Starting phenix.real_space_refine (version: 1.21rc1) on Tue Apr 25 03:56:17 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nyy_0552/04_2023/6nyy_0552_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nyy_0552/04_2023/6nyy_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_0552/04_2023/6nyy_0552.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nyy_0552/04_2023/6nyy_0552.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nyy_0552/04_2023/6nyy_0552_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nyy_0552/04_2023/6nyy_0552_updated.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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: 10.71, per 1000 atoms: 0.56 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: 7.72 Conformation dependent library (CDL) restraints added in 3.3 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: 1.86 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: 5.84 Time building geometry restraints manager: 8.20 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: 11533 34.48 - 68.95: 66 68.95 - 103.43: 5 103.43 - 137.91: 4 137.91 - 172.38: 3 Dihedral angle restraints: 11611 sinusoidal: 4745 harmonic: 6866 Sorted by residual: dihedral pdb=" C5' ADP E 801 " pdb=" O5' ADP E 801 " pdb=" PA ADP E 801 " pdb=" O2A ADP E 801 " ideal model delta sinusoidal sigma weight residual -60.00 112.39 -172.38 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" O2A ADP E 801 " pdb=" O3A ADP E 801 " pdb=" PA ADP E 801 " pdb=" PB ADP E 801 " ideal model delta sinusoidal sigma weight residual -60.00 66.09 -126.09 1 2.00e+01 2.50e-03 3.81e+01 dihedral pdb=" O1B ADP E 801 " pdb=" O3A ADP E 801 " pdb=" PB ADP E 801 " pdb=" PA ADP E 801 " ideal model delta sinusoidal sigma weight residual -60.00 59.48 -119.49 1 2.00e+01 2.50e-03 3.58e+01 ... (remaining 11608 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 2468 0.069 - 0.138: 407 0.138 - 0.207: 30 0.207 - 0.276: 7 0.276 - 0.345: 3 Chirality restraints: 2915 Sorted by residual: chirality pdb=" CB ILE B 449 " pdb=" CA ILE B 449 " pdb=" CG1 ILE B 449 " pdb=" CG2 ILE B 449 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.35 2.00e-01 2.50e+01 2.98e+00 chirality pdb=" C3' ANP D 801 " pdb=" C2' ANP D 801 " pdb=" C4' ANP D 801 " pdb=" O3' ANP D 801 " both_signs ideal model delta sigma weight residual False -2.36 -2.65 0.29 2.00e-01 2.50e+01 2.16e+00 chirality pdb=" C3' ANP C 803 " pdb=" C2' ANP C 803 " pdb=" C4' ANP C 803 " pdb=" O3' ANP C 803 " both_signs ideal model delta sigma weight residual False -2.36 -2.65 0.29 2.00e-01 2.50e+01 2.11e+00 ... (remaining 2912 not shown) Planarity restraints: 3334 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 552 " 0.028 2.00e-02 2.50e+03 5.61e-02 3.15e+01 pdb=" C VAL A 552 " -0.097 2.00e-02 2.50e+03 pdb=" O VAL A 552 " 0.037 2.00e-02 2.50e+03 pdb=" N ILE A 553 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 523 " 0.016 2.00e-02 2.50e+03 3.14e-02 9.87e+00 pdb=" CG ASN C 523 " -0.054 2.00e-02 2.50e+03 pdb=" OD1 ASN C 523 " 0.020 2.00e-02 2.50e+03 pdb=" ND2 ASN C 523 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY B 385 " -0.046 5.00e-02 4.00e+02 6.91e-02 7.64e+00 pdb=" N PRO B 386 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO B 386 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 386 " -0.038 5.00e-02 4.00e+02 ... (remaining 3331 not shown) Histogram of nonbonded interaction distances: 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: 0.090 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: 2.540 Check model and map are aligned: 0.250 Set scattering table: 0.170 Process input model: 55.090 Find NCS groups from input model: 1.860 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.460 ------------------------------------------------------------------------------- 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 : 10.084 172.382 7191 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 % 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 *********************** 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 : 2.470 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 outliers start: 1 outliers final: 1 residues processed: 527 average time/residue: 1.4908 time to fit residues: 871.3416 Evaluate side-chains 318 residues out of total 2375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 317 time to evaluate : 2.278 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 3.2484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 119 optimal weight: 0.9990 chunk 73 optimal weight: 6.9990 chunk 145 optimal weight: 0.9990 chunk 115 optimal weight: 9.9990 chunk 223 optimal weight: 4.9990 chunk 86 optimal weight: 0.9990 chunk 135 optimal weight: 0.9990 chunk 166 optimal weight: 8.9990 chunk 258 optimal weight: 50.0000 overall best weight: 1.7990 ------------------------------------------------------------------------------- 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 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 433 GLN D 526 ASN D 535 HIS D 541 ASN D 547 GLN D 561 GLN D 575 GLN D 655 GLN E 408 GLN E 454 ASN E 663 GLN F 667 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6266 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 19031 Z= 0.199 Angle : 0.603 11.172 25717 Z= 0.308 Chirality : 0.041 0.149 2915 Planarity : 0.005 0.056 3334 Dihedral : 9.256 170.371 2589 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer Outliers : 4.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.22 (0.15), residues: 2372 helix: -2.14 (0.12), residues: 1240 sheet: -1.45 (0.39), residues: 150 loop : -2.05 (0.18), residues: 982 *********************** 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 412 residues out of total 2375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 333 time to evaluate : 2.420 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 outliers start: 79 outliers final: 24 residues processed: 383 average time/residue: 1.4724 time to fit residues: 629.3730 Evaluate side-chains 306 residues out of total 2375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 282 time to evaluate : 2.610 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 16 residues processed: 9 average time/residue: 0.6064 time to fit residues: 10.2785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 143 optimal weight: 7.9990 chunk 80 optimal weight: 10.0000 chunk 215 optimal weight: 7.9990 chunk 176 optimal weight: 4.9990 chunk 71 optimal weight: 8.9990 chunk 259 optimal weight: 50.0000 chunk 280 optimal weight: 10.0000 chunk 230 optimal weight: 0.6980 chunk 257 optimal weight: 50.0000 chunk 88 optimal weight: 1.9990 chunk 208 optimal weight: 0.0370 overall best weight: 3.1464 ------------------------------------------------------------------------------- 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 C 739 ASN D 561 GLN D 647 GLN E 663 GLN F 667 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6307 moved from start: 0.3025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 19031 Z= 0.257 Angle : 0.594 11.261 25717 Z= 0.296 Chirality : 0.042 0.151 2915 Planarity : 0.005 0.053 3334 Dihedral : 8.847 158.033 2589 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer Outliers : 4.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.14 (0.16), residues: 2372 helix: -1.06 (0.14), residues: 1249 sheet: -1.08 (0.40), residues: 150 loop : -1.81 (0.19), residues: 973 *********************** 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 402 residues out of total 2375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 312 time to evaluate : 2.352 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 outliers start: 90 outliers final: 33 residues processed: 370 average time/residue: 1.4125 time to fit residues: 584.9571 Evaluate side-chains 310 residues out of total 2375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 277 time to evaluate : 2.527 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 24 residues processed: 11 average time/residue: 0.4585 time to fit residues: 10.6909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 10.0000 chunk 134 optimal weight: 2.9990 chunk 28 optimal weight: 8.9990 chunk 123 optimal weight: 3.9990 chunk 174 optimal weight: 7.9990 chunk 260 optimal weight: 50.0000 chunk 275 optimal weight: 9.9990 chunk 135 optimal weight: 0.9980 chunk 246 optimal weight: 50.0000 chunk 74 optimal weight: 8.9990 overall best weight: 4.9988 ------------------------------------------------------------------------------- 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 472 GLN C 587 HIS C 613 GLN C 663 GLN D 561 GLN D 647 GLN E 408 GLN E 542 GLN E 663 GLN F 667 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6346 moved from start: 0.3638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.051 19031 Z= 0.371 Angle : 0.662 11.653 25717 Z= 0.329 Chirality : 0.045 0.209 2915 Planarity : 0.005 0.056 3334 Dihedral : 8.841 155.318 2589 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer Outliers : 5.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.79 (0.16), residues: 2372 helix: -0.70 (0.14), residues: 1248 sheet: -1.02 (0.40), residues: 148 loop : -1.76 (0.19), residues: 976 *********************** 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 392 residues out of total 2375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 287 time to evaluate : 2.177 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 outliers start: 105 outliers final: 43 residues processed: 347 average time/residue: 1.3922 time to fit residues: 541.9035 Evaluate side-chains 320 residues out of total 2375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 277 time to evaluate : 2.318 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 27 residues processed: 17 average time/residue: 0.4480 time to fit residues: 14.0000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 229 optimal weight: 2.9990 chunk 156 optimal weight: 0.9980 chunk 4 optimal weight: 50.0000 chunk 205 optimal weight: 0.9990 chunk 113 optimal weight: 6.9990 chunk 235 optimal weight: 7.9990 chunk 190 optimal weight: 9.9990 chunk 0 optimal weight: 50.0000 chunk 140 optimal weight: 0.0370 chunk 247 optimal weight: 50.0000 chunk 69 optimal weight: 7.9990 overall best weight: 2.4064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 663 GLN D 561 GLN ** D 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 0.6307 moved from start: 0.3815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 19031 Z= 0.211 Angle : 0.561 10.901 25717 Z= 0.277 Chirality : 0.041 0.162 2915 Planarity : 0.004 0.056 3334 Dihedral : 8.434 156.492 2589 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer Outliers : 3.97 % 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: -1.19 (0.17), residues: 2372 helix: -0.15 (0.15), residues: 1234 sheet: -0.75 (0.41), residues: 148 loop : -1.54 (0.19), residues: 990 *********************** 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: 78 poor density : 301 time to evaluate : 2.560 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. outliers start: 78 outliers final: 34 residues processed: 348 average time/residue: 1.3645 time to fit residues: 534.9475 Evaluate side-chains 305 residues out of total 2375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 271 time to evaluate : 2.342 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 27 residues processed: 7 average time/residue: 0.3262 time to fit residues: 6.5690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 92 optimal weight: 4.9990 chunk 248 optimal weight: 50.0000 chunk 54 optimal weight: 6.9990 chunk 161 optimal weight: 2.9990 chunk 68 optimal weight: 7.9990 chunk 275 optimal weight: 0.7980 chunk 228 optimal weight: 8.9990 chunk 127 optimal weight: 4.9990 chunk 22 optimal weight: 50.0000 chunk 91 optimal weight: 7.9990 chunk 144 optimal weight: 3.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN ** B 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 663 GLN C 667 ASN D 561 GLN ** 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: 0.6328 moved from start: 0.4075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 19031 Z= 0.279 Angle : 0.598 9.223 25717 Z= 0.296 Chirality : 0.043 0.163 2915 Planarity : 0.004 0.058 3334 Dihedral : 8.433 155.222 2589 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer Outliers : 4.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.00 (0.17), residues: 2372 helix: 0.05 (0.15), residues: 1231 sheet: -0.82 (0.40), residues: 158 loop : -1.49 (0.19), residues: 983 *********************** 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 363 residues out of total 2375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 283 time to evaluate : 2.358 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. outliers start: 80 outliers final: 45 residues processed: 331 average time/residue: 1.3532 time to fit residues: 505.2905 Evaluate side-chains 310 residues out of total 2375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 265 time to evaluate : 2.488 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 29 residues processed: 16 average time/residue: 0.6078 time to fit residues: 15.7025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 265 optimal weight: 8.9990 chunk 31 optimal weight: 6.9990 chunk 157 optimal weight: 4.9990 chunk 201 optimal weight: 3.9990 chunk 156 optimal weight: 5.9990 chunk 232 optimal weight: 7.9990 chunk 153 optimal weight: 6.9990 chunk 274 optimal weight: 6.9990 chunk 171 optimal weight: 5.9990 chunk 167 optimal weight: 5.9990 chunk 126 optimal weight: 0.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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 ** D 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 587 HIS E 663 GLN F 667 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6338 moved from start: 0.4261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.047 19031 Z= 0.327 Angle : 0.622 12.024 25717 Z= 0.309 Chirality : 0.044 0.160 2915 Planarity : 0.004 0.064 3334 Dihedral : 8.499 156.418 2589 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer Outliers : 4.38 % 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: -0.95 (0.17), residues: 2372 helix: 0.08 (0.15), residues: 1233 sheet: -0.74 (0.40), residues: 160 loop : -1.45 (0.19), residues: 979 *********************** 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 357 residues out of total 2375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 271 time to evaluate : 2.456 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 outliers start: 86 outliers final: 42 residues processed: 327 average time/residue: 1.3922 time to fit residues: 512.0808 Evaluate side-chains 303 residues out of total 2375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 261 time to evaluate : 2.342 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 30 residues processed: 12 average time/residue: 0.3819 time to fit residues: 9.8561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0670 chunk 82 optimal weight: 2.9990 chunk 53 optimal weight: 0.0670 chunk 174 optimal weight: 3.9990 chunk 187 optimal weight: 7.9990 chunk 135 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 chunk 215 optimal weight: 7.9990 chunk 249 optimal weight: 50.0000 overall best weight: 2.6262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 433 GLN ** B 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 564 GLN C 663 GLN ** 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6313 moved from start: 0.4343 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= 0.228 Angle : 0.576 12.563 25717 Z= 0.285 Chirality : 0.041 0.151 2915 Planarity : 0.004 0.060 3334 Dihedral : 8.287 157.101 2589 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer Outliers : 3.16 % 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: -0.68 (0.17), residues: 2372 helix: 0.32 (0.15), residues: 1229 sheet: -0.61 (0.41), residues: 154 loop : -1.36 (0.19), residues: 989 *********************** 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 346 residues out of total 2375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 284 time to evaluate : 2.453 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. outliers start: 62 outliers final: 41 residues processed: 326 average time/residue: 1.3076 time to fit residues: 482.7045 Evaluate side-chains 308 residues out of total 2375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 267 time to evaluate : 2.332 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 33 residues processed: 8 average time/residue: 0.4523 time to fit residues: 8.2611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 chunk 111 optimal weight: 0.9990 chunk 201 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 231 optimal weight: 0.9980 chunk 242 optimal weight: 50.0000 chunk 168 optimal weight: 4.9990 chunk 270 optimal weight: 0.1980 overall best weight: 1.4184 ------------------------------------------------------------------------------- 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 541 ASN ** D 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 542 GLN E 663 GLN F 667 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6278 moved from start: 0.4459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 19031 Z= 0.168 Angle : 0.550 14.454 25717 Z= 0.273 Chirality : 0.040 0.232 2915 Planarity : 0.004 0.060 3334 Dihedral : 7.959 159.529 2589 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer Outliers : 2.44 % 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: -0.35 (0.18), residues: 2372 helix: 0.64 (0.15), residues: 1229 sheet: -0.57 (0.42), residues: 154 loop : -1.25 (0.20), residues: 989 *********************** 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 330 residues out of total 2375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 282 time to evaluate : 2.401 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. outliers start: 48 outliers final: 37 residues processed: 319 average time/residue: 1.3411 time to fit residues: 484.6416 Evaluate side-chains 300 residues out of total 2375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 263 time to evaluate : 2.320 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 34 residues processed: 3 average time/residue: 0.7016 time to fit residues: 5.8535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 165 optimal weight: 9.9990 chunk 128 optimal weight: 8.9990 chunk 188 optimal weight: 5.9990 chunk 283 optimal weight: 20.0000 chunk 261 optimal weight: 50.0000 chunk 226 optimal weight: 4.9990 chunk 23 optimal weight: 20.0000 chunk 174 optimal weight: 6.9990 chunk 138 optimal weight: 10.0000 chunk 179 optimal weight: 0.9980 chunk 240 optimal weight: 50.0000 overall best weight: 5.5988 ------------------------------------------------------------------------------- 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 ** D 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 424 GLN ** E 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 667 ASN ** F 739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6343 moved from start: 0.4565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.052 19031 Z= 0.396 Angle : 0.675 13.529 25717 Z= 0.333 Chirality : 0.046 0.233 2915 Planarity : 0.005 0.061 3334 Dihedral : 8.294 147.427 2589 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer Outliers : 2.44 % 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: -0.74 (0.17), residues: 2372 helix: 0.27 (0.15), residues: 1232 sheet: -0.59 (0.41), residues: 150 loop : -1.40 (0.19), residues: 990 ********************** 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 317 residues out of total 2375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 269 time to evaluate : 2.598 Fit side-chains TARDY: cannot create tardy model for: "MET A 321 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 380 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 438 " (corrupted residue). Skipping it. revert: symmetry clash 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. outliers start: 48 outliers final: 36 residues processed: 307 average time/residue: 1.3979 time to fit residues: 483.8684 Evaluate side-chains 299 residues out of total 2375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 263 time to evaluate : 2.388 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 29 residues processed: 7 average time/residue: 0.3887 time to fit residues: 7.3137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 69 optimal weight: 9.9990 chunk 208 optimal weight: 6.9990 chunk 33 optimal weight: 8.9990 chunk 62 optimal weight: 0.9990 chunk 226 optimal weight: 0.9980 chunk 94 optimal weight: 10.0000 chunk 232 optimal weight: 0.0970 chunk 28 optimal weight: 6.9990 chunk 41 optimal weight: 7.9990 chunk 198 optimal weight: 3.9990 chunk 12 optimal weight: 50.0000 overall best weight: 2.6184 ------------------------------------------------------------------------------- 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** ** D 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 663 GLN F 667 ASN ** F 739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.159555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.136864 restraints weight = 26428.352| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 1.87 r_work: 0.3554 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3413 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7044 moved from start: 0.4611 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= 0.233 Angle : 0.597 13.231 25717 Z= 0.296 Chirality : 0.042 0.200 2915 Planarity : 0.004 0.061 3334 Dihedral : 8.072 147.447 2589 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer Outliers : 2.09 % 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: -0.51 (0.17), residues: 2372 helix: 0.49 (0.15), residues: 1231 sheet: -0.46 (0.42), residues: 144 loop : -1.33 (0.19), residues: 997 =============================================================================== Job complete usr+sys time: 7977.89 seconds wall clock time: 141 minutes 41.13 seconds (8501.13 seconds total)