.0000 chunk 196 optimal weight: 10.0000 chunk 270 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 133 optimal weight: 0.9990 chunk 66 optimal weight: 8.9990 chunk 236 optimal weight: 9.9990 chunk 131 optimal weight: 0.9980 chunk 185 optimal weight: 0.2980 chunk 171 optimal weight: 0.9990 chunk 154 optimal weight: 7.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 472 GLN B 575 GLN B 667 ASN C 667 ASN E 667 ASN F 655 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 = 0.4051 r_free = 0.4051 target = 0.165410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.141836 restraints weight = 26376.882| |-----------------------------------------------------------------------------| r_work (start): 0.3735 rms_B_bonded: 2.09 r_work: 0.3618 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3475 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6995 moved from start: 0.3371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 19044 Z= 0.102 Angle : 0.542 11.128 25717 Z= 0.272 Chirality : 0.040 0.189 2915 Planarity : 0.004 0.043 3334 Dihedral : 9.101 166.641 2673 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.90 % Allowed : 16.54 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.17), residues: 2372 helix: -0.01 (0.15), residues: 1258 sheet: -1.11 (0.41), residues: 148 loop : -1.54 (0.20), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 583 HIS 0.003 0.001 HIS D 544 PHE 0.016 0.001 PHE C 638 TYR 0.021 0.001 TYR C 605 ARG 0.006 0.000 ARG C 624 Details of bonding type rmsd hydrogen bonds : bond 0.03357 ( 799) hydrogen bonds : angle 4.36604 ( 2340) metal coordination : bond 0.00095 ( 10) covalent geometry : bond 0.00229 (19031) covalent geometry : angle 0.54234 (25717) Misc. bond : bond 0.00052 ( 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 383 residues out of total 2375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 326 time to evaluate : 2.276 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: 0.3053 (tpp) cc_final: 0.0449 (pmm) REVERT: A 733 LYS cc_start: 0.7836 (mtpt) cc_final: 0.7012 (tptp) REVERT: B 370 ILE cc_start: 0.7604 (OUTLIER) cc_final: 0.7333 (mt) REVERT: B 402 CYS cc_start: 0.7794 (p) cc_final: 0.7450 (p) REVERT: B 404 LEU cc_start: 0.8021 (tt) cc_final: 0.7786 (tp) REVERT: B 433 GLN cc_start: 0.7694 (tp40) cc_final: 0.7489 (tm-30) REVERT: B 636 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.8005 (mm-30) REVERT: B 683 MET cc_start: 0.6187 (ptp) cc_final: 0.4783 (pmm) REVERT: C 328 LYS cc_start: 0.8648 (ttmm) cc_final: 0.8132 (mmmm) REVERT: C 408 GLN cc_start: 0.8211 (OUTLIER) cc_final: 0.5858 (mp10) REVERT: C 472 GLN cc_start: 0.8418 (OUTLIER) cc_final: 0.8064 (mt0) REVERT: C 547 GLN cc_start: 0.8193 (mt0) cc_final: 0.7977 (mt0) REVERT: C 636 GLU cc_start: 0.8084 (tt0) cc_final: 0.7838 (pt0) REVERT: C 666 MET cc_start: 0.8399 (mmt) cc_final: 0.7159 (mtt) REVERT: C 695 ARG cc_start: 0.7953 (ttp80) cc_final: 0.7520 (ttp80) REVERT: C 699 ASP cc_start: 0.7713 (m-30) cc_final: 0.7486 (m-30) REVERT: D 404 LEU cc_start: 0.8147 (tt) cc_final: 0.7893 (tp) REVERT: D 424 GLN cc_start: 0.7491 (mt0) cc_final: 0.7285 (mt0) REVERT: D 504 LYS cc_start: 0.8463 (mtpm) cc_final: 0.8165 (mttm) REVERT: D 543 LYS cc_start: 0.8678 (mttt) cc_final: 0.8433 (mtmm) REVERT: D 547 GLN cc_start: 0.8381 (mt0) cc_final: 0.8141 (mt0) REVERT: D 568 LYS cc_start: 0.8382 (OUTLIER) cc_final: 0.8174 (mttm) REVERT: D 573 TYR cc_start: 0.8381 (m-80) cc_final: 0.7975 (m-10) REVERT: D 624 ARG cc_start: 0.7952 (ttm-80) cc_final: 0.7601 (mtt-85) REVERT: D 687 LYS cc_start: 0.8601 (mttp) cc_final: 0.8383 (mttt) REVERT: D 734 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7100 (mt-10) REVERT: E 309 ASP cc_start: 0.8065 (m-30) cc_final: 0.7848 (m-30) REVERT: E 318 LEU cc_start: 0.8830 (mt) cc_final: 0.8582 (mp) REVERT: E 407 ASP cc_start: 0.7795 (t0) cc_final: 0.7579 (t0) REVERT: E 543 LYS cc_start: 0.8453 (mmtt) cc_final: 0.8066 (tptt) REVERT: E 619 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7629 (mp0) REVERT: E 669 LYS cc_start: 0.8817 (OUTLIER) cc_final: 0.8614 (mtpp) REVERT: F 619 GLU cc_start: 0.7816 (mp0) cc_final: 0.7591 (mp0) REVERT: F 627 MET cc_start: 0.8118 (tmm) cc_final: 0.7841 (tmm) REVERT: F 660 GLN cc_start: 0.8285 (tt0) cc_final: 0.7849 (tt0) REVERT: F 700 GLU cc_start: 0.8185 (mm-30) cc_final: 0.7965 (mm-30) REVERT: F 732 GLU cc_start: 0.7759 (mm-30) cc_final: 0.7443 (mt-10) REVERT: F 734 GLU cc_start: 0.7674 (mt-10) cc_final: 0.6845 (tm-30) outliers start: 57 outliers final: 11 residues processed: 358 average time/residue: 1.4179 time to fit residues: 566.7088 Evaluate side-chains 314 residues out of total 2375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 295 time to evaluate : 2.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 370 ILE Chi-restraints excluded: chain B residue 449 ILE 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 329 ASN Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 408 GLN Chi-restraints excluded: chain C residue 472 GLN Chi-restraints excluded: chain C residue 539 SER Chi-restraints excluded: chain D residue 457 ASP Chi-restraints excluded: chain D residue 553 ILE Chi-restraints excluded: chain D residue 568 LYS Chi-restraints excluded: chain D residue 734 GLU Chi-restraints excluded: chain D residue 739 ASN Chi-restraints excluded: chain E residue 619 GLU Chi-restraints excluded: chain E residue 669 LYS Chi-restraints excluded: chain F residue 728 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 178 optimal weight: 0.7980 chunk 282 optimal weight: 9.9990 chunk 244 optimal weight: 50.0000 chunk 256 optimal weight: 50.0000 chunk 140 optimal weight: 6.9990 chunk 55 optimal weight: 0.6980 chunk 43 optimal weight: 4.9990 chunk 278 optimal weight: 0.8980 chunk 254 optimal weight: 50.0000 chunk 264 optimal weight: 6.9990 chunk 218 optimal weight: 0.0570 overall best weight: 1.4900 ------------------------------------------------------------------------------- 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** C 663 GLN E 613 GLN E 663 GLN F 655 GLN F 667 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.164110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.140965 restraints weight = 26649.602| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 2.03 r_work: 0.3612 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3471 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6994 moved from start: 0.3580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19044 Z= 0.115 Angle : 0.549 10.308 25717 Z= 0.273 Chirality : 0.040 0.190 2915 Planarity : 0.004 0.065 3334 Dihedral : 8.899 169.989 2673 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.60 % Allowed : 17.71 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.17), residues: 2372 helix: 0.37 (0.15), residues: 1251 sheet: -1.05 (0.41), residues: 150 loop : -1.41 (0.20), residues: 971 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 583 HIS 0.005 0.001 HIS D 578 PHE 0.015 0.001 PHE C 638 TYR 0.021 0.001 TYR C 605 ARG 0.011 0.000 ARG E 534 Details of bonding type rmsd hydrogen bonds : bond 0.03336 ( 799) hydrogen bonds : angle 4.30191 ( 2340) metal coordination : bond 0.00154 ( 10) covalent geometry : bond 0.00268 (19031) covalent geometry : angle 0.54876 (25717) Misc. bond : bond 0.00081 ( 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 358 residues out of total 2375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 307 time to evaluate : 2.176 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 683 MET cc_start: 0.3279 (tpp) cc_final: 0.0611 (pmm) REVERT: A 733 LYS cc_start: 0.7816 (mtpt) cc_final: 0.7034 (tptp) REVERT: A 741 MET cc_start: 0.7439 (mmt) cc_final: 0.7072 (mmp) REVERT: B 370 ILE cc_start: 0.7573 (OUTLIER) cc_final: 0.7281 (mt) REVERT: B 402 CYS cc_start: 0.7829 (p) cc_final: 0.7489 (p) REVERT: B 404 LEU cc_start: 0.8017 (tt) cc_final: 0.7795 (tp) REVERT: B 636 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7974 (mm-30) REVERT: B 641 ARG cc_start: 0.8270 (OUTLIER) cc_final: 0.8043 (mtm180) REVERT: B 683 MET cc_start: 0.6082 (ptp) cc_final: 0.5665 (ttt) REVERT: C 408 GLN cc_start: 0.8228 (OUTLIER) cc_final: 0.5944 (mp10) REVERT: C 472 GLN cc_start: 0.8452 (OUTLIER) cc_final: 0.8097 (mt0) REVERT: C 547 GLN cc_start: 0.8141 (mt0) cc_final: 0.7913 (mt0) REVERT: C 666 MET cc_start: 0.8358 (mmt) cc_final: 0.7132 (mmt) REVERT: C 672 GLN cc_start: 0.8062 (mp10) cc_final: 0.7752 (mp10) REVERT: C 683 MET cc_start: 0.5608 (ttt) cc_final: 0.5292 (tmm) REVERT: C 695 ARG cc_start: 0.7984 (ttp80) cc_final: 0.7554 (ttp80) REVERT: C 699 ASP cc_start: 0.7685 (m-30) cc_final: 0.7474 (m-30) REVERT: D 404 LEU cc_start: 0.8149 (tt) cc_final: 0.7874 (tp) REVERT: D 503 ASP cc_start: 0.7743 (m-30) cc_final: 0.7334 (p0) REVERT: D 504 LYS cc_start: 0.8368 (mtpm) cc_final: 0.7712 (mttm) REVERT: D 543 LYS cc_start: 0.8646 (mttt) cc_final: 0.8421 (mtmm) REVERT: D 547 GLN cc_start: 0.8329 (mt0) cc_final: 0.8080 (mt0) REVERT: D 556 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8411 (tp) REVERT: D 568 LYS cc_start: 0.8404 (OUTLIER) cc_final: 0.8185 (mttm) REVERT: D 573 TYR cc_start: 0.8409 (m-80) cc_final: 0.8052 (m-80) REVERT: D 624 ARG cc_start: 0.7971 (ttm-80) cc_final: 0.7618 (mtt-85) REVERT: D 683 MET cc_start: 0.5518 (ptt) cc_final: 0.5242 (ptt) REVERT: E 309 ASP cc_start: 0.8071 (m-30) cc_final: 0.7836 (m-30) REVERT: E 318 LEU cc_start: 0.8848 (mt) cc_final: 0.8599 (mp) REVERT: E 407 ASP cc_start: 0.7601 (t0) cc_final: 0.7391 (t0) REVERT: E 543 LYS cc_start: 0.8526 (mmtt) cc_final: 0.8146 (tmtm) REVERT: E 619 GLU cc_start: 0.7888 (OUTLIER) cc_final: 0.7542 (mp0) REVERT: E 632 ARG cc_start: 0.8555 (OUTLIER) cc_final: 0.8313 (tpt170) REVERT: F 627 MET cc_start: 0.8115 (tmm) cc_final: 0.7889 (tmm) REVERT: F 660 GLN cc_start: 0.8350 (tt0) cc_final: 0.7921 (tt0) REVERT: F 732 GLU cc_start: 0.7696 (mm-30) cc_final: 0.7385 (mt-10) REVERT: F 734 GLU cc_start: 0.7699 (mt-10) cc_final: 0.6864 (tm-30) outliers start: 51 outliers final: 16 residues processed: 335 average time/residue: 1.4539 time to fit residues: 542.6934 Evaluate side-chains 301 residues out of total 2375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 276 time to evaluate : 2.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain B residue 370 ILE Chi-restraints excluded: chain B residue 449 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 329 ASN Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain C residue 408 GLN Chi-restraints excluded: chain C residue 472 GLN Chi-restraints excluded: chain C residue 539 SER Chi-restraints excluded: chain C residue 735 VAL Chi-restraints excluded: chain D residue 457 ASP Chi-restraints excluded: chain D residue 556 LEU Chi-restraints excluded: chain D residue 568 LYS Chi-restraints excluded: chain D residue 669 LYS 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 619 GLU Chi-restraints excluded: chain E residue 632 ARG Chi-restraints excluded: chain F residue 562 VAL Chi-restraints excluded: chain F residue 728 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 123 optimal weight: 5.9990 chunk 70 optimal weight: 9.9990 chunk 235 optimal weight: 1.9990 chunk 130 optimal weight: 7.9990 chunk 211 optimal weight: 6.9990 chunk 197 optimal weight: 5.9990 chunk 39 optimal weight: 0.2980 chunk 122 optimal weight: 20.0000 chunk 136 optimal weight: 0.7980 chunk 6 optimal weight: 50.0000 chunk 9 optimal weight: 50.0000 overall best weight: 3.0186 ------------------------------------------------------------------------------- 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** C 325 ASN C 332 GLN C 663 GLN ** D 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 663 GLN F 655 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 = 0.4000 r_free = 0.4000 target = 0.161397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.138347 restraints weight = 26604.760| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 1.83 r_work: 0.3565 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3419 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7061 moved from start: 0.3783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 19044 Z= 0.161 Angle : 0.595 12.561 25717 Z= 0.295 Chirality : 0.042 0.189 2915 Planarity : 0.004 0.054 3334 Dihedral : 8.959 175.312 2673 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 3.21 % Allowed : 18.22 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.18), residues: 2372 helix: 0.44 (0.15), residues: 1256 sheet: -1.04 (0.41), residues: 153 loop : -1.32 (0.20), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 583 HIS 0.007 0.002 HIS C 578 PHE 0.019 0.002 PHE D 638 TYR 0.021 0.002 TYR C 605 ARG 0.007 0.001 ARG C 624 Details of bonding type rmsd hydrogen bonds : bond 0.03769 ( 799) hydrogen bonds : angle 4.35056 ( 2340) metal coordination : bond 0.00336 ( 10) covalent geometry : bond 0.00387 (19031) covalent geometry : angle 0.59508 (25717) Misc. bond : bond 0.00145 ( 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 340 residues out of total 2375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 277 time to evaluate : 2.245 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: 0.3327 (tpp) cc_final: 0.0607 (pmm) REVERT: A 733 LYS cc_start: 0.7898 (mtpt) cc_final: 0.7061 (tptp) REVERT: A 741 MET cc_start: 0.7479 (mmt) cc_final: 0.7072 (mmp) REVERT: B 370 ILE cc_start: 0.7600 (OUTLIER) cc_final: 0.7388 (mt) REVERT: B 402 CYS cc_start: 0.7868 (p) cc_final: 0.7608 (p) REVERT: B 404 LEU cc_start: 0.8127 (tt) cc_final: 0.7911 (tp) REVERT: B 433 GLN cc_start: 0.7583 (tm-30) cc_final: 0.7219 (tm-30) REVERT: B 458 ILE cc_start: 0.8951 (OUTLIER) cc_final: 0.8549 (pt) REVERT: B 465 ARG cc_start: 0.6055 (mtt-85) cc_final: 0.5615 (tpt170) REVERT: B 469 PHE cc_start: 0.8326 (m-10) cc_final: 0.8027 (m-10) REVERT: B 501 GLU cc_start: 0.7082 (pm20) cc_final: 0.6852 (pm20) REVERT: B 601 LYS cc_start: 0.7904 (OUTLIER) cc_final: 0.7627 (mttt) REVERT: B 636 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7967 (mm-30) REVERT: B 641 ARG cc_start: 0.8358 (OUTLIER) cc_final: 0.8033 (mtm-85) REVERT: B 683 MET cc_start: 0.6174 (ptp) cc_final: 0.5749 (ttt) REVERT: C 408 GLN cc_start: 0.8267 (OUTLIER) cc_final: 0.6082 (mp10) REVERT: C 472 GLN cc_start: 0.8468 (OUTLIER) cc_final: 0.8159 (mt0) REVERT: C 611 LYS cc_start: 0.8320 (OUTLIER) cc_final: 0.7825 (mttp) REVERT: C 683 MET cc_start: 0.6288 (ttt) cc_final: 0.5853 (tmm) REVERT: C 695 ARG cc_start: 0.8042 (ttp80) cc_final: 0.7614 (ttp80) REVERT: C 699 ASP cc_start: 0.7714 (m-30) cc_final: 0.7492 (m-30) REVERT: C 777 LYS cc_start: 0.8211 (OUTLIER) cc_final: 0.7725 (mptm) REVERT: D 333 TYR cc_start: 0.8540 (m-80) cc_final: 0.8243 (m-80) REVERT: D 404 LEU cc_start: 0.8204 (tt) cc_final: 0.7912 (tp) REVERT: D 556 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8483 (tp) REVERT: D 568 LYS cc_start: 0.8400 (OUTLIER) cc_final: 0.8198 (mttm) REVERT: D 624 ARG cc_start: 0.7994 (ttm-80) cc_final: 0.7632 (mtt-85) REVERT: D 734 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.7167 (mt-10) REVERT: E 309 ASP cc_start: 0.8074 (m-30) cc_final: 0.7852 (m-30) REVERT: E 318 LEU cc_start: 0.8888 (mt) cc_final: 0.8633 (mp) REVERT: E 407 ASP cc_start: 0.7607 (t0) cc_final: 0.7387 (t0) REVERT: E 415 LYS cc_start: 0.8399 (tttt) cc_final: 0.8118 (ttmm) REVERT: E 516 PHE cc_start: 0.8322 (m-80) cc_final: 0.8056 (m-80) REVERT: E 543 LYS cc_start: 0.8516 (mmtt) cc_final: 0.8120 (tptt) REVERT: E 619 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7718 (mp0) REVERT: F 627 MET cc_start: 0.8119 (tmm) cc_final: 0.7884 (tmm) REVERT: F 660 GLN cc_start: 0.8446 (tt0) cc_final: 0.8052 (tt0) REVERT: F 669 LYS cc_start: 0.7860 (OUTLIER) cc_final: 0.7512 (tttp) REVERT: F 732 GLU cc_start: 0.7799 (mm-30) cc_final: 0.7441 (mt-10) outliers start: 63 outliers final: 23 residues processed: 308 average time/residue: 1.4505 time to fit residues: 498.5290 Evaluate side-chains 302 residues out of total 2375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 265 time to evaluate : 2.127 ------------------------------------------------------------------------------- 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 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 601 LYS 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 329 ASN Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain C residue 408 GLN Chi-restraints excluded: chain C residue 472 GLN Chi-restraints excluded: chain C residue 538 ASP Chi-restraints excluded: chain C residue 539 SER Chi-restraints excluded: chain C residue 611 LYS Chi-restraints excluded: chain C residue 735 VAL 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 541 ASN Chi-restraints excluded: chain D residue 556 LEU Chi-restraints excluded: chain D residue 568 LYS 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 553 ILE Chi-restraints excluded: chain E residue 619 GLU Chi-restraints excluded: chain E residue 729 LEU Chi-restraints excluded: chain F residue 666 MET Chi-restraints excluded: chain F residue 669 LYS 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 114 optimal weight: 5.9990 chunk 80 optimal weight: 9.9990 chunk 274 optimal weight: 6.9990 chunk 159 optimal weight: 5.9990 chunk 211 optimal weight: 20.0000 chunk 222 optimal weight: 10.0000 chunk 136 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 chunk 110 optimal weight: 0.8980 chunk 111 optimal weight: 5.9990 chunk 55 optimal weight: 0.0970 overall best weight: 2.9984 ------------------------------------------------------------------------------- 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** C 587 HIS C 667 ASN ** D 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 663 GLN F 667 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.161261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.138193 restraints weight = 26499.479| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 1.85 r_work: 0.3561 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3417 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7057 moved from start: 0.3953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 19044 Z= 0.156 Angle : 0.591 12.575 25717 Z= 0.292 Chirality : 0.042 0.153 2915 Planarity : 0.004 0.050 3334 Dihedral : 8.893 179.636 2673 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.05 % Allowed : 18.98 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.18), residues: 2372 helix: 0.56 (0.15), residues: 1257 sheet: -0.97 (0.42), residues: 144 loop : -1.27 (0.20), residues: 971 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 583 HIS 0.006 0.001 HIS D 574 PHE 0.017 0.002 PHE D 638 TYR 0.025 0.002 TYR D 605 ARG 0.007 0.001 ARG C 624 Details of bonding type rmsd hydrogen bonds : bond 0.03657 ( 799) hydrogen bonds : angle 4.31475 ( 2340) metal coordination : bond 0.00302 ( 10) covalent geometry : bond 0.00379 (19031) covalent geometry : angle 0.59091 (25717) Misc. bond : bond 0.00140 ( 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 341 residues out of total 2375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 281 time to evaluate : 2.107 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: 0.3189 (tpp) cc_final: 0.0516 (pmm) REVERT: A 733 LYS cc_start: 0.7876 (mtpt) cc_final: 0.7090 (tptp) REVERT: B 404 LEU cc_start: 0.8050 (tt) cc_final: 0.7843 (tp) REVERT: B 433 GLN cc_start: 0.7804 (tm-30) cc_final: 0.7418 (tm-30) REVERT: B 458 ILE cc_start: 0.8990 (OUTLIER) cc_final: 0.8567 (pt) REVERT: B 465 ARG cc_start: 0.6055 (mtt-85) cc_final: 0.5505 (tpt170) REVERT: B 469 PHE cc_start: 0.8280 (m-10) cc_final: 0.7958 (m-10) REVERT: B 601 LYS cc_start: 0.7969 (OUTLIER) cc_final: 0.7673 (mttt) REVERT: B 636 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7987 (mm-30) REVERT: B 641 ARG cc_start: 0.8324 (OUTLIER) cc_final: 0.7993 (mtm-85) REVERT: B 683 MET cc_start: 0.6229 (ptp) cc_final: 0.5788 (ttt) REVERT: C 408 GLN cc_start: 0.8231 (OUTLIER) cc_final: 0.6131 (mp10) REVERT: C 472 GLN cc_start: 0.8444 (OUTLIER) cc_final: 0.8146 (mt0) REVERT: C 611 LYS cc_start: 0.8355 (OUTLIER) cc_final: 0.7848 (mttp) REVERT: C 683 MET cc_start: 0.6264 (ttt) cc_final: 0.5723 (tmm) REVERT: C 695 ARG cc_start: 0.8051 (ttp80) cc_final: 0.7609 (ttp80) REVERT: C 699 ASP cc_start: 0.7682 (m-30) cc_final: 0.7476 (m-30) REVERT: D 333 TYR cc_start: 0.8568 (m-80) cc_final: 0.8251 (m-80) REVERT: D 404 LEU cc_start: 0.8187 (tt) cc_final: 0.7885 (tp) REVERT: D 624 ARG cc_start: 0.7979 (ttm-80) cc_final: 0.7619 (mtt-85) REVERT: D 683 MET cc_start: 0.5373 (ptt) cc_final: 0.5159 (ptt) REVERT: D 734 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7174 (mt-10) REVERT: E 309 ASP cc_start: 0.8051 (m-30) cc_final: 0.7791 (m-30) REVERT: E 318 LEU cc_start: 0.8862 (mt) cc_final: 0.8594 (mp) REVERT: E 415 LYS cc_start: 0.8396 (tttt) cc_final: 0.8125 (ttmm) REVERT: E 516 PHE cc_start: 0.8389 (m-80) cc_final: 0.8165 (m-80) REVERT: E 543 LYS cc_start: 0.8619 (mmtt) cc_final: 0.8202 (tptt) REVERT: E 619 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7714 (mp0) REVERT: F 627 MET cc_start: 0.8141 (tmm) cc_final: 0.7766 (tmm) REVERT: F 660 GLN cc_start: 0.8427 (tt0) cc_final: 0.8012 (tt0) REVERT: F 669 LYS cc_start: 0.7893 (OUTLIER) cc_final: 0.7559 (tttp) REVERT: F 732 GLU cc_start: 0.7788 (mm-30) cc_final: 0.7411 (mt-10) REVERT: F 734 GLU cc_start: 0.7737 (mt-10) cc_final: 0.6912 (tm-30) outliers start: 60 outliers final: 28 residues processed: 316 average time/residue: 1.5418 time to fit residues: 546.6044 Evaluate side-chains 319 residues out of total 2375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 281 time to evaluate : 2.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 684 VAL 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 601 LYS 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 329 ASN Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain C residue 408 GLN Chi-restraints excluded: chain C residue 472 GLN Chi-restraints excluded: chain C residue 538 ASP Chi-restraints excluded: chain C residue 539 SER Chi-restraints excluded: chain C residue 611 LYS Chi-restraints excluded: chain C residue 687 LYS Chi-restraints excluded: chain C residue 735 VAL Chi-restraints excluded: chain D residue 371 THR 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 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 525 CYS Chi-restraints excluded: chain E residue 619 GLU Chi-restraints excluded: chain E residue 729 LEU Chi-restraints excluded: chain F residue 562 VAL Chi-restraints excluded: chain F residue 637 ILE Chi-restraints excluded: chain F residue 648 ASP Chi-restraints excluded: chain F residue 656 SER Chi-restraints excluded: chain F residue 669 LYS Chi-restraints excluded: chain F residue 705 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 261 optimal weight: 50.0000 chunk 187 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 chunk 132 optimal weight: 20.0000 chunk 15 optimal weight: 50.0000 chunk 176 optimal weight: 7.9990 chunk 271 optimal weight: 9.9990 chunk 50 optimal weight: 8.9990 chunk 179 optimal weight: 3.9990 chunk 64 optimal weight: 7.9990 chunk 231 optimal weight: 0.9980 overall best weight: 4.7988 ------------------------------------------------------------------------------- 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** ** C 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 442 ASN E 663 GLN F 667 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.158606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.135368 restraints weight = 26636.314| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 2.03 r_work: 0.3523 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3379 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7078 moved from start: 0.4147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 19044 Z= 0.226 Angle : 0.680 13.341 25717 Z= 0.334 Chirality : 0.045 0.169 2915 Planarity : 0.005 0.050 3334 Dihedral : 8.960 174.189 2673 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.90 % Allowed : 19.24 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.17), residues: 2372 helix: 0.39 (0.15), residues: 1259 sheet: -1.08 (0.41), residues: 143 loop : -1.33 (0.20), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP F 583 HIS 0.008 0.002 HIS C 578 PHE 0.022 0.002 PHE C 750 TYR 0.028 0.002 TYR D 573 ARG 0.015 0.001 ARG E 483 Details of bonding type rmsd hydrogen bonds : bond 0.04198 ( 799) hydrogen bonds : angle 4.47807 ( 2340) metal coordination : bond 0.00516 ( 10) covalent geometry : bond 0.00553 (19031) covalent geometry : angle 0.67973 (25717) Misc. bond : bond 0.00226 ( 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 338 residues out of total 2375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 281 time to evaluate : 2.310 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: 0.3621 (tpp) cc_final: 0.0685 (pmm) REVERT: A 733 LYS cc_start: 0.7887 (mtpt) cc_final: 0.7087 (tptp) REVERT: B 433 GLN cc_start: 0.7809 (tm-30) cc_final: 0.7380 (tm-30) REVERT: B 458 ILE cc_start: 0.8963 (OUTLIER) cc_final: 0.8534 (pt) REVERT: B 465 ARG cc_start: 0.6007 (mtt-85) cc_final: 0.5550 (tpt170) REVERT: B 601 LYS cc_start: 0.8104 (OUTLIER) cc_final: 0.7738 (mttt) REVERT: B 641 ARG cc_start: 0.8382 (OUTLIER) cc_final: 0.8069 (mtm-85) REVERT: B 683 MET cc_start: 0.6295 (ptp) cc_final: 0.5796 (ttt) REVERT: C 408 GLN cc_start: 0.8267 (OUTLIER) cc_final: 0.6118 (mp10) REVERT: C 472 GLN cc_start: 0.8462 (OUTLIER) cc_final: 0.8182 (mt0) REVERT: C 611 LYS cc_start: 0.8391 (OUTLIER) cc_final: 0.7868 (mttp) REVERT: C 683 MET cc_start: 0.6362 (ttt) cc_final: 0.5868 (tmm) REVERT: C 695 ARG cc_start: 0.8124 (ttp80) cc_final: 0.7712 (ttp80) REVERT: C 699 ASP cc_start: 0.7736 (m-30) cc_final: 0.7507 (m-30) REVERT: D 333 TYR cc_start: 0.8674 (m-80) cc_final: 0.8348 (m-80) REVERT: D 556 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8211 (mt) REVERT: D 766 LEU cc_start: 0.7985 (tm) cc_final: 0.7619 (tp) REVERT: D 767 ASP cc_start: 0.7911 (m-30) cc_final: 0.7707 (m-30) REVERT: E 309 ASP cc_start: 0.7923 (m-30) cc_final: 0.7468 (m-30) REVERT: E 331 LYS cc_start: 0.7987 (tttm) cc_final: 0.7759 (pmtt) REVERT: E 375 SER cc_start: 0.8486 (p) cc_final: 0.7916 (m) REVERT: E 407 ASP cc_start: 0.7585 (t0) cc_final: 0.7375 (t0) REVERT: E 415 LYS cc_start: 0.8346 (tttt) cc_final: 0.8064 (ttmm) REVERT: E 523 ASN cc_start: 0.6725 (m110) cc_final: 0.6401 (m110) REVERT: E 543 LYS cc_start: 0.8610 (mmtt) cc_final: 0.8138 (tptt) REVERT: E 619 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7823 (mp0) REVERT: F 627 MET cc_start: 0.8037 (tmm) cc_final: 0.7615 (tmm) REVERT: F 660 GLN cc_start: 0.8400 (tt0) cc_final: 0.8033 (tt0) REVERT: F 732 GLU cc_start: 0.7861 (mm-30) cc_final: 0.7451 (mt-10) REVERT: F 734 GLU cc_start: 0.7673 (mt-10) cc_final: 0.6604 (pm20) REVERT: F 744 LEU cc_start: 0.7138 (OUTLIER) cc_final: 0.6471 (mp) outliers start: 57 outliers final: 35 residues processed: 310 average time/residue: 1.6875 time to fit residues: 586.7131 Evaluate side-chains 308 residues out of total 2375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 264 time to evaluate : 2.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 684 VAL 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 562 VAL Chi-restraints excluded: chain B residue 601 LYS 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 329 ASN Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 408 GLN Chi-restraints excluded: chain C residue 472 GLN Chi-restraints excluded: chain C residue 538 ASP Chi-restraints excluded: chain C residue 539 SER 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 D residue 371 THR Chi-restraints excluded: chain D residue 453 THR Chi-restraints excluded: chain D residue 457 ASP 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 556 LEU Chi-restraints excluded: chain D residue 669 LYS Chi-restraints excluded: chain D residue 739 ASN Chi-restraints excluded: chain D residue 772 LEU Chi-restraints excluded: chain E residue 619 GLU Chi-restraints excluded: chain E residue 676 ASP Chi-restraints excluded: chain E residue 729 LEU Chi-restraints excluded: chain E residue 736 LEU Chi-restraints excluded: chain F residue 562 VAL Chi-restraints excluded: chain F residue 592 LEU Chi-restraints excluded: chain F residue 637 ILE Chi-restraints excluded: chain F residue 648 ASP Chi-restraints excluded: chain F residue 656 SER Chi-restraints excluded: chain F residue 666 MET Chi-restraints excluded: chain F residue 705 ILE Chi-restraints excluded: chain F residue 744 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 199 optimal weight: 10.0000 chunk 6 optimal weight: 50.0000 chunk 153 optimal weight: 7.9990 chunk 145 optimal weight: 3.9990 chunk 167 optimal weight: 7.9990 chunk 131 optimal weight: 0.0010 chunk 282 optimal weight: 3.9990 chunk 215 optimal weight: 5.9990 chunk 120 optimal weight: 2.9990 chunk 119 optimal weight: 0.9980 chunk 0 optimal weight: 50.0000 overall best weight: 2.3992 ------------------------------------------------------------------------------- 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** ** 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 = 0.3985 r_free = 0.3985 target = 0.160347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.137060 restraints weight = 26813.161| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 2.04 r_work: 0.3553 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3411 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7045 moved from start: 0.4258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 19044 Z= 0.144 Angle : 0.605 14.070 25717 Z= 0.299 Chirality : 0.042 0.149 2915 Planarity : 0.004 0.046 3334 Dihedral : 8.472 169.861 2673 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.24 % Allowed : 20.15 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.18), residues: 2372 helix: 0.70 (0.15), residues: 1255 sheet: -1.11 (0.42), residues: 137 loop : -1.28 (0.20), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 583 HIS 0.005 0.001 HIS D 578 PHE 0.044 0.002 PHE B 469 TYR 0.020 0.002 TYR D 605 ARG 0.014 0.001 ARG E 483 Details of bonding type rmsd hydrogen bonds : bond 0.03597 ( 799) hydrogen bonds : angle 4.36068 ( 2340) metal coordination : bond 0.00245 ( 10) covalent geometry : bond 0.00347 (19031) covalent geometry : angle 0.60536 (25717) Misc. bond : bond 0.00168 ( 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 317 residues out of total 2375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 273 time to evaluate : 2.176 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: 0.3305 (tpp) cc_final: 0.0578 (pmm) REVERT: B 433 GLN cc_start: 0.7792 (tm-30) cc_final: 0.7473 (tm-30) REVERT: B 458 ILE cc_start: 0.8966 (OUTLIER) cc_final: 0.8527 (pt) REVERT: B 465 ARG cc_start: 0.6101 (mtt-85) cc_final: 0.5592 (tpt170) REVERT: B 601 LYS cc_start: 0.8085 (OUTLIER) cc_final: 0.7755 (mttt) REVERT: B 641 ARG cc_start: 0.8317 (OUTLIER) cc_final: 0.8070 (mtm180) REVERT: B 666 MET cc_start: 0.8051 (OUTLIER) cc_final: 0.6898 (mtt) REVERT: B 683 MET cc_start: 0.6284 (ptp) cc_final: 0.5723 (ttt) REVERT: C 408 GLN cc_start: 0.8238 (OUTLIER) cc_final: 0.6149 (mp10) REVERT: C 472 GLN cc_start: 0.8436 (OUTLIER) cc_final: 0.8151 (mt0) REVERT: C 611 LYS cc_start: 0.8365 (OUTLIER) cc_final: 0.7878 (mttp) REVERT: C 624 ARG cc_start: 0.7723 (ttm-80) cc_final: 0.6975 (mpt180) REVERT: C 683 MET cc_start: 0.6359 (ttt) cc_final: 0.5870 (tmm) REVERT: C 695 ARG cc_start: 0.8064 (ttp80) cc_final: 0.7588 (ttp80) REVERT: C 699 ASP cc_start: 0.7648 (m-30) cc_final: 0.7428 (m-30) REVERT: D 333 TYR cc_start: 0.8612 (m-80) cc_final: 0.8275 (m-80) REVERT: D 556 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.8177 (mt) REVERT: D 624 ARG cc_start: 0.7923 (ttm-80) cc_final: 0.7571 (mtt-85) REVERT: E 309 ASP cc_start: 0.7927 (m-30) cc_final: 0.7503 (m-30) REVERT: E 415 LYS cc_start: 0.8380 (tttt) cc_final: 0.8101 (ttmm) REVERT: E 517 SER cc_start: 0.7670 (p) cc_final: 0.7448 (m) REVERT: E 530 LEU cc_start: 0.7885 (mp) cc_final: 0.7647 (pp) REVERT: E 543 LYS cc_start: 0.8615 (mmtt) cc_final: 0.8158 (tmtm) REVERT: E 619 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7723 (mp0) REVERT: F 627 MET cc_start: 0.8069 (tmm) cc_final: 0.7678 (tmm) REVERT: F 660 GLN cc_start: 0.8379 (tt0) cc_final: 0.7979 (tt0) REVERT: F 732 GLU cc_start: 0.7772 (mm-30) cc_final: 0.7530 (mt-10) REVERT: F 734 GLU cc_start: 0.7666 (mt-10) cc_final: 0.6595 (pm20) outliers start: 44 outliers final: 25 residues processed: 299 average time/residue: 1.3928 time to fit residues: 464.9597 Evaluate side-chains 292 residues out of total 2375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 258 time to evaluate : 2.108 ------------------------------------------------------------------------------- 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 556 LEU Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain B residue 601 LYS Chi-restraints excluded: chain B residue 641 ARG Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 666 MET Chi-restraints excluded: chain B residue 744 LEU Chi-restraints excluded: chain C residue 329 ASN Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 408 GLN Chi-restraints excluded: chain C residue 472 GLN Chi-restraints excluded: chain C residue 538 ASP Chi-restraints excluded: chain C residue 539 SER Chi-restraints excluded: chain C residue 611 LYS Chi-restraints excluded: chain C residue 687 LYS Chi-restraints excluded: chain D residue 371 THR 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 556 LEU Chi-restraints excluded: chain D residue 669 LYS Chi-restraints excluded: chain D residue 739 ASN Chi-restraints excluded: chain E residue 619 GLU Chi-restraints excluded: chain E residue 729 LEU Chi-restraints excluded: chain F residue 562 VAL Chi-restraints excluded: chain F residue 648 ASP Chi-restraints excluded: chain F residue 656 SER Chi-restraints excluded: chain F residue 666 MET Chi-restraints excluded: chain F residue 705 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 162 optimal weight: 9.9990 chunk 185 optimal weight: 9.9990 chunk 157 optimal weight: 8.9990 chunk 54 optimal weight: 0.9980 chunk 237 optimal weight: 50.0000 chunk 244 optimal weight: 50.0000 chunk 56 optimal weight: 8.9990 chunk 233 optimal weight: 0.9980 chunk 154 optimal weight: 4.9990 chunk 61 optimal weight: 8.9990 chunk 38 optimal weight: 0.2980 overall best weight: 3.2584 ------------------------------------------------------------------------------- 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** ** C 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 667 ASN 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 = 0.3985 r_free = 0.3985 target = 0.160498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.137228 restraints weight = 26824.419| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 1.95 r_work: 0.3551 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3409 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7047 moved from start: 0.4354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 19044 Z= 0.170 Angle : 0.629 13.977 25717 Z= 0.310 Chirality : 0.043 0.156 2915 Planarity : 0.004 0.049 3334 Dihedral : 8.319 167.505 2673 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.19 % Allowed : 20.71 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.18), residues: 2372 helix: 0.73 (0.15), residues: 1251 sheet: -1.00 (0.42), residues: 144 loop : -1.30 (0.20), residues: 977 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 583 HIS 0.006 0.001 HIS C 578 PHE 0.047 0.002 PHE B 469 TYR 0.029 0.002 TYR D 605 ARG 0.014 0.001 ARG E 483 Details of bonding type rmsd hydrogen bonds : bond 0.03736 ( 799) hydrogen bonds : angle 4.40607 ( 2340) metal coordination : bond 0.00332 ( 10) covalent geometry : bond 0.00412 (19031) covalent geometry : angle 0.62858 (25717) Misc. bond : bond 0.00215 ( 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 312 residues out of total 2375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 269 time to evaluate : 2.123 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: 0.3310 (tpp) cc_final: 0.0598 (pmm) REVERT: A 734 GLU cc_start: 0.7321 (tm-30) cc_final: 0.7077 (tm-30) REVERT: A 741 MET cc_start: 0.7091 (mmp) cc_final: 0.6718 (mmt) REVERT: B 433 GLN cc_start: 0.7975 (tm-30) cc_final: 0.7700 (tm-30) REVERT: B 458 ILE cc_start: 0.8931 (OUTLIER) cc_final: 0.8533 (pt) REVERT: B 465 ARG cc_start: 0.6064 (mtt-85) cc_final: 0.5552 (mmt180) REVERT: B 601 LYS cc_start: 0.8079 (OUTLIER) cc_final: 0.7844 (mttt) REVERT: B 641 ARG cc_start: 0.8301 (OUTLIER) cc_final: 0.7919 (mtm-85) REVERT: B 666 MET cc_start: 0.8074 (OUTLIER) cc_final: 0.6895 (mtt) REVERT: B 673 ILE cc_start: 0.8587 (OUTLIER) cc_final: 0.8386 (pp) REVERT: B 683 MET cc_start: 0.6304 (ptp) cc_final: 0.5808 (ttt) REVERT: C 408 GLN cc_start: 0.8238 (OUTLIER) cc_final: 0.6155 (mp10) REVERT: C 472 GLN cc_start: 0.8382 (OUTLIER) cc_final: 0.8101 (mt0) REVERT: C 564 GLN cc_start: 0.7604 (OUTLIER) cc_final: 0.6916 (mm-40) REVERT: C 611 LYS cc_start: 0.8363 (OUTLIER) cc_final: 0.7875 (mttp) REVERT: C 624 ARG cc_start: 0.7731 (ttm-80) cc_final: 0.6984 (mpt180) REVERT: C 683 MET cc_start: 0.6369 (ttt) cc_final: 0.5930 (tmm) REVERT: C 695 ARG cc_start: 0.8047 (ttp80) cc_final: 0.7601 (ttp80) REVERT: C 699 ASP cc_start: 0.7691 (m-30) cc_final: 0.7453 (m-30) REVERT: D 333 TYR cc_start: 0.8637 (m-80) cc_final: 0.8246 (m-80) REVERT: D 404 LEU cc_start: 0.8106 (OUTLIER) cc_final: 0.7564 (mt) REVERT: D 624 ARG cc_start: 0.7930 (ttm-80) cc_final: 0.7596 (mtt-85) REVERT: E 309 ASP cc_start: 0.7962 (m-30) cc_final: 0.7559 (m-30) REVERT: E 415 LYS cc_start: 0.8381 (tttt) cc_final: 0.8080 (ttmm) REVERT: E 523 ASN cc_start: 0.6830 (m110) cc_final: 0.6520 (m110) REVERT: E 530 LEU cc_start: 0.7911 (mp) cc_final: 0.7685 (pp) REVERT: E 543 LYS cc_start: 0.8584 (mmtt) cc_final: 0.8112 (tmtm) REVERT: E 619 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7824 (mp0) REVERT: F 627 MET cc_start: 0.8064 (tmm) cc_final: 0.7688 (tmm) REVERT: F 660 GLN cc_start: 0.8387 (tt0) cc_final: 0.7949 (tt0) REVERT: F 666 MET cc_start: 0.8842 (OUTLIER) cc_final: 0.8406 (mtp) REVERT: F 732 GLU cc_start: 0.7671 (mm-30) cc_final: 0.7445 (mt-10) REVERT: F 734 GLU cc_start: 0.7403 (mt-10) cc_final: 0.6462 (pm20) outliers start: 43 outliers final: 27 residues processed: 294 average time/residue: 1.3326 time to fit residues: 439.4568 Evaluate side-chains 301 residues out of total 2375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 262 time to evaluate : 2.112 ------------------------------------------------------------------------------- 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 556 LEU Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain B residue 601 LYS Chi-restraints excluded: chain B residue 641 ARG Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 666 MET Chi-restraints excluded: chain B residue 673 ILE Chi-restraints excluded: chain B residue 744 LEU Chi-restraints excluded: chain C residue 329 ASN Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 408 GLN Chi-restraints excluded: chain C residue 410 ASP Chi-restraints excluded: chain C residue 472 GLN Chi-restraints excluded: chain C residue 538 ASP Chi-restraints excluded: chain C residue 539 SER Chi-restraints excluded: chain C residue 564 GLN 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 D residue 371 THR Chi-restraints excluded: chain D residue 404 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 541 ASN Chi-restraints excluded: chain D residue 669 LYS Chi-restraints excluded: chain D residue 739 ASN Chi-restraints excluded: chain E residue 619 GLU Chi-restraints excluded: chain E residue 729 LEU Chi-restraints excluded: chain F residue 562 VAL Chi-restraints excluded: chain F residue 648 ASP Chi-restraints excluded: chain F residue 656 SER Chi-restraints excluded: chain F residue 666 MET Chi-restraints excluded: chain F residue 705 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 24 optimal weight: 3.9990 chunk 264 optimal weight: 7.9990 chunk 188 optimal weight: 3.9990 chunk 195 optimal weight: 0.8980 chunk 266 optimal weight: 0.9980 chunk 56 optimal weight: 9.9990 chunk 10 optimal weight: 50.0000 chunk 208 optimal weight: 1.9990 chunk 153 optimal weight: 0.0040 chunk 5 optimal weight: 50.0000 chunk 83 optimal weight: 0.9990 overall best weight: 0.9796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4021 r_free = 0.4021 target = 0.163346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.139910 restraints weight = 26855.336| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 2.12 r_work: 0.3587 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3444 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6995 moved from start: 0.4442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 19044 Z= 0.105 Angle : 0.571 13.407 25717 Z= 0.281 Chirality : 0.040 0.153 2915 Planarity : 0.004 0.042 3334 Dihedral : 7.928 158.719 2673 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.88 % Allowed : 21.07 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.18), residues: 2372 helix: 1.06 (0.15), residues: 1256 sheet: -0.81 (0.43), residues: 137 loop : -1.20 (0.20), residues: 979 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 583 HIS 0.004 0.001 HIS D 578 PHE 0.034 0.001 PHE B 469 TYR 0.024 0.001 TYR D 605 ARG 0.011 0.001 ARG E 483 Details of bonding type rmsd hydrogen bonds : bond 0.03129 ( 799) hydrogen bonds : angle 4.25777 ( 2340) metal coordination : bond 0.00119 ( 10) covalent geometry : bond 0.00241 (19031) covalent geometry : angle 0.57062 (25717) Misc. bond : bond 0.00140 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15111.16 seconds wall clock time: 261 minutes 29.90 seconds (15689.90 seconds total)