Starting phenix.real_space_refine on Sat Sep 12 22:26:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6nyy_0552/09_2026/6nyy_0552.cif Found real_map, /net/cci-nas-00/data/ceres_data/6nyy_0552/09_2026/6nyy_0552.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6nyy_0552/09_2026/6nyy_0552.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6nyy_0552/09_2026/6nyy_0552.map" model { file = "/net/cci-nas-00/data/ceres_data/6nyy_0552/09_2026/6nyy_0552.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6nyy_0552/09_2026/6nyy_0552.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6nyy_0552/09_2026/6nyy_0552.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6nyy_0552/09_2026/6nyy_0552.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.010 sd= 0.024 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 6 6.06 5 P 11 5.49 5 Mg 3 5.21 5 S 60 5.16 5 C 12356 2.51 5 N 3221 2.21 5 O 3569 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19226 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 2038 Classifications: {'peptide': 459} Incomplete info: {'c_alpha_only': 231, 'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 436} Unresolved chain links: 231 Unresolved chain link angles: 707 Unresolved chain link dihedrals: 693 Unresolved non-hydrogen bonds: 1564 Unresolved non-hydrogen angles: 1718 Unresolved non-hydrogen dihedrals: 533 Unresolved non-hydrogen chiralities: 281 Planarities with less than four sites: {'PHE:plan': 14, 'GLU:plan': 13, 'ASP:plan': 15, 'ASN:plan1': 10, 'GLN:plan1': 7, 'TYR:plan': 1, 'ARG:plan': 12, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 352 Chain: "B" Number of atoms: 3786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 3786 Classifications: {'peptide': 487} Link IDs: {'PTRANS': 23, 'TRANS': 463} Chain breaks: 1 Chain: "C" Number of atoms: 3818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3818 Classifications: {'peptide': 491} Link IDs: {'PTRANS': 23, 'TRANS': 467} Chain: "D" Number of atoms: 3818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3818 Classifications: {'peptide': 491} Link IDs: {'PTRANS': 23, 'TRANS': 467} Chain: "E" Number of atoms: 3640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3640 Classifications: {'peptide': 467} Link IDs: {'PTRANS': 21, 'TRANS': 445} Chain breaks: 1 Chain: "F" Number of atoms: 1802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 1802 Classifications: {'peptide': 460} Incomplete info: {'c_alpha_only': 267} Link IDs: {'PTRANS': 22, 'TRANS': 437} Unresolved chain links: 267 Unresolved chain link angles: 815 Unresolved chain link dihedrals: 801 Unresolved non-hydrogen bonds: 1809 Unresolved non-hydrogen angles: 1988 Unresolved non-hydrogen dihedrals: 615 Unresolved non-hydrogen chiralities: 324 Planarities with less than four sites: {'PHE:plan': 15, 'GLU:plan': 17, 'ASP:plan': 16, 'ASN:plan1': 12, 'GLN:plan1': 10, 'TYR:plan': 1, 'ARG:plan': 14, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 421 Chain: "G" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 55 Classifications: {'peptide': 11} Link IDs: {'TRANS': 10} Chain: "H" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 55 Classifications: {'peptide': 11} Link IDs: {'TRANS': 10} Chain: "I" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 45 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Chain: "J" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 40 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' ZN': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.98, per 1000 atoms: 0.26 Number of scatterers: 19226 At special positions: 0 Unit cell: (140.3, 135.7, 100.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 6 29.99 S 60 16.00 P 11 15.00 Mg 3 11.99 O 3569 8.00 N 3221 7.00 C 12356 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.16 Conformation dependent library (CDL) restraints added in 550.0 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 801 " pdb="ZN ZN A 801 " - pdb=" NE2 HIS A 574 " pdb=" ZN B 803 " pdb="ZN ZN B 803 " - pdb=" NE2 HIS B 574 " pdb="ZN ZN B 803 " - pdb=" NE2 HIS B 578 " pdb=" ZN C 802 " pdb="ZN ZN C 802 " - pdb=" NE2 HIS C 578 " pdb="ZN ZN C 802 " - pdb=" NE2 HIS C 574 " pdb=" ZN D 803 " pdb="ZN ZN D 803 " - pdb=" NE2 HIS D 578 " pdb="ZN ZN D 803 " - pdb=" NE2 HIS D 574 " pdb=" ZN E 802 " pdb="ZN ZN E 802 " - pdb=" NE2 HIS E 574 " pdb=" ZN F 801 " pdb="ZN ZN F 801 " - pdb=" NE2 HIS F 574 " pdb="ZN ZN F 801 " - pdb=" NE2 HIS F 578 " 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4420 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 9 sheets defined 43.7% alpha, 3.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 526 through 533 Processing helix chain 'A' and resid 542 through 553 removed outlier: 3.518A pdb=" N GLU A 546 " --> pdb=" O GLN A 542 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLN A 547 " --> pdb=" O LYS A 543 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG A 551 " --> pdb=" O GLN A 547 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL A 552 " --> pdb=" O ALA A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 585 removed outlier: 3.862A pdb=" N THR A 570 " --> pdb=" O GLU A 566 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU A 585 " --> pdb=" O ALA A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 617 through 629 removed outlier: 3.606A pdb=" N ASP A 623 " --> pdb=" O GLU A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 638 Processing helix chain 'A' and resid 646 through 662 removed outlier: 3.753A pdb=" N LYS A 652 " --> pdb=" O ASP A 648 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ALA A 659 " --> pdb=" O GLN A 655 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLN A 660 " --> pdb=" O SER A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 719 removed outlier: 3.604A pdb=" N ILE A 703 " --> pdb=" O ASP A 699 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU A 718 " --> pdb=" O ALA A 714 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 734 Processing helix chain 'A' and resid 737 through 746 Processing helix chain 'B' and resid 306 through 310 removed outlier: 3.688A pdb=" N VAL B 310 " --> pdb=" O PHE B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 329 removed outlier: 3.579A pdb=" N LEU B 327 " --> pdb=" O PHE B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 365 Processing helix chain 'B' and resid 375 through 377 No H-bonds generated for 'chain 'B' and resid 375 through 377' Processing helix chain 'B' and resid 384 through 399 removed outlier: 3.893A pdb=" N VAL B 389 " --> pdb=" O GLY B 385 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N ARG B 390 " --> pdb=" O PRO B 386 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ARG B 397 " --> pdb=" O PHE B 393 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS B 398 " --> pdb=" O ALA B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 412 Processing helix chain 'B' and resid 421 through 440 removed outlier: 4.216A pdb=" N GLN B 427 " --> pdb=" O GLY B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 491 removed outlier: 3.674A pdb=" N SER B 485 " --> pdb=" O LYS B 481 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL B 489 " --> pdb=" O SER B 485 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N HIS B 490 " --> pdb=" O ILE B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 513 Processing helix chain 'B' and resid 517 through 535 removed outlier: 3.508A pdb=" N VAL B 521 " --> pdb=" O SER B 517 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA B 522 " --> pdb=" O GLY B 518 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ALA B 529 " --> pdb=" O CYS B 525 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N HIS B 535 " --> pdb=" O ILE B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 555 removed outlier: 3.732A pdb=" N PHE B 545 " --> pdb=" O ASN B 541 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU B 550 " --> pdb=" O GLU B 546 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE B 553 " --> pdb=" O ILE B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 566 through 585 removed outlier: 3.676A pdb=" N VAL B 571 " --> pdb=" O GLU B 567 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLY B 577 " --> pdb=" O TYR B 573 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N HIS B 578 " --> pdb=" O HIS B 574 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA B 579 " --> pdb=" O GLN B 575 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA B 581 " --> pdb=" O GLY B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 617 through 629 removed outlier: 3.789A pdb=" N ARG B 624 " --> pdb=" O GLN B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 629 through 639 Processing helix chain 'B' and resid 647 through 662 removed outlier: 3.663A pdb=" N LYS B 652 " --> pdb=" O ASP B 648 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ALA B 659 " --> pdb=" O GLN B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 690 through 719 removed outlier: 3.679A pdb=" N ARG B 702 " --> pdb=" O ASP B 698 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLU B 718 " --> pdb=" O ALA B 714 " (cutoff:3.500A) Processing helix chain 'B' and resid 719 through 734 Processing helix chain 'B' and resid 738 through 746 Processing helix chain 'B' and resid 755 through 760 Processing helix chain 'C' and resid 306 through 310 Processing helix chain 'C' and resid 313 through 329 removed outlier: 4.224A pdb=" N GLU C 319 " --> pdb=" O GLU C 315 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE C 320 " --> pdb=" O ALA C 316 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N PHE C 323 " --> pdb=" O GLU C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 335 Processing helix chain 'C' and resid 355 through 365 removed outlier: 3.622A pdb=" N THR C 361 " --> pdb=" O LEU C 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 399 removed outlier: 4.345A pdb=" N ASP C 391 " --> pdb=" O ALA C 387 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU C 395 " --> pdb=" O ASP C 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 412 Processing helix chain 'C' and resid 421 through 439 removed outlier: 3.960A pdb=" N SER C 425 " --> pdb=" O PHE C 421 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N GLU C 426 " --> pdb=" O GLY C 422 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N GLN C 427 " --> pdb=" O GLY C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 459 removed outlier: 3.835A pdb=" N ILE C 458 " --> pdb=" O ARG C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 479 through 491 removed outlier: 3.647A pdb=" N SER C 485 " --> pdb=" O LYS C 481 " (cutoff:3.500A) Processing helix chain 'C' and resid 501 through 512 removed outlier: 3.830A pdb=" N ALA C 506 " --> pdb=" O LYS C 502 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG C 507 " --> pdb=" O ASP C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 533 removed outlier: 3.516A pdb=" N ALA C 528 " --> pdb=" O VAL C 524 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ALA C 529 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing helix chain 'C' and resid 542 through 554 removed outlier: 3.513A pdb=" N GLU C 546 " --> pdb=" O GLN C 542 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLN C 547 " --> pdb=" O LYS C 543 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG C 551 " --> pdb=" O GLN C 547 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL C 552 " --> pdb=" O ALA C 548 " (cutoff:3.500A) Processing helix chain 'C' and resid 567 through 585 removed outlier: 3.709A pdb=" N VAL C 571 " --> pdb=" O GLU C 567 " (cutoff:3.500A) Processing helix chain 'C' and resid 617 through 629 removed outlier: 3.567A pdb=" N LEU C 621 " --> pdb=" O THR C 617 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N MET C 627 " --> pdb=" O ASP C 623 " (cutoff:3.500A) Processing helix chain 'C' and resid 629 through 639 Processing helix chain 'C' and resid 646 through 659 removed outlier: 3.587A pdb=" N LYS C 652 " --> pdb=" O ASP C 648 " (cutoff:3.500A) Processing helix chain 'C' and resid 690 through 714 removed outlier: 3.537A pdb=" N ILE C 703 " --> pdb=" O ASP C 699 " (cutoff:3.500A) Processing helix chain 'C' and resid 719 through 734 removed outlier: 3.579A pdb=" N LEU C 729 " --> pdb=" O LYS C 725 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLU C 732 " --> pdb=" O LEU C 728 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 746 Processing helix chain 'C' and resid 773 through 777 removed outlier: 3.984A pdb=" N LYS C 777 " --> pdb=" O GLU C 774 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 310 Processing helix chain 'D' and resid 313 through 329 removed outlier: 4.059A pdb=" N GLU D 319 " --> pdb=" O GLU D 315 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE D 320 " --> pdb=" O ALA D 316 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N PHE D 323 " --> pdb=" O GLU D 319 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL D 324 " --> pdb=" O ILE D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 329 through 335 removed outlier: 4.027A pdb=" N TYR D 333 " --> pdb=" O ASN D 329 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 365 removed outlier: 3.580A pdb=" N THR D 361 " --> pdb=" O LEU D 357 " (cutoff:3.500A) Processing helix chain 'D' and resid 375 through 377 No H-bonds generated for 'chain 'D' and resid 375 through 377' Processing helix chain 'D' and resid 385 through 399 removed outlier: 3.817A pdb=" N ASP D 391 " --> pdb=" O ALA D 387 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASN D 399 " --> pdb=" O LEU D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 409 through 412 Processing helix chain 'D' and resid 424 through 439 removed outlier: 3.524A pdb=" N GLU D 428 " --> pdb=" O GLN D 424 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR D 430 " --> pdb=" O GLU D 426 " (cutoff:3.500A) Processing helix chain 'D' and resid 479 through 491 removed outlier: 3.770A pdb=" N SER D 485 " --> pdb=" O LYS D 481 " (cutoff:3.500A) Processing helix chain 'D' and resid 501 through 513 removed outlier: 3.515A pdb=" N ALA D 506 " --> pdb=" O LYS D 502 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG D 507 " --> pdb=" O ASP D 503 " (cutoff:3.500A) Processing helix chain 'D' and resid 517 through 535 removed outlier: 3.830A pdb=" N VAL D 521 " --> pdb=" O SER D 517 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA D 522 " --> pdb=" O GLY D 518 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASN D 523 " --> pdb=" O ALA D 519 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA D 529 " --> pdb=" O CYS D 525 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N HIS D 535 " --> pdb=" O ILE D 531 " (cutoff:3.500A) Processing helix chain 'D' and resid 542 through 555 removed outlier: 3.676A pdb=" N ALA D 548 " --> pdb=" O HIS D 544 " (cutoff:3.500A) Processing helix chain 'D' and resid 564 through 585 removed outlier: 3.671A pdb=" N LYS D 569 " --> pdb=" O PRO D 565 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N THR D 570 " --> pdb=" O GLU D 566 " (cutoff:3.500A) Processing helix chain 'D' and resid 617 through 629 removed outlier: 3.787A pdb=" N ARG D 624 " --> pdb=" O GLN D 620 " (cutoff:3.500A) Processing helix chain 'D' and resid 629 through 638 removed outlier: 3.509A pdb=" N GLU D 635 " --> pdb=" O GLY D 631 " (cutoff:3.500A) Processing helix chain 'D' and resid 646 through 662 removed outlier: 3.625A pdb=" N LYS D 652 " --> pdb=" O ASP D 648 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL D 653 " --> pdb=" O ASP D 649 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLN D 660 " --> pdb=" O SER D 656 " (cutoff:3.500A) Processing helix chain 'D' and resid 690 through 714 removed outlier: 3.548A pdb=" N ALA D 694 " --> pdb=" O SER D 690 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG D 702 " --> pdb=" O ASP D 698 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS D 710 " --> pdb=" O ASN D 706 " (cutoff:3.500A) Processing helix chain 'D' and resid 719 through 733 removed outlier: 3.581A pdb=" N LEU D 729 " --> pdb=" O LYS D 725 " (cutoff:3.500A) Processing helix chain 'D' and resid 738 through 746 removed outlier: 3.502A pdb=" N LEU D 744 " --> pdb=" O ASP D 740 " (cutoff:3.500A) Processing helix chain 'D' and resid 755 through 761 removed outlier: 3.505A pdb=" N GLU D 761 " --> pdb=" O GLU D 757 " (cutoff:3.500A) Processing helix chain 'D' and resid 773 through 777 removed outlier: 3.722A pdb=" N LYS D 777 " --> pdb=" O GLU D 774 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 310 removed outlier: 3.501A pdb=" N VAL E 310 " --> pdb=" O PHE E 307 " (cutoff:3.500A) Processing helix chain 'E' and resid 313 through 329 removed outlier: 3.779A pdb=" N LEU E 318 " --> pdb=" O GLU E 314 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N GLU E 319 " --> pdb=" O GLU E 315 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE E 320 " --> pdb=" O ALA E 316 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLU E 322 " --> pdb=" O LEU E 318 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N PHE E 323 " --> pdb=" O GLU E 319 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL E 324 " --> pdb=" O ILE E 320 " (cutoff:3.500A) Processing helix chain 'E' and resid 329 through 335 removed outlier: 4.172A pdb=" N TYR E 333 " --> pdb=" O ASN E 329 " (cutoff:3.500A) Processing helix chain 'E' and resid 353 through 366 removed outlier: 3.545A pdb=" N THR E 361 " --> pdb=" O LEU E 357 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ALA E 365 " --> pdb=" O THR E 361 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 399 removed outlier: 3.670A pdb=" N ASP E 391 " --> pdb=" O ALA E 387 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN E 399 " --> pdb=" O LEU E 395 " (cutoff:3.500A) Processing helix chain 'E' and resid 409 through 412 Processing helix chain 'E' and resid 424 through 439 removed outlier: 3.512A pdb=" N GLU E 428 " --> pdb=" O GLN E 424 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N MET E 438 " --> pdb=" O LEU E 434 " (cutoff:3.500A) Processing helix chain 'E' and resid 455 through 459 removed outlier: 3.701A pdb=" N ILE E 458 " --> pdb=" O ARG E 455 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU E 459 " --> pdb=" O PRO E 456 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 455 through 459' Processing helix chain 'E' and resid 479 through 492 removed outlier: 3.917A pdb=" N SER E 485 " --> pdb=" O LYS E 481 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ARG E 492 " --> pdb=" O LYS E 488 " (cutoff:3.500A) Processing helix chain 'E' and resid 501 through 510 removed outlier: 4.001A pdb=" N ARG E 507 " --> pdb=" O ASP E 503 " (cutoff:3.500A) Processing helix chain 'E' and resid 517 through 535 removed outlier: 3.545A pdb=" N ASN E 526 " --> pdb=" O ALA E 522 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ALA E 529 " --> pdb=" O CYS E 525 " (cutoff:3.500A) Processing helix chain 'E' and resid 541 through 554 removed outlier: 3.680A pdb=" N ILE E 549 " --> pdb=" O PHE E 545 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLU E 550 " --> pdb=" O GLU E 546 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG E 551 " --> pdb=" O GLN E 547 " (cutoff:3.500A) Processing helix chain 'E' and resid 564 through 585 removed outlier: 3.848A pdb=" N THR E 570 " --> pdb=" O GLU E 566 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY E 577 " --> pdb=" O TYR E 573 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N HIS E 578 " --> pdb=" O HIS E 574 " (cutoff:3.500A) Processing helix chain 'E' and resid 618 through 629 removed outlier: 4.072A pdb=" N ARG E 624 " --> pdb=" O GLN E 620 " (cutoff:3.500A) Processing helix chain 'E' and resid 629 through 638 removed outlier: 4.105A pdb=" N GLU E 635 " --> pdb=" O GLY E 631 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU E 636 " --> pdb=" O ARG E 632 " (cutoff:3.500A) Processing helix chain 'E' and resid 644 through 646 No H-bonds generated for 'chain 'E' and resid 644 through 646' Processing helix chain 'E' and resid 647 through 662 removed outlier: 3.777A pdb=" N LYS E 652 " --> pdb=" O ASP E 648 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N VAL E 653 " --> pdb=" O ASP E 649 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N GLN E 660 " --> pdb=" O SER E 656 " (cutoff:3.500A) Processing helix chain 'E' and resid 690 through 717 removed outlier: 3.665A pdb=" N ILE E 703 " --> pdb=" O ASP E 699 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG E 711 " --> pdb=" O ASP E 707 " (cutoff:3.500A) Processing helix chain 'E' and resid 719 through 731 removed outlier: 3.545A pdb=" N LEU E 728 " --> pdb=" O GLU E 724 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LEU E 729 " --> pdb=" O LYS E 725 " (cutoff:3.500A) Processing helix chain 'E' and resid 737 through 746 removed outlier: 3.577A pdb=" N GLU E 743 " --> pdb=" O ASN E 739 " (cutoff:3.500A) Processing helix chain 'F' and resid 564 through 582 removed outlier: 3.548A pdb=" N LYS F 569 " --> pdb=" O PRO F 565 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR F 570 " --> pdb=" O GLU F 566 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY F 577 " --> pdb=" O TYR F 573 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N HIS F 578 " --> pdb=" O HIS F 574 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA F 579 " --> pdb=" O GLN F 575 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL F 580 " --> pdb=" O ALA F 576 " (cutoff:3.500A) Processing helix chain 'F' and resid 617 through 629 removed outlier: 3.580A pdb=" N LEU F 622 " --> pdb=" O LYS F 618 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ARG F 624 " --> pdb=" O GLN F 620 " (cutoff:3.500A) Processing helix chain 'F' and resid 629 through 639 removed outlier: 3.533A pdb=" N VAL F 633 " --> pdb=" O LEU F 629 " (cutoff:3.500A) Processing helix chain 'F' and resid 646 through 660 Processing helix chain 'F' and resid 690 through 717 removed outlier: 3.816A pdb=" N ILE F 703 " --> pdb=" O ASP F 699 " (cutoff:3.500A) Processing helix chain 'F' and resid 719 through 734 removed outlier: 3.513A pdb=" N GLU F 724 " --> pdb=" O LYS F 720 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LEU F 729 " --> pdb=" O LYS F 725 " (cutoff:3.500A) Processing helix chain 'F' and resid 737 through 746 Processing sheet with id=AA1, first strand: chain 'A' and resid 591 through 595 Processing sheet with id=AA2, first strand: chain 'B' and resid 297 through 299 removed outlier: 3.910A pdb=" N LYS B 297 " --> pdb=" O THR B 371 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N THR B 371 " --> pdb=" O LYS B 297 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N PHE B 369 " --> pdb=" O LEU B 299 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ILE B 370 " --> pdb=" O PHE B 405 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N ASP B 407 " --> pdb=" O ILE B 370 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N VAL B 372 " --> pdb=" O ASP B 407 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N LEU B 404 " --> pdb=" O LEU B 450 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N GLY B 452 " --> pdb=" O LEU B 404 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ILE B 406 " --> pdb=" O GLY B 452 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 605 through 608 Processing sheet with id=AA4, first strand: chain 'C' and resid 297 through 298 removed outlier: 3.550A pdb=" N LYS C 297 " --> pdb=" O THR C 371 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ILE C 370 " --> pdb=" O PHE C 405 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N ASP C 407 " --> pdb=" O ILE C 370 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL C 372 " --> pdb=" O ASP C 407 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG C 471 " --> pdb=" O GLY C 343 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 602 through 605 removed outlier: 6.152A pdb=" N ALA I 6 " --> pdb=" O LEU C 603 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 297 through 298 removed outlier: 3.690A pdb=" N LYS D 297 " --> pdb=" O THR D 371 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR D 371 " --> pdb=" O LYS D 297 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ALA D 344 " --> pdb=" O ALA D 451 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N THR D 453 " --> pdb=" O ALA D 344 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N LEU D 346 " --> pdb=" O THR D 453 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 735 through 736 removed outlier: 3.650A pdb=" N ALA J 4 " --> pdb=" O ALA D 606 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 369 through 373 removed outlier: 6.150A pdb=" N ILE E 370 " --> pdb=" O PHE E 405 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N ASP E 407 " --> pdb=" O ILE E 370 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N VAL E 372 " --> pdb=" O ASP E 407 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N LEU E 404 " --> pdb=" O LEU E 450 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N GLY E 452 " --> pdb=" O LEU E 404 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ILE E 406 " --> pdb=" O GLY E 452 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 594 through 595 799 hydrogen bonds defined for protein. 2340 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.96 Time building geometry restraints manager: 1.53 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: 11533 34.48 - 68.95: 66 68.95 - 103.43: 5 103.43 - 137.91: 4 137.91 - 172.38: 3 Dihedral angle restraints: 11611 sinusoidal: 4745 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 11608 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: 0.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 17.880 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6601 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 : 10.084 172.382 7191 Min Nonbonded Distance : 1.264 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 0.05 % Allowed : 1.68 % Favored : 98.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.40 (0.12), residues: 2372 helix: -4.34 (0.06), residues: 1246 sheet: -1.97 (0.37), residues: 149 loop : -2.51 (0.17), residues: 977 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 465 TYR 0.020 0.002 TYR E 584 PHE 0.041 0.004 PHE E 750 TRP 0.019 0.003 TRP C 583 HIS 0.011 0.002 HIS E 578 Details of bonding type rmsd/Z covalent geometry : bond 0.00728 / 0.32 (19031) covalent geometry : angle 0.89925 / 0.46 (25717) hydrogen bonds : bond 0.31768 / 20.91 ( 799) hydrogen bonds : angle 10.42684 / 7.22 ( 2340) metal coordination : bond 0.14665 / 8.35 ( 10) Misc. bond : bond 0.27608 / 13.80 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 527 residues out of total 2375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 526 time to evaluate : 0.530 Fit side-chains TARDY: cannot create tardy model for: "MET A 321 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 380 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 438 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET F 321 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 380 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 438 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 575 GLN cc_start: 0.8496 (mm-40) cc_final: 0.8150 (mm-40) REVERT: A 593 LYS cc_start: 0.6676 (ttmt) cc_final: 0.6274 (mtpp) REVERT: A 652 LYS cc_start: 0.7842 (mttt) cc_final: 0.7582 (mtmt) REVERT: A 683 MET cc_start: 0.3221 (tpp) cc_final: 0.0465 (pmm) REVERT: A 687 LYS cc_start: 0.7500 (mmtp) cc_final: 0.7287 (mmtm) REVERT: A 700 GLU cc_start: 0.7139 (mm-30) cc_final: 0.6867 (mm-30) REVERT: A 733 LYS cc_start: 0.7475 (mtpt) cc_final: 0.6680 (tptp) REVERT: A 744 LEU cc_start: 0.7480 (tp) cc_final: 0.7231 (tp) REVERT: B 428 GLU cc_start: 0.6344 (tt0) cc_final: 0.6119 (mm-30) REVERT: B 465 ARG cc_start: 0.5940 (mtt-85) cc_final: 0.5676 (tpt170) REVERT: B 503 ASP cc_start: 0.7522 (m-30) cc_final: 0.7319 (m-30) REVERT: B 520 ASP cc_start: 0.7113 (m-30) cc_final: 0.6800 (m-30) REVERT: B 722 ASP cc_start: 0.7543 (m-30) cc_final: 0.7316 (m-30) REVERT: C 520 ASP cc_start: 0.7207 (m-30) cc_final: 0.7000 (m-30) REVERT: C 569 LYS cc_start: 0.8526 (tttt) cc_final: 0.8198 (ttmt) REVERT: C 666 MET cc_start: 0.7234 (mmt) cc_final: 0.6965 (mmt) REVERT: C 672 GLN cc_start: 0.7309 (mm-40) cc_final: 0.6988 (mp10) REVERT: C 673 ILE cc_start: 0.8324 (mt) cc_final: 0.8069 (tt) REVERT: C 685 LEU cc_start: 0.7221 (OUTLIER) cc_final: 0.6955 (pp) REVERT: C 695 ARG cc_start: 0.7074 (ttp80) cc_final: 0.6746 (ttp-110) REVERT: C 699 ASP cc_start: 0.7352 (m-30) cc_final: 0.7040 (m-30) REVERT: C 711 ARG cc_start: 0.7897 (ttt180) cc_final: 0.7653 (mtp-110) REVERT: C 774 GLU cc_start: 0.7851 (mp0) cc_final: 0.7604 (mp0) REVERT: D 306 LYS cc_start: 0.8330 (mmtt) cc_final: 0.8009 (mmtm) REVERT: D 321 MET cc_start: 0.8365 (mtp) cc_final: 0.7931 (mtm) REVERT: D 395 LEU cc_start: 0.7526 (tp) cc_final: 0.7249 (tt) REVERT: D 404 LEU cc_start: 0.7627 (tt) cc_final: 0.7360 (tp) REVERT: D 424 GLN cc_start: 0.6684 (mt0) cc_final: 0.6232 (mm-40) REVERT: D 500 LEU cc_start: 0.7874 (mt) cc_final: 0.7663 (mt) REVERT: D 504 LYS cc_start: 0.8298 (mttp) cc_final: 0.8061 (mtpm) REVERT: D 544 HIS cc_start: 0.8171 (m170) cc_final: 0.7915 (m170) REVERT: D 547 GLN cc_start: 0.8539 (mt0) cc_final: 0.8264 (mt0) REVERT: D 559 LYS cc_start: 0.8091 (mtpt) cc_final: 0.7742 (mtpt) REVERT: D 561 GLN cc_start: 0.8268 (tt0) cc_final: 0.7982 (tt0) REVERT: D 619 GLU cc_start: 0.7588 (mp0) cc_final: 0.7259 (mp0) REVERT: D 673 ILE cc_start: 0.7877 (mt) cc_final: 0.7475 (pp) REVERT: D 753 LYS cc_start: 0.8691 (mtmt) cc_final: 0.8476 (mtmm) REVERT: E 309 ASP cc_start: 0.7572 (m-30) cc_final: 0.7171 (t0) REVERT: E 321 MET cc_start: 0.7338 (mtm) cc_final: 0.6902 (mtp) REVERT: E 375 SER cc_start: 0.8253 (p) cc_final: 0.7974 (m) REVERT: E 376 GLU cc_start: 0.7808 (mt-10) cc_final: 0.7572 (tt0) REVERT: E 408 GLN cc_start: 0.7715 (mm-40) cc_final: 0.7440 (tp40) REVERT: E 455 ARG cc_start: 0.8251 (mtp180) cc_final: 0.7830 (mmm-85) REVERT: E 543 LYS cc_start: 0.8383 (mmtt) cc_final: 0.8066 (ttpp) REVERT: E 656 SER cc_start: 0.8280 (t) cc_final: 0.8012 (m) REVERT: F 616 TYR cc_start: 0.8050 (m-80) cc_final: 0.7825 (m-80) REVERT: F 627 MET cc_start: 0.7246 (tmm) cc_final: 0.6918 (tmm) REVERT: F 641 ARG cc_start: 0.7043 (mmt-90) cc_final: 0.6775 (ptp-110) outliers start: 1 outliers final: 1 residues processed: 527 average time/residue: 0.6653 time to fit residues: 390.1336 Evaluate side-chains 337 residues out of total 2375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 335 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 391 ASP Chi-restraints excluded: chain C residue 685 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 50.0000 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 50.0000 chunk 248 optimal weight: 50.0000 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 50.0000 chunk 183 optimal weight: 3.9990 chunk 111 optimal weight: 0.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 578 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 672 GLN B 332 GLN B 663 GLN ** B 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 472 GLN C 613 GLN C 647 GLN ** C 667 ASN ** 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 542 GLN E 663 GLN F 667 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.161837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.138129 restraints weight = 26592.118| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 2.04 r_work: 0.3574 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3434 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 19044 Z= 0.221 Angle : 0.697 11.023 25717 Z= 0.356 Chirality : 0.044 0.159 2915 Planarity : 0.006 0.055 3334 Dihedral : 9.596 179.471 2593 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 3.72 % Allowed : 11.09 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.22 (0.15), residues: 2372 helix: -2.07 (0.12), residues: 1267 sheet: -1.52 (0.40), residues: 135 loop : -2.13 (0.18), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 468 TYR 0.018 0.002 TYR C 605 PHE 0.028 0.003 PHE A 750 TRP 0.015 0.002 TRP D 583 HIS 0.009 0.002 HIS C 578 Details of bonding type rmsd/Z covalent geometry : bond 0.00522 / 0.22 (19031) covalent geometry : angle 0.69741 / 0.36 (25717) hydrogen bonds : bond 0.05322 / 3.53 ( 799) hydrogen bonds : angle 5.28313 / 3.61 ( 2340) metal coordination : bond 0.00316 / 0.19 ( 10) Misc. bond : bond 0.00187 / 0.10 ( 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 427 residues out of total 2375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 354 time to evaluate : 0.676 Fit side-chains TARDY: cannot create tardy model for: "MET A 321 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 380 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 438 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET F 321 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 380 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 438 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 619 GLU cc_start: 0.7422 (OUTLIER) cc_final: 0.7132 (pp20) REVERT: A 683 MET cc_start: 0.3316 (tpp) cc_final: 0.0614 (pmm) REVERT: A 733 LYS cc_start: 0.7736 (mtpt) cc_final: 0.6990 (tptp) REVERT: B 370 ILE cc_start: 0.7650 (OUTLIER) cc_final: 0.7241 (mt) REVERT: B 402 CYS cc_start: 0.7844 (p) cc_final: 0.7442 (p) REVERT: B 404 LEU cc_start: 0.8216 (tt) cc_final: 0.7971 (tp) REVERT: B 427 GLN cc_start: 0.7316 (OUTLIER) cc_final: 0.6755 (tm-30) REVERT: B 428 GLU cc_start: 0.7028 (tt0) cc_final: 0.6705 (mm-30) REVERT: B 458 ILE cc_start: 0.8837 (OUTLIER) cc_final: 0.8561 (pp) REVERT: B 465 ARG cc_start: 0.6201 (mtt-85) cc_final: 0.5944 (tpt170) REVERT: B 619 GLU cc_start: 0.7799 (pm20) cc_final: 0.7592 (mp0) REVERT: B 673 ILE cc_start: 0.8658 (OUTLIER) cc_final: 0.8424 (pp) REVERT: C 398 LYS cc_start: 0.8367 (mttt) cc_final: 0.8129 (mmtm) REVERT: C 408 GLN cc_start: 0.8227 (OUTLIER) cc_final: 0.5964 (mp10) REVERT: C 547 GLN cc_start: 0.8396 (mt0) cc_final: 0.8195 (mt0) REVERT: C 636 GLU cc_start: 0.8115 (tt0) cc_final: 0.7665 (pt0) REVERT: C 695 ARG cc_start: 0.7991 (ttp80) cc_final: 0.7702 (ttp80) REVERT: C 699 ASP cc_start: 0.7704 (m-30) cc_final: 0.7431 (m-30) REVERT: D 424 GLN cc_start: 0.7594 (mt0) cc_final: 0.7321 (mt0) REVERT: D 507 ARG cc_start: 0.8789 (OUTLIER) cc_final: 0.8032 (mtm-85) REVERT: D 556 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8121 (tp) REVERT: D 734 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.7133 (mt-10) REVERT: E 309 ASP cc_start: 0.8042 (m-30) cc_final: 0.7812 (m-30) REVERT: E 455 ARG cc_start: 0.8356 (mtp180) cc_final: 0.8089 (mmm-85) REVERT: E 543 LYS cc_start: 0.8251 (mmtt) cc_final: 0.8023 (tptt) REVERT: E 668 GLU cc_start: 0.7280 (OUTLIER) cc_final: 0.6874 (mp0) REVERT: F 584 TYR cc_start: 0.8067 (m-10) cc_final: 0.7733 (m-10) REVERT: F 589 ASP cc_start: 0.7256 (m-30) cc_final: 0.6596 (t0) REVERT: F 616 TYR cc_start: 0.8608 (m-80) cc_final: 0.8390 (m-80) REVERT: F 627 MET cc_start: 0.8246 (tmm) cc_final: 0.7850 (tmm) REVERT: F 660 GLN cc_start: 0.8315 (tt0) cc_final: 0.8031 (tt0) outliers start: 73 outliers final: 27 residues processed: 397 average time/residue: 0.6439 time to fit residues: 284.1115 Evaluate side-chains 321 residues out of total 2375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 284 time to evaluate : 0.727 ------------------------------------------------------------------------------- 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 370 ILE Chi-restraints excluded: chain B residue 427 GLN Chi-restraints excluded: chain B residue 458 ILE Chi-restraints excluded: chain B residue 504 LYS Chi-restraints excluded: chain B residue 556 LEU Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 627 MET Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 673 ILE Chi-restraints excluded: chain B residue 744 LEU Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 371 THR Chi-restraints excluded: chain C residue 391 ASP Chi-restraints excluded: chain C residue 408 GLN Chi-restraints excluded: chain C residue 538 ASP Chi-restraints excluded: chain C residue 539 SER Chi-restraints excluded: chain C residue 541 ASN Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 435 LEU Chi-restraints excluded: chain D residue 457 ASP Chi-restraints excluded: chain D residue 499 THR Chi-restraints excluded: chain D residue 507 ARG Chi-restraints excluded: chain D residue 535 HIS Chi-restraints excluded: chain D residue 556 LEU Chi-restraints excluded: chain D residue 669 LYS Chi-restraints excluded: chain D residue 713 VAL Chi-restraints excluded: chain D residue 734 GLU Chi-restraints excluded: chain D residue 739 ASN Chi-restraints excluded: chain E residue 335 ASP Chi-restraints excluded: chain E residue 382 VAL Chi-restraints excluded: chain E residue 668 GLU Chi-restraints excluded: chain E residue 669 LYS Chi-restraints excluded: chain F residue 705 ILE Chi-restraints excluded: chain F residue 744 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 178 optimal weight: 7.9990 chunk 134 optimal weight: 1.9990 chunk 63 optimal weight: 9.9990 chunk 80 optimal weight: 3.9990 chunk 87 optimal weight: 0.8980 chunk 152 optimal weight: 0.7980 chunk 121 optimal weight: 5.9990 chunk 256 optimal weight: 50.0000 chunk 21 optimal weight: 50.0000 chunk 206 optimal weight: 0.0060 chunk 272 optimal weight: 0.9990 overall best weight: 0.9400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 667 ASN C 541 ASN C 613 GLN ** C 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 739 ASN D 535 HIS E 433 GLN E 663 GLN F 667 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.164538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.140957 restraints weight = 26596.239| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 2.08 r_work: 0.3620 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3482 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.3048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 19044 Z= 0.110 Angle : 0.564 10.702 25717 Z= 0.284 Chirality : 0.040 0.147 2915 Planarity : 0.004 0.048 3334 Dihedral : 8.794 153.331 2591 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.85 % Allowed : 14.96 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.85 (0.17), residues: 2372 helix: -0.72 (0.14), residues: 1265 sheet: -1.38 (0.40), residues: 150 loop : -1.77 (0.19), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 534 TYR 0.021 0.001 TYR C 605 PHE 0.014 0.001 PHE E 750 TRP 0.008 0.001 TRP D 583 HIS 0.005 0.001 HIS D 535 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (19031) covalent geometry : angle 0.56437 / 0.28 (25717) hydrogen bonds : bond 0.03829 / 2.55 ( 799) hydrogen bonds : angle 4.66870 / 3.18 ( 2340) metal coordination : bond 0.00144 / 0.08 ( 10) Misc. bond : bond 0.00053 / 0.03 ( 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 372 residues out of total 2375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 316 time to evaluate : 0.760 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 619 GLU cc_start: 0.7446 (OUTLIER) cc_final: 0.7087 (pp20) REVERT: A 683 MET cc_start: 0.3148 (tpp) cc_final: 0.0493 (pmm) REVERT: B 402 CYS cc_start: 0.7728 (p) cc_final: 0.7359 (p) REVERT: B 404 LEU cc_start: 0.8020 (tt) cc_final: 0.7813 (tp) REVERT: B 427 GLN cc_start: 0.7221 (OUTLIER) cc_final: 0.6650 (tm-30) REVERT: B 428 GLU cc_start: 0.6874 (tt0) cc_final: 0.6572 (mm-30) REVERT: B 433 GLN cc_start: 0.7765 (tp40) cc_final: 0.7511 (tm-30) REVERT: B 465 ARG cc_start: 0.6258 (mtt-85) cc_final: 0.5901 (tpt170) REVERT: B 469 PHE cc_start: 0.8478 (m-10) cc_final: 0.8243 (m-10) REVERT: B 501 GLU cc_start: 0.7239 (pt0) cc_final: 0.6988 (pt0) REVERT: B 636 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7880 (mm-30) REVERT: B 683 MET cc_start: 0.6456 (ptp) cc_final: 0.4769 (pmm) REVERT: C 328 LYS cc_start: 0.8640 (ttmm) cc_final: 0.8145 (mmmm) REVERT: C 332 GLN cc_start: 0.7743 (mt0) cc_final: 0.7538 (pt0) REVERT: C 547 GLN cc_start: 0.8336 (mt0) cc_final: 0.8116 (mt0) REVERT: C 636 GLU cc_start: 0.8094 (tt0) cc_final: 0.7761 (pt0) REVERT: C 695 ARG cc_start: 0.8006 (ttp80) cc_final: 0.7589 (ttp80) REVERT: C 699 ASP cc_start: 0.7739 (m-30) cc_final: 0.7445 (m-30) REVERT: D 376 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.7514 (tm-30) REVERT: D 404 LEU cc_start: 0.8184 (tt) cc_final: 0.7962 (tp) REVERT: D 504 LYS cc_start: 0.8343 (mtpm) cc_final: 0.8045 (mttm) REVERT: D 557 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.8164 (tm-30) REVERT: D 573 TYR cc_start: 0.8290 (m-80) cc_final: 0.7781 (m-10) REVERT: D 624 ARG cc_start: 0.7942 (ttm-80) cc_final: 0.7606 (mtt-85) REVERT: E 309 ASP cc_start: 0.8018 (m-30) cc_final: 0.7784 (m-30) REVERT: E 318 LEU cc_start: 0.8790 (mt) cc_final: 0.8557 (mp) REVERT: E 407 ASP cc_start: 0.7815 (t0) cc_final: 0.7609 (t0) REVERT: E 455 ARG cc_start: 0.8323 (mtp180) cc_final: 0.8003 (mmm-85) REVERT: E 543 LYS cc_start: 0.8329 (mmtt) cc_final: 0.8072 (tmtm) REVERT: E 619 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7609 (mp0) REVERT: F 616 TYR cc_start: 0.8523 (m-80) cc_final: 0.8311 (m-80) REVERT: F 619 GLU cc_start: 0.7731 (mp0) cc_final: 0.7530 (mp0) REVERT: F 660 GLN cc_start: 0.8257 (tt0) cc_final: 0.7905 (tt0) REVERT: F 732 GLU cc_start: 0.7611 (mm-30) cc_final: 0.7217 (mt-10) outliers start: 56 outliers final: 10 residues processed: 351 average time/residue: 0.6419 time to fit residues: 251.2193 Evaluate side-chains 298 residues out of total 2375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 282 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain B residue 427 GLN Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 636 GLU Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 744 LEU Chi-restraints excluded: chain C residue 538 ASP Chi-restraints excluded: chain C residue 539 SER Chi-restraints excluded: chain C residue 541 ASN Chi-restraints excluded: chain D residue 376 GLU Chi-restraints excluded: chain D residue 457 ASP Chi-restraints excluded: chain D residue 557 GLU Chi-restraints excluded: chain D residue 739 ASN Chi-restraints excluded: chain E residue 335 ASP Chi-restraints excluded: chain E residue 619 GLU Chi-restraints excluded: chain F residue 562 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 83 optimal weight: 10.0000 chunk 31 optimal weight: 8.9990 chunk 34 optimal weight: 1.9990 chunk 116 optimal weight: 8.9990 chunk 101 optimal weight: 5.9990 chunk 234 optimal weight: 6.9990 chunk 90 optimal weight: 0.1980 chunk 0 optimal weight: 50.0000 chunk 131 optimal weight: 0.9980 chunk 104 optimal weight: 0.8980 chunk 249 optimal weight: 50.0000 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 472 GLN B 575 GLN C 663 GLN ** C 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 535 HIS ** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.163409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.140082 restraints weight = 26521.713| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 1.98 r_work: 0.3600 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3462 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.3331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19044 Z= 0.130 Angle : 0.566 11.690 25717 Z= 0.283 Chirality : 0.041 0.155 2915 Planarity : 0.004 0.044 3334 Dihedral : 8.416 148.996 2589 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 3.05 % Allowed : 15.67 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.17), residues: 2372 helix: -0.15 (0.15), residues: 1264 sheet: -1.20 (0.41), residues: 147 loop : -1.58 (0.20), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 624 TYR 0.021 0.001 TYR C 605 PHE 0.019 0.002 PHE E 638 TRP 0.008 0.001 TRP F 583 HIS 0.006 0.001 HIS D 578 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 (19031) covalent geometry : angle 0.56599 / 0.28 (25717) hydrogen bonds : bond 0.03675 / 2.45 ( 799) hydrogen bonds : angle 4.45885 / 3.03 ( 2340) metal coordination : bond 0.00202 / 0.12 ( 10) Misc. bond : bond 0.00094 / 0.05 ( 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 349 residues out of total 2375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 289 time to evaluate : 0.757 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 669 LYS cc_start: 0.8758 (mtpm) cc_final: 0.8535 (mtpp) REVERT: A 683 MET cc_start: 0.3235 (tpp) cc_final: 0.0509 (pmm) REVERT: B 402 CYS cc_start: 0.7902 (p) cc_final: 0.7526 (p) REVERT: B 404 LEU cc_start: 0.8099 (tt) cc_final: 0.7869 (tp) REVERT: B 427 GLN cc_start: 0.7197 (OUTLIER) cc_final: 0.6634 (tm-30) REVERT: B 428 GLU cc_start: 0.6887 (tt0) cc_final: 0.6546 (mm-30) REVERT: B 433 GLN cc_start: 0.7753 (tp40) cc_final: 0.7516 (tm-30) REVERT: B 469 PHE cc_start: 0.8442 (m-10) cc_final: 0.8210 (m-10) REVERT: B 636 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7876 (mm-30) REVERT: B 641 ARG cc_start: 0.8309 (OUTLIER) cc_final: 0.8081 (mtm180) REVERT: B 683 MET cc_start: 0.6211 (ptp) cc_final: 0.5767 (ttt) REVERT: C 408 GLN cc_start: 0.8242 (OUTLIER) cc_final: 0.5971 (mp10) REVERT: C 547 GLN cc_start: 0.8287 (mt0) cc_final: 0.8063 (mt0) REVERT: C 666 MET cc_start: 0.8369 (mmt) cc_final: 0.7025 (mmt) REVERT: C 695 ARG cc_start: 0.8008 (ttp80) cc_final: 0.7545 (ttp80) REVERT: C 699 ASP cc_start: 0.7712 (m-30) cc_final: 0.7455 (m-30) REVERT: D 376 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.7530 (tm-30) REVERT: D 404 LEU cc_start: 0.8155 (tt) cc_final: 0.7890 (tp) REVERT: D 573 TYR cc_start: 0.8376 (m-80) cc_final: 0.7807 (m-80) REVERT: D 624 ARG cc_start: 0.7944 (ttm-80) cc_final: 0.7621 (mtt-85) REVERT: D 734 GLU cc_start: 0.7743 (OUTLIER) cc_final: 0.7055 (mt-10) REVERT: E 309 ASP cc_start: 0.8066 (m-30) cc_final: 0.7863 (m-30) REVERT: E 318 LEU cc_start: 0.8861 (mt) cc_final: 0.8621 (mp) REVERT: E 407 ASP cc_start: 0.7652 (t0) cc_final: 0.7415 (t0) REVERT: E 455 ARG cc_start: 0.8350 (mtp180) cc_final: 0.8032 (mmm-85) REVERT: E 543 LYS cc_start: 0.8493 (mmtt) cc_final: 0.8116 (tptt) REVERT: E 619 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7668 (mp0) REVERT: E 632 ARG cc_start: 0.8456 (OUTLIER) cc_final: 0.7481 (tpt170) REVERT: F 616 TYR cc_start: 0.8541 (m-80) cc_final: 0.8331 (m-80) REVERT: F 660 GLN cc_start: 0.8351 (tt0) cc_final: 0.7981 (tt0) REVERT: F 732 GLU cc_start: 0.7798 (mm-30) cc_final: 0.7427 (mt-10) outliers start: 60 outliers final: 18 residues processed: 327 average time/residue: 0.6161 time to fit residues: 225.5264 Evaluate side-chains 304 residues out of total 2375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 278 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 689 TYR Chi-restraints excluded: chain B residue 427 GLN Chi-restraints excluded: chain B residue 449 ILE 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 408 GLN Chi-restraints excluded: chain C residue 538 ASP Chi-restraints excluded: chain C residue 673 ILE Chi-restraints excluded: chain D residue 376 GLU Chi-restraints excluded: chain D residue 453 THR Chi-restraints excluded: chain D residue 457 ASP Chi-restraints excluded: chain D residue 535 HIS Chi-restraints excluded: chain D residue 553 ILE 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 E residue 380 MET Chi-restraints excluded: chain E residue 619 GLU Chi-restraints excluded: chain E residue 632 ARG Chi-restraints excluded: chain E residue 736 LEU Chi-restraints excluded: chain F residue 562 VAL Chi-restraints excluded: chain F residue 705 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 3 optimal weight: 50.0000 chunk 12 optimal weight: 50.0000 chunk 259 optimal weight: 50.0000 chunk 8 optimal weight: 50.0000 chunk 72 optimal weight: 6.9990 chunk 232 optimal weight: 0.9980 chunk 277 optimal weight: 2.9990 chunk 185 optimal weight: 8.9990 chunk 106 optimal weight: 6.9990 chunk 47 optimal weight: 0.9990 chunk 263 optimal weight: 30.0000 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 325 ASN C 332 GLN ** C 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.161130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.137862 restraints weight = 26452.940| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 2.02 r_work: 0.3559 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3417 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.3538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 19044 Z= 0.186 Angle : 0.613 11.983 25717 Z= 0.304 Chirality : 0.043 0.152 2915 Planarity : 0.004 0.074 3334 Dihedral : 8.457 147.429 2589 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.61 % Allowed : 15.88 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.17), residues: 2372 helix: 0.03 (0.15), residues: 1261 sheet: -1.26 (0.39), residues: 153 loop : -1.55 (0.20), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 624 TYR 0.020 0.002 TYR C 605 PHE 0.017 0.002 PHE D 638 TRP 0.010 0.002 TRP F 583 HIS 0.011 0.002 HIS D 535 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.19 (19031) covalent geometry : angle 0.61305 / 0.30 (25717) hydrogen bonds : bond 0.03944 / 2.62 ( 799) hydrogen bonds : angle 4.46019 / 3.03 ( 2340) metal coordination : bond 0.00355 / 0.21 ( 10) Misc. bond : bond 0.00174 / 0.09 ( 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 361 residues out of total 2375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 290 time to evaluate : 0.672 Fit side-chains TARDY: cannot create tardy model for: "MET A 321 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 380 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 438 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET F 321 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 380 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 438 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 619 GLU cc_start: 0.7496 (OUTLIER) cc_final: 0.7207 (pt0) REVERT: A 683 MET cc_start: 0.3429 (tpp) cc_final: 0.0553 (pmm) REVERT: A 741 MET cc_start: 0.7037 (mmp) cc_final: 0.6767 (mmt) REVERT: B 402 CYS cc_start: 0.7944 (p) cc_final: 0.7525 (p) REVERT: B 404 LEU cc_start: 0.8076 (tt) cc_final: 0.7850 (tp) REVERT: B 427 GLN cc_start: 0.7185 (OUTLIER) cc_final: 0.6676 (tm-30) REVERT: B 428 GLU cc_start: 0.6907 (tt0) cc_final: 0.6554 (mm-30) REVERT: B 433 GLN cc_start: 0.7779 (tp40) cc_final: 0.7536 (tm-30) REVERT: B 465 ARG cc_start: 0.6066 (mtt-85) cc_final: 0.5628 (mmt180) REVERT: B 469 PHE cc_start: 0.8521 (m-10) cc_final: 0.8283 (m-10) REVERT: B 641 ARG cc_start: 0.8346 (OUTLIER) cc_final: 0.8113 (mtm180) REVERT: B 683 MET cc_start: 0.6074 (ptp) cc_final: 0.5674 (ttt) REVERT: C 408 GLN cc_start: 0.8237 (OUTLIER) cc_final: 0.5971 (mp10) REVERT: C 611 LYS cc_start: 0.8339 (OUTLIER) cc_final: 0.7826 (mttp) REVERT: C 683 MET cc_start: 0.6146 (ttt) cc_final: 0.5754 (tmm) REVERT: C 695 ARG cc_start: 0.8033 (ttp80) cc_final: 0.7578 (ttp80) REVERT: C 699 ASP cc_start: 0.7729 (m-30) cc_final: 0.7470 (m-30) REVERT: C 777 LYS cc_start: 0.8160 (OUTLIER) cc_final: 0.7711 (mptm) REVERT: D 376 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7666 (tm-30) REVERT: D 556 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8441 (tp) REVERT: D 624 ARG cc_start: 0.7979 (ttm-80) cc_final: 0.7638 (mtt-85) REVERT: D 666 MET cc_start: 0.7717 (OUTLIER) cc_final: 0.5982 (mmt) REVERT: D 685 LEU cc_start: 0.7030 (OUTLIER) cc_final: 0.6701 (tt) REVERT: D 734 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.7104 (mt-10) REVERT: E 318 LEU cc_start: 0.8866 (mt) cc_final: 0.8617 (mp) REVERT: E 407 ASP cc_start: 0.7645 (t0) cc_final: 0.7438 (t0) REVERT: E 543 LYS cc_start: 0.8509 (mmtt) cc_final: 0.8105 (tptt) REVERT: E 619 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7702 (mp0) REVERT: E 632 ARG cc_start: 0.8587 (OUTLIER) cc_final: 0.7784 (tpt170) REVERT: F 619 GLU cc_start: 0.7795 (mp0) cc_final: 0.7548 (mp0) REVERT: F 625 MET cc_start: 0.8058 (ttm) cc_final: 0.7683 (ttm) REVERT: F 660 GLN cc_start: 0.8404 (tt0) cc_final: 0.8055 (tt0) REVERT: F 732 GLU cc_start: 0.7853 (mm-30) cc_final: 0.7427 (mt-10) REVERT: F 734 GLU cc_start: 0.7700 (mt-10) cc_final: 0.6879 (tm-30) outliers start: 71 outliers final: 31 residues processed: 329 average time/residue: 0.6353 time to fit residues: 232.7684 Evaluate side-chains 312 residues out of total 2375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 268 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 689 TYR Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 370 ILE Chi-restraints excluded: chain B residue 427 GLN Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain B residue 556 LEU Chi-restraints excluded: chain B residue 641 ARG Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 744 LEU Chi-restraints excluded: chain C residue 329 ASN Chi-restraints excluded: chain C residue 408 GLN Chi-restraints excluded: chain C residue 500 LEU Chi-restraints excluded: chain C residue 538 ASP Chi-restraints excluded: chain C residue 539 SER Chi-restraints excluded: chain C residue 541 ASN Chi-restraints excluded: chain C residue 611 LYS Chi-restraints excluded: chain C residue 673 ILE Chi-restraints excluded: chain C residue 687 LYS Chi-restraints excluded: chain C residue 735 VAL Chi-restraints excluded: chain C residue 777 LYS Chi-restraints excluded: chain D residue 376 GLU Chi-restraints excluded: chain D residue 453 THR Chi-restraints excluded: chain D residue 457 ASP Chi-restraints excluded: chain D residue 499 THR Chi-restraints excluded: chain D residue 556 LEU Chi-restraints excluded: chain D residue 666 MET Chi-restraints excluded: chain D residue 669 LYS Chi-restraints excluded: chain D residue 685 LEU Chi-restraints excluded: chain D residue 734 GLU Chi-restraints excluded: chain D residue 739 ASN Chi-restraints excluded: chain D residue 772 LEU Chi-restraints excluded: chain E residue 380 MET Chi-restraints excluded: chain E residue 553 ILE Chi-restraints excluded: chain E residue 619 GLU Chi-restraints excluded: chain E residue 632 ARG Chi-restraints excluded: chain E residue 736 LEU Chi-restraints excluded: chain F residue 562 VAL Chi-restraints excluded: chain F residue 642 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 63 optimal weight: 0.8980 chunk 111 optimal weight: 3.9990 chunk 268 optimal weight: 10.0000 chunk 136 optimal weight: 9.9990 chunk 175 optimal weight: 1.9990 chunk 239 optimal weight: 50.0000 chunk 80 optimal weight: 8.9990 chunk 249 optimal weight: 50.0000 chunk 158 optimal weight: 3.9990 chunk 207 optimal weight: 20.0000 chunk 152 optimal weight: 4.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 667 ASN C 587 HIS ** C 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 442 ASN E 663 GLN 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 = 0.3992 r_free = 0.3992 target = 0.160650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.137115 restraints weight = 26408.482| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 2.03 r_work: 0.3554 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3412 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.3794 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= 0.164 Angle : 0.599 12.258 25717 Z= 0.297 Chirality : 0.042 0.164 2915 Planarity : 0.004 0.070 3334 Dihedral : 8.302 142.236 2589 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.51 % Allowed : 16.79 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.17), residues: 2372 helix: 0.26 (0.15), residues: 1261 sheet: -1.20 (0.40), residues: 153 loop : -1.43 (0.20), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 624 TYR 0.020 0.002 TYR C 605 PHE 0.020 0.002 PHE D 638 TRP 0.009 0.001 TRP A 583 HIS 0.006 0.002 HIS C 578 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.16 (19031) covalent geometry : angle 0.59927 / 0.30 (25717) hydrogen bonds : bond 0.03751 / 2.50 ( 799) hydrogen bonds : angle 4.39150 / 2.98 ( 2340) metal coordination : bond 0.00323 / 0.19 ( 10) Misc. bond : bond 0.00146 / 0.07 ( 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 347 residues out of total 2375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 278 time to evaluate : 0.625 Fit side-chains TARDY: cannot create tardy model for: "MET A 321 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 380 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 438 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET F 321 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 380 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 438 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 619 GLU cc_start: 0.7547 (OUTLIER) cc_final: 0.7255 (pt0) REVERT: A 683 MET cc_start: 0.3594 (tpp) cc_final: 0.0648 (pmm) REVERT: B 402 CYS cc_start: 0.7984 (p) cc_final: 0.7511 (p) REVERT: B 404 LEU cc_start: 0.8033 (tt) cc_final: 0.7830 (tp) REVERT: B 427 GLN cc_start: 0.7111 (OUTLIER) cc_final: 0.6537 (tm-30) REVERT: B 428 GLU cc_start: 0.6835 (tt0) cc_final: 0.6482 (mm-30) REVERT: B 433 GLN cc_start: 0.7688 (tp40) cc_final: 0.7465 (tm-30) REVERT: B 458 ILE cc_start: 0.8981 (OUTLIER) cc_final: 0.8588 (pt) REVERT: B 465 ARG cc_start: 0.6078 (mtt-85) cc_final: 0.5514 (tpt170) REVERT: B 469 PHE cc_start: 0.8526 (m-10) cc_final: 0.8270 (m-10) REVERT: B 501 GLU cc_start: 0.7080 (pm20) cc_final: 0.6833 (pm20) REVERT: B 504 LYS cc_start: 0.7673 (mtpt) cc_final: 0.7363 (mtpt) REVERT: B 636 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.8064 (mm-30) REVERT: B 641 ARG cc_start: 0.8347 (OUTLIER) cc_final: 0.8105 (mtm180) REVERT: B 667 ASN cc_start: 0.8598 (OUTLIER) cc_final: 0.8381 (t0) REVERT: B 683 MET cc_start: 0.6179 (ptp) cc_final: 0.5646 (ttt) REVERT: C 408 GLN cc_start: 0.8229 (OUTLIER) cc_final: 0.6110 (mp10) REVERT: C 500 LEU cc_start: 0.7585 (OUTLIER) cc_final: 0.7350 (tp) REVERT: C 611 LYS cc_start: 0.8342 (OUTLIER) cc_final: 0.7835 (mttp) REVERT: C 683 MET cc_start: 0.6143 (ttt) cc_final: 0.5735 (tmm) REVERT: C 695 ARG cc_start: 0.8069 (ttp80) cc_final: 0.7591 (ttp80) REVERT: C 699 ASP cc_start: 0.7702 (m-30) cc_final: 0.7492 (m-30) REVERT: C 777 LYS cc_start: 0.8182 (OUTLIER) cc_final: 0.7700 (mptm) REVERT: D 376 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7647 (tm-30) REVERT: D 504 LYS cc_start: 0.8208 (mtpm) cc_final: 0.7912 (mttt) REVERT: D 559 LYS cc_start: 0.8455 (mtpp) cc_final: 0.8207 (mttm) REVERT: D 624 ARG cc_start: 0.7983 (ttm-80) cc_final: 0.7634 (mtt-85) REVERT: D 666 MET cc_start: 0.7651 (OUTLIER) cc_final: 0.5870 (mmt) REVERT: D 668 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7631 (mt-10) REVERT: D 673 ILE cc_start: 0.8508 (OUTLIER) cc_final: 0.8234 (pp) REVERT: D 683 MET cc_start: 0.5524 (ptt) cc_final: 0.5296 (ptt) REVERT: D 685 LEU cc_start: 0.7105 (OUTLIER) cc_final: 0.6772 (tt) REVERT: E 318 LEU cc_start: 0.8858 (mt) cc_final: 0.8609 (mp) REVERT: E 407 ASP cc_start: 0.7617 (t0) cc_final: 0.7403 (t0) REVERT: E 415 LYS cc_start: 0.8363 (tttt) cc_final: 0.8073 (ttmm) REVERT: E 543 LYS cc_start: 0.8538 (mmtt) cc_final: 0.8126 (tptt) REVERT: E 619 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7750 (mp0) REVERT: E 632 ARG cc_start: 0.8605 (OUTLIER) cc_final: 0.7596 (tpt170) REVERT: F 619 GLU cc_start: 0.7796 (mp0) cc_final: 0.7584 (mp0) REVERT: F 625 MET cc_start: 0.8052 (ttm) cc_final: 0.7630 (ttm) REVERT: F 660 GLN cc_start: 0.8414 (tt0) cc_final: 0.8017 (tt0) REVERT: F 666 MET cc_start: 0.8854 (OUTLIER) cc_final: 0.8436 (mtp) REVERT: F 732 GLU cc_start: 0.7852 (mm-30) cc_final: 0.7401 (mt-10) outliers start: 69 outliers final: 27 residues processed: 317 average time/residue: 0.6266 time to fit residues: 222.5825 Evaluate side-chains 309 residues out of total 2375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 264 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain B residue 370 ILE 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 636 GLU Chi-restraints excluded: chain B residue 641 ARG Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 667 ASN Chi-restraints excluded: chain B residue 744 LEU Chi-restraints excluded: chain C residue 329 ASN Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 408 GLN Chi-restraints excluded: chain C residue 500 LEU Chi-restraints excluded: chain C residue 538 ASP Chi-restraints excluded: chain C residue 539 SER Chi-restraints excluded: chain C residue 541 ASN Chi-restraints excluded: chain C residue 562 VAL Chi-restraints excluded: chain C residue 611 LYS Chi-restraints excluded: chain C residue 673 ILE Chi-restraints excluded: chain C residue 687 LYS Chi-restraints excluded: chain C residue 735 VAL Chi-restraints excluded: chain C residue 777 LYS Chi-restraints excluded: chain D residue 376 GLU Chi-restraints excluded: chain D residue 453 THR Chi-restraints excluded: chain D residue 457 ASP Chi-restraints excluded: chain D residue 499 THR Chi-restraints excluded: chain D residue 541 ASN Chi-restraints excluded: chain D residue 666 MET Chi-restraints excluded: chain D residue 668 GLU Chi-restraints excluded: chain D residue 669 LYS Chi-restraints excluded: chain D residue 673 ILE Chi-restraints excluded: chain D residue 685 LEU Chi-restraints excluded: chain D residue 739 ASN 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 E residue 729 LEU Chi-restraints excluded: chain F residue 648 ASP Chi-restraints excluded: chain F residue 666 MET Chi-restraints excluded: chain F residue 705 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 177 optimal weight: 6.9990 chunk 47 optimal weight: 8.9990 chunk 260 optimal weight: 50.0000 chunk 101 optimal weight: 10.0000 chunk 249 optimal weight: 50.0000 chunk 281 optimal weight: 0.9990 chunk 83 optimal weight: 0.9990 chunk 184 optimal weight: 0.6980 chunk 59 optimal weight: 5.9990 chunk 22 optimal weight: 50.0000 chunk 148 optimal weight: 1.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 433 GLN B 667 ASN ** C 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 613 GLN 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 = 0.4001 r_free = 0.4001 target = 0.161422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.138163 restraints weight = 26551.202| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 1.96 r_work: 0.3569 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3428 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.3931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19044 Z= 0.132 Angle : 0.574 13.402 25717 Z= 0.284 Chirality : 0.041 0.153 2915 Planarity : 0.004 0.049 3334 Dihedral : 8.088 138.686 2589 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.95 % Allowed : 18.37 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.18), residues: 2372 helix: 0.50 (0.15), residues: 1257 sheet: -1.13 (0.40), residues: 153 loop : -1.35 (0.20), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 534 TYR 0.021 0.002 TYR C 605 PHE 0.016 0.001 PHE D 638 TRP 0.009 0.001 TRP F 583 HIS 0.005 0.001 HIS C 578 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.13 (19031) covalent geometry : angle 0.57407 / 0.28 (25717) hydrogen bonds : bond 0.03461 / 2.31 ( 799) hydrogen bonds : angle 4.30540 / 2.93 ( 2340) metal coordination : bond 0.00223 / 0.13 ( 10) Misc. bond : bond 0.00092 / 0.05 ( 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 336 residues out of total 2375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 278 time to evaluate : 0.598 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 619 GLU cc_start: 0.7525 (OUTLIER) cc_final: 0.7224 (pt0) REVERT: A 683 MET cc_start: 0.3298 (tpp) cc_final: 0.0519 (pmm) REVERT: A 686 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.7552 (tt0) REVERT: A 741 MET cc_start: 0.7045 (mmp) cc_final: 0.6843 (mmt) REVERT: B 402 CYS cc_start: 0.7956 (p) cc_final: 0.7734 (p) REVERT: B 427 GLN cc_start: 0.7069 (OUTLIER) cc_final: 0.6494 (tm-30) REVERT: B 428 GLU cc_start: 0.6835 (tt0) cc_final: 0.6483 (mm-30) REVERT: B 458 ILE cc_start: 0.8986 (OUTLIER) cc_final: 0.8584 (pt) REVERT: B 465 ARG cc_start: 0.6107 (mtt-85) cc_final: 0.5580 (mmt180) REVERT: B 469 PHE cc_start: 0.8492 (m-10) cc_final: 0.8267 (m-10) REVERT: B 641 ARG cc_start: 0.8296 (OUTLIER) cc_final: 0.8066 (mtm180) REVERT: B 683 MET cc_start: 0.6209 (ptp) cc_final: 0.5663 (ttt) REVERT: C 408 GLN cc_start: 0.8244 (OUTLIER) cc_final: 0.6082 (mp10) REVERT: C 611 LYS cc_start: 0.8352 (OUTLIER) cc_final: 0.7847 (mttp) REVERT: C 683 MET cc_start: 0.6332 (ttt) cc_final: 0.5924 (tmm) REVERT: C 695 ARG cc_start: 0.8049 (ttp80) cc_final: 0.7583 (ttp80) REVERT: C 699 ASP cc_start: 0.7693 (m-30) cc_final: 0.7486 (m-30) REVERT: C 777 LYS cc_start: 0.8158 (OUTLIER) cc_final: 0.7670 (mptm) REVERT: D 376 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7578 (tm-30) REVERT: D 504 LYS cc_start: 0.8193 (mtpm) cc_final: 0.7901 (mttt) REVERT: D 559 LYS cc_start: 0.8465 (mtpp) cc_final: 0.8235 (mttm) REVERT: D 624 ARG cc_start: 0.7954 (ttm-80) cc_final: 0.7610 (mtt-85) REVERT: D 666 MET cc_start: 0.7592 (OUTLIER) cc_final: 0.5858 (mmt) REVERT: D 668 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7599 (mt-10) REVERT: D 673 ILE cc_start: 0.8500 (OUTLIER) cc_final: 0.8246 (pp) REVERT: D 685 LEU cc_start: 0.7008 (OUTLIER) cc_final: 0.6685 (tt) REVERT: D 734 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.7079 (mt-10) REVERT: E 318 LEU cc_start: 0.8831 (mt) cc_final: 0.8591 (mp) REVERT: E 415 LYS cc_start: 0.8370 (tttt) cc_final: 0.8078 (ttmm) REVERT: E 543 LYS cc_start: 0.8578 (mmtt) cc_final: 0.8182 (tmtm) REVERT: E 619 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7647 (mp0) REVERT: E 632 ARG cc_start: 0.8598 (OUTLIER) cc_final: 0.7386 (tpt170) REVERT: F 619 GLU cc_start: 0.7789 (mp0) cc_final: 0.7564 (mp0) REVERT: F 625 MET cc_start: 0.8060 (ttm) cc_final: 0.7641 (ttm) REVERT: F 660 GLN cc_start: 0.8373 (tt0) cc_final: 0.7933 (tt0) REVERT: F 666 MET cc_start: 0.8824 (OUTLIER) cc_final: 0.8413 (mtp) REVERT: F 732 GLU cc_start: 0.7846 (mm-30) cc_final: 0.7413 (mt-10) outliers start: 58 outliers final: 26 residues processed: 312 average time/residue: 0.6071 time to fit residues: 211.8449 Evaluate side-chains 310 residues out of total 2375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 267 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 686 GLU 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 562 VAL Chi-restraints excluded: chain B residue 641 ARG Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 744 LEU Chi-restraints excluded: chain C residue 329 ASN Chi-restraints excluded: chain C residue 408 GLN Chi-restraints excluded: chain C residue 538 ASP Chi-restraints excluded: chain C residue 539 SER Chi-restraints excluded: chain C residue 541 ASN Chi-restraints excluded: chain C residue 611 LYS Chi-restraints excluded: chain C residue 673 ILE Chi-restraints excluded: chain C residue 687 LYS Chi-restraints excluded: chain C residue 735 VAL Chi-restraints excluded: chain C residue 777 LYS Chi-restraints excluded: chain D residue 376 GLU Chi-restraints excluded: chain D residue 453 THR Chi-restraints excluded: chain D residue 457 ASP Chi-restraints excluded: chain D residue 541 ASN Chi-restraints excluded: chain D residue 666 MET Chi-restraints excluded: chain D residue 668 GLU Chi-restraints excluded: chain D residue 669 LYS Chi-restraints excluded: chain D residue 673 ILE Chi-restraints excluded: chain D residue 685 LEU Chi-restraints excluded: chain D residue 734 GLU Chi-restraints excluded: chain D residue 739 ASN Chi-restraints excluded: chain E residue 335 ASP Chi-restraints excluded: chain E residue 553 ILE Chi-restraints excluded: chain E residue 619 GLU Chi-restraints excluded: chain E residue 632 ARG 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 648 ASP Chi-restraints excluded: chain F residue 666 MET 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 97 optimal weight: 1.9990 chunk 130 optimal weight: 0.0070 chunk 152 optimal weight: 0.8980 chunk 106 optimal weight: 0.0270 chunk 254 optimal weight: 50.0000 chunk 194 optimal weight: 2.9990 chunk 63 optimal weight: 7.9990 chunk 93 optimal weight: 7.9990 chunk 212 optimal weight: 0.4980 chunk 176 optimal weight: 0.7980 chunk 1 optimal weight: 50.0000 overall best weight: 0.4456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 667 ASN ** C 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.164754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.141772 restraints weight = 26503.611| |-----------------------------------------------------------------------------| r_work (start): 0.3738 rms_B_bonded: 1.92 r_work: 0.3622 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3483 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.4097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 19044 Z= 0.099 Angle : 0.542 13.018 25717 Z= 0.269 Chirality : 0.039 0.154 2915 Planarity : 0.004 0.045 3334 Dihedral : 7.627 132.567 2589 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.14 % Allowed : 19.59 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.18), residues: 2372 helix: 0.89 (0.15), residues: 1250 sheet: -1.00 (0.41), residues: 151 loop : -1.24 (0.21), residues: 971 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG E 483 TYR 0.021 0.001 TYR C 605 PHE 0.011 0.001 PHE E 393 TRP 0.010 0.001 TRP F 583 HIS 0.004 0.001 HIS E 535 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.10 (19031) covalent geometry : angle 0.54160 / 0.27 (25717) hydrogen bonds : bond 0.03002 / 2.01 ( 799) hydrogen bonds : angle 4.19015 / 2.84 ( 2340) metal coordination : bond 0.00057 / 0.03 ( 10) Misc. bond : bond 0.00034 / 0.02 ( 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 342 residues out of total 2375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 300 time to evaluate : 0.725 Fit side-chains TARDY: cannot create tardy model for: "MET A 321 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 380 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 438 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET F 321 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 380 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 438 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 619 GLU cc_start: 0.7434 (OUTLIER) cc_final: 0.7141 (pt0) REVERT: A 683 MET cc_start: 0.3018 (tpp) cc_final: 0.0470 (pmm) REVERT: A 741 MET cc_start: 0.6987 (mmp) cc_final: 0.6747 (mmt) REVERT: B 402 CYS cc_start: 0.7772 (p) cc_final: 0.7500 (p) REVERT: B 427 GLN cc_start: 0.7084 (OUTLIER) cc_final: 0.6640 (tm-30) REVERT: B 428 GLU cc_start: 0.6865 (tt0) cc_final: 0.6494 (mm-30) REVERT: B 465 ARG cc_start: 0.6130 (mtt-85) cc_final: 0.5599 (tpt170) REVERT: B 469 PHE cc_start: 0.8296 (m-10) cc_final: 0.8068 (m-10) REVERT: B 471 ARG cc_start: 0.7981 (mtp85) cc_final: 0.7775 (mtp85) REVERT: B 504 LYS cc_start: 0.7454 (mtpt) cc_final: 0.7105 (tppt) REVERT: B 636 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.8080 (mm-30) REVERT: B 641 ARG cc_start: 0.8193 (OUTLIER) cc_final: 0.7985 (mtm180) REVERT: B 667 ASN cc_start: 0.8327 (OUTLIER) cc_final: 0.8023 (t0) REVERT: B 669 LYS cc_start: 0.8727 (OUTLIER) cc_final: 0.8471 (ttmt) REVERT: B 683 MET cc_start: 0.6164 (ptp) cc_final: 0.5635 (ttt) REVERT: C 328 LYS cc_start: 0.8661 (ttmm) cc_final: 0.8222 (mmmm) REVERT: C 611 LYS cc_start: 0.8322 (OUTLIER) cc_final: 0.7826 (mttp) REVERT: C 666 MET cc_start: 0.8386 (mmt) cc_final: 0.6852 (mtt) REVERT: C 672 GLN cc_start: 0.8054 (mp10) cc_final: 0.7706 (mp10) REVERT: C 695 ARG cc_start: 0.8001 (ttp80) cc_final: 0.7503 (ttp80) REVERT: C 699 ASP cc_start: 0.7587 (m-30) cc_final: 0.7382 (m-30) REVERT: D 404 LEU cc_start: 0.8042 (tt) cc_final: 0.7814 (tp) REVERT: D 504 LYS cc_start: 0.8149 (mtpm) cc_final: 0.7875 (mttt) REVERT: D 559 LYS cc_start: 0.8442 (mtpp) cc_final: 0.8202 (mttm) REVERT: D 624 ARG cc_start: 0.7850 (ttm-80) cc_final: 0.7512 (mtt-85) REVERT: D 668 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7562 (mt-10) REVERT: D 685 LEU cc_start: 0.6825 (OUTLIER) cc_final: 0.6490 (tt) REVERT: D 734 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.7000 (mt-10) REVERT: E 318 LEU cc_start: 0.8742 (mt) cc_final: 0.8450 (mp) REVERT: E 415 LYS cc_start: 0.8362 (tttt) cc_final: 0.8076 (ttmm) REVERT: E 543 LYS cc_start: 0.8559 (mmtt) cc_final: 0.8132 (tptt) REVERT: E 619 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7476 (mp0) REVERT: F 625 MET cc_start: 0.8027 (ttm) cc_final: 0.7626 (ttm) REVERT: F 660 GLN cc_start: 0.8257 (tt0) cc_final: 0.7817 (tt0) REVERT: F 666 MET cc_start: 0.8819 (OUTLIER) cc_final: 0.8376 (mtp) REVERT: F 732 GLU cc_start: 0.7759 (mm-30) cc_final: 0.7393 (mt-10) REVERT: F 734 GLU cc_start: 0.7659 (mt-10) cc_final: 0.6653 (pm20) outliers start: 42 outliers final: 18 residues processed: 322 average time/residue: 0.5968 time to fit residues: 215.6486 Evaluate side-chains 305 residues out of total 2375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 275 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain B residue 427 GLN Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain B residue 636 GLU Chi-restraints excluded: chain B residue 641 ARG Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 667 ASN Chi-restraints excluded: chain B residue 669 LYS Chi-restraints excluded: chain C residue 391 ASP Chi-restraints excluded: chain C residue 539 SER Chi-restraints excluded: chain C residue 541 ASN Chi-restraints excluded: chain C residue 562 VAL Chi-restraints excluded: chain C residue 611 LYS Chi-restraints excluded: chain C residue 687 LYS Chi-restraints excluded: chain C residue 735 VAL Chi-restraints excluded: chain D residue 457 ASP Chi-restraints excluded: chain D residue 553 ILE Chi-restraints excluded: chain D residue 668 GLU Chi-restraints excluded: chain D residue 669 LYS Chi-restraints excluded: chain D residue 685 LEU Chi-restraints excluded: chain D residue 734 GLU Chi-restraints excluded: chain D residue 739 ASN Chi-restraints excluded: chain E residue 335 ASP Chi-restraints excluded: chain E residue 553 ILE 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 666 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 50 optimal weight: 9.9990 chunk 80 optimal weight: 7.9990 chunk 74 optimal weight: 1.9990 chunk 249 optimal weight: 50.0000 chunk 157 optimal weight: 20.0000 chunk 284 optimal weight: 30.0000 chunk 36 optimal weight: 2.9990 chunk 187 optimal weight: 8.9990 chunk 188 optimal weight: 6.9990 chunk 39 optimal weight: 0.4980 chunk 78 optimal weight: 8.9990 overall best weight: 4.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 523 ASN ** B 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 544 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.160022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.137096 restraints weight = 26608.564| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 1.87 r_work: 0.3546 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3402 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.4146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 19044 Z= 0.200 Angle : 0.642 14.179 25717 Z= 0.316 Chirality : 0.044 0.165 2915 Planarity : 0.004 0.052 3334 Dihedral : 7.988 134.275 2589 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 2.04 % Allowed : 20.20 % Favored : 77.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.18), residues: 2372 helix: 0.66 (0.15), residues: 1257 sheet: -0.92 (0.42), residues: 143 loop : -1.31 (0.20), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG E 483 TYR 0.026 0.002 TYR D 573 PHE 0.019 0.002 PHE D 638 TRP 0.010 0.002 TRP F 583 HIS 0.009 0.002 HIS C 578 Details of bonding type rmsd/Z covalent geometry : bond 0.00489 / 0.20 (19031) covalent geometry : angle 0.64215 / 0.32 (25717) hydrogen bonds : bond 0.03907 / 2.60 ( 799) hydrogen bonds : angle 4.31045 / 2.93 ( 2340) metal coordination : bond 0.00413 / 0.25 ( 10) Misc. bond : bond 0.00165 / 0.09 ( 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 311 residues out of total 2375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 271 time to evaluate : 0.748 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 619 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.7259 (pt0) REVERT: A 683 MET cc_start: 0.3207 (tpp) cc_final: 0.0515 (pmm) REVERT: A 741 MET cc_start: 0.7298 (mmp) cc_final: 0.6911 (mmt) REVERT: B 402 CYS cc_start: 0.7922 (p) cc_final: 0.7715 (p) REVERT: B 427 GLN cc_start: 0.7103 (OUTLIER) cc_final: 0.6558 (tm-30) REVERT: B 428 GLU cc_start: 0.6821 (tt0) cc_final: 0.6501 (mm-30) REVERT: B 433 GLN cc_start: 0.7768 (tm-30) cc_final: 0.7532 (tm-30) REVERT: B 465 ARG cc_start: 0.5974 (mtt-85) cc_final: 0.5493 (mmt180) REVERT: B 469 PHE cc_start: 0.8449 (m-10) cc_final: 0.8215 (m-10) REVERT: B 641 ARG cc_start: 0.8346 (OUTLIER) cc_final: 0.8077 (mtm-85) REVERT: B 683 MET cc_start: 0.6189 (ptp) cc_final: 0.5667 (ttt) REVERT: C 611 LYS cc_start: 0.8372 (OUTLIER) cc_final: 0.7882 (mttp) REVERT: C 695 ARG cc_start: 0.8107 (ttp80) cc_final: 0.7628 (ttp80) REVERT: C 699 ASP cc_start: 0.7661 (m-30) cc_final: 0.7446 (m-30) REVERT: D 559 LYS cc_start: 0.8471 (mtpp) cc_final: 0.8236 (mttm) REVERT: D 607 GLN cc_start: 0.8385 (OUTLIER) cc_final: 0.7474 (tm-30) REVERT: D 624 ARG cc_start: 0.7972 (ttm-80) cc_final: 0.7657 (mtt-85) REVERT: D 668 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7669 (mt-10) REVERT: D 685 LEU cc_start: 0.6800 (OUTLIER) cc_final: 0.6596 (tt) REVERT: D 734 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.7082 (mt-10) REVERT: D 767 ASP cc_start: 0.7840 (m-30) cc_final: 0.7625 (m-30) REVERT: E 318 LEU cc_start: 0.8790 (mt) cc_final: 0.8509 (mp) REVERT: E 415 LYS cc_start: 0.8380 (tttt) cc_final: 0.8093 (ttmm) REVERT: E 516 PHE cc_start: 0.8192 (m-80) cc_final: 0.7880 (m-80) REVERT: E 523 ASN cc_start: 0.6757 (m110) cc_final: 0.6497 (m110) REVERT: E 543 LYS cc_start: 0.8614 (mmtt) cc_final: 0.8146 (tptt) REVERT: E 619 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7735 (mp0) REVERT: F 625 MET cc_start: 0.8060 (ttm) cc_final: 0.7681 (ttm) REVERT: F 660 GLN cc_start: 0.8425 (tt0) cc_final: 0.8039 (tt0) REVERT: F 732 GLU cc_start: 0.7863 (mm-30) cc_final: 0.7476 (mt-10) REVERT: F 734 GLU cc_start: 0.7697 (mt-10) cc_final: 0.6597 (pm20) outliers start: 40 outliers final: 18 residues processed: 292 average time/residue: 0.6051 time to fit residues: 198.2448 Evaluate side-chains 290 residues out of total 2375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 263 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain B residue 370 ILE Chi-restraints excluded: chain B residue 427 GLN Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain B residue 641 ARG Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 538 ASP Chi-restraints excluded: chain C residue 541 ASN Chi-restraints excluded: chain C residue 562 VAL Chi-restraints excluded: chain C residue 611 LYS Chi-restraints excluded: chain C residue 687 LYS Chi-restraints excluded: chain C residue 735 VAL Chi-restraints excluded: chain D residue 457 ASP Chi-restraints excluded: chain D residue 607 GLN Chi-restraints excluded: chain D residue 668 GLU Chi-restraints excluded: chain D residue 669 LYS Chi-restraints excluded: chain D residue 685 LEU Chi-restraints excluded: chain D residue 734 GLU Chi-restraints excluded: chain D residue 739 ASN Chi-restraints excluded: chain E residue 619 GLU Chi-restraints excluded: chain E residue 729 LEU Chi-restraints excluded: chain F residue 562 VAL Chi-restraints excluded: chain F residue 642 ILE Chi-restraints excluded: chain F residue 648 ASP Chi-restraints excluded: chain F residue 666 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 102 optimal weight: 0.7980 chunk 64 optimal weight: 4.9990 chunk 171 optimal weight: 0.3980 chunk 18 optimal weight: 50.0000 chunk 146 optimal weight: 0.9980 chunk 9 optimal weight: 50.0000 chunk 211 optimal weight: 6.9990 chunk 116 optimal weight: 2.9990 chunk 256 optimal weight: 50.0000 chunk 219 optimal weight: 0.9980 chunk 31 optimal weight: 9.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 667 ASN ** C 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.162641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.139568 restraints weight = 26524.067| |-----------------------------------------------------------------------------| r_work (start): 0.3706 rms_B_bonded: 2.04 r_work: 0.3588 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3446 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.4268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19044 Z= 0.111 Angle : 0.575 14.208 25717 Z= 0.283 Chirality : 0.040 0.155 2915 Planarity : 0.004 0.044 3334 Dihedral : 7.703 130.085 2589 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.73 % Allowed : 21.17 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.18), residues: 2372 helix: 0.94 (0.15), residues: 1252 sheet: -0.82 (0.42), residues: 142 loop : -1.24 (0.20), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 483 TYR 0.021 0.001 TYR D 605 PHE 0.014 0.001 PHE E 638 TRP 0.007 0.001 TRP A 583 HIS 0.005 0.001 HIS D 578 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.11 (19031) covalent geometry : angle 0.57504 / 0.28 (25717) hydrogen bonds : bond 0.03223 / 2.15 ( 799) hydrogen bonds : angle 4.21226 / 2.86 ( 2340) metal coordination : bond 0.00131 / 0.08 ( 10) Misc. bond : bond 0.00047 / 0.02 ( 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 305 residues out of total 2375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 271 time to evaluate : 0.699 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 567 GLU cc_start: 0.7475 (OUTLIER) cc_final: 0.6836 (mt-10) REVERT: A 619 GLU cc_start: 0.7524 (OUTLIER) cc_final: 0.7228 (pt0) REVERT: A 683 MET cc_start: 0.2991 (tpp) cc_final: 0.0475 (pmm) REVERT: B 427 GLN cc_start: 0.7069 (OUTLIER) cc_final: 0.6538 (tm-30) REVERT: B 428 GLU cc_start: 0.6839 (tt0) cc_final: 0.6483 (mm-30) REVERT: B 465 ARG cc_start: 0.6088 (mtt-85) cc_final: 0.5554 (tpt170) REVERT: B 469 PHE cc_start: 0.8331 (m-10) cc_final: 0.8096 (m-10) REVERT: B 636 GLU cc_start: 0.8395 (tt0) cc_final: 0.8110 (mm-30) REVERT: B 641 ARG cc_start: 0.8247 (OUTLIER) cc_final: 0.8045 (mtm180) REVERT: B 667 ASN cc_start: 0.8434 (OUTLIER) cc_final: 0.7918 (t0) REVERT: B 683 MET cc_start: 0.6117 (ptp) cc_final: 0.5666 (ttt) REVERT: C 328 LYS cc_start: 0.8684 (ttmm) cc_final: 0.8255 (mmmm) REVERT: C 611 LYS cc_start: 0.8355 (OUTLIER) cc_final: 0.7869 (mttp) REVERT: C 695 ARG cc_start: 0.8037 (ttp80) cc_final: 0.7540 (ttp80) REVERT: C 699 ASP cc_start: 0.7613 (m-30) cc_final: 0.7387 (m-30) REVERT: C 732 GLU cc_start: 0.7106 (OUTLIER) cc_final: 0.6879 (pm20) REVERT: D 404 LEU cc_start: 0.8091 (tt) cc_final: 0.7885 (tp) REVERT: D 504 LYS cc_start: 0.8148 (mtpm) cc_final: 0.7864 (mttt) REVERT: D 559 LYS cc_start: 0.8482 (mtpp) cc_final: 0.8201 (mttm) REVERT: D 624 ARG cc_start: 0.7927 (ttm-80) cc_final: 0.7594 (mtt-85) REVERT: D 668 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.7586 (mt-10) REVERT: D 673 ILE cc_start: 0.8478 (OUTLIER) cc_final: 0.8268 (pp) REVERT: D 734 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.7033 (mt-10) REVERT: D 767 ASP cc_start: 0.7812 (m-30) cc_final: 0.7601 (m-30) REVERT: E 318 LEU cc_start: 0.8751 (mt) cc_final: 0.8450 (mp) REVERT: E 391 ASP cc_start: 0.8093 (t0) cc_final: 0.7521 (t0) REVERT: E 415 LYS cc_start: 0.8380 (tttt) cc_final: 0.8080 (ttmm) REVERT: E 516 PHE cc_start: 0.8191 (m-80) cc_final: 0.7943 (m-80) REVERT: E 523 ASN cc_start: 0.6730 (m110) cc_final: 0.6471 (m110) REVERT: E 530 LEU cc_start: 0.7937 (mp) cc_final: 0.7704 (pp) REVERT: E 543 LYS cc_start: 0.8616 (mmtt) cc_final: 0.8135 (tptt) REVERT: E 619 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7672 (mp0) REVERT: F 625 MET cc_start: 0.8013 (ttm) cc_final: 0.7635 (ttm) REVERT: F 660 GLN cc_start: 0.8328 (tt0) cc_final: 0.7911 (tt0) REVERT: F 732 GLU cc_start: 0.7795 (mm-30) cc_final: 0.7405 (mt-10) REVERT: F 734 GLU cc_start: 0.7680 (mt-10) cc_final: 0.6629 (pm20) outliers start: 34 outliers final: 13 residues processed: 290 average time/residue: 0.6335 time to fit residues: 205.6211 Evaluate side-chains 288 residues out of total 2375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 264 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 567 GLU Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain B residue 427 GLN Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain B residue 641 ARG Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 667 ASN Chi-restraints excluded: chain C residue 541 ASN Chi-restraints excluded: chain C residue 562 VAL Chi-restraints excluded: chain C residue 611 LYS Chi-restraints excluded: chain C residue 687 LYS Chi-restraints excluded: chain C residue 732 GLU Chi-restraints excluded: chain C residue 735 VAL Chi-restraints excluded: chain D residue 457 ASP Chi-restraints excluded: chain D residue 668 GLU Chi-restraints excluded: chain D residue 669 LYS Chi-restraints excluded: chain D residue 673 ILE Chi-restraints excluded: chain D residue 734 GLU Chi-restraints excluded: chain D residue 739 ASN Chi-restraints excluded: chain E residue 619 GLU Chi-restraints excluded: chain F residue 562 VAL Chi-restraints excluded: chain F residue 648 ASP Chi-restraints excluded: chain F residue 666 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 219 optimal weight: 5.9990 chunk 188 optimal weight: 5.9990 chunk 112 optimal weight: 1.9990 chunk 92 optimal weight: 40.0000 chunk 205 optimal weight: 0.6980 chunk 83 optimal weight: 5.9990 chunk 275 optimal weight: 9.9990 chunk 130 optimal weight: 0.1980 chunk 245 optimal weight: 50.0000 chunk 46 optimal weight: 8.9990 chunk 104 optimal weight: 2.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 472 GLN B 667 ASN ** C 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.162553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.139363 restraints weight = 26573.855| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 2.00 r_work: 0.3589 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3446 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.4281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.132 19044 Z= 0.156 Angle : 0.745 59.200 25717 Z= 0.410 Chirality : 0.045 0.959 2915 Planarity : 0.004 0.073 3334 Dihedral : 7.701 130.038 2589 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.58 % Allowed : 21.27 % Favored : 77.15 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.18), residues: 2372 helix: 0.95 (0.15), residues: 1252 sheet: -0.81 (0.42), residues: 142 loop : -1.25 (0.20), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 483 TYR 0.019 0.001 TYR C 605 PHE 0.013 0.001 PHE E 638 TRP 0.007 0.001 TRP A 583 HIS 0.004 0.001 HIS D 578 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.16 (19031) covalent geometry : angle 0.74491 / 0.41 (25717) hydrogen bonds : bond 0.03254 / 2.17 ( 799) hydrogen bonds : angle 4.21246 / 2.86 ( 2340) metal coordination : bond 0.00178 / 0.11 ( 10) Misc. bond : bond 0.00073 / 0.04 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6316.26 seconds wall clock time: 108 minutes 14.35 seconds (6494.35 seconds total)