Starting phenix.real_space_refine on Sat Feb 17 16:02:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nyy_0552/02_2024/6nyy_0552_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nyy_0552/02_2024/6nyy_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nyy_0552/02_2024/6nyy_0552.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nyy_0552/02_2024/6nyy_0552.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nyy_0552/02_2024/6nyy_0552_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nyy_0552/02_2024/6nyy_0552_updated.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.010 sd= 0.024 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 6 6.06 5 P 11 5.49 5 Mg 3 5.21 5 S 60 5.16 5 C 12356 2.51 5 N 3221 2.21 5 O 3569 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 689": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 414": "NH1" <-> "NH2" Residue "C ARG 468": "NH1" <-> "NH2" Residue "C TYR 689": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 465": "NH1" <-> "NH2" Residue "D TYR 689": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 397": "NH1" <-> "NH2" Residue "E ARG 483": "NH1" <-> "NH2" Residue "E ARG 492": "NH1" <-> "NH2" Residue "E TYR 605": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 689": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 689": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 19226 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 2038 Classifications: {'peptide': 459} Incomplete info: {'c_alpha_only': 231, 'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 436} Unresolved chain links: 231 Unresolved chain link angles: 707 Unresolved chain link dihedrals: 693 Unresolved non-hydrogen bonds: 1564 Unresolved non-hydrogen angles: 1718 Unresolved non-hydrogen dihedrals: 533 Unresolved non-hydrogen chiralities: 281 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 10, 'ASP:plan': 15, 'PHE:plan': 14, 'GLU:plan': 13, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 352 Chain: "B" Number of atoms: 3786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 3786 Classifications: {'peptide': 487} Link IDs: {'PTRANS': 23, 'TRANS': 463} Chain breaks: 1 Chain: "C" Number of atoms: 3818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3818 Classifications: {'peptide': 491} Link IDs: {'PTRANS': 23, 'TRANS': 467} Chain: "D" Number of atoms: 3818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3818 Classifications: {'peptide': 491} Link IDs: {'PTRANS': 23, 'TRANS': 467} Chain: "E" Number of atoms: 3640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3640 Classifications: {'peptide': 467} Link IDs: {'PTRANS': 21, 'TRANS': 445} Chain breaks: 1 Chain: "F" Number of atoms: 1802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 1802 Classifications: {'peptide': 460} Incomplete info: {'c_alpha_only': 267} Link IDs: {'PTRANS': 22, 'TRANS': 437} Unresolved chain links: 267 Unresolved chain link angles: 815 Unresolved chain link dihedrals: 801 Unresolved non-hydrogen bonds: 1809 Unresolved non-hydrogen angles: 1988 Unresolved non-hydrogen dihedrals: 615 Unresolved non-hydrogen chiralities: 324 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 12, 'ASP:plan': 16, 'PHE:plan': 15, 'GLU:plan': 17, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 421 Chain: "G" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 55 Classifications: {'peptide': 11} Link IDs: {'TRANS': 10} Chain: "H" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 55 Classifications: {'peptide': 11} Link IDs: {'TRANS': 10} Chain: "I" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 45 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Chain: "J" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 40 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' ZN': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 10.88, per 1000 atoms: 0.57 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 - 3.50 Amino acid : False - 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 7.38 Conformation dependent library (CDL) restraints added in 3.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 801 " pdb="ZN ZN A 801 " - pdb=" NE2 HIS A 574 " pdb=" ZN B 803 " pdb="ZN ZN B 803 " - pdb=" NE2 HIS B 574 " pdb="ZN ZN B 803 " - pdb=" NE2 HIS B 578 " pdb=" ZN C 802 " pdb="ZN ZN C 802 " - pdb=" NE2 HIS C 578 " pdb="ZN ZN C 802 " - pdb=" NE2 HIS C 574 " pdb=" ZN D 803 " pdb="ZN ZN D 803 " - pdb=" NE2 HIS D 578 " pdb="ZN ZN D 803 " - pdb=" NE2 HIS D 574 " pdb=" ZN E 802 " pdb="ZN ZN E 802 " - pdb=" NE2 HIS E 574 " pdb=" ZN F 801 " pdb="ZN ZN F 801 " - pdb=" NE2 HIS F 574 " pdb="ZN ZN F 801 " - pdb=" NE2 HIS F 578 " 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4420 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 91 helices and 7 sheets defined 38.5% alpha, 3.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.95 Creating SS restraints... Processing helix chain 'A' and resid 527 through 532 Processing helix chain 'A' and resid 542 through 552 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 565 through 584 removed outlier: 3.862A pdb=" N THR A 570 " --> pdb=" O GLU A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 638 removed outlier: 3.606A pdb=" N ASP A 623 " --> pdb=" O GLU A 619 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLY A 631 " --> pdb=" O MET A 627 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N ARG A 632 " --> pdb=" O THR A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 661 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 691 through 718 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 720 through 733 Processing helix chain 'A' and resid 738 through 745 Processing helix chain 'B' and resid 307 through 309 No H-bonds generated for 'chain 'B' and resid 307 through 309' Processing helix chain 'B' and resid 318 through 328 removed outlier: 3.579A pdb=" N LEU B 327 " --> pdb=" O PHE B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 364 Processing helix chain 'B' and resid 374 through 376 No H-bonds generated for 'chain 'B' and resid 374 through 376' Processing helix chain 'B' and resid 385 through 398 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 411 No H-bonds generated for 'chain 'B' and resid 409 through 411' Processing helix chain 'B' and resid 422 through 441 removed outlier: 4.216A pdb=" N GLN B 427 " --> pdb=" O GLY B 423 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N PHE B 441 " --> pdb=" O GLU B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 464 Processing helix chain 'B' and resid 480 through 490 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 504 through 512 Processing helix chain 'B' and resid 518 through 534 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) Processing helix chain 'B' and resid 542 through 554 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 567 through 584 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 618 through 638 removed outlier: 3.789A pdb=" N ARG B 624 " --> pdb=" O GLN B 620 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLY B 630 " --> pdb=" O CYS B 626 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLY B 631 " --> pdb=" O MET B 627 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N ARG B 632 " --> pdb=" O THR B 628 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 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 691 through 718 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 720 through 730 Processing helix chain 'B' and resid 738 through 745 Processing helix chain 'B' and resid 756 through 759 No H-bonds generated for 'chain 'B' and resid 756 through 759' Processing helix chain 'C' and resid 307 through 309 No H-bonds generated for 'chain 'C' and resid 307 through 309' Processing helix chain 'C' and resid 314 through 328 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 334 removed outlier: 3.926A pdb=" N GLN C 334 " --> pdb=" O LYS C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 364 removed outlier: 3.622A pdb=" N THR C 361 " --> pdb=" O LEU C 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 398 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 411 No H-bonds generated for 'chain 'C' and resid 409 through 411' Processing helix chain 'C' and resid 422 through 438 removed outlier: 3.587A pdb=" N SER C 425 " --> pdb=" O GLY C 422 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLU C 426 " --> pdb=" O GLY C 423 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASN C 429 " --> pdb=" O GLU C 426 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASN C 432 " --> pdb=" O ASN C 429 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLN C 433 " --> pdb=" O THR C 430 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU C 435 " --> pdb=" O ASN C 432 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU C 437 " --> pdb=" O LEU C 434 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N MET C 438 " --> pdb=" O LEU C 435 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 490 removed outlier: 3.647A pdb=" N SER C 485 " --> pdb=" O LYS C 481 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 511 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 520 through 532 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 553 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 568 through 584 Processing helix chain 'C' and resid 618 through 638 removed outlier: 3.550A pdb=" N MET C 627 " --> pdb=" O ASP C 623 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLY C 630 " --> pdb=" O CYS C 626 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N GLY C 631 " --> pdb=" O MET C 627 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N ARG C 632 " --> pdb=" O THR C 628 " (cutoff:3.500A) Processing helix chain 'C' and resid 647 through 658 removed outlier: 3.587A pdb=" N LYS C 652 " --> pdb=" O ASP C 648 " (cutoff:3.500A) Processing helix chain 'C' and resid 691 through 716 removed outlier: 3.537A pdb=" N ILE C 703 " --> pdb=" O ASP C 699 " (cutoff:3.500A) Processing helix chain 'C' and resid 720 through 733 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 738 through 745 Processing helix chain 'C' and resid 756 through 759 No H-bonds generated for 'chain 'C' and resid 756 through 759' Processing helix chain 'C' and resid 774 through 776 No H-bonds generated for 'chain 'C' and resid 774 through 776' Processing helix chain 'D' and resid 307 through 309 No H-bonds generated for 'chain 'D' and resid 307 through 309' Processing helix chain 'D' and resid 314 through 328 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 330 through 334 Processing helix chain 'D' and resid 356 through 364 removed outlier: 3.580A pdb=" N THR D 361 " --> pdb=" O LEU D 357 " (cutoff:3.500A) Processing helix chain 'D' and resid 374 through 376 No H-bonds generated for 'chain 'D' and resid 374 through 376' Processing helix chain 'D' and resid 386 through 398 removed outlier: 3.817A pdb=" N ASP D 391 " --> pdb=" O ALA D 387 " (cutoff:3.500A) Processing helix chain 'D' and resid 409 through 411 No H-bonds generated for 'chain 'D' and resid 409 through 411' Processing helix chain 'D' and resid 425 through 438 removed outlier: 3.668A pdb=" N THR D 430 " --> pdb=" O GLU D 426 " (cutoff:3.500A) Processing helix chain 'D' and resid 480 through 490 removed outlier: 3.770A pdb=" N SER D 485 " --> pdb=" O LYS D 481 " (cutoff:3.500A) Processing helix chain 'D' and resid 502 through 512 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 518 through 534 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) Processing helix chain 'D' and resid 542 through 554 removed outlier: 3.676A pdb=" N ALA D 548 " --> pdb=" O HIS D 544 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 584 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 618 through 628 removed outlier: 3.787A pdb=" N ARG D 624 " --> pdb=" O GLN D 620 " (cutoff:3.500A) Processing helix chain 'D' and resid 630 through 637 removed outlier: 3.509A pdb=" N GLU D 635 " --> pdb=" O GLY D 631 " (cutoff:3.500A) Processing helix chain 'D' and resid 647 through 661 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 691 through 716 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 720 through 732 removed outlier: 3.581A pdb=" N LEU D 729 " --> pdb=" O LYS D 725 " (cutoff:3.500A) Processing helix chain 'D' and resid 739 through 745 removed outlier: 3.502A pdb=" N LEU D 744 " --> pdb=" O ASP D 740 " (cutoff:3.500A) Processing helix chain 'D' and resid 756 through 760 Processing helix chain 'D' and resid 774 through 776 No H-bonds generated for 'chain 'D' and resid 774 through 776' Processing helix chain 'E' and resid 307 through 309 No H-bonds generated for 'chain 'E' and resid 307 through 309' Processing helix chain 'E' and resid 314 through 328 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 330 through 334 Processing helix chain 'E' and resid 354 through 365 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 384 through 398 removed outlier: 3.670A pdb=" N ASP E 391 " --> pdb=" O ALA E 387 " (cutoff:3.500A) Processing helix chain 'E' and resid 409 through 411 No H-bonds generated for 'chain 'E' and resid 409 through 411' Processing helix chain 'E' and resid 424 through 438 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 456 through 458 No H-bonds generated for 'chain 'E' and resid 456 through 458' Processing helix chain 'E' and resid 480 through 491 removed outlier: 3.917A pdb=" N SER E 485 " --> pdb=" O LYS E 481 " (cutoff:3.500A) Processing helix chain 'E' and resid 502 through 512 removed outlier: 4.001A pdb=" N ARG E 507 " --> pdb=" O ASP E 503 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER E 511 " --> pdb=" O ARG E 507 " (cutoff:3.500A) Processing helix chain 'E' and resid 518 through 534 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 542 through 553 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 565 through 584 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 619 through 637 removed outlier: 4.072A pdb=" N ARG E 624 " --> pdb=" O GLN E 620 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N GLY E 631 " --> pdb=" O MET E 627 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N ARG E 632 " --> pdb=" O THR E 628 " (cutoff:3.500A) 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 645 through 661 removed outlier: 4.331A pdb=" N ASP E 648 " --> pdb=" O GLY E 645 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASP E 649 " --> pdb=" O ALA E 646 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ARG E 651 " --> pdb=" O ASP E 648 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N LYS E 652 " --> pdb=" O ASP E 649 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL E 653 " --> pdb=" O LEU E 650 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLN E 655 " --> pdb=" O LYS E 652 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N SER E 656 " --> pdb=" O VAL E 653 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR E 658 " --> pdb=" O GLN E 655 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N ALA E 659 " --> pdb=" O SER E 656 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLN E 660 " --> pdb=" O ALA E 657 " (cutoff:3.500A) Processing helix chain 'E' and resid 691 through 716 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 720 through 730 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 738 through 745 removed outlier: 3.577A pdb=" N GLU E 743 " --> pdb=" O ASN E 739 " (cutoff:3.500A) Processing helix chain 'F' and resid 565 through 584 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) removed outlier: 3.997A pdb=" N TRP F 583 " --> pdb=" O ALA F 579 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 638 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) removed outlier: 4.662A pdb=" N GLY F 631 " --> pdb=" O MET F 627 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N ARG F 632 " --> pdb=" O THR F 628 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL F 633 " --> pdb=" O LEU F 629 " (cutoff:3.500A) Processing helix chain 'F' and resid 645 through 659 removed outlier: 4.244A pdb=" N ASP F 648 " --> pdb=" O GLY F 645 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU F 650 " --> pdb=" O GLN F 647 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL F 653 " --> pdb=" O LEU F 650 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLN F 655 " --> pdb=" O LYS F 652 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N SER F 656 " --> pdb=" O VAL F 653 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N TYR F 658 " --> pdb=" O GLN F 655 " (cutoff:3.500A) Processing helix chain 'F' and resid 691 through 716 removed outlier: 3.816A pdb=" N ILE F 703 " --> pdb=" O ASP F 699 " (cutoff:3.500A) Processing helix chain 'F' and resid 720 through 733 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 738 through 745 Processing sheet with id= A, first strand: chain 'A' and resid 590 through 595 removed outlier: 6.700A pdb=" N GLN A 607 " --> pdb=" O LEU A 592 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N VAL A 594 " --> pdb=" O TYR A 605 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N TYR A 605 " --> pdb=" O VAL A 594 " (cutoff:3.500A) Processing sheet with id= B, 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: 7.433A pdb=" N LEU B 450 " --> pdb=" O ILE B 406 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 735 through 737 removed outlier: 6.640A pdb=" N GLN B 607 " --> pdb=" O LEU B 592 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N VAL B 594 " --> pdb=" O TYR B 605 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N TYR B 605 " --> pdb=" O VAL B 594 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 471 through 474 removed outlier: 3.658A pdb=" N ARG C 471 " --> pdb=" O GLY C 343 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ILE C 449 " --> pdb=" O ALA C 344 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N LEU C 346 " --> pdb=" O ILE C 449 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ALA C 451 " --> pdb=" O LEU C 346 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 471 through 474 removed outlier: 6.405A pdb=" N ILE D 449 " --> pdb=" O ALA D 344 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N LEU D 346 " --> pdb=" O ILE D 449 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ALA D 451 " --> pdb=" O LEU D 346 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 590 through 595 removed outlier: 6.726A pdb=" N GLN D 607 " --> pdb=" O LEU D 592 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N VAL D 594 " --> pdb=" O TYR D 605 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N TYR D 605 " --> pdb=" O VAL D 594 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'E' and resid 471 through 474 removed outlier: 5.918A pdb=" N ILE E 449 " --> pdb=" O ALA E 344 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N LEU E 346 " --> pdb=" O ILE E 449 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ALA E 451 " --> pdb=" O LEU E 346 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE E 370 " --> pdb=" O ILE E 403 " (cutoff:3.500A) 657 hydrogen bonds defined for protein. 1914 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.43 Time building geometry restraints manager: 7.91 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: 98.55 - 105.97: 467 105.97 - 113.40: 10551 113.40 - 120.82: 8910 120.82 - 128.24: 5696 128.24 - 135.66: 93 Bond angle restraints: 25717 Sorted by residual: angle pdb=" N LEU F 563 " pdb=" CA LEU F 563 " pdb=" C LEU F 563 " ideal model delta sigma weight residual 108.79 119.17 -10.38 1.53e+00 4.27e-01 4.60e+01 angle pdb=" PB ANP C 803 " pdb=" N3B ANP C 803 " pdb=" PG ANP C 803 " ideal model delta sigma weight residual 126.95 107.90 19.05 3.00e+00 1.11e-01 4.03e+01 angle pdb=" PB ANP B 801 " pdb=" N3B ANP B 801 " pdb=" PG ANP B 801 " ideal model delta sigma weight residual 126.95 109.10 17.85 3.00e+00 1.11e-01 3.54e+01 angle pdb=" PB ANP D 801 " pdb=" N3B ANP D 801 " pdb=" PG ANP D 801 " ideal model delta sigma weight residual 126.95 109.67 17.28 3.00e+00 1.11e-01 3.32e+01 angle pdb=" N GLY A 554 " pdb=" CA GLY A 554 " pdb=" C GLY A 554 " ideal model delta sigma weight residual 112.77 119.12 -6.35 1.28e+00 6.10e-01 2.46e+01 ... (remaining 25712 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.48: 11589 34.48 - 68.95: 82 68.95 - 103.43: 17 103.43 - 137.91: 4 137.91 - 172.38: 3 Dihedral angle restraints: 11695 sinusoidal: 4829 harmonic: 6866 Sorted by residual: dihedral pdb=" C5' ADP E 801 " pdb=" O5' ADP E 801 " pdb=" PA ADP E 801 " pdb=" O2A ADP E 801 " ideal model delta sinusoidal sigma weight residual -60.00 112.39 -172.38 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" O2A ADP E 801 " pdb=" O3A ADP E 801 " pdb=" PA ADP E 801 " pdb=" PB ADP E 801 " ideal model delta sinusoidal sigma weight residual -60.00 66.09 -126.09 1 2.00e+01 2.50e-03 3.81e+01 dihedral pdb=" O1B ADP E 801 " pdb=" O3A ADP E 801 " pdb=" PB ADP E 801 " pdb=" PA ADP E 801 " ideal model delta sinusoidal sigma weight residual -60.00 59.48 -119.49 1 2.00e+01 2.50e-03 3.58e+01 ... (remaining 11692 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 2468 0.069 - 0.138: 407 0.138 - 0.207: 30 0.207 - 0.276: 7 0.276 - 0.345: 3 Chirality restraints: 2915 Sorted by residual: chirality pdb=" CB ILE B 449 " pdb=" CA ILE B 449 " pdb=" CG1 ILE B 449 " pdb=" CG2 ILE B 449 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.35 2.00e-01 2.50e+01 2.98e+00 chirality pdb=" C3' ANP D 801 " pdb=" C2' ANP D 801 " pdb=" C4' ANP D 801 " pdb=" O3' ANP D 801 " both_signs ideal model delta sigma weight residual False -2.36 -2.65 0.29 2.00e-01 2.50e+01 2.16e+00 chirality pdb=" C3' ANP C 803 " pdb=" C2' ANP C 803 " pdb=" C4' ANP C 803 " pdb=" O3' ANP C 803 " both_signs ideal model delta sigma weight residual False -2.36 -2.65 0.29 2.00e-01 2.50e+01 2.11e+00 ... (remaining 2912 not shown) Planarity restraints: 3334 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 552 " 0.028 2.00e-02 2.50e+03 5.61e-02 3.15e+01 pdb=" C VAL A 552 " -0.097 2.00e-02 2.50e+03 pdb=" O VAL A 552 " 0.037 2.00e-02 2.50e+03 pdb=" N ILE A 553 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 523 " 0.016 2.00e-02 2.50e+03 3.14e-02 9.87e+00 pdb=" CG ASN C 523 " -0.054 2.00e-02 2.50e+03 pdb=" OD1 ASN C 523 " 0.020 2.00e-02 2.50e+03 pdb=" ND2 ASN C 523 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY B 385 " -0.046 5.00e-02 4.00e+02 6.91e-02 7.64e+00 pdb=" N PRO B 386 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO B 386 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 386 " -0.038 5.00e-02 4.00e+02 ... (remaining 3331 not shown) Histogram of nonbonded interaction distances: 0.95 - 1.74: 4 1.74 - 2.53: 142 2.53 - 3.32: 21411 3.32 - 4.11: 45389 4.11 - 4.90: 84150 Warning: very small nonbonded interaction distances. Nonbonded interactions: 151096 Sorted by model distance: nonbonded pdb=" NH2 ARG E 534 " pdb=" CA GLU F 322 " model vdw 0.952 3.550 nonbonded pdb=" CZ ARG E 534 " pdb=" CA GLU F 322 " model vdw 1.242 3.700 nonbonded pdb=" OD1 ASN A 526 " pdb=" N LYS B 339 " model vdw 1.264 2.520 nonbonded pdb=" ND2 ASN A 526 " pdb=" O LYS B 339 " model vdw 1.540 2.520 nonbonded pdb=" NH1 ARG E 534 " pdb=" CA GLU F 322 " model vdw 1.765 3.550 ... (remaining 151091 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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: 1.810 Check model and map are aligned: 0.330 Set scattering table: 0.170 Process input model: 54.140 Find NCS groups from input model: 1.930 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6249 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.154 19031 Z= 0.472 Angle : 0.899 19.046 25717 Z= 0.461 Chirality : 0.052 0.345 2915 Planarity : 0.007 0.069 3334 Dihedral : 10.823 172.382 7275 Min Nonbonded Distance : 0.952 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 0.05 % Allowed : 1.68 % Favored : 98.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.40 (0.12), residues: 2372 helix: -4.34 (0.06), residues: 1246 sheet: -1.97 (0.37), residues: 149 loop : -2.51 (0.17), residues: 977 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP C 583 HIS 0.011 0.002 HIS E 578 PHE 0.041 0.004 PHE E 750 TYR 0.020 0.002 TYR E 584 ARG 0.014 0.001 ARG C 465 *********************** 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 fitting. rotamer outliers: 1 poor density : 526 time to evaluate : 2.196 Fit side-chains TARDY: cannot create tardy model for: "MET A 321 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 380 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 438 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET F 321 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 380 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 438 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 575 GLN cc_start: 0.8496 (mm-40) cc_final: 0.8149 (mm-40) REVERT: A 593 LYS cc_start: 0.6676 (ttmt) cc_final: 0.6274 (mtpp) REVERT: A 652 LYS cc_start: 0.7842 (mttt) cc_final: 0.7583 (mtmt) REVERT: A 683 MET cc_start: 0.3221 (tpp) cc_final: 0.0465 (pmm) REVERT: A 687 LYS cc_start: 0.7500 (mmtp) cc_final: 0.7287 (mmtm) REVERT: A 700 GLU cc_start: 0.7139 (mm-30) cc_final: 0.6867 (mm-30) REVERT: A 733 LYS cc_start: 0.7475 (mtpt) cc_final: 0.6680 (tptp) REVERT: A 744 LEU cc_start: 0.7480 (tp) cc_final: 0.7231 (tp) REVERT: B 428 GLU cc_start: 0.6344 (tt0) cc_final: 0.6120 (mm-30) REVERT: B 465 ARG cc_start: 0.5940 (mtt-85) cc_final: 0.5686 (mmt180) REVERT: B 503 ASP cc_start: 0.7522 (m-30) cc_final: 0.7318 (m-30) REVERT: B 520 ASP cc_start: 0.7113 (m-30) cc_final: 0.6801 (m-30) REVERT: B 722 ASP cc_start: 0.7543 (m-30) cc_final: 0.7316 (m-30) REVERT: C 520 ASP cc_start: 0.7207 (m-30) cc_final: 0.6999 (m-30) REVERT: C 569 LYS cc_start: 0.8526 (tttt) cc_final: 0.8198 (ttmt) REVERT: C 666 MET cc_start: 0.7234 (mmt) cc_final: 0.6964 (mmt) REVERT: C 672 GLN cc_start: 0.7309 (mm-40) cc_final: 0.6988 (mp10) REVERT: C 673 ILE cc_start: 0.8324 (mt) cc_final: 0.8069 (tt) REVERT: C 685 LEU cc_start: 0.7221 (OUTLIER) cc_final: 0.6955 (pp) REVERT: C 695 ARG cc_start: 0.7074 (ttp80) cc_final: 0.6746 (ttp-110) REVERT: C 699 ASP cc_start: 0.7352 (m-30) cc_final: 0.7040 (m-30) REVERT: C 711 ARG cc_start: 0.7897 (ttt180) cc_final: 0.7652 (mtp-110) REVERT: C 774 GLU cc_start: 0.7851 (mp0) cc_final: 0.7603 (mp0) REVERT: D 306 LYS cc_start: 0.8330 (mmtt) cc_final: 0.8009 (mmtm) REVERT: D 321 MET cc_start: 0.8365 (mtp) cc_final: 0.7931 (mtm) REVERT: D 395 LEU cc_start: 0.7526 (tp) cc_final: 0.7249 (tt) REVERT: D 404 LEU cc_start: 0.7626 (tt) cc_final: 0.7360 (tp) REVERT: D 424 GLN cc_start: 0.6684 (mt0) cc_final: 0.6233 (mm-40) REVERT: D 500 LEU cc_start: 0.7874 (mt) cc_final: 0.7663 (mt) REVERT: D 504 LYS cc_start: 0.8298 (mttp) cc_final: 0.8061 (mtpm) REVERT: D 544 HIS cc_start: 0.8171 (m170) cc_final: 0.7915 (m170) REVERT: D 547 GLN cc_start: 0.8539 (mt0) cc_final: 0.8264 (mt0) REVERT: D 559 LYS cc_start: 0.8091 (mtpt) cc_final: 0.7742 (mtpt) REVERT: D 561 GLN cc_start: 0.8268 (tt0) cc_final: 0.7982 (tt0) REVERT: D 619 GLU cc_start: 0.7588 (mp0) cc_final: 0.7259 (mp0) REVERT: D 673 ILE cc_start: 0.7877 (mt) cc_final: 0.7475 (pp) REVERT: D 753 LYS cc_start: 0.8691 (mtmt) cc_final: 0.8476 (mtmm) REVERT: E 309 ASP cc_start: 0.7572 (m-30) cc_final: 0.7172 (t0) REVERT: E 321 MET cc_start: 0.7339 (mtm) cc_final: 0.6902 (mtp) REVERT: E 375 SER cc_start: 0.8253 (p) cc_final: 0.7974 (m) REVERT: E 376 GLU cc_start: 0.7808 (mt-10) cc_final: 0.7572 (tt0) REVERT: E 408 GLN cc_start: 0.7715 (mm-40) cc_final: 0.7440 (tp40) REVERT: E 455 ARG cc_start: 0.8251 (mtp180) cc_final: 0.7830 (mmm-85) REVERT: E 543 LYS cc_start: 0.8383 (mmtt) cc_final: 0.8066 (ttpp) REVERT: E 656 SER cc_start: 0.8280 (t) cc_final: 0.8012 (m) REVERT: F 616 TYR cc_start: 0.8050 (m-80) cc_final: 0.7825 (m-80) REVERT: F 627 MET cc_start: 0.7246 (tmm) cc_final: 0.6919 (tmm) REVERT: F 641 ARG cc_start: 0.7043 (mmt-90) cc_final: 0.6775 (ptp-110) outliers start: 1 outliers final: 1 residues processed: 527 average time/residue: 1.5047 time to fit residues: 876.9990 Evaluate side-chains 336 residues out of total 2375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 334 time to evaluate : 2.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 391 ASP Chi-restraints excluded: chain C residue 685 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 240 optimal weight: 50.0000 chunk 216 optimal weight: 0.9990 chunk 119 optimal weight: 0.9990 chunk 73 optimal weight: 6.9990 chunk 145 optimal weight: 0.8980 chunk 115 optimal weight: 9.9990 chunk 223 optimal weight: 4.9990 chunk 86 optimal weight: 4.9990 chunk 135 optimal weight: 7.9990 chunk 166 optimal weight: 5.9990 chunk 258 optimal weight: 50.0000 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 578 HIS A 672 GLN B 332 GLN ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 663 GLN C 472 GLN C 647 GLN ** C 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 706 ASN D 433 GLN D 526 ASN D 535 HIS D 575 GLN D 655 GLN E 454 ASN E 663 GLN F 667 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6284 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 19031 Z= 0.229 Angle : 0.611 11.166 25717 Z= 0.311 Chirality : 0.042 0.149 2915 Planarity : 0.005 0.051 3334 Dihedral : 10.651 174.387 2677 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 3.72 % Allowed : 10.79 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.27 (0.15), residues: 2372 helix: -2.18 (0.12), residues: 1242 sheet: -1.46 (0.39), residues: 149 loop : -2.07 (0.18), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP F 583 HIS 0.007 0.002 HIS B 578 PHE 0.020 0.002 PHE E 750 TYR 0.021 0.002 TYR C 605 ARG 0.007 0.001 ARG C 624 *********************** 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 424 residues out of total 2375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 351 time to evaluate : 2.610 Fit side-chains TARDY: cannot create tardy model for: "MET A 321 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 380 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 438 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET F 321 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 380 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 438 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 575 GLN cc_start: 0.8034 (mm-40) cc_final: 0.7814 (mm110) REVERT: A 593 LYS cc_start: 0.6888 (ttmt) cc_final: 0.6664 (ttpp) REVERT: A 619 GLU cc_start: 0.6322 (OUTLIER) cc_final: 0.5832 (pp20) REVERT: A 627 MET cc_start: 0.7232 (tmm) cc_final: 0.6958 (tmm) REVERT: A 683 MET cc_start: 0.2995 (tpp) cc_final: 0.0370 (pmm) REVERT: A 687 LYS cc_start: 0.7452 (mmtp) cc_final: 0.7183 (mmtm) REVERT: A 733 LYS cc_start: 0.7470 (mtpt) cc_final: 0.6619 (tptp) REVERT: B 370 ILE cc_start: 0.7316 (OUTLIER) cc_final: 0.7081 (mt) REVERT: B 427 GLN cc_start: 0.6711 (OUTLIER) cc_final: 0.6264 (tm130) REVERT: B 428 GLU cc_start: 0.6387 (tt0) cc_final: 0.6029 (mm-30) REVERT: B 465 ARG cc_start: 0.5776 (mtt-85) cc_final: 0.5530 (tpt170) REVERT: C 314 GLU cc_start: 0.7728 (tp30) cc_final: 0.7528 (tp30) REVERT: C 328 LYS cc_start: 0.8153 (ttmm) cc_final: 0.7562 (mmmm) REVERT: C 391 ASP cc_start: 0.7034 (t70) cc_final: 0.6793 (t70) REVERT: C 504 LYS cc_start: 0.8307 (mttt) cc_final: 0.8017 (mttt) REVERT: C 547 GLN cc_start: 0.8112 (mt0) cc_final: 0.7785 (mt0) REVERT: C 648 ASP cc_start: 0.7435 (t0) cc_final: 0.7065 (p0) REVERT: C 672 GLN cc_start: 0.7382 (mm-40) cc_final: 0.7126 (mp10) REVERT: C 673 ILE cc_start: 0.8318 (mt) cc_final: 0.8014 (tt) REVERT: C 695 ARG cc_start: 0.6981 (ttp80) cc_final: 0.6635 (ttp80) REVERT: C 699 ASP cc_start: 0.7264 (m-30) cc_final: 0.6933 (m-30) REVERT: C 774 GLU cc_start: 0.7898 (mp0) cc_final: 0.7686 (mp0) REVERT: D 306 LYS cc_start: 0.8272 (mmtt) cc_final: 0.7922 (mmtm) REVERT: D 424 GLN cc_start: 0.6828 (mt0) cc_final: 0.6337 (mt0) REVERT: D 507 ARG cc_start: 0.8164 (OUTLIER) cc_final: 0.7963 (mpp80) REVERT: D 547 GLN cc_start: 0.8211 (mt0) cc_final: 0.7787 (mt0) REVERT: D 561 GLN cc_start: 0.8188 (tt0) cc_final: 0.7899 (tt0) REVERT: D 673 ILE cc_start: 0.7942 (mt) cc_final: 0.7529 (pp) REVERT: E 309 ASP cc_start: 0.7627 (m-30) cc_final: 0.7166 (t0) REVERT: E 321 MET cc_start: 0.7362 (mtm) cc_final: 0.6903 (mtp) REVERT: E 375 SER cc_start: 0.8262 (p) cc_final: 0.8010 (m) REVERT: E 408 GLN cc_start: 0.7913 (mm-40) cc_final: 0.7577 (tp40) REVERT: E 455 ARG cc_start: 0.8151 (mtp180) cc_final: 0.7690 (mmm-85) REVERT: E 543 LYS cc_start: 0.8276 (mmtt) cc_final: 0.7910 (tptt) REVERT: E 656 SER cc_start: 0.8341 (t) cc_final: 0.8045 (m) REVERT: E 668 GLU cc_start: 0.6756 (OUTLIER) cc_final: 0.6501 (mp0) REVERT: F 616 TYR cc_start: 0.8080 (m-80) cc_final: 0.7849 (m-80) REVERT: F 627 MET cc_start: 0.7078 (tmm) cc_final: 0.6664 (tmm) REVERT: F 660 GLN cc_start: 0.7793 (tt0) cc_final: 0.7392 (tt0) outliers start: 73 outliers final: 30 residues processed: 398 average time/residue: 1.4897 time to fit residues: 658.2604 Evaluate side-chains 323 residues out of total 2375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 288 time to evaluate : 2.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 567 GLU Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 689 TYR Chi-restraints excluded: chain A residue 690 SER Chi-restraints excluded: chain B residue 370 ILE Chi-restraints excluded: chain B residue 427 GLN 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 591 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 308 LYS Chi-restraints excluded: chain C residue 329 ASN Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain C residue 437 GLU Chi-restraints excluded: chain C residue 538 ASP Chi-restraints excluded: chain C residue 541 ASN Chi-restraints excluded: chain C residue 755 THR Chi-restraints excluded: chain D residue 457 ASP Chi-restraints excluded: chain D residue 499 THR Chi-restraints excluded: chain D residue 507 ARG Chi-restraints excluded: chain D residue 535 HIS Chi-restraints excluded: chain D residue 739 ASN Chi-restraints excluded: chain E residue 382 VAL Chi-restraints excluded: chain E residue 399 ASN Chi-restraints excluded: chain E residue 457 ASP Chi-restraints excluded: chain E residue 556 LEU Chi-restraints excluded: chain E residue 668 GLU Chi-restraints excluded: chain E residue 669 LYS Chi-restraints excluded: chain E residue 676 ASP Chi-restraints excluded: chain F residue 656 SER 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 143 optimal weight: 6.9990 chunk 80 optimal weight: 6.9990 chunk 215 optimal weight: 4.9990 chunk 176 optimal weight: 0.6980 chunk 71 optimal weight: 8.9990 chunk 259 optimal weight: 50.0000 chunk 280 optimal weight: 10.0000 chunk 230 optimal weight: 1.9990 chunk 257 optimal weight: 50.0000 chunk 88 optimal weight: 0.5980 chunk 208 optimal weight: 6.9990 overall best weight: 3.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 578 HIS ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 663 GLN ** C 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 739 ASN D 541 ASN E 663 GLN F 667 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6308 moved from start: 0.2868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 19031 Z= 0.247 Angle : 0.586 11.090 25717 Z= 0.291 Chirality : 0.042 0.155 2915 Planarity : 0.004 0.048 3334 Dihedral : 9.728 169.092 2673 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.92 % Allowed : 14.30 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.16), residues: 2372 helix: -1.11 (0.14), residues: 1253 sheet: -1.07 (0.41), residues: 150 loop : -1.84 (0.19), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 583 HIS 0.008 0.002 HIS D 535 PHE 0.021 0.002 PHE A 750 TYR 0.020 0.002 TYR C 605 ARG 0.006 0.000 ARG E 551 *********************** 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 401 residues out of total 2375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 324 time to evaluate : 2.348 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 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: 0.8086 (mm-40) cc_final: 0.7864 (mm110) REVERT: A 593 LYS cc_start: 0.6895 (ttmt) cc_final: 0.6657 (ttpp) REVERT: A 607 GLN cc_start: 0.6253 (tt0) cc_final: 0.6021 (tt0) REVERT: A 619 GLU cc_start: 0.6561 (OUTLIER) cc_final: 0.6252 (pp20) REVERT: A 683 MET cc_start: 0.3118 (tpp) cc_final: 0.0414 (pmm) REVERT: A 733 LYS cc_start: 0.7582 (mtpt) cc_final: 0.6715 (tptp) REVERT: B 427 GLN cc_start: 0.6629 (OUTLIER) cc_final: 0.6086 (tm-30) REVERT: B 428 GLU cc_start: 0.6222 (tt0) cc_final: 0.5874 (mm-30) REVERT: B 433 GLN cc_start: 0.7340 (tp40) cc_final: 0.6889 (tm-30) REVERT: B 469 PHE cc_start: 0.8310 (m-10) cc_final: 0.8042 (m-10) REVERT: B 501 GLU cc_start: 0.7294 (pt0) cc_final: 0.6870 (pt0) REVERT: B 683 MET cc_start: 0.6302 (ptp) cc_final: 0.4578 (pmm) REVERT: B 724 GLU cc_start: 0.7469 (OUTLIER) cc_final: 0.6847 (tm-30) REVERT: C 314 GLU cc_start: 0.7745 (tp30) cc_final: 0.7508 (mm-30) REVERT: C 391 ASP cc_start: 0.6972 (t70) cc_final: 0.6704 (t70) REVERT: C 408 GLN cc_start: 0.7656 (OUTLIER) cc_final: 0.5187 (mp10) REVERT: C 437 GLU cc_start: 0.6526 (OUTLIER) cc_final: 0.6213 (tp30) REVERT: C 547 GLN cc_start: 0.8171 (mt0) cc_final: 0.7882 (mt0) REVERT: C 611 LYS cc_start: 0.8238 (OUTLIER) cc_final: 0.7661 (mttp) REVERT: C 648 ASP cc_start: 0.7406 (t0) cc_final: 0.7018 (p0) REVERT: C 672 GLN cc_start: 0.7468 (mm-40) cc_final: 0.7170 (mp10) REVERT: C 673 ILE cc_start: 0.8311 (mt) cc_final: 0.7992 (tt) REVERT: C 683 MET cc_start: 0.5948 (ttt) cc_final: 0.5677 (tmm) REVERT: C 695 ARG cc_start: 0.6952 (ttp80) cc_final: 0.6501 (ttp80) REVERT: C 699 ASP cc_start: 0.7289 (m-30) cc_final: 0.6937 (m-30) REVERT: C 774 GLU cc_start: 0.7888 (mp0) cc_final: 0.7670 (mp0) REVERT: D 424 GLN cc_start: 0.6834 (mt0) cc_final: 0.6473 (mt0) REVERT: D 504 LYS cc_start: 0.7875 (mtpm) cc_final: 0.7433 (mttm) REVERT: D 547 GLN cc_start: 0.8162 (mt0) cc_final: 0.7929 (mt0) REVERT: D 561 GLN cc_start: 0.8251 (tt0) cc_final: 0.7964 (tt0) REVERT: D 683 MET cc_start: 0.5908 (OUTLIER) cc_final: 0.5687 (ptt) REVERT: D 734 GLU cc_start: 0.7434 (OUTLIER) cc_final: 0.6654 (mt-10) REVERT: E 318 LEU cc_start: 0.8417 (mt) cc_final: 0.8164 (mp) REVERT: E 375 SER cc_start: 0.8317 (p) cc_final: 0.7903 (m) REVERT: E 455 ARG cc_start: 0.8197 (mtp180) cc_final: 0.7748 (mmm-85) REVERT: E 543 LYS cc_start: 0.8324 (mmtt) cc_final: 0.7959 (tptt) REVERT: E 593 LYS cc_start: 0.7658 (tttt) cc_final: 0.7446 (ttmm) REVERT: E 625 MET cc_start: 0.7739 (ttp) cc_final: 0.7490 (ttp) REVERT: E 656 SER cc_start: 0.8346 (t) cc_final: 0.7993 (m) REVERT: E 717 THR cc_start: 0.8172 (t) cc_final: 0.7853 (p) REVERT: E 718 GLU cc_start: 0.7045 (mt-10) cc_final: 0.6642 (mp0) REVERT: F 619 GLU cc_start: 0.6856 (mp0) cc_final: 0.6637 (mp0) REVERT: F 627 MET cc_start: 0.7156 (tmm) cc_final: 0.6672 (tmm) REVERT: F 656 SER cc_start: 0.8106 (OUTLIER) cc_final: 0.7869 (p) REVERT: F 660 GLN cc_start: 0.7824 (tt0) cc_final: 0.7349 (tt0) REVERT: F 668 GLU cc_start: 0.7968 (tt0) cc_final: 0.7230 (pm20) REVERT: F 732 GLU cc_start: 0.7401 (mm-30) cc_final: 0.6875 (mt-10) outliers start: 77 outliers final: 32 residues processed: 372 average time/residue: 1.4236 time to fit residues: 590.0014 Evaluate side-chains 340 residues out of total 2375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 299 time to evaluate : 2.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 689 TYR Chi-restraints excluded: chain B residue 427 GLN Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain B residue 556 LEU Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 724 GLU Chi-restraints excluded: chain B residue 744 LEU Chi-restraints excluded: chain C residue 308 LYS Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 408 GLN Chi-restraints excluded: chain C residue 437 GLU Chi-restraints excluded: chain C residue 500 LEU Chi-restraints excluded: chain C residue 501 GLU Chi-restraints excluded: chain C residue 538 ASP Chi-restraints excluded: chain C residue 541 ASN Chi-restraints excluded: chain C residue 611 LYS Chi-restraints excluded: chain C residue 687 LYS Chi-restraints excluded: chain C residue 755 THR Chi-restraints excluded: chain D residue 308 LYS Chi-restraints excluded: chain D residue 457 ASP Chi-restraints excluded: chain D residue 479 ASP Chi-restraints excluded: chain D residue 499 THR Chi-restraints excluded: chain D residue 507 ARG Chi-restraints excluded: chain D residue 669 LYS Chi-restraints excluded: chain D residue 683 MET 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 372 VAL Chi-restraints excluded: chain E residue 382 VAL Chi-restraints excluded: chain E residue 457 ASP Chi-restraints excluded: chain E residue 669 LYS Chi-restraints excluded: chain E residue 676 ASP Chi-restraints excluded: chain F residue 562 VAL Chi-restraints excluded: chain F residue 656 SER Chi-restraints excluded: chain F residue 690 SER Chi-restraints excluded: chain F residue 705 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 256 optimal weight: 50.0000 chunk 194 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 chunk 28 optimal weight: 7.9990 chunk 123 optimal weight: 6.9990 chunk 174 optimal weight: 0.9980 chunk 260 optimal weight: 50.0000 chunk 275 optimal weight: 7.9990 chunk 135 optimal weight: 0.3980 chunk 246 optimal weight: 50.0000 chunk 74 optimal weight: 7.9990 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 663 GLN ** C 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 542 GLN E 663 GLN E 667 ASN F 667 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6310 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 19031 Z= 0.232 Angle : 0.559 11.577 25717 Z= 0.277 Chirality : 0.041 0.183 2915 Planarity : 0.004 0.044 3334 Dihedral : 9.287 174.515 2673 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 4.12 % Allowed : 15.47 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.17), residues: 2372 helix: -0.48 (0.15), residues: 1246 sheet: -0.94 (0.41), residues: 148 loop : -1.64 (0.19), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 583 HIS 0.006 0.002 HIS C 578 PHE 0.020 0.002 PHE C 393 TYR 0.021 0.002 TYR C 605 ARG 0.005 0.000 ARG E 468 *********************** 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 395 residues out of total 2375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 314 time to evaluate : 2.464 Fit side-chains TARDY: cannot create tardy model for: "MET A 321 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 380 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 438 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET F 321 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 380 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 438 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 575 GLN cc_start: 0.8100 (mm-40) cc_final: 0.7770 (mm110) REVERT: A 589 ASP cc_start: 0.7281 (m-30) cc_final: 0.6989 (t0) REVERT: A 593 LYS cc_start: 0.6919 (ttmt) cc_final: 0.6634 (ttpp) REVERT: A 607 GLN cc_start: 0.6165 (tt0) cc_final: 0.5889 (tt0) REVERT: A 619 GLU cc_start: 0.6487 (OUTLIER) cc_final: 0.6186 (pp20) REVERT: A 683 MET cc_start: 0.3158 (tpp) cc_final: 0.0357 (pmm) REVERT: A 733 LYS cc_start: 0.7614 (mtpt) cc_final: 0.6746 (tptp) REVERT: B 427 GLN cc_start: 0.6550 (OUTLIER) cc_final: 0.5996 (tm-30) REVERT: B 428 GLU cc_start: 0.6198 (tt0) cc_final: 0.5839 (mm-30) REVERT: B 433 GLN cc_start: 0.7235 (tp40) cc_final: 0.6942 (tm-30) REVERT: B 465 ARG cc_start: 0.5677 (mtt-85) cc_final: 0.5252 (tpt170) REVERT: B 469 PHE cc_start: 0.8290 (m-10) cc_final: 0.8084 (m-10) REVERT: B 541 ASN cc_start: 0.8187 (OUTLIER) cc_final: 0.7955 (p0) REVERT: B 601 LYS cc_start: 0.7876 (OUTLIER) cc_final: 0.7537 (mttt) REVERT: B 683 MET cc_start: 0.6057 (ptp) cc_final: 0.5653 (ttt) REVERT: B 724 GLU cc_start: 0.7551 (OUTLIER) cc_final: 0.6912 (tm-30) REVERT: C 314 GLU cc_start: 0.7614 (tp30) cc_final: 0.7374 (mm-30) REVERT: C 391 ASP cc_start: 0.7090 (t70) cc_final: 0.6808 (t70) REVERT: C 408 GLN cc_start: 0.7674 (OUTLIER) cc_final: 0.7282 (mp10) REVERT: C 437 GLU cc_start: 0.6660 (OUTLIER) cc_final: 0.5488 (mp0) REVERT: C 547 GLN cc_start: 0.8136 (mt0) cc_final: 0.7848 (mt0) REVERT: C 648 ASP cc_start: 0.7420 (t0) cc_final: 0.6995 (p0) REVERT: C 672 GLN cc_start: 0.7512 (mm-40) cc_final: 0.7273 (mp10) REVERT: C 673 ILE cc_start: 0.8258 (mt) cc_final: 0.7982 (tt) REVERT: C 695 ARG cc_start: 0.6962 (ttp80) cc_final: 0.6399 (ttp80) REVERT: C 699 ASP cc_start: 0.7237 (m-30) cc_final: 0.6912 (m-30) REVERT: C 774 GLU cc_start: 0.7985 (mp0) cc_final: 0.7747 (mp0) REVERT: D 503 ASP cc_start: 0.7234 (m-30) cc_final: 0.6736 (p0) REVERT: D 507 ARG cc_start: 0.8186 (OUTLIER) cc_final: 0.7208 (mtm-85) REVERT: D 561 GLN cc_start: 0.8355 (tt0) cc_final: 0.8038 (tt0) REVERT: D 568 LYS cc_start: 0.7756 (OUTLIER) cc_final: 0.7470 (mttm) REVERT: D 668 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7088 (mm-30) REVERT: D 673 ILE cc_start: 0.7995 (mt) cc_final: 0.7640 (pp) REVERT: D 734 GLU cc_start: 0.7417 (OUTLIER) cc_final: 0.6611 (mt-10) REVERT: E 318 LEU cc_start: 0.8374 (mt) cc_final: 0.8141 (mp) REVERT: E 359 LYS cc_start: 0.7618 (mttt) cc_final: 0.7318 (mtpm) REVERT: E 455 ARG cc_start: 0.8172 (mtp180) cc_final: 0.7739 (mmm-85) REVERT: E 543 LYS cc_start: 0.8324 (mmtt) cc_final: 0.7967 (tmtm) REVERT: E 616 TYR cc_start: 0.8120 (m-80) cc_final: 0.7904 (m-80) REVERT: E 625 MET cc_start: 0.7729 (ttp) cc_final: 0.7512 (ttp) REVERT: E 656 SER cc_start: 0.8340 (t) cc_final: 0.7973 (m) REVERT: E 717 THR cc_start: 0.8217 (t) cc_final: 0.7919 (p) REVERT: E 718 GLU cc_start: 0.7060 (mt-10) cc_final: 0.6671 (mp0) REVERT: F 619 GLU cc_start: 0.6859 (mp0) cc_final: 0.6632 (mp0) REVERT: F 627 MET cc_start: 0.7155 (tmm) cc_final: 0.6652 (tmm) REVERT: F 656 SER cc_start: 0.8060 (OUTLIER) cc_final: 0.7794 (p) REVERT: F 660 GLN cc_start: 0.7785 (tt0) cc_final: 0.7295 (tt0) REVERT: F 666 MET cc_start: 0.8602 (OUTLIER) cc_final: 0.8297 (mtp) REVERT: F 728 LEU cc_start: 0.6684 (OUTLIER) cc_final: 0.6338 (mm) REVERT: F 732 GLU cc_start: 0.7699 (mm-30) cc_final: 0.7133 (mt-10) REVERT: F 734 GLU cc_start: 0.7551 (mt-10) cc_final: 0.6586 (tm-30) REVERT: F 744 LEU cc_start: 0.6711 (OUTLIER) cc_final: 0.6153 (mp) outliers start: 81 outliers final: 30 residues processed: 363 average time/residue: 1.4250 time to fit residues: 578.6042 Evaluate side-chains 332 residues out of total 2375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 287 time to evaluate : 2.281 ------------------------------------------------------------------------------- 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 427 GLN Chi-restraints excluded: chain B residue 541 ASN Chi-restraints excluded: chain B residue 556 LEU Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 601 LYS Chi-restraints excluded: chain B residue 724 GLU Chi-restraints excluded: chain B residue 744 LEU Chi-restraints excluded: chain C residue 308 LYS Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 408 GLN Chi-restraints excluded: chain C residue 437 GLU Chi-restraints excluded: chain C residue 454 ASN Chi-restraints excluded: chain C residue 470 ASP Chi-restraints excluded: chain C residue 500 LEU 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 740 ASP Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 453 THR Chi-restraints excluded: chain D residue 457 ASP Chi-restraints excluded: chain D residue 499 THR Chi-restraints excluded: chain D residue 507 ARG Chi-restraints excluded: chain D residue 541 ASN Chi-restraints excluded: chain D residue 568 LYS Chi-restraints excluded: chain D residue 668 GLU Chi-restraints excluded: chain D residue 734 GLU Chi-restraints excluded: chain D residue 739 ASN Chi-restraints excluded: chain E residue 335 ASP Chi-restraints excluded: chain E residue 380 MET Chi-restraints excluded: chain E residue 382 VAL Chi-restraints excluded: chain E residue 444 THR Chi-restraints excluded: chain E residue 457 ASP Chi-restraints excluded: chain E residue 669 LYS Chi-restraints excluded: chain E residue 676 ASP Chi-restraints excluded: chain F residue 656 SER Chi-restraints excluded: chain F residue 666 MET Chi-restraints excluded: chain F residue 690 SER Chi-restraints excluded: chain F residue 705 ILE Chi-restraints excluded: chain F residue 728 LEU Chi-restraints excluded: chain F residue 744 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 229 optimal weight: 30.0000 chunk 156 optimal weight: 5.9990 chunk 4 optimal weight: 50.0000 chunk 205 optimal weight: 0.7980 chunk 113 optimal weight: 8.9990 chunk 235 optimal weight: 5.9990 chunk 190 optimal weight: 7.9990 chunk 0 optimal weight: 50.0000 chunk 140 optimal weight: 4.9990 chunk 247 optimal weight: 50.0000 chunk 69 optimal weight: 9.9990 overall best weight: 5.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 607 GLN A 613 GLN ** B 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 587 HIS C 613 GLN ** 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 667 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6356 moved from start: 0.3713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 19031 Z= 0.381 Angle : 0.654 9.591 25717 Z= 0.323 Chirality : 0.045 0.168 2915 Planarity : 0.005 0.057 3334 Dihedral : 9.477 179.476 2673 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 4.58 % Allowed : 15.57 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.17), residues: 2372 helix: -0.42 (0.14), residues: 1245 sheet: -0.97 (0.40), residues: 153 loop : -1.64 (0.19), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP F 583 HIS 0.011 0.002 HIS C 578 PHE 0.030 0.003 PHE D 638 TYR 0.030 0.002 TYR D 573 ARG 0.010 0.001 ARG E 468 *********************** 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 379 residues out of total 2375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 289 time to evaluate : 2.316 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 575 GLN cc_start: 0.8120 (mm-40) cc_final: 0.7780 (mm-40) REVERT: A 589 ASP cc_start: 0.7350 (m-30) cc_final: 0.6927 (t0) REVERT: A 593 LYS cc_start: 0.6926 (ttmt) cc_final: 0.6680 (ttpp) REVERT: A 607 GLN cc_start: 0.6173 (tt0) cc_final: 0.5950 (tt0) REVERT: A 619 GLU cc_start: 0.6580 (OUTLIER) cc_final: 0.6281 (pp20) REVERT: A 683 MET cc_start: 0.3475 (tpp) cc_final: 0.0504 (pmm) REVERT: A 733 LYS cc_start: 0.7626 (mtpt) cc_final: 0.6716 (tptp) REVERT: B 427 GLN cc_start: 0.6553 (OUTLIER) cc_final: 0.5988 (tm-30) REVERT: B 428 GLU cc_start: 0.6152 (tt0) cc_final: 0.5859 (mm-30) REVERT: B 465 ARG cc_start: 0.5524 (mtt-85) cc_final: 0.5049 (mmt180) REVERT: B 592 LEU cc_start: 0.7254 (OUTLIER) cc_final: 0.6889 (mp) REVERT: B 601 LYS cc_start: 0.8013 (OUTLIER) cc_final: 0.7806 (mttp) REVERT: B 683 MET cc_start: 0.6039 (ptp) cc_final: 0.5580 (ttt) REVERT: B 724 GLU cc_start: 0.7398 (OUTLIER) cc_final: 0.6858 (tm-30) REVERT: C 380 MET cc_start: 0.7973 (ptm) cc_final: 0.7647 (ptp) REVERT: C 391 ASP cc_start: 0.7253 (t70) cc_final: 0.7018 (t70) REVERT: C 408 GLN cc_start: 0.7696 (OUTLIER) cc_final: 0.5482 (mp10) REVERT: C 559 LYS cc_start: 0.7756 (mtpt) cc_final: 0.7462 (mtmt) REVERT: C 564 GLN cc_start: 0.7478 (OUTLIER) cc_final: 0.6715 (mm-40) REVERT: C 611 LYS cc_start: 0.8338 (OUTLIER) cc_final: 0.7754 (mttp) REVERT: C 636 GLU cc_start: 0.7515 (tt0) cc_final: 0.7057 (pt0) REVERT: C 672 GLN cc_start: 0.7673 (mm-40) cc_final: 0.7345 (mp10) REVERT: C 673 ILE cc_start: 0.8267 (mt) cc_final: 0.7951 (tt) REVERT: C 695 ARG cc_start: 0.7014 (ttp80) cc_final: 0.6471 (ttp80) REVERT: C 699 ASP cc_start: 0.7296 (m-30) cc_final: 0.6962 (m-30) REVERT: C 774 GLU cc_start: 0.8016 (mp0) cc_final: 0.7740 (mp0) REVERT: D 559 LYS cc_start: 0.8400 (mttm) cc_final: 0.8166 (mttm) REVERT: D 561 GLN cc_start: 0.8268 (tt0) cc_final: 0.8004 (tt0) REVERT: D 568 LYS cc_start: 0.7666 (OUTLIER) cc_final: 0.7210 (mttm) REVERT: D 666 MET cc_start: 0.7504 (OUTLIER) cc_final: 0.5716 (mmt) REVERT: D 668 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7367 (mt-10) REVERT: D 683 MET cc_start: 0.5627 (ptt) cc_final: 0.5425 (ptm) REVERT: E 318 LEU cc_start: 0.8362 (mt) cc_final: 0.8128 (mp) REVERT: E 359 LYS cc_start: 0.7632 (mttt) cc_final: 0.7343 (mtpm) REVERT: E 455 ARG cc_start: 0.8147 (mtp180) cc_final: 0.7637 (mmm-85) REVERT: E 543 LYS cc_start: 0.8314 (mmtt) cc_final: 0.7892 (tptt) REVERT: E 573 TYR cc_start: 0.7878 (m-80) cc_final: 0.7670 (m-80) REVERT: E 593 LYS cc_start: 0.7644 (tttt) cc_final: 0.7422 (tttm) REVERT: E 656 SER cc_start: 0.8525 (t) cc_final: 0.8153 (m) REVERT: E 668 GLU cc_start: 0.6924 (OUTLIER) cc_final: 0.6697 (mp0) REVERT: F 627 MET cc_start: 0.6810 (tmm) cc_final: 0.6207 (tmm) REVERT: F 732 GLU cc_start: 0.7761 (mm-30) cc_final: 0.7189 (mt-10) REVERT: F 744 LEU cc_start: 0.6788 (OUTLIER) cc_final: 0.6227 (mp) outliers start: 90 outliers final: 42 residues processed: 348 average time/residue: 1.4048 time to fit residues: 545.6825 Evaluate side-chains 331 residues out of total 2375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 276 time to evaluate : 2.199 ------------------------------------------------------------------------------- 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 735 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 427 GLN Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain B residue 481 LYS Chi-restraints excluded: chain B residue 541 ASN Chi-restraints excluded: chain B residue 556 LEU Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 601 LYS Chi-restraints excluded: chain B residue 724 GLU Chi-restraints excluded: chain B residue 744 LEU Chi-restraints excluded: chain C residue 308 LYS Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 408 GLN Chi-restraints excluded: chain C residue 454 ASN Chi-restraints excluded: chain C residue 500 LEU Chi-restraints excluded: chain C residue 501 GLU 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 564 GLN Chi-restraints excluded: chain C residue 611 LYS Chi-restraints excluded: chain C residue 687 LYS Chi-restraints excluded: chain C residue 740 ASP Chi-restraints excluded: chain C residue 755 THR Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 453 THR Chi-restraints excluded: chain D residue 479 ASP Chi-restraints excluded: chain D residue 499 THR Chi-restraints excluded: chain D residue 507 ARG Chi-restraints excluded: chain D residue 541 ASN Chi-restraints excluded: chain D residue 568 LYS Chi-restraints excluded: chain D residue 666 MET Chi-restraints excluded: chain D residue 668 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 399 ASN Chi-restraints excluded: chain E residue 457 ASP Chi-restraints excluded: chain E residue 648 ASP Chi-restraints excluded: chain E residue 668 GLU Chi-restraints excluded: chain E residue 669 LYS Chi-restraints excluded: chain E residue 676 ASP Chi-restraints excluded: chain F residue 642 ILE Chi-restraints excluded: chain F residue 690 SER Chi-restraints excluded: chain F residue 705 ILE Chi-restraints excluded: chain F residue 719 LYS Chi-restraints excluded: chain F residue 740 ASP Chi-restraints excluded: chain F residue 744 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 92 optimal weight: 0.8980 chunk 248 optimal weight: 50.0000 chunk 54 optimal weight: 2.9990 chunk 161 optimal weight: 0.9990 chunk 68 optimal weight: 5.9990 chunk 275 optimal weight: 0.0470 chunk 228 optimal weight: 4.9990 chunk 127 optimal weight: 0.9980 chunk 22 optimal weight: 50.0000 chunk 91 optimal weight: 20.0000 chunk 144 optimal weight: 2.9990 overall best weight: 1.1882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 655 GLN ** B 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 454 ASN ** D 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 663 GLN F 667 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6288 moved from start: 0.3818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 19031 Z= 0.153 Angle : 0.521 12.092 25717 Z= 0.259 Chirality : 0.040 0.140 2915 Planarity : 0.004 0.044 3334 Dihedral : 8.678 175.199 2673 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.00 % Allowed : 18.07 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.17), residues: 2372 helix: 0.17 (0.15), residues: 1236 sheet: -0.77 (0.42), residues: 151 loop : -1.34 (0.20), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 583 HIS 0.003 0.001 HIS E 544 PHE 0.013 0.001 PHE D 638 TYR 0.020 0.001 TYR C 605 ARG 0.006 0.000 ARG F 641 *********************** 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 360 residues out of total 2375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 301 time to evaluate : 2.237 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 593 LYS cc_start: 0.6921 (ttmt) cc_final: 0.6638 (ttpp) REVERT: A 607 GLN cc_start: 0.6154 (tt0) cc_final: 0.5943 (tt0) REVERT: A 619 GLU cc_start: 0.6520 (OUTLIER) cc_final: 0.6274 (pp20) REVERT: A 683 MET cc_start: 0.3232 (tpp) cc_final: 0.0393 (pmm) REVERT: A 725 LYS cc_start: 0.7151 (mtpm) cc_final: 0.6863 (mtmp) REVERT: A 733 LYS cc_start: 0.7677 (mtpt) cc_final: 0.6808 (tptp) REVERT: B 427 GLN cc_start: 0.6563 (OUTLIER) cc_final: 0.5978 (tm-30) REVERT: B 428 GLU cc_start: 0.6133 (tt0) cc_final: 0.5795 (mm-30) REVERT: B 458 ILE cc_start: 0.8512 (OUTLIER) cc_final: 0.8101 (pt) REVERT: B 465 ARG cc_start: 0.5467 (mtt-85) cc_final: 0.5102 (tpt170) REVERT: B 469 PHE cc_start: 0.8319 (m-10) cc_final: 0.8082 (m-10) REVERT: B 601 LYS cc_start: 0.7921 (OUTLIER) cc_final: 0.7633 (mttt) REVERT: B 683 MET cc_start: 0.6045 (ptp) cc_final: 0.5588 (ttt) REVERT: C 328 LYS cc_start: 0.7848 (ttmm) cc_final: 0.7599 (ttmm) REVERT: C 380 MET cc_start: 0.7926 (OUTLIER) cc_final: 0.7603 (ptp) REVERT: C 391 ASP cc_start: 0.7230 (t70) cc_final: 0.6975 (t70) REVERT: C 408 GLN cc_start: 0.7714 (OUTLIER) cc_final: 0.7400 (mp10) REVERT: C 559 LYS cc_start: 0.7681 (mtpt) cc_final: 0.7462 (mtmt) REVERT: C 611 LYS cc_start: 0.8295 (OUTLIER) cc_final: 0.7699 (mttp) REVERT: C 648 ASP cc_start: 0.7257 (t0) cc_final: 0.6883 (p0) REVERT: C 672 GLN cc_start: 0.7595 (mm-40) cc_final: 0.7373 (mp10) REVERT: C 673 ILE cc_start: 0.8227 (mt) cc_final: 0.8010 (tt) REVERT: C 695 ARG cc_start: 0.6960 (ttp80) cc_final: 0.6378 (ttp80) REVERT: C 699 ASP cc_start: 0.7189 (m-30) cc_final: 0.6883 (m-30) REVERT: C 774 GLU cc_start: 0.7967 (mp0) cc_final: 0.7714 (mp0) REVERT: D 507 ARG cc_start: 0.8144 (OUTLIER) cc_final: 0.7236 (mtm-85) REVERT: D 559 LYS cc_start: 0.8372 (mttm) cc_final: 0.8149 (mttm) REVERT: D 561 GLN cc_start: 0.8227 (tt0) cc_final: 0.7970 (tt0) REVERT: D 568 LYS cc_start: 0.7697 (OUTLIER) cc_final: 0.7339 (mttm) REVERT: D 668 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7326 (mt-10) REVERT: D 673 ILE cc_start: 0.8002 (mt) cc_final: 0.7641 (pp) REVERT: D 734 GLU cc_start: 0.7384 (OUTLIER) cc_final: 0.6592 (mt-10) REVERT: E 318 LEU cc_start: 0.8361 (mt) cc_final: 0.8116 (mp) REVERT: E 359 LYS cc_start: 0.7607 (mttt) cc_final: 0.7314 (mtpm) REVERT: E 415 LYS cc_start: 0.7800 (tttt) cc_final: 0.7392 (ttmm) REVERT: E 455 ARG cc_start: 0.8257 (mtp180) cc_final: 0.7866 (mmm-85) REVERT: E 543 LYS cc_start: 0.8461 (mmtt) cc_final: 0.7955 (tptt) REVERT: E 656 SER cc_start: 0.8317 (t) cc_final: 0.7958 (m) REVERT: F 627 MET cc_start: 0.6996 (tmm) cc_final: 0.6586 (tmm) REVERT: F 660 GLN cc_start: 0.7527 (tt0) cc_final: 0.7039 (mt0) REVERT: F 666 MET cc_start: 0.8592 (OUTLIER) cc_final: 0.8261 (mtp) REVERT: F 732 GLU cc_start: 0.7665 (mm-30) cc_final: 0.7108 (mt-10) REVERT: F 734 GLU cc_start: 0.7616 (mt-10) cc_final: 0.6755 (pt0) REVERT: F 744 LEU cc_start: 0.6500 (OUTLIER) cc_final: 0.6280 (mp) outliers start: 59 outliers final: 18 residues processed: 341 average time/residue: 1.4135 time to fit residues: 536.9623 Evaluate side-chains 311 residues out of total 2375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 280 time to evaluate : 2.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain B residue 427 GLN Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain B residue 458 ILE Chi-restraints excluded: chain B residue 556 LEU Chi-restraints excluded: chain B residue 601 LYS Chi-restraints excluded: chain B residue 744 LEU Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain C residue 380 MET Chi-restraints excluded: chain C residue 408 GLN 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 755 THR Chi-restraints excluded: chain D residue 479 ASP Chi-restraints excluded: chain D residue 507 ARG Chi-restraints excluded: chain D residue 568 LYS Chi-restraints excluded: chain D residue 668 GLU 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 335 ASP Chi-restraints excluded: chain E residue 485 SER Chi-restraints excluded: chain E residue 663 GLN Chi-restraints excluded: chain E residue 669 LYS Chi-restraints excluded: chain F residue 666 MET Chi-restraints excluded: chain F residue 744 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 265 optimal weight: 20.0000 chunk 31 optimal weight: 7.9990 chunk 157 optimal weight: 5.9990 chunk 201 optimal weight: 2.9990 chunk 156 optimal weight: 3.9990 chunk 232 optimal weight: 4.9990 chunk 153 optimal weight: 4.9990 chunk 274 optimal weight: 9.9990 chunk 171 optimal weight: 9.9990 chunk 167 optimal weight: 3.9990 chunk 126 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 433 GLN B 472 GLN ** B 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 663 GLN ** C 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 667 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6334 moved from start: 0.3973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 19031 Z= 0.301 Angle : 0.594 11.257 25717 Z= 0.292 Chirality : 0.043 0.277 2915 Planarity : 0.004 0.048 3334 Dihedral : 8.458 165.174 2673 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 3.97 % Allowed : 17.61 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.17), residues: 2372 helix: 0.16 (0.15), residues: 1235 sheet: -0.69 (0.42), residues: 153 loop : -1.41 (0.20), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 583 HIS 0.008 0.002 HIS C 578 PHE 0.020 0.002 PHE B 638 TYR 0.025 0.002 TYR D 605 ARG 0.010 0.001 ARG C 624 *********************** 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 354 residues out of total 2375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 276 time to evaluate : 2.513 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: 0.7178 (OUTLIER) cc_final: 0.6542 (tt0) REVERT: A 593 LYS cc_start: 0.6913 (ttmt) cc_final: 0.6634 (ttpp) REVERT: A 619 GLU cc_start: 0.6529 (OUTLIER) cc_final: 0.6281 (pp20) REVERT: A 683 MET cc_start: 0.3319 (tpp) cc_final: 0.0435 (pmm) REVERT: A 733 LYS cc_start: 0.7728 (mtpt) cc_final: 0.6838 (tptp) REVERT: B 427 GLN cc_start: 0.6535 (OUTLIER) cc_final: 0.6000 (tm-30) REVERT: B 428 GLU cc_start: 0.6156 (tt0) cc_final: 0.5855 (mm-30) REVERT: B 433 GLN cc_start: 0.7128 (tp-100) cc_final: 0.6834 (tm-30) REVERT: B 458 ILE cc_start: 0.8521 (OUTLIER) cc_final: 0.8111 (pt) REVERT: B 465 ARG cc_start: 0.5511 (mtt-85) cc_final: 0.4986 (mmt180) REVERT: B 471 ARG cc_start: 0.7522 (OUTLIER) cc_final: 0.7203 (mtp85) REVERT: B 541 ASN cc_start: 0.8208 (OUTLIER) cc_final: 0.7970 (p0) REVERT: B 592 LEU cc_start: 0.7211 (OUTLIER) cc_final: 0.6929 (mp) REVERT: B 683 MET cc_start: 0.6079 (ptp) cc_final: 0.5566 (ttt) REVERT: C 391 ASP cc_start: 0.7267 (t70) cc_final: 0.7017 (t70) REVERT: C 408 GLN cc_start: 0.7755 (OUTLIER) cc_final: 0.5469 (mp10) REVERT: C 559 LYS cc_start: 0.7713 (mtpt) cc_final: 0.7458 (mtmt) REVERT: C 611 LYS cc_start: 0.8337 (OUTLIER) cc_final: 0.7743 (mttp) REVERT: C 648 ASP cc_start: 0.7395 (t0) cc_final: 0.6936 (p0) REVERT: C 672 GLN cc_start: 0.7659 (mm-40) cc_final: 0.7294 (mp10) REVERT: C 673 ILE cc_start: 0.8259 (mt) cc_final: 0.7962 (tt) REVERT: C 683 MET cc_start: 0.6209 (ttt) cc_final: 0.5739 (tmm) REVERT: C 695 ARG cc_start: 0.7039 (ttp80) cc_final: 0.6467 (ttp80) REVERT: C 699 ASP cc_start: 0.7246 (m-30) cc_final: 0.6936 (m-30) REVERT: C 774 GLU cc_start: 0.8024 (mp0) cc_final: 0.7769 (mp0) REVERT: D 561 GLN cc_start: 0.8424 (tt0) cc_final: 0.8151 (tt0) REVERT: D 568 LYS cc_start: 0.7667 (OUTLIER) cc_final: 0.7324 (mttm) REVERT: D 668 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7393 (mt-10) REVERT: D 673 ILE cc_start: 0.8116 (mt) cc_final: 0.7760 (pp) REVERT: E 318 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.8055 (mp) REVERT: E 359 LYS cc_start: 0.7677 (mttt) cc_final: 0.7360 (mtpm) REVERT: E 455 ARG cc_start: 0.8270 (mtp180) cc_final: 0.7904 (mmm-85) REVERT: E 543 LYS cc_start: 0.8458 (mmtt) cc_final: 0.7958 (tptt) REVERT: E 656 SER cc_start: 0.8375 (t) cc_final: 0.8018 (m) REVERT: F 627 MET cc_start: 0.6934 (tmm) cc_final: 0.6491 (tmm) REVERT: F 660 GLN cc_start: 0.7661 (tt0) cc_final: 0.7202 (mt0) REVERT: F 666 MET cc_start: 0.8635 (OUTLIER) cc_final: 0.8301 (mtp) REVERT: F 732 GLU cc_start: 0.7696 (mm-30) cc_final: 0.7097 (mt-10) REVERT: F 744 LEU cc_start: 0.6821 (OUTLIER) cc_final: 0.6250 (mp) outliers start: 78 outliers final: 35 residues processed: 328 average time/residue: 1.4088 time to fit residues: 515.9888 Evaluate side-chains 325 residues out of total 2375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 276 time to evaluate : 2.309 ------------------------------------------------------------------------------- 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 684 VAL Chi-restraints excluded: chain B residue 427 GLN Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain B residue 458 ILE Chi-restraints excluded: chain B residue 471 ARG Chi-restraints excluded: chain B residue 541 ASN Chi-restraints excluded: chain B residue 556 LEU Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 744 LEU Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 408 GLN Chi-restraints excluded: chain C residue 454 ASN Chi-restraints excluded: chain C residue 500 LEU Chi-restraints excluded: chain C residue 520 ASP 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 755 THR Chi-restraints excluded: chain D residue 457 ASP Chi-restraints excluded: chain D residue 479 ASP Chi-restraints excluded: chain D residue 507 ARG Chi-restraints excluded: chain D residue 541 ASN Chi-restraints excluded: chain D residue 568 LYS Chi-restraints excluded: chain D residue 668 GLU Chi-restraints excluded: chain D residue 669 LYS Chi-restraints excluded: chain D residue 739 ASN Chi-restraints excluded: chain D residue 772 LEU Chi-restraints excluded: chain E residue 318 LEU Chi-restraints excluded: chain E residue 335 ASP Chi-restraints excluded: chain E residue 382 VAL Chi-restraints excluded: chain E residue 457 ASP Chi-restraints excluded: chain E residue 485 SER Chi-restraints excluded: chain E residue 669 LYS Chi-restraints excluded: chain E residue 676 ASP Chi-restraints excluded: chain F residue 562 VAL Chi-restraints excluded: chain F residue 656 SER Chi-restraints excluded: chain F residue 666 MET Chi-restraints excluded: chain F residue 705 ILE Chi-restraints excluded: chain F residue 740 ASP Chi-restraints excluded: chain F residue 743 GLU Chi-restraints excluded: chain F residue 744 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 169 optimal weight: 6.9990 chunk 109 optimal weight: 6.9990 chunk 164 optimal weight: 0.6980 chunk 82 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 174 optimal weight: 1.9990 chunk 187 optimal weight: 2.9990 chunk 135 optimal weight: 0.8980 chunk 25 optimal weight: 30.0000 chunk 215 optimal weight: 6.9990 chunk 249 optimal weight: 50.0000 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 663 GLN ** C 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 663 GLN F 667 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6301 moved from start: 0.4061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19031 Z= 0.195 Angle : 0.535 12.361 25717 Z= 0.266 Chirality : 0.040 0.155 2915 Planarity : 0.004 0.044 3334 Dihedral : 7.969 156.713 2673 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.21 % Allowed : 18.58 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.17), residues: 2372 helix: 0.50 (0.15), residues: 1227 sheet: -0.62 (0.42), residues: 153 loop : -1.27 (0.20), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 583 HIS 0.005 0.001 HIS C 578 PHE 0.013 0.001 PHE B 638 TYR 0.020 0.001 TYR C 605 ARG 0.009 0.000 ARG C 624 *********************** 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 349 residues out of total 2375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 286 time to evaluate : 2.327 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: 0.7144 (OUTLIER) cc_final: 0.6539 (tt0) REVERT: A 575 GLN cc_start: 0.8118 (mm-40) cc_final: 0.7873 (mm110) REVERT: A 593 LYS cc_start: 0.6921 (ttmt) cc_final: 0.6647 (ttpp) REVERT: A 619 GLU cc_start: 0.6516 (OUTLIER) cc_final: 0.6300 (pp20) REVERT: A 673 ILE cc_start: 0.8510 (OUTLIER) cc_final: 0.8130 (pp) REVERT: A 683 MET cc_start: 0.3163 (tpp) cc_final: 0.0412 (pmm) REVERT: A 733 LYS cc_start: 0.7706 (mtpt) cc_final: 0.6789 (tptp) REVERT: B 427 GLN cc_start: 0.6426 (OUTLIER) cc_final: 0.5901 (tm-30) REVERT: B 428 GLU cc_start: 0.6134 (tt0) cc_final: 0.5829 (mm-30) REVERT: B 433 GLN cc_start: 0.7037 (tp-100) cc_final: 0.6764 (tm-30) REVERT: B 458 ILE cc_start: 0.8556 (OUTLIER) cc_final: 0.8156 (pt) REVERT: B 465 ARG cc_start: 0.5496 (mtt-85) cc_final: 0.5007 (tpt170) REVERT: B 541 ASN cc_start: 0.8161 (OUTLIER) cc_final: 0.7925 (p0) REVERT: B 636 GLU cc_start: 0.7744 (mm-30) cc_final: 0.7457 (mm-30) REVERT: B 683 MET cc_start: 0.6085 (ptp) cc_final: 0.5568 (ttt) REVERT: C 391 ASP cc_start: 0.7239 (t70) cc_final: 0.7003 (t70) REVERT: C 408 GLN cc_start: 0.7710 (OUTLIER) cc_final: 0.7323 (mp10) REVERT: C 559 LYS cc_start: 0.7697 (mtpt) cc_final: 0.7452 (mtmt) REVERT: C 611 LYS cc_start: 0.8328 (OUTLIER) cc_final: 0.7731 (mttp) REVERT: C 648 ASP cc_start: 0.7333 (t0) cc_final: 0.6929 (p0) REVERT: C 672 GLN cc_start: 0.7618 (mm-40) cc_final: 0.7284 (mp10) REVERT: C 673 ILE cc_start: 0.8251 (mt) cc_final: 0.7987 (tt) REVERT: C 683 MET cc_start: 0.6252 (ttt) cc_final: 0.5760 (tmm) REVERT: C 695 ARG cc_start: 0.7030 (ttp80) cc_final: 0.6437 (ttp80) REVERT: C 699 ASP cc_start: 0.7130 (m-30) cc_final: 0.6826 (m-30) REVERT: C 774 GLU cc_start: 0.8035 (mp0) cc_final: 0.7805 (mp0) REVERT: D 507 ARG cc_start: 0.8151 (OUTLIER) cc_final: 0.7144 (mtm-85) REVERT: D 561 GLN cc_start: 0.8414 (tt0) cc_final: 0.8107 (tt0) REVERT: D 568 LYS cc_start: 0.7706 (OUTLIER) cc_final: 0.7370 (mttm) REVERT: D 641 ARG cc_start: 0.8092 (mtm-85) cc_final: 0.7842 (mtm-85) REVERT: D 668 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7360 (mt-10) REVERT: D 673 ILE cc_start: 0.8073 (mt) cc_final: 0.7717 (pp) REVERT: E 359 LYS cc_start: 0.7678 (mttt) cc_final: 0.7371 (mtpm) REVERT: E 415 LYS cc_start: 0.7809 (tttt) cc_final: 0.7402 (ttmm) REVERT: E 455 ARG cc_start: 0.8236 (mtp180) cc_final: 0.7841 (mmm-85) REVERT: E 543 LYS cc_start: 0.8439 (mmtt) cc_final: 0.7894 (tptt) REVERT: E 656 SER cc_start: 0.8350 (t) cc_final: 0.7979 (m) REVERT: E 668 GLU cc_start: 0.6827 (OUTLIER) cc_final: 0.6530 (pm20) REVERT: E 718 GLU cc_start: 0.7113 (mt-10) cc_final: 0.6646 (mp0) REVERT: F 627 MET cc_start: 0.7004 (tmm) cc_final: 0.6455 (tmm) REVERT: F 660 GLN cc_start: 0.7609 (tt0) cc_final: 0.7119 (mt0) REVERT: F 666 MET cc_start: 0.8605 (OUTLIER) cc_final: 0.8257 (mtp) REVERT: F 732 GLU cc_start: 0.7691 (mm-30) cc_final: 0.7092 (mt-10) REVERT: F 734 GLU cc_start: 0.7607 (mt-10) cc_final: 0.6772 (pt0) REVERT: F 744 LEU cc_start: 0.6622 (OUTLIER) cc_final: 0.6387 (mp) outliers start: 63 outliers final: 30 residues processed: 328 average time/residue: 1.4339 time to fit residues: 524.8491 Evaluate side-chains 314 residues out of total 2375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 270 time to evaluate : 2.372 ------------------------------------------------------------------------------- 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 673 ILE Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain B residue 427 GLN Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain B residue 458 ILE Chi-restraints excluded: chain B residue 541 ASN Chi-restraints excluded: chain B residue 556 LEU Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain B residue 744 LEU Chi-restraints excluded: chain B residue 760 VAL Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 408 GLN Chi-restraints excluded: chain C residue 410 ASP Chi-restraints excluded: chain C residue 454 ASN 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 643 THR Chi-restraints excluded: chain C residue 687 LYS Chi-restraints excluded: chain C residue 755 THR Chi-restraints excluded: chain D residue 479 ASP Chi-restraints excluded: chain D residue 507 ARG Chi-restraints excluded: chain D residue 541 ASN Chi-restraints excluded: chain D residue 568 LYS Chi-restraints excluded: chain D residue 668 GLU Chi-restraints excluded: chain D residue 669 LYS Chi-restraints excluded: chain D residue 739 ASN Chi-restraints excluded: chain D residue 772 LEU Chi-restraints excluded: chain E residue 320 ILE Chi-restraints excluded: chain E residue 335 ASP Chi-restraints excluded: chain E residue 382 VAL Chi-restraints excluded: chain E residue 485 SER Chi-restraints excluded: chain E residue 668 GLU Chi-restraints excluded: chain E residue 669 LYS Chi-restraints excluded: chain E residue 676 ASP Chi-restraints excluded: chain F residue 562 VAL Chi-restraints excluded: chain F residue 656 SER Chi-restraints excluded: chain F residue 666 MET Chi-restraints excluded: chain F residue 705 ILE Chi-restraints excluded: chain F residue 743 GLU Chi-restraints excluded: chain F residue 744 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 263 optimal weight: 20.0000 chunk 240 optimal weight: 50.0000 chunk 255 optimal weight: 50.0000 chunk 154 optimal weight: 9.9990 chunk 111 optimal weight: 7.9990 chunk 201 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 231 optimal weight: 7.9990 chunk 242 optimal weight: 50.0000 chunk 168 optimal weight: 4.9990 chunk 270 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 433 GLN C 663 GLN ** C 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 325 ASN E 329 ASN E 424 GLN ** E 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 587 HIS F 667 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6353 moved from start: 0.4233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 19031 Z= 0.398 Angle : 0.663 13.472 25717 Z= 0.327 Chirality : 0.046 0.166 2915 Planarity : 0.005 0.056 3334 Dihedral : 8.397 163.163 2673 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 3.56 % Allowed : 18.78 % Favored : 77.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.17), residues: 2372 helix: 0.17 (0.15), residues: 1233 sheet: -0.65 (0.42), residues: 153 loop : -1.45 (0.19), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP F 583 HIS 0.008 0.002 HIS C 578 PHE 0.024 0.002 PHE C 393 TYR 0.029 0.002 TYR D 605 ARG 0.010 0.001 ARG C 624 *********************** 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 346 residues out of total 2375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 276 time to evaluate : 2.377 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 567 GLU cc_start: 0.7150 (OUTLIER) cc_final: 0.6570 (tt0) REVERT: A 575 GLN cc_start: 0.8126 (mm-40) cc_final: 0.7805 (mm110) REVERT: A 593 LYS cc_start: 0.6911 (ttmt) cc_final: 0.6668 (ttpp) REVERT: A 619 GLU cc_start: 0.6558 (OUTLIER) cc_final: 0.6298 (pp20) REVERT: A 673 ILE cc_start: 0.8543 (OUTLIER) cc_final: 0.8170 (pp) REVERT: A 683 MET cc_start: 0.3366 (tpp) cc_final: 0.0553 (pmm) REVERT: A 733 LYS cc_start: 0.7655 (mtpt) cc_final: 0.6689 (tptp) REVERT: B 404 LEU cc_start: 0.7400 (tt) cc_final: 0.7183 (tp) REVERT: B 427 GLN cc_start: 0.6506 (OUTLIER) cc_final: 0.5930 (tm-30) REVERT: B 428 GLU cc_start: 0.6109 (tt0) cc_final: 0.5821 (mm-30) REVERT: B 433 GLN cc_start: 0.7014 (tp-100) cc_final: 0.6773 (tm130) REVERT: B 458 ILE cc_start: 0.8530 (OUTLIER) cc_final: 0.8112 (pt) REVERT: B 465 ARG cc_start: 0.5784 (mtt-85) cc_final: 0.5209 (tpt170) REVERT: B 541 ASN cc_start: 0.8242 (OUTLIER) cc_final: 0.8001 (p0) REVERT: B 592 LEU cc_start: 0.7249 (OUTLIER) cc_final: 0.6867 (mp) REVERT: B 636 GLU cc_start: 0.7724 (mm-30) cc_final: 0.7495 (mm-30) REVERT: B 683 MET cc_start: 0.6085 (ptp) cc_final: 0.5580 (ttt) REVERT: C 391 ASP cc_start: 0.7259 (t70) cc_final: 0.7012 (t70) REVERT: C 408 GLN cc_start: 0.7748 (OUTLIER) cc_final: 0.5496 (mp10) REVERT: C 559 LYS cc_start: 0.7745 (mtpt) cc_final: 0.7444 (mtmt) REVERT: C 611 LYS cc_start: 0.8354 (OUTLIER) cc_final: 0.7764 (mttp) REVERT: C 636 GLU cc_start: 0.7552 (tt0) cc_final: 0.7070 (pt0) REVERT: C 648 ASP cc_start: 0.7432 (t0) cc_final: 0.6959 (p0) REVERT: C 672 GLN cc_start: 0.7720 (mm-40) cc_final: 0.7428 (mp10) REVERT: C 673 ILE cc_start: 0.8284 (mt) cc_final: 0.7953 (tt) REVERT: C 683 MET cc_start: 0.6231 (ttt) cc_final: 0.5749 (tmm) REVERT: C 695 ARG cc_start: 0.7079 (ttp80) cc_final: 0.6517 (ttp80) REVERT: C 699 ASP cc_start: 0.7263 (m-30) cc_final: 0.6970 (m-30) REVERT: C 774 GLU cc_start: 0.8024 (mp0) cc_final: 0.7787 (mp0) REVERT: D 561 GLN cc_start: 0.8441 (tt0) cc_final: 0.8099 (tt0) REVERT: D 568 LYS cc_start: 0.7665 (OUTLIER) cc_final: 0.7296 (mttm) REVERT: D 668 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7412 (mt-10) REVERT: E 318 LEU cc_start: 0.8317 (mt) cc_final: 0.8059 (mp) REVERT: E 359 LYS cc_start: 0.7680 (mttt) cc_final: 0.7393 (mtpm) REVERT: E 455 ARG cc_start: 0.8174 (mtp180) cc_final: 0.7651 (mmm-85) REVERT: E 543 LYS cc_start: 0.8338 (mmtt) cc_final: 0.7913 (tptt) REVERT: E 656 SER cc_start: 0.8378 (t) cc_final: 0.8011 (m) REVERT: E 668 GLU cc_start: 0.6884 (OUTLIER) cc_final: 0.6668 (mp0) REVERT: E 718 GLU cc_start: 0.7123 (mt-10) cc_final: 0.6720 (mp0) REVERT: F 627 MET cc_start: 0.6899 (tmm) cc_final: 0.6506 (tmm) REVERT: F 732 GLU cc_start: 0.7533 (mm-30) cc_final: 0.6982 (mt-10) REVERT: F 734 GLU cc_start: 0.7548 (mt-10) cc_final: 0.6671 (pt0) REVERT: F 744 LEU cc_start: 0.6663 (OUTLIER) cc_final: 0.6096 (mp) outliers start: 70 outliers final: 36 residues processed: 322 average time/residue: 1.4223 time to fit residues: 511.7608 Evaluate side-chains 323 residues out of total 2375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 274 time to evaluate : 2.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 567 GLU Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 673 ILE Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 689 TYR 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 541 ASN Chi-restraints excluded: chain B residue 556 LEU Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain C residue 408 GLN Chi-restraints excluded: chain C residue 410 ASP Chi-restraints excluded: chain C residue 454 ASN Chi-restraints excluded: chain C residue 501 GLU Chi-restraints excluded: chain C residue 520 ASP 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 755 THR Chi-restraints excluded: chain D residue 479 ASP Chi-restraints excluded: chain D residue 499 THR Chi-restraints excluded: chain D residue 507 ARG Chi-restraints excluded: chain D residue 541 ASN Chi-restraints excluded: chain D residue 568 LYS Chi-restraints excluded: chain D residue 668 GLU Chi-restraints excluded: chain D residue 669 LYS Chi-restraints excluded: chain D residue 739 ASN Chi-restraints excluded: chain D residue 772 LEU Chi-restraints excluded: chain E residue 320 ILE Chi-restraints excluded: chain E residue 335 ASP Chi-restraints excluded: chain E residue 382 VAL Chi-restraints excluded: chain E residue 485 SER Chi-restraints excluded: chain E residue 668 GLU Chi-restraints excluded: chain E residue 676 ASP Chi-restraints excluded: chain E residue 736 LEU Chi-restraints excluded: chain F residue 562 VAL Chi-restraints excluded: chain F residue 656 SER Chi-restraints excluded: chain F residue 666 MET Chi-restraints excluded: chain F residue 705 ILE Chi-restraints excluded: chain F residue 740 ASP Chi-restraints excluded: chain F residue 743 GLU Chi-restraints excluded: chain F residue 744 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 165 optimal weight: 5.9990 chunk 128 optimal weight: 8.9990 chunk 188 optimal weight: 0.5980 chunk 283 optimal weight: 40.0000 chunk 261 optimal weight: 50.0000 chunk 226 optimal weight: 5.9990 chunk 23 optimal weight: 30.0000 chunk 174 optimal weight: 5.9990 chunk 138 optimal weight: 0.7980 chunk 179 optimal weight: 0.8980 chunk 240 optimal weight: 50.0000 overall best weight: 2.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 433 GLN ** C 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 663 GLN F 667 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6317 moved from start: 0.4288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 19031 Z= 0.235 Angle : 0.567 13.466 25717 Z= 0.282 Chirality : 0.041 0.150 2915 Planarity : 0.004 0.045 3334 Dihedral : 8.033 156.153 2673 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.85 % Allowed : 19.69 % Favored : 77.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.17), residues: 2372 helix: 0.46 (0.15), residues: 1228 sheet: -0.53 (0.43), residues: 147 loop : -1.35 (0.19), residues: 997 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 583 HIS 0.006 0.001 HIS C 578 PHE 0.017 0.002 PHE B 469 TYR 0.019 0.002 TYR C 605 ARG 0.009 0.001 ARG C 624 ********************** 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 338 residues out of total 2375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 282 time to evaluate : 2.336 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 567 GLU cc_start: 0.7179 (OUTLIER) cc_final: 0.6629 (tt0) REVERT: A 593 LYS cc_start: 0.6931 (ttmt) cc_final: 0.6670 (ttpp) REVERT: A 619 GLU cc_start: 0.6549 (OUTLIER) cc_final: 0.6326 (pp20) REVERT: A 673 ILE cc_start: 0.8540 (OUTLIER) cc_final: 0.8173 (pp) REVERT: A 683 MET cc_start: 0.3336 (tpp) cc_final: 0.0577 (pmm) REVERT: A 733 LYS cc_start: 0.7645 (mtpt) cc_final: 0.6677 (tptp) REVERT: B 402 CYS cc_start: 0.7027 (p) cc_final: 0.6212 (t) REVERT: B 404 LEU cc_start: 0.7212 (tt) cc_final: 0.6973 (tp) REVERT: B 427 GLN cc_start: 0.6350 (OUTLIER) cc_final: 0.5786 (tm-30) REVERT: B 428 GLU cc_start: 0.6104 (tt0) cc_final: 0.5822 (mm-30) REVERT: B 433 GLN cc_start: 0.7091 (tp-100) cc_final: 0.6793 (tm130) REVERT: B 454 ASN cc_start: 0.8275 (OUTLIER) cc_final: 0.7886 (p0) REVERT: B 458 ILE cc_start: 0.8564 (OUTLIER) cc_final: 0.8180 (pt) REVERT: B 465 ARG cc_start: 0.5740 (mtt-85) cc_final: 0.5068 (mmt180) REVERT: B 541 ASN cc_start: 0.8187 (OUTLIER) cc_final: 0.7949 (p0) REVERT: B 592 LEU cc_start: 0.7140 (OUTLIER) cc_final: 0.6872 (mp) REVERT: B 636 GLU cc_start: 0.7748 (mm-30) cc_final: 0.7460 (mm-30) REVERT: B 683 MET cc_start: 0.6135 (ptp) cc_final: 0.5576 (ttt) REVERT: C 391 ASP cc_start: 0.7255 (t70) cc_final: 0.7014 (t70) REVERT: C 408 GLN cc_start: 0.7735 (OUTLIER) cc_final: 0.7398 (mp10) REVERT: C 559 LYS cc_start: 0.7662 (mtpt) cc_final: 0.7361 (mtmt) REVERT: C 564 GLN cc_start: 0.7275 (OUTLIER) cc_final: 0.6662 (mm-40) REVERT: C 611 LYS cc_start: 0.8325 (OUTLIER) cc_final: 0.7737 (mttp) REVERT: C 648 ASP cc_start: 0.7389 (t0) cc_final: 0.6947 (p0) REVERT: C 672 GLN cc_start: 0.7664 (mm-40) cc_final: 0.7268 (mp10) REVERT: C 673 ILE cc_start: 0.8257 (mt) cc_final: 0.7995 (tt) REVERT: C 683 MET cc_start: 0.6228 (ttt) cc_final: 0.5758 (tmm) REVERT: C 695 ARG cc_start: 0.7024 (ttp80) cc_final: 0.6436 (ttp80) REVERT: C 699 ASP cc_start: 0.7227 (m-30) cc_final: 0.6921 (m-30) REVERT: C 774 GLU cc_start: 0.8028 (mp0) cc_final: 0.7782 (mp0) REVERT: D 507 ARG cc_start: 0.8184 (OUTLIER) cc_final: 0.7932 (mtp180) REVERT: D 561 GLN cc_start: 0.8449 (tt0) cc_final: 0.8103 (tt0) REVERT: D 568 LYS cc_start: 0.7646 (OUTLIER) cc_final: 0.7301 (mttm) REVERT: D 641 ARG cc_start: 0.8056 (mtm-85) cc_final: 0.7825 (mtm-85) REVERT: D 668 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7384 (mt-10) REVERT: D 673 ILE cc_start: 0.8129 (mt) cc_final: 0.7775 (pp) REVERT: E 318 LEU cc_start: 0.8299 (mt) cc_final: 0.8030 (mp) REVERT: E 359 LYS cc_start: 0.7675 (mttt) cc_final: 0.7382 (mtpm) REVERT: E 455 ARG cc_start: 0.8323 (mtp180) cc_final: 0.7943 (mmm-85) REVERT: E 543 LYS cc_start: 0.8356 (mmtt) cc_final: 0.7911 (tptt) REVERT: E 608 TYR cc_start: 0.7559 (m-80) cc_final: 0.6931 (m-80) REVERT: E 656 SER cc_start: 0.8347 (t) cc_final: 0.7997 (m) REVERT: E 729 LEU cc_start: 0.7756 (mt) cc_final: 0.7506 (mt) REVERT: F 627 MET cc_start: 0.6956 (tmm) cc_final: 0.6530 (tmm) REVERT: F 660 GLN cc_start: 0.7617 (tt0) cc_final: 0.7141 (mt0) REVERT: F 732 GLU cc_start: 0.7551 (mm-30) cc_final: 0.7011 (mt-10) REVERT: F 734 GLU cc_start: 0.7676 (mt-10) cc_final: 0.6803 (pt0) REVERT: F 744 LEU cc_start: 0.6733 (OUTLIER) cc_final: 0.6156 (mp) outliers start: 56 outliers final: 31 residues processed: 320 average time/residue: 1.3648 time to fit residues: 488.3658 Evaluate side-chains 317 residues out of total 2375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 271 time to evaluate : 2.185 ------------------------------------------------------------------------------- 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 673 ILE Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain B residue 427 GLN Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain B residue 454 ASN Chi-restraints excluded: chain B residue 458 ILE Chi-restraints excluded: chain B residue 541 ASN Chi-restraints excluded: chain B residue 556 LEU Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 408 GLN Chi-restraints excluded: chain C residue 454 ASN 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 564 GLN Chi-restraints excluded: chain C residue 611 LYS Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 687 LYS Chi-restraints excluded: chain C residue 755 THR Chi-restraints excluded: chain D residue 479 ASP Chi-restraints excluded: chain D residue 507 ARG Chi-restraints excluded: chain D residue 541 ASN Chi-restraints excluded: chain D residue 568 LYS Chi-restraints excluded: chain D residue 668 GLU Chi-restraints excluded: chain D residue 669 LYS Chi-restraints excluded: chain D residue 739 ASN Chi-restraints excluded: chain D residue 772 LEU Chi-restraints excluded: chain E residue 320 ILE Chi-restraints excluded: chain E residue 335 ASP Chi-restraints excluded: chain E residue 382 VAL Chi-restraints excluded: chain E residue 399 ASN Chi-restraints excluded: chain E residue 485 SER Chi-restraints excluded: chain E residue 663 GLN Chi-restraints excluded: chain E residue 676 ASP Chi-restraints excluded: chain E residue 736 LEU Chi-restraints excluded: chain F residue 562 VAL Chi-restraints excluded: chain F residue 656 SER Chi-restraints excluded: chain F residue 666 MET Chi-restraints excluded: chain F residue 705 ILE Chi-restraints excluded: chain F residue 743 GLU Chi-restraints excluded: chain F residue 744 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 69 optimal weight: 20.0000 chunk 208 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 226 optimal weight: 6.9990 chunk 94 optimal weight: 8.9990 chunk 232 optimal weight: 5.9990 chunk 28 optimal weight: 8.9990 chunk 41 optimal weight: 5.9990 chunk 198 optimal weight: 3.9990 chunk 12 optimal weight: 50.0000 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 663 GLN F 667 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.158680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.135537 restraints weight = 26601.976| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 2.01 r_work: 0.3531 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3389 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7074 moved from start: 0.4350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 19031 Z= 0.278 Angle : 0.591 13.825 25717 Z= 0.293 Chirality : 0.043 0.151 2915 Planarity : 0.004 0.046 3334 Dihedral : 8.007 155.961 2673 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 2.75 % Allowed : 20.15 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.17), residues: 2372 helix: 0.48 (0.15), residues: 1226 sheet: -0.52 (0.42), residues: 154 loop : -1.37 (0.19), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 583 HIS 0.007 0.001 HIS C 578 PHE 0.018 0.002 PHE B 469 TYR 0.020 0.002 TYR D 605 ARG 0.009 0.001 ARG C 624 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8357.99 seconds wall clock time: 148 minutes 18.36 seconds (8898.36 seconds total)