Starting phenix.real_space_refine on Sat Sep 28 01:56:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a1s_15086/09_2024/8a1s_15086.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a1s_15086/09_2024/8a1s_15086.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a1s_15086/09_2024/8a1s_15086.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a1s_15086/09_2024/8a1s_15086.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a1s_15086/09_2024/8a1s_15086.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a1s_15086/09_2024/8a1s_15086.cif" } resolution = 4.0 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= 0.000 sd= 0.005 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: 4 Type Number sf(0) Gaussians S 432 5.16 5 C 42912 2.51 5 N 11008 2.21 5 O 12800 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 137 residue(s): 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 67152 Number of models: 1 Model: "" Number of chains: 32 Chain: "A" Number of atoms: 4148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4148 Classifications: {'peptide': 533} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 27, 'TRANS': 503} Chain breaks: 2 Chain: "B" Number of atoms: 4148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4148 Classifications: {'peptide': 533} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 27, 'TRANS': 503} Chain breaks: 2 Chain: "C" Number of atoms: 4148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4148 Classifications: {'peptide': 533} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 27, 'TRANS': 503} Chain breaks: 2 Chain: "D" Number of atoms: 4148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4148 Classifications: {'peptide': 533} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 27, 'TRANS': 503} Chain breaks: 2 Chain: "E" Number of atoms: 4148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4148 Classifications: {'peptide': 533} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 27, 'TRANS': 503} Chain breaks: 2 Chain: "F" Number of atoms: 4148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4148 Classifications: {'peptide': 533} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 27, 'TRANS': 503} Chain breaks: 2 Chain: "G" Number of atoms: 4148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4148 Classifications: {'peptide': 533} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 27, 'TRANS': 503} Chain breaks: 2 Chain: "H" Number of atoms: 4148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4148 Classifications: {'peptide': 533} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 27, 'TRANS': 503} Chain breaks: 2 Chain: "I" Number of atoms: 4148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4148 Classifications: {'peptide': 533} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 27, 'TRANS': 503} Chain breaks: 2 Chain: "J" Number of atoms: 4148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4148 Classifications: {'peptide': 533} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 27, 'TRANS': 503} Chain breaks: 2 Chain: "K" Number of atoms: 4148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4148 Classifications: {'peptide': 533} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 27, 'TRANS': 503} Chain breaks: 2 Chain: "L" Number of atoms: 4148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4148 Classifications: {'peptide': 533} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 27, 'TRANS': 503} Chain breaks: 2 Chain: "M" Number of atoms: 4148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4148 Classifications: {'peptide': 533} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 27, 'TRANS': 503} Chain breaks: 2 Chain: "N" Number of atoms: 4148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4148 Classifications: {'peptide': 533} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 27, 'TRANS': 503} Chain breaks: 2 Chain: "O" Number of atoms: 4148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4148 Classifications: {'peptide': 533} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 27, 'TRANS': 503} Chain breaks: 2 Chain: "P" Number of atoms: 4148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4148 Classifications: {'peptide': 533} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 27, 'TRANS': 503} Chain breaks: 2 Chain: "A" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 49 Unusual residues: {'MA4': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 49 Unusual residues: {'MA4': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 49 Unusual residues: {'MA4': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 49 Unusual residues: {'MA4': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 49 Unusual residues: {'MA4': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 49 Unusual residues: {'MA4': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 49 Unusual residues: {'MA4': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 49 Unusual residues: {'MA4': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 49 Unusual residues: {'MA4': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "J" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 49 Unusual residues: {'MA4': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 49 Unusual residues: {'MA4': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 49 Unusual residues: {'MA4': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "M" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 49 Unusual residues: {'MA4': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "N" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 49 Unusual residues: {'MA4': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "O" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 49 Unusual residues: {'MA4': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "P" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 49 Unusual residues: {'MA4': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 29.00, per 1000 atoms: 0.43 Number of scatterers: 67152 At special positions: 0 Unit cell: (212.541, 214.635, 157.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 432 16.00 O 12800 8.00 N 11008 7.00 C 42912 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=128, symmetry=0 Simple disulfide: pdb=" SG CYS A 34 " - pdb=" SG CYS A 70 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 394 " distance=2.03 Simple disulfide: pdb=" SG CYS A 409 " - pdb=" SG CYS A 462 " distance=2.03 Simple disulfide: pdb=" SG CYS A 432 " - pdb=" SG CYS A 446 " distance=2.03 Simple disulfide: pdb=" SG CYS A 436 " - pdb=" SG CYS A 442 " distance=2.03 Simple disulfide: pdb=" SG CYS A 494 " - pdb=" SG CYS A 510 " distance=2.03 Simple disulfide: pdb=" SG CYS A 531 " - pdb=" SG CYS A 569 " distance=2.03 Simple disulfide: pdb=" SG CYS A 554 " - pdb=" SG CYS A 574 " distance=2.03 Simple disulfide: pdb=" SG CYS B 34 " - pdb=" SG CYS B 70 " distance=2.04 Simple disulfide: pdb=" SG CYS B 385 " - pdb=" SG CYS B 394 " distance=2.03 Simple disulfide: pdb=" SG CYS B 409 " - pdb=" SG CYS B 462 " distance=2.03 Simple disulfide: pdb=" SG CYS B 432 " - pdb=" SG CYS B 446 " distance=2.03 Simple disulfide: pdb=" SG CYS B 436 " - pdb=" SG CYS B 442 " distance=2.03 Simple disulfide: pdb=" SG CYS B 494 " - pdb=" SG CYS B 510 " distance=2.03 Simple disulfide: pdb=" SG CYS B 531 " - pdb=" SG CYS B 569 " distance=2.03 Simple disulfide: pdb=" SG CYS B 554 " - pdb=" SG CYS B 574 " distance=2.03 Simple disulfide: pdb=" SG CYS C 34 " - pdb=" SG CYS C 70 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 394 " distance=2.03 Simple disulfide: pdb=" SG CYS C 409 " - pdb=" SG CYS C 462 " distance=2.03 Simple disulfide: pdb=" SG CYS C 432 " - pdb=" SG CYS C 446 " distance=2.03 Simple disulfide: pdb=" SG CYS C 436 " - pdb=" SG CYS C 442 " distance=2.03 Simple disulfide: pdb=" SG CYS C 494 " - pdb=" SG CYS C 510 " distance=2.03 Simple disulfide: pdb=" SG CYS C 531 " - pdb=" SG CYS C 569 " distance=2.03 Simple disulfide: pdb=" SG CYS C 554 " - pdb=" SG CYS C 574 " distance=2.03 Simple disulfide: pdb=" SG CYS D 34 " - pdb=" SG CYS D 70 " distance=2.03 Simple disulfide: pdb=" SG CYS D 385 " - pdb=" SG CYS D 394 " distance=2.03 Simple disulfide: pdb=" SG CYS D 409 " - pdb=" SG CYS D 462 " distance=2.03 Simple disulfide: pdb=" SG CYS D 432 " - pdb=" SG CYS D 446 " distance=2.03 Simple disulfide: pdb=" SG CYS D 436 " - pdb=" SG CYS D 442 " distance=2.03 Simple disulfide: pdb=" SG CYS D 494 " - pdb=" SG CYS D 510 " distance=2.03 Simple disulfide: pdb=" SG CYS D 531 " - pdb=" SG CYS D 569 " distance=2.03 Simple disulfide: pdb=" SG CYS D 554 " - pdb=" SG CYS D 574 " distance=2.03 Simple disulfide: pdb=" SG CYS E 34 " - pdb=" SG CYS E 70 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 394 " distance=2.03 Simple disulfide: pdb=" SG CYS E 409 " - pdb=" SG CYS E 462 " distance=2.03 Simple disulfide: pdb=" SG CYS E 432 " - pdb=" SG CYS E 446 " distance=2.03 Simple disulfide: pdb=" SG CYS E 436 " - pdb=" SG CYS E 442 " distance=2.03 Simple disulfide: pdb=" SG CYS E 494 " - pdb=" SG CYS E 510 " distance=2.03 Simple disulfide: pdb=" SG CYS E 531 " - pdb=" SG CYS E 569 " distance=2.03 Simple disulfide: pdb=" SG CYS E 554 " - pdb=" SG CYS E 574 " distance=2.03 Simple disulfide: pdb=" SG CYS F 34 " - pdb=" SG CYS F 70 " distance=2.04 Simple disulfide: pdb=" SG CYS F 385 " - pdb=" SG CYS F 394 " distance=2.03 Simple disulfide: pdb=" SG CYS F 409 " - pdb=" SG CYS F 462 " distance=2.03 Simple disulfide: pdb=" SG CYS F 432 " - pdb=" SG CYS F 446 " distance=2.03 Simple disulfide: pdb=" SG CYS F 436 " - pdb=" SG CYS F 442 " distance=2.03 Simple disulfide: pdb=" SG CYS F 494 " - pdb=" SG CYS F 510 " distance=2.03 Simple disulfide: pdb=" SG CYS F 531 " - pdb=" SG CYS F 569 " distance=2.03 Simple disulfide: pdb=" SG CYS F 554 " - pdb=" SG CYS F 574 " distance=2.03 Simple disulfide: pdb=" SG CYS G 34 " - pdb=" SG CYS G 70 " distance=2.03 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 394 " distance=2.03 Simple disulfide: pdb=" SG CYS G 409 " - pdb=" SG CYS G 462 " distance=2.03 Simple disulfide: pdb=" SG CYS G 432 " - pdb=" SG CYS G 446 " distance=2.03 Simple disulfide: pdb=" SG CYS G 436 " - pdb=" SG CYS G 442 " distance=2.03 Simple disulfide: pdb=" SG CYS G 494 " - pdb=" SG CYS G 510 " distance=2.03 Simple disulfide: pdb=" SG CYS G 531 " - pdb=" SG CYS G 569 " distance=2.03 Simple disulfide: pdb=" SG CYS G 554 " - pdb=" SG CYS G 574 " distance=2.03 Simple disulfide: pdb=" SG CYS H 34 " - pdb=" SG CYS H 70 " distance=2.03 Simple disulfide: pdb=" SG CYS H 385 " - pdb=" SG CYS H 394 " distance=2.03 Simple disulfide: pdb=" SG CYS H 409 " - pdb=" SG CYS H 462 " distance=2.03 Simple disulfide: pdb=" SG CYS H 432 " - pdb=" SG CYS H 446 " distance=2.03 Simple disulfide: pdb=" SG CYS H 436 " - pdb=" SG CYS H 442 " distance=2.03 Simple disulfide: pdb=" SG CYS H 494 " - pdb=" SG CYS H 510 " distance=2.03 Simple disulfide: pdb=" SG CYS H 531 " - pdb=" SG CYS H 569 " distance=2.03 Simple disulfide: pdb=" SG CYS H 554 " - pdb=" SG CYS H 574 " distance=2.03 Simple disulfide: pdb=" SG CYS I 34 " - pdb=" SG CYS I 70 " distance=2.03 Simple disulfide: pdb=" SG CYS I 385 " - pdb=" SG CYS I 394 " distance=2.03 Simple disulfide: pdb=" SG CYS I 409 " - pdb=" SG CYS I 462 " distance=2.03 Simple disulfide: pdb=" SG CYS I 432 " - pdb=" SG CYS I 446 " distance=2.03 Simple disulfide: pdb=" SG CYS I 436 " - pdb=" SG CYS I 442 " distance=2.03 Simple disulfide: pdb=" SG CYS I 494 " - pdb=" SG CYS I 510 " distance=2.03 Simple disulfide: pdb=" SG CYS I 531 " - pdb=" SG CYS I 569 " distance=2.03 Simple disulfide: pdb=" SG CYS I 554 " - pdb=" SG CYS I 574 " distance=2.03 Simple disulfide: pdb=" SG CYS J 34 " - pdb=" SG CYS J 70 " distance=2.04 Simple disulfide: pdb=" SG CYS J 385 " - pdb=" SG CYS J 394 " distance=2.03 Simple disulfide: pdb=" SG CYS J 409 " - pdb=" SG CYS J 462 " distance=2.03 Simple disulfide: pdb=" SG CYS J 432 " - pdb=" SG CYS J 446 " distance=2.03 Simple disulfide: pdb=" SG CYS J 436 " - pdb=" SG CYS J 442 " distance=2.03 Simple disulfide: pdb=" SG CYS J 494 " - pdb=" SG CYS J 510 " distance=2.03 Simple disulfide: pdb=" SG CYS J 531 " - pdb=" SG CYS J 569 " distance=2.03 Simple disulfide: pdb=" SG CYS J 554 " - pdb=" SG CYS J 574 " distance=2.03 Simple disulfide: pdb=" SG CYS K 34 " - pdb=" SG CYS K 70 " distance=2.03 Simple disulfide: pdb=" SG CYS K 385 " - pdb=" SG CYS K 394 " distance=2.03 Simple disulfide: pdb=" SG CYS K 409 " - pdb=" SG CYS K 462 " distance=2.03 Simple disulfide: pdb=" SG CYS K 432 " - pdb=" SG CYS K 446 " distance=2.03 Simple disulfide: pdb=" SG CYS K 436 " - pdb=" SG CYS K 442 " distance=2.03 Simple disulfide: pdb=" SG CYS K 494 " - pdb=" SG CYS K 510 " distance=2.03 Simple disulfide: pdb=" SG CYS K 531 " - pdb=" SG CYS K 569 " distance=2.03 Simple disulfide: pdb=" SG CYS K 554 " - pdb=" SG CYS K 574 " distance=2.03 Simple disulfide: pdb=" SG CYS L 34 " - pdb=" SG CYS L 70 " distance=2.03 Simple disulfide: pdb=" SG CYS L 385 " - pdb=" SG CYS L 394 " distance=2.03 Simple disulfide: pdb=" SG CYS L 409 " - pdb=" SG CYS L 462 " distance=2.03 Simple disulfide: pdb=" SG CYS L 432 " - pdb=" SG CYS L 446 " distance=2.03 Simple disulfide: pdb=" SG CYS L 436 " - pdb=" SG CYS L 442 " distance=2.03 Simple disulfide: pdb=" SG CYS L 494 " - pdb=" SG CYS L 510 " distance=2.03 Simple disulfide: pdb=" SG CYS L 531 " - pdb=" SG CYS L 569 " distance=2.03 Simple disulfide: pdb=" SG CYS L 554 " - pdb=" SG CYS L 574 " distance=2.03 Simple disulfide: pdb=" SG CYS M 34 " - pdb=" SG CYS M 70 " distance=2.03 Simple disulfide: pdb=" SG CYS M 385 " - pdb=" SG CYS M 394 " distance=2.03 Simple disulfide: pdb=" SG CYS M 409 " - pdb=" SG CYS M 462 " distance=2.03 Simple disulfide: pdb=" SG CYS M 432 " - pdb=" SG CYS M 446 " distance=2.03 Simple disulfide: pdb=" SG CYS M 436 " - pdb=" SG CYS M 442 " distance=2.03 Simple disulfide: pdb=" SG CYS M 494 " - pdb=" SG CYS M 510 " distance=2.03 Simple disulfide: pdb=" SG CYS M 531 " - pdb=" SG CYS M 569 " distance=2.03 Simple disulfide: pdb=" SG CYS M 554 " - pdb=" SG CYS M 574 " distance=2.03 Simple disulfide: pdb=" SG CYS N 34 " - pdb=" SG CYS N 70 " distance=2.04 Simple disulfide: pdb=" SG CYS N 385 " - pdb=" SG CYS N 394 " distance=2.03 Simple disulfide: pdb=" SG CYS N 409 " - pdb=" SG CYS N 462 " distance=2.03 Simple disulfide: pdb=" SG CYS N 432 " - pdb=" SG CYS N 446 " distance=2.03 Simple disulfide: pdb=" SG CYS N 436 " - pdb=" SG CYS N 442 " distance=2.03 Simple disulfide: pdb=" SG CYS N 494 " - pdb=" SG CYS N 510 " distance=2.03 Simple disulfide: pdb=" SG CYS N 531 " - pdb=" SG CYS N 569 " distance=2.03 Simple disulfide: pdb=" SG CYS N 554 " - pdb=" SG CYS N 574 " distance=2.03 Simple disulfide: pdb=" SG CYS O 34 " - pdb=" SG CYS O 70 " distance=2.03 Simple disulfide: pdb=" SG CYS O 385 " - pdb=" SG CYS O 394 " distance=2.03 Simple disulfide: pdb=" SG CYS O 409 " - pdb=" SG CYS O 462 " distance=2.03 Simple disulfide: pdb=" SG CYS O 432 " - pdb=" SG CYS O 446 " distance=2.03 Simple disulfide: pdb=" SG CYS O 436 " - pdb=" SG CYS O 442 " distance=2.03 Simple disulfide: pdb=" SG CYS O 494 " - pdb=" SG CYS O 510 " distance=2.03 Simple disulfide: pdb=" SG CYS O 531 " - pdb=" SG CYS O 569 " distance=2.03 Simple disulfide: pdb=" SG CYS O 554 " - pdb=" SG CYS O 574 " distance=2.03 Simple disulfide: pdb=" SG CYS P 34 " - pdb=" SG CYS P 70 " distance=2.03 Simple disulfide: pdb=" SG CYS P 385 " - pdb=" SG CYS P 394 " distance=2.03 Simple disulfide: pdb=" SG CYS P 409 " - pdb=" SG CYS P 462 " distance=2.03 Simple disulfide: pdb=" SG CYS P 432 " - pdb=" SG CYS P 446 " distance=2.03 Simple disulfide: pdb=" SG CYS P 436 " - pdb=" SG CYS P 442 " distance=2.03 Simple disulfide: pdb=" SG CYS P 494 " - pdb=" SG CYS P 510 " distance=2.03 Simple disulfide: pdb=" SG CYS P 531 " - pdb=" SG CYS P 569 " distance=2.03 Simple disulfide: pdb=" SG CYS P 554 " - pdb=" SG CYS P 574 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 701 " - " ASN A 269 " " NAG B 701 " - " ASN B 269 " " NAG C 701 " - " ASN C 269 " " NAG D 701 " - " ASN D 269 " " NAG E 701 " - " ASN E 269 " " NAG F 701 " - " ASN F 269 " " NAG G 701 " - " ASN G 269 " " NAG H 701 " - " ASN H 269 " " NAG I 701 " - " ASN I 269 " " NAG J 701 " - " ASN J 269 " " NAG K 701 " - " ASN K 269 " " NAG L 701 " - " ASN L 269 " " NAG M 701 " - " ASN M 269 " " NAG N 701 " - " ASN N 269 " " NAG O 701 " - " ASN O 269 " " NAG P 701 " - " ASN P 269 " Time building additional restraints: 12.33 Conformation dependent library (CDL) restraints added in 6.6 seconds 16864 Ramachandran restraints generated. 8432 Oldfield, 0 Emsley, 8432 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15808 Finding SS restraints... Secondary structure from input PDB file: 149 helices and 64 sheets defined 18.1% alpha, 37.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.97 Creating SS restraints... Processing helix chain 'A' and resid 31 through 39 Processing helix chain 'A' and resid 168 through 184 Processing helix chain 'A' and resid 186 through 202 Processing helix chain 'A' and resid 288 through 294 Processing helix chain 'A' and resid 311 through 314 Processing helix chain 'A' and resid 315 through 319 Processing helix chain 'A' and resid 323 through 345 removed outlier: 3.674A pdb=" N ASN A 345 " --> pdb=" O TYR A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 398 removed outlier: 3.746A pdb=" N GLU A 398 " --> pdb=" O CYS A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 521 Processing helix chain 'B' and resid 31 through 39 Processing helix chain 'B' and resid 168 through 184 Processing helix chain 'B' and resid 186 through 202 removed outlier: 3.806A pdb=" N ALA B 190 " --> pdb=" O GLN B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 294 Processing helix chain 'B' and resid 311 through 313 No H-bonds generated for 'chain 'B' and resid 311 through 313' Processing helix chain 'B' and resid 315 through 319 Processing helix chain 'B' and resid 323 through 345 removed outlier: 3.501A pdb=" N ASN B 345 " --> pdb=" O TYR B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 398 removed outlier: 3.832A pdb=" N GLU B 398 " --> pdb=" O CYS B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 440 No H-bonds generated for 'chain 'B' and resid 438 through 440' Processing helix chain 'B' and resid 514 through 520 Processing helix chain 'C' and resid 31 through 39 Processing helix chain 'C' and resid 168 through 184 Processing helix chain 'C' and resid 186 through 202 removed outlier: 3.695A pdb=" N ALA C 190 " --> pdb=" O GLN C 186 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N THR C 191 " --> pdb=" O THR C 187 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR C 192 " --> pdb=" O LYS C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 294 Processing helix chain 'C' and resid 311 through 314 Processing helix chain 'C' and resid 315 through 319 Processing helix chain 'C' and resid 323 through 345 removed outlier: 3.524A pdb=" N ASN C 345 " --> pdb=" O TYR C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 396 removed outlier: 3.700A pdb=" N GLN C 395 " --> pdb=" O VAL C 392 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASN C 396 " --> pdb=" O LEU C 393 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 392 through 396' Processing helix chain 'C' and resid 514 through 521 Processing helix chain 'D' and resid 31 through 39 Processing helix chain 'D' and resid 168 through 184 Processing helix chain 'D' and resid 186 through 202 removed outlier: 3.809A pdb=" N ALA D 190 " --> pdb=" O GLN D 186 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR D 191 " --> pdb=" O THR D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 294 Processing helix chain 'D' and resid 311 through 314 Processing helix chain 'D' and resid 315 through 319 Processing helix chain 'D' and resid 323 through 345 removed outlier: 3.697A pdb=" N ASN D 345 " --> pdb=" O TYR D 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 392 through 396 removed outlier: 3.667A pdb=" N GLN D 395 " --> pdb=" O VAL D 392 " (cutoff:3.500A) Processing helix chain 'D' and resid 514 through 521 Processing helix chain 'E' and resid 31 through 39 Processing helix chain 'E' and resid 168 through 184 Processing helix chain 'E' and resid 186 through 202 Processing helix chain 'E' and resid 288 through 295 Processing helix chain 'E' and resid 311 through 314 Processing helix chain 'E' and resid 323 through 345 removed outlier: 3.600A pdb=" N ASN E 345 " --> pdb=" O TYR E 341 " (cutoff:3.500A) Processing helix chain 'E' and resid 393 through 398 removed outlier: 3.746A pdb=" N LEU E 397 " --> pdb=" O LEU E 393 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLU E 398 " --> pdb=" O CYS E 394 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 393 through 398' Processing helix chain 'E' and resid 514 through 521 Processing helix chain 'F' and resid 31 through 39 Processing helix chain 'F' and resid 168 through 184 Processing helix chain 'F' and resid 186 through 202 removed outlier: 3.541A pdb=" N THR F 191 " --> pdb=" O THR F 187 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TYR F 192 " --> pdb=" O LYS F 188 " (cutoff:3.500A) Processing helix chain 'F' and resid 288 through 295 Processing helix chain 'F' and resid 311 through 314 Processing helix chain 'F' and resid 315 through 319 Processing helix chain 'F' and resid 323 through 345 Processing helix chain 'F' and resid 392 through 396 removed outlier: 3.820A pdb=" N GLN F 395 " --> pdb=" O VAL F 392 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASN F 396 " --> pdb=" O LEU F 393 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 392 through 396' Processing helix chain 'F' and resid 438 through 440 No H-bonds generated for 'chain 'F' and resid 438 through 440' Processing helix chain 'F' and resid 514 through 521 Processing helix chain 'G' and resid 31 through 39 Processing helix chain 'G' and resid 168 through 184 Processing helix chain 'G' and resid 186 through 202 removed outlier: 3.554A pdb=" N THR G 191 " --> pdb=" O THR G 187 " (cutoff:3.500A) Processing helix chain 'G' and resid 288 through 294 Processing helix chain 'G' and resid 311 through 314 Processing helix chain 'G' and resid 315 through 319 Processing helix chain 'G' and resid 323 through 345 removed outlier: 3.706A pdb=" N ASN G 345 " --> pdb=" O TYR G 341 " (cutoff:3.500A) Processing helix chain 'G' and resid 393 through 398 removed outlier: 4.001A pdb=" N GLU G 398 " --> pdb=" O CYS G 394 " (cutoff:3.500A) Processing helix chain 'G' and resid 438 through 440 No H-bonds generated for 'chain 'G' and resid 438 through 440' Processing helix chain 'G' and resid 514 through 521 Processing helix chain 'H' and resid 31 through 39 Processing helix chain 'H' and resid 168 through 184 Processing helix chain 'H' and resid 186 through 202 Processing helix chain 'H' and resid 288 through 294 Processing helix chain 'H' and resid 311 through 314 Processing helix chain 'H' and resid 315 through 319 Processing helix chain 'H' and resid 323 through 345 removed outlier: 3.537A pdb=" N ASN H 345 " --> pdb=" O TYR H 341 " (cutoff:3.500A) Processing helix chain 'H' and resid 392 through 396 removed outlier: 3.680A pdb=" N GLN H 395 " --> pdb=" O VAL H 392 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASN H 396 " --> pdb=" O LEU H 393 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 392 through 396' Processing helix chain 'H' and resid 514 through 521 Processing helix chain 'I' and resid 31 through 39 Processing helix chain 'I' and resid 168 through 184 Processing helix chain 'I' and resid 186 through 202 removed outlier: 3.539A pdb=" N ALA I 190 " --> pdb=" O GLN I 186 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR I 191 " --> pdb=" O THR I 187 " (cutoff:3.500A) Processing helix chain 'I' and resid 288 through 294 Processing helix chain 'I' and resid 311 through 314 Processing helix chain 'I' and resid 315 through 319 Processing helix chain 'I' and resid 323 through 345 removed outlier: 3.673A pdb=" N ASN I 345 " --> pdb=" O TYR I 341 " (cutoff:3.500A) Processing helix chain 'I' and resid 393 through 398 removed outlier: 3.748A pdb=" N GLU I 398 " --> pdb=" O CYS I 394 " (cutoff:3.500A) Processing helix chain 'I' and resid 514 through 520 Processing helix chain 'J' and resid 31 through 39 Processing helix chain 'J' and resid 168 through 184 Processing helix chain 'J' and resid 186 through 202 removed outlier: 3.624A pdb=" N THR J 191 " --> pdb=" O THR J 187 " (cutoff:3.500A) Processing helix chain 'J' and resid 288 through 294 Processing helix chain 'J' and resid 311 through 313 No H-bonds generated for 'chain 'J' and resid 311 through 313' Processing helix chain 'J' and resid 315 through 319 Processing helix chain 'J' and resid 323 through 345 removed outlier: 3.505A pdb=" N ASN J 345 " --> pdb=" O TYR J 341 " (cutoff:3.500A) Processing helix chain 'J' and resid 393 through 398 removed outlier: 3.829A pdb=" N GLU J 398 " --> pdb=" O CYS J 394 " (cutoff:3.500A) Processing helix chain 'J' and resid 438 through 440 No H-bonds generated for 'chain 'J' and resid 438 through 440' Processing helix chain 'J' and resid 514 through 520 Processing helix chain 'K' and resid 31 through 39 Processing helix chain 'K' and resid 168 through 184 Processing helix chain 'K' and resid 186 through 202 removed outlier: 3.725A pdb=" N ALA K 190 " --> pdb=" O GLN K 186 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N THR K 191 " --> pdb=" O THR K 187 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TYR K 192 " --> pdb=" O LYS K 188 " (cutoff:3.500A) Processing helix chain 'K' and resid 288 through 294 Processing helix chain 'K' and resid 311 through 314 Processing helix chain 'K' and resid 315 through 319 Processing helix chain 'K' and resid 323 through 345 Processing helix chain 'K' and resid 392 through 396 removed outlier: 3.675A pdb=" N GLN K 395 " --> pdb=" O VAL K 392 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN K 396 " --> pdb=" O LEU K 393 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 392 through 396' Processing helix chain 'K' and resid 514 through 521 Processing helix chain 'L' and resid 31 through 39 Processing helix chain 'L' and resid 168 through 184 Processing helix chain 'L' and resid 186 through 202 removed outlier: 3.766A pdb=" N ALA L 190 " --> pdb=" O GLN L 186 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THR L 191 " --> pdb=" O THR L 187 " (cutoff:3.500A) Processing helix chain 'L' and resid 288 through 294 Processing helix chain 'L' and resid 311 through 314 Processing helix chain 'L' and resid 315 through 319 Processing helix chain 'L' and resid 323 through 345 removed outlier: 3.566A pdb=" N ASN L 345 " --> pdb=" O TYR L 341 " (cutoff:3.500A) Processing helix chain 'L' and resid 393 through 398 removed outlier: 3.507A pdb=" N LEU L 397 " --> pdb=" O LEU L 393 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLU L 398 " --> pdb=" O CYS L 394 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 393 through 398' Processing helix chain 'L' and resid 514 through 521 Processing helix chain 'M' and resid 31 through 39 Processing helix chain 'M' and resid 168 through 184 Processing helix chain 'M' and resid 186 through 202 removed outlier: 3.588A pdb=" N TYR M 192 " --> pdb=" O LYS M 188 " (cutoff:3.500A) Processing helix chain 'M' and resid 288 through 295 Processing helix chain 'M' and resid 311 through 314 Processing helix chain 'M' and resid 315 through 319 Processing helix chain 'M' and resid 323 through 345 removed outlier: 3.599A pdb=" N ASN M 345 " --> pdb=" O TYR M 341 " (cutoff:3.500A) Processing helix chain 'M' and resid 393 through 398 removed outlier: 3.736A pdb=" N LEU M 397 " --> pdb=" O LEU M 393 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLU M 398 " --> pdb=" O CYS M 394 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 393 through 398' Processing helix chain 'M' and resid 514 through 521 Processing helix chain 'N' and resid 31 through 39 Processing helix chain 'N' and resid 168 through 184 Processing helix chain 'N' and resid 186 through 202 removed outlier: 3.557A pdb=" N TYR N 192 " --> pdb=" O LYS N 188 " (cutoff:3.500A) Processing helix chain 'N' and resid 288 through 295 Processing helix chain 'N' and resid 311 through 314 Processing helix chain 'N' and resid 315 through 319 Processing helix chain 'N' and resid 323 through 345 removed outlier: 3.509A pdb=" N ASN N 345 " --> pdb=" O TYR N 341 " (cutoff:3.500A) Processing helix chain 'N' and resid 392 through 396 removed outlier: 3.822A pdb=" N GLN N 395 " --> pdb=" O VAL N 392 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ASN N 396 " --> pdb=" O LEU N 393 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 392 through 396' Processing helix chain 'N' and resid 438 through 440 No H-bonds generated for 'chain 'N' and resid 438 through 440' Processing helix chain 'N' and resid 514 through 521 Processing helix chain 'O' and resid 31 through 39 Processing helix chain 'O' and resid 168 through 184 Processing helix chain 'O' and resid 186 through 202 removed outlier: 3.527A pdb=" N THR O 191 " --> pdb=" O THR O 187 " (cutoff:3.500A) Processing helix chain 'O' and resid 288 through 294 Processing helix chain 'O' and resid 311 through 314 Processing helix chain 'O' and resid 315 through 319 Processing helix chain 'O' and resid 323 through 345 removed outlier: 3.675A pdb=" N ASN O 345 " --> pdb=" O TYR O 341 " (cutoff:3.500A) Processing helix chain 'O' and resid 393 through 398 removed outlier: 3.963A pdb=" N GLU O 398 " --> pdb=" O CYS O 394 " (cutoff:3.500A) Processing helix chain 'O' and resid 438 through 440 No H-bonds generated for 'chain 'O' and resid 438 through 440' Processing helix chain 'O' and resid 514 through 521 Processing helix chain 'P' and resid 31 through 39 Processing helix chain 'P' and resid 168 through 184 Processing helix chain 'P' and resid 186 through 202 Processing helix chain 'P' and resid 288 through 294 Processing helix chain 'P' and resid 311 through 314 Processing helix chain 'P' and resid 315 through 319 Processing helix chain 'P' and resid 323 through 345 removed outlier: 3.529A pdb=" N ASN P 345 " --> pdb=" O TYR P 341 " (cutoff:3.500A) Processing helix chain 'P' and resid 392 through 396 removed outlier: 3.674A pdb=" N GLN P 395 " --> pdb=" O VAL P 392 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASN P 396 " --> pdb=" O LEU P 393 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 392 through 396' Processing helix chain 'P' and resid 514 through 522 Processing sheet with id=AA1, first strand: chain 'A' and resid 49 through 52 removed outlier: 4.209A pdb=" N GLY A 60 " --> pdb=" O GLY A 50 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N ASP A 52 " --> pdb=" O ASP A 58 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ASP A 58 " --> pdb=" O ASP A 52 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 84 through 121 removed outlier: 5.919A pdb=" N TYR A 85 " --> pdb=" O THR A 161 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N THR A 161 " --> pdb=" O TYR A 85 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N ILE A 87 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N VAL A 159 " --> pdb=" O ILE A 87 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N GLN A 89 " --> pdb=" O TYR A 157 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N TYR A 157 " --> pdb=" O GLN A 89 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ALA A 211 " --> pdb=" O ILE A 156 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N THR A 158 " --> pdb=" O VAL A 209 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N VAL A 209 " --> pdb=" O THR A 158 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N LYS A 160 " --> pdb=" O THR A 207 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N THR A 207 " --> pdb=" O LYS A 160 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 248 through 278 current: chain 'B' and resid 125 through 161 removed outlier: 6.626A pdb=" N ALA B 211 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N THR B 158 " --> pdb=" O VAL B 209 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N VAL B 209 " --> pdb=" O THR B 158 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N LYS B 160 " --> pdb=" O THR B 207 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N THR B 207 " --> pdb=" O LYS B 160 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 248 through 278 current: chain 'C' and resid 57 through 61 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 57 through 61 current: chain 'C' and resid 125 through 161 removed outlier: 6.615A pdb=" N ALA C 211 " --> pdb=" O ILE C 156 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N THR C 158 " --> pdb=" O VAL C 209 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N VAL C 209 " --> pdb=" O THR C 158 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N LYS C 160 " --> pdb=" O THR C 207 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N THR C 207 " --> pdb=" O LYS C 160 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 248 through 278 current: chain 'D' and resid 125 through 161 removed outlier: 6.642A pdb=" N ALA D 211 " --> pdb=" O ILE D 156 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N THR D 158 " --> pdb=" O VAL D 209 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N VAL D 209 " --> pdb=" O THR D 158 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N LYS D 160 " --> pdb=" O THR D 207 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N THR D 207 " --> pdb=" O LYS D 160 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 248 through 278 current: chain 'E' and resid 125 through 161 removed outlier: 6.690A pdb=" N ALA E 211 " --> pdb=" O ILE E 156 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N THR E 158 " --> pdb=" O VAL E 209 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N VAL E 209 " --> pdb=" O THR E 158 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N LYS E 160 " --> pdb=" O THR E 207 " (cutoff:3.500A) removed outlier: 8.245A pdb=" N THR E 207 " --> pdb=" O LYS E 160 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 248 through 278 current: chain 'F' and resid 125 through 161 removed outlier: 6.720A pdb=" N ALA F 211 " --> pdb=" O ILE F 156 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N THR F 158 " --> pdb=" O VAL F 209 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N VAL F 209 " --> pdb=" O THR F 158 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N LYS F 160 " --> pdb=" O THR F 207 " (cutoff:3.500A) removed outlier: 8.149A pdb=" N THR F 207 " --> pdb=" O LYS F 160 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 248 through 278 current: chain 'G' and resid 125 through 161 removed outlier: 6.643A pdb=" N ALA G 211 " --> pdb=" O ILE G 156 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N THR G 158 " --> pdb=" O VAL G 209 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N VAL G 209 " --> pdb=" O THR G 158 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N LYS G 160 " --> pdb=" O THR G 207 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N THR G 207 " --> pdb=" O LYS G 160 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 248 through 278 current: chain 'H' and resid 125 through 161 removed outlier: 6.704A pdb=" N ALA H 211 " --> pdb=" O ILE H 156 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N THR H 158 " --> pdb=" O VAL H 209 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N VAL H 209 " --> pdb=" O THR H 158 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N LYS H 160 " --> pdb=" O THR H 207 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N THR H 207 " --> pdb=" O LYS H 160 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 248 through 278 current: chain 'I' and resid 125 through 161 removed outlier: 6.662A pdb=" N ALA I 211 " --> pdb=" O ILE I 156 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N THR I 158 " --> pdb=" O VAL I 209 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N VAL I 209 " --> pdb=" O THR I 158 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N LYS I 160 " --> pdb=" O THR I 207 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N THR I 207 " --> pdb=" O LYS I 160 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 248 through 278 current: chain 'J' and resid 125 through 161 removed outlier: 6.651A pdb=" N ALA J 211 " --> pdb=" O ILE J 156 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N THR J 158 " --> pdb=" O VAL J 209 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N VAL J 209 " --> pdb=" O THR J 158 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N LYS J 160 " --> pdb=" O THR J 207 " (cutoff:3.500A) removed outlier: 8.153A pdb=" N THR J 207 " --> pdb=" O LYS J 160 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 248 through 278 current: chain 'K' and resid 125 through 161 removed outlier: 6.623A pdb=" N ALA K 211 " --> pdb=" O ILE K 156 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N THR K 158 " --> pdb=" O VAL K 209 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N VAL K 209 " --> pdb=" O THR K 158 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N LYS K 160 " --> pdb=" O THR K 207 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N THR K 207 " --> pdb=" O LYS K 160 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 248 through 278 current: chain 'L' and resid 125 through 161 removed outlier: 6.676A pdb=" N ALA L 211 " --> pdb=" O ILE L 156 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N THR L 158 " --> pdb=" O VAL L 209 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N VAL L 209 " --> pdb=" O THR L 158 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N LYS L 160 " --> pdb=" O THR L 207 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N THR L 207 " --> pdb=" O LYS L 160 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 248 through 278 current: chain 'M' and resid 125 through 161 removed outlier: 6.720A pdb=" N ALA M 211 " --> pdb=" O ILE M 156 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N THR M 158 " --> pdb=" O VAL M 209 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VAL M 209 " --> pdb=" O THR M 158 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N LYS M 160 " --> pdb=" O THR M 207 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N THR M 207 " --> pdb=" O LYS M 160 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 248 through 278 current: chain 'N' and resid 125 through 161 removed outlier: 6.720A pdb=" N ALA N 211 " --> pdb=" O ILE N 156 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N THR N 158 " --> pdb=" O VAL N 209 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N VAL N 209 " --> pdb=" O THR N 158 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N LYS N 160 " --> pdb=" O THR N 207 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N THR N 207 " --> pdb=" O LYS N 160 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 248 through 278 current: chain 'O' and resid 125 through 161 removed outlier: 6.654A pdb=" N ALA O 211 " --> pdb=" O ILE O 156 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N THR O 158 " --> pdb=" O VAL O 209 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N VAL O 209 " --> pdb=" O THR O 158 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N LYS O 160 " --> pdb=" O THR O 207 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N THR O 207 " --> pdb=" O LYS O 160 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 248 through 278 current: chain 'P' and resid 125 through 161 removed outlier: 6.733A pdb=" N ALA P 211 " --> pdb=" O ILE P 156 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N THR P 158 " --> pdb=" O VAL P 209 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N VAL P 209 " --> pdb=" O THR P 158 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N LYS P 160 " --> pdb=" O THR P 207 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N THR P 207 " --> pdb=" O LYS P 160 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 378 through 387 removed outlier: 7.863A pdb=" N PHE A 378 " --> pdb=" O ALA A 464 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ALA A 464 " --> pdb=" O PHE A 378 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLY A 380 " --> pdb=" O CYS A 462 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N TYR A 382 " --> pdb=" O TYR A 460 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N TRP A 461 " --> pdb=" O HIS A 417 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N HIS A 417 " --> pdb=" O TRP A 461 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N VAL A 463 " --> pdb=" O PRO A 415 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 475 through 481 removed outlier: 3.690A pdb=" N LEU A 475 " --> pdb=" O SER A 512 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER A 512 " --> pdb=" O LEU A 475 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N CYS A 510 " --> pdb=" O GLY A 477 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N VAL A 479 " --> pdb=" O LYS A 508 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N LYS A 508 " --> pdb=" O VAL A 479 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 525 through 530 removed outlier: 6.324A pdb=" N CYS A 574 " --> pdb=" O GLY A 526 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N PHE A 528 " --> pdb=" O SER A 572 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N SER A 572 " --> pdb=" O PHE A 528 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N SER A 530 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N GLN A 570 " --> pdb=" O SER A 530 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N CYS A 569 " --> pdb=" O ILE A 565 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ILE A 565 " --> pdb=" O CYS A 569 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VAL A 571 " --> pdb=" O ALA A 563 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 49 through 52 removed outlier: 4.127A pdb=" N GLY B 60 " --> pdb=" O GLY B 50 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N ASP B 52 " --> pdb=" O ASP B 58 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N ASP B 58 " --> pdb=" O ASP B 52 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 378 through 387 removed outlier: 7.606A pdb=" N PHE B 378 " --> pdb=" O ALA B 464 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ALA B 464 " --> pdb=" O PHE B 378 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLY B 380 " --> pdb=" O CYS B 462 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N TRP B 461 " --> pdb=" O HIS B 417 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N HIS B 417 " --> pdb=" O TRP B 461 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N VAL B 463 " --> pdb=" O PRO B 415 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 475 through 481 removed outlier: 3.808A pdb=" N LEU B 475 " --> pdb=" O SER B 512 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER B 512 " --> pdb=" O LEU B 475 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N CYS B 510 " --> pdb=" O GLY B 477 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N VAL B 479 " --> pdb=" O LYS B 508 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N LYS B 508 " --> pdb=" O VAL B 479 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 525 through 529 removed outlier: 6.349A pdb=" N CYS B 574 " --> pdb=" O GLY B 526 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N PHE B 528 " --> pdb=" O SER B 572 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N SER B 572 " --> pdb=" O PHE B 528 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N CYS B 569 " --> pdb=" O ILE B 565 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ILE B 565 " --> pdb=" O CYS B 569 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N VAL B 571 " --> pdb=" O ALA B 563 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 378 through 387 removed outlier: 7.543A pdb=" N PHE C 378 " --> pdb=" O ALA C 464 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ALA C 464 " --> pdb=" O PHE C 378 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLY C 380 " --> pdb=" O CYS C 462 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N TRP C 461 " --> pdb=" O HIS C 417 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N HIS C 417 " --> pdb=" O TRP C 461 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N VAL C 463 " --> pdb=" O PRO C 415 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 475 through 480 removed outlier: 3.834A pdb=" N LEU C 475 " --> pdb=" O SER C 512 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N SER C 512 " --> pdb=" O LEU C 475 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N CYS C 510 " --> pdb=" O GLY C 477 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N VAL C 479 " --> pdb=" O LYS C 508 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N LYS C 508 " --> pdb=" O VAL C 479 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 525 through 529 removed outlier: 6.365A pdb=" N CYS C 574 " --> pdb=" O GLY C 526 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N PHE C 528 " --> pdb=" O SER C 572 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N SER C 572 " --> pdb=" O PHE C 528 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N CYS C 569 " --> pdb=" O ILE C 565 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ILE C 565 " --> pdb=" O CYS C 569 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N VAL C 571 " --> pdb=" O ALA C 563 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 49 through 52 removed outlier: 4.173A pdb=" N GLY D 60 " --> pdb=" O GLY D 50 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N ASP D 52 " --> pdb=" O ASP D 58 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N ASP D 58 " --> pdb=" O ASP D 52 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 378 through 387 removed outlier: 7.774A pdb=" N PHE D 378 " --> pdb=" O ALA D 464 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N ALA D 464 " --> pdb=" O PHE D 378 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLY D 380 " --> pdb=" O CYS D 462 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TYR D 382 " --> pdb=" O TYR D 460 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N PHE D 441 " --> pdb=" O CYS D 436 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N CYS D 436 " --> pdb=" O PHE D 441 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N LYS D 443 " --> pdb=" O LYS D 434 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N LYS D 434 " --> pdb=" O LYS D 443 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N VAL D 445 " --> pdb=" O CYS D 432 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N CYS D 432 " --> pdb=" O VAL D 445 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N GLU D 447 " --> pdb=" O LEU D 430 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N LEU D 430 " --> pdb=" O GLU D 447 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N VAL D 449 " --> pdb=" O SER D 428 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N SER D 428 " --> pdb=" O VAL D 449 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ARG D 451 " --> pdb=" O GLY D 426 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N GLY D 426 " --> pdb=" O ARG D 451 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ALA D 453 " --> pdb=" O GLU D 424 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N GLU D 424 " --> pdb=" O ALA D 453 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ALA D 455 " --> pdb=" O THR D 422 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N THR D 422 " --> pdb=" O ALA D 455 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N PHE D 457 " --> pdb=" O SER D 420 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N SER D 420 " --> pdb=" O PHE D 457 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ALA D 459 " --> pdb=" O LEU D 418 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 479 through 480 Processing sheet with id=AB7, first strand: chain 'D' and resid 558 through 566 removed outlier: 3.559A pdb=" N HIS D 561 " --> pdb=" O TYR D 573 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N VAL D 571 " --> pdb=" O ALA D 563 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ILE D 565 " --> pdb=" O CYS D 569 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N CYS D 569 " --> pdb=" O ILE D 565 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 49 through 52 removed outlier: 4.033A pdb=" N GLY E 60 " --> pdb=" O GLY E 50 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N ASP E 52 " --> pdb=" O ASP E 58 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N ASP E 58 " --> pdb=" O ASP E 52 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 378 through 387 removed outlier: 7.966A pdb=" N PHE E 378 " --> pdb=" O ALA E 464 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ALA E 464 " --> pdb=" O PHE E 378 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLY E 380 " --> pdb=" O CYS E 462 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N TYR E 382 " --> pdb=" O TYR E 460 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N TRP E 461 " --> pdb=" O HIS E 417 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N HIS E 417 " --> pdb=" O TRP E 461 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N VAL E 463 " --> pdb=" O PRO E 415 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 479 through 480 Processing sheet with id=AC2, first strand: chain 'E' and resid 558 through 566 removed outlier: 3.711A pdb=" N HIS E 561 " --> pdb=" O TYR E 573 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TYR E 573 " --> pdb=" O HIS E 561 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N VAL E 571 " --> pdb=" O ALA E 563 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ILE E 565 " --> pdb=" O CYS E 569 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N CYS E 569 " --> pdb=" O ILE E 565 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 49 through 52 removed outlier: 4.139A pdb=" N GLY F 60 " --> pdb=" O GLY F 50 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N ASP F 52 " --> pdb=" O ASP F 58 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N ASP F 58 " --> pdb=" O ASP F 52 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 383 through 387 removed outlier: 6.520A pdb=" N TRP F 461 " --> pdb=" O HIS F 417 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N HIS F 417 " --> pdb=" O TRP F 461 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N VAL F 463 " --> pdb=" O PRO F 415 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 479 through 480 Processing sheet with id=AC6, first strand: chain 'F' and resid 525 through 529 removed outlier: 6.513A pdb=" N CYS F 574 " --> pdb=" O GLY F 526 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N PHE F 528 " --> pdb=" O SER F 572 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N SER F 572 " --> pdb=" O PHE F 528 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N CYS F 569 " --> pdb=" O ILE F 565 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ILE F 565 " --> pdb=" O CYS F 569 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N VAL F 571 " --> pdb=" O ALA F 563 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR F 573 " --> pdb=" O HIS F 561 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N HIS F 561 " --> pdb=" O TYR F 573 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 49 through 52 removed outlier: 3.832A pdb=" N GLY G 60 " --> pdb=" O GLY G 50 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N ASP G 52 " --> pdb=" O ASP G 58 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N ASP G 58 " --> pdb=" O ASP G 52 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 378 through 387 removed outlier: 7.793A pdb=" N PHE G 378 " --> pdb=" O ALA G 464 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ALA G 464 " --> pdb=" O PHE G 378 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLY G 380 " --> pdb=" O CYS G 462 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N TRP G 461 " --> pdb=" O HIS G 417 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N HIS G 417 " --> pdb=" O TRP G 461 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL G 463 " --> pdb=" O PRO G 415 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 475 through 480 removed outlier: 4.572A pdb=" N LEU G 475 " --> pdb=" O SER G 512 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N SER G 512 " --> pdb=" O LEU G 475 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N CYS G 510 " --> pdb=" O GLY G 477 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N VAL G 479 " --> pdb=" O LYS G 508 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N LYS G 508 " --> pdb=" O VAL G 479 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 525 through 529 removed outlier: 6.562A pdb=" N CYS G 574 " --> pdb=" O GLY G 526 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N PHE G 528 " --> pdb=" O SER G 572 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N SER G 572 " --> pdb=" O PHE G 528 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N CYS G 569 " --> pdb=" O ILE G 565 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ILE G 565 " --> pdb=" O CYS G 569 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N VAL G 571 " --> pdb=" O ALA G 563 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N HIS G 561 " --> pdb=" O TYR G 573 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 49 through 52 removed outlier: 4.085A pdb=" N GLY H 60 " --> pdb=" O GLY H 50 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N ASP H 52 " --> pdb=" O ASP H 58 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N ASP H 58 " --> pdb=" O ASP H 52 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 378 through 387 removed outlier: 7.859A pdb=" N PHE H 378 " --> pdb=" O ALA H 464 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N ALA H 464 " --> pdb=" O PHE H 378 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLY H 380 " --> pdb=" O CYS H 462 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR H 382 " --> pdb=" O TYR H 460 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N TRP H 461 " --> pdb=" O HIS H 417 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N HIS H 417 " --> pdb=" O TRP H 461 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N VAL H 463 " --> pdb=" O PRO H 415 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 475 through 481 removed outlier: 3.566A pdb=" N LEU H 475 " --> pdb=" O SER H 512 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N CYS H 510 " --> pdb=" O GLY H 477 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N VAL H 479 " --> pdb=" O LYS H 508 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N LYS H 508 " --> pdb=" O VAL H 479 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 525 through 529 removed outlier: 6.381A pdb=" N CYS H 574 " --> pdb=" O GLY H 526 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N PHE H 528 " --> pdb=" O SER H 572 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N SER H 572 " --> pdb=" O PHE H 528 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N CYS H 569 " --> pdb=" O ILE H 565 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ILE H 565 " --> pdb=" O CYS H 569 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N VAL H 571 " --> pdb=" O ALA H 563 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 49 through 52 removed outlier: 4.150A pdb=" N GLY I 60 " --> pdb=" O GLY I 50 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N ASP I 52 " --> pdb=" O ASP I 58 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ASP I 58 " --> pdb=" O ASP I 52 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 378 through 387 removed outlier: 7.862A pdb=" N PHE I 378 " --> pdb=" O ALA I 464 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N ALA I 464 " --> pdb=" O PHE I 378 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLY I 380 " --> pdb=" O CYS I 462 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N TYR I 382 " --> pdb=" O TYR I 460 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N TRP I 461 " --> pdb=" O HIS I 417 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N HIS I 417 " --> pdb=" O TRP I 461 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N VAL I 463 " --> pdb=" O PRO I 415 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 475 through 481 removed outlier: 3.676A pdb=" N LEU I 475 " --> pdb=" O SER I 512 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER I 512 " --> pdb=" O LEU I 475 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N CYS I 510 " --> pdb=" O GLY I 477 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N VAL I 479 " --> pdb=" O LYS I 508 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N LYS I 508 " --> pdb=" O VAL I 479 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 525 through 530 removed outlier: 6.279A pdb=" N CYS I 574 " --> pdb=" O GLY I 526 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N PHE I 528 " --> pdb=" O SER I 572 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N SER I 572 " --> pdb=" O PHE I 528 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N SER I 530 " --> pdb=" O GLN I 570 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N GLN I 570 " --> pdb=" O SER I 530 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N CYS I 569 " --> pdb=" O ILE I 565 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ILE I 565 " --> pdb=" O CYS I 569 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N VAL I 571 " --> pdb=" O ALA I 563 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 49 through 52 removed outlier: 4.074A pdb=" N GLY J 60 " --> pdb=" O GLY J 50 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N ASP J 52 " --> pdb=" O ASP J 58 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ASP J 58 " --> pdb=" O ASP J 52 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 378 through 387 removed outlier: 7.609A pdb=" N PHE J 378 " --> pdb=" O ALA J 464 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ALA J 464 " --> pdb=" O PHE J 378 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLY J 380 " --> pdb=" O CYS J 462 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N PHE J 441 " --> pdb=" O CYS J 436 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N CYS J 436 " --> pdb=" O PHE J 441 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N LYS J 443 " --> pdb=" O LYS J 434 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N LYS J 434 " --> pdb=" O LYS J 443 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N VAL J 445 " --> pdb=" O CYS J 432 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N CYS J 432 " --> pdb=" O VAL J 445 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N GLU J 447 " --> pdb=" O LEU J 430 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N LEU J 430 " --> pdb=" O GLU J 447 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N VAL J 449 " --> pdb=" O SER J 428 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N SER J 428 " --> pdb=" O VAL J 449 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ARG J 451 " --> pdb=" O GLY J 426 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N GLY J 426 " --> pdb=" O ARG J 451 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ALA J 453 " --> pdb=" O GLU J 424 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N GLU J 424 " --> pdb=" O ALA J 453 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ALA J 455 " --> pdb=" O THR J 422 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N THR J 422 " --> pdb=" O ALA J 455 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N PHE J 457 " --> pdb=" O SER J 420 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N SER J 420 " --> pdb=" O PHE J 457 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ALA J 459 " --> pdb=" O LEU J 418 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 475 through 481 removed outlier: 3.712A pdb=" N LEU J 475 " --> pdb=" O SER J 512 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N CYS J 510 " --> pdb=" O GLY J 477 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N VAL J 479 " --> pdb=" O LYS J 508 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N LYS J 508 " --> pdb=" O VAL J 479 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 525 through 529 removed outlier: 6.349A pdb=" N CYS J 574 " --> pdb=" O GLY J 526 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N PHE J 528 " --> pdb=" O SER J 572 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N SER J 572 " --> pdb=" O PHE J 528 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N CYS J 569 " --> pdb=" O ILE J 565 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ILE J 565 " --> pdb=" O CYS J 569 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N VAL J 571 " --> pdb=" O ALA J 563 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'K' and resid 49 through 52 removed outlier: 4.045A pdb=" N GLY K 60 " --> pdb=" O GLY K 50 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N ASP K 52 " --> pdb=" O ASP K 58 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N ASP K 58 " --> pdb=" O ASP K 52 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 378 through 387 removed outlier: 7.569A pdb=" N PHE K 378 " --> pdb=" O ALA K 464 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ALA K 464 " --> pdb=" O PHE K 378 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLY K 380 " --> pdb=" O CYS K 462 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N TRP K 461 " --> pdb=" O HIS K 417 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N HIS K 417 " --> pdb=" O TRP K 461 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N VAL K 463 " --> pdb=" O PRO K 415 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'K' and resid 479 through 480 Processing sheet with id=AE8, first strand: chain 'K' and resid 525 through 529 removed outlier: 6.353A pdb=" N CYS K 574 " --> pdb=" O GLY K 526 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N PHE K 528 " --> pdb=" O SER K 572 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N SER K 572 " --> pdb=" O PHE K 528 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N CYS K 569 " --> pdb=" O ILE K 565 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ILE K 565 " --> pdb=" O CYS K 569 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N VAL K 571 " --> pdb=" O ALA K 563 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'L' and resid 49 through 52 removed outlier: 4.145A pdb=" N GLY L 60 " --> pdb=" O GLY L 50 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N ASP L 52 " --> pdb=" O ASP L 58 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N ASP L 58 " --> pdb=" O ASP L 52 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'L' and resid 378 through 387 removed outlier: 7.766A pdb=" N PHE L 378 " --> pdb=" O ALA L 464 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ALA L 464 " --> pdb=" O PHE L 378 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLY L 380 " --> pdb=" O CYS L 462 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR L 382 " --> pdb=" O TYR L 460 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N PHE L 441 " --> pdb=" O CYS L 436 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N CYS L 436 " --> pdb=" O PHE L 441 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N LYS L 443 " --> pdb=" O LYS L 434 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N LYS L 434 " --> pdb=" O LYS L 443 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N VAL L 445 " --> pdb=" O CYS L 432 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N CYS L 432 " --> pdb=" O VAL L 445 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N GLU L 447 " --> pdb=" O LEU L 430 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N LEU L 430 " --> pdb=" O GLU L 447 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N VAL L 449 " --> pdb=" O SER L 428 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N SER L 428 " --> pdb=" O VAL L 449 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ARG L 451 " --> pdb=" O GLY L 426 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N GLY L 426 " --> pdb=" O ARG L 451 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ALA L 453 " --> pdb=" O GLU L 424 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLU L 424 " --> pdb=" O ALA L 453 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ALA L 455 " --> pdb=" O THR L 422 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N THR L 422 " --> pdb=" O ALA L 455 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N PHE L 457 " --> pdb=" O SER L 420 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N SER L 420 " --> pdb=" O PHE L 457 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ALA L 459 " --> pdb=" O LEU L 418 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'L' and resid 479 through 480 Processing sheet with id=AF3, first strand: chain 'L' and resid 558 through 566 removed outlier: 3.592A pdb=" N HIS L 561 " --> pdb=" O TYR L 573 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL L 571 " --> pdb=" O ALA L 563 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ILE L 565 " --> pdb=" O CYS L 569 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N CYS L 569 " --> pdb=" O ILE L 565 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'M' and resid 49 through 52 removed outlier: 4.003A pdb=" N GLY M 60 " --> pdb=" O GLY M 50 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N ASP M 52 " --> pdb=" O ASP M 58 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N ASP M 58 " --> pdb=" O ASP M 52 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'M' and resid 378 through 387 removed outlier: 7.948A pdb=" N PHE M 378 " --> pdb=" O ALA M 464 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ALA M 464 " --> pdb=" O PHE M 378 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLY M 380 " --> pdb=" O CYS M 462 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYR M 382 " --> pdb=" O TYR M 460 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N TRP M 461 " --> pdb=" O HIS M 417 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N HIS M 417 " --> pdb=" O TRP M 461 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N VAL M 463 " --> pdb=" O PRO M 415 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'M' and resid 479 through 480 Processing sheet with id=AF7, first strand: chain 'M' and resid 558 through 566 removed outlier: 3.747A pdb=" N HIS M 561 " --> pdb=" O TYR M 573 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N TYR M 573 " --> pdb=" O HIS M 561 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N VAL M 571 " --> pdb=" O ALA M 563 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ILE M 565 " --> pdb=" O CYS M 569 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N CYS M 569 " --> pdb=" O ILE M 565 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'N' and resid 49 through 52 removed outlier: 4.170A pdb=" N GLY N 60 " --> pdb=" O GLY N 50 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N ASP N 52 " --> pdb=" O ASP N 58 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ASP N 58 " --> pdb=" O ASP N 52 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'N' and resid 383 through 387 removed outlier: 6.500A pdb=" N TRP N 461 " --> pdb=" O HIS N 417 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N HIS N 417 " --> pdb=" O TRP N 461 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N VAL N 463 " --> pdb=" O PRO N 415 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'N' and resid 479 through 480 Processing sheet with id=AG2, first strand: chain 'N' and resid 525 through 529 removed outlier: 6.374A pdb=" N CYS N 574 " --> pdb=" O GLY N 526 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N PHE N 528 " --> pdb=" O SER N 572 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N SER N 572 " --> pdb=" O PHE N 528 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N CYS N 569 " --> pdb=" O ILE N 565 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ILE N 565 " --> pdb=" O CYS N 569 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N VAL N 571 " --> pdb=" O ALA N 563 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N TYR N 573 " --> pdb=" O HIS N 561 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N HIS N 561 " --> pdb=" O TYR N 573 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'O' and resid 49 through 52 removed outlier: 3.932A pdb=" N GLY O 60 " --> pdb=" O GLY O 50 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N ASP O 52 " --> pdb=" O ASP O 58 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ASP O 58 " --> pdb=" O ASP O 52 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'O' and resid 378 through 387 removed outlier: 7.800A pdb=" N PHE O 378 " --> pdb=" O ALA O 464 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ALA O 464 " --> pdb=" O PHE O 378 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLY O 380 " --> pdb=" O CYS O 462 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR O 382 " --> pdb=" O TYR O 460 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N TRP O 461 " --> pdb=" O HIS O 417 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N HIS O 417 " --> pdb=" O TRP O 461 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N VAL O 463 " --> pdb=" O PRO O 415 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'O' and resid 476 through 480 removed outlier: 4.861A pdb=" N CYS O 510 " --> pdb=" O GLY O 477 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N VAL O 479 " --> pdb=" O LYS O 508 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N LYS O 508 " --> pdb=" O VAL O 479 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'O' and resid 525 through 529 removed outlier: 6.547A pdb=" N CYS O 574 " --> pdb=" O GLY O 526 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N PHE O 528 " --> pdb=" O SER O 572 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N SER O 572 " --> pdb=" O PHE O 528 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N CYS O 569 " --> pdb=" O ILE O 565 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ILE O 565 " --> pdb=" O CYS O 569 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N VAL O 571 " --> pdb=" O ALA O 563 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'P' and resid 49 through 52 removed outlier: 4.064A pdb=" N GLY P 60 " --> pdb=" O GLY P 50 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N ASP P 52 " --> pdb=" O ASP P 58 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ASP P 58 " --> pdb=" O ASP P 52 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'P' and resid 378 through 387 removed outlier: 7.861A pdb=" N PHE P 378 " --> pdb=" O ALA P 464 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N ALA P 464 " --> pdb=" O PHE P 378 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLY P 380 " --> pdb=" O CYS P 462 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N TYR P 382 " --> pdb=" O TYR P 460 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N TRP P 461 " --> pdb=" O HIS P 417 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N HIS P 417 " --> pdb=" O TRP P 461 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N VAL P 463 " --> pdb=" O PRO P 415 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'P' and resid 475 through 481 removed outlier: 3.535A pdb=" N LEU P 475 " --> pdb=" O SER P 512 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N CYS P 510 " --> pdb=" O GLY P 477 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N VAL P 479 " --> pdb=" O LYS P 508 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N LYS P 508 " --> pdb=" O VAL P 479 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'P' and resid 525 through 529 removed outlier: 6.370A pdb=" N CYS P 574 " --> pdb=" O GLY P 526 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N PHE P 528 " --> pdb=" O SER P 572 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N SER P 572 " --> pdb=" O PHE P 528 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N CYS P 569 " --> pdb=" O ILE P 565 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ILE P 565 " --> pdb=" O CYS P 569 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N VAL P 571 " --> pdb=" O ALA P 563 " (cutoff:3.500A) 2497 hydrogen bonds defined for protein. 7287 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: 20.16 Time building geometry restraints manager: 14.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 20981 1.33 - 1.46: 12946 1.46 - 1.58: 34101 1.58 - 1.70: 4 1.70 - 1.82: 592 Bond restraints: 68624 Sorted by residual: bond pdb=" CB PRO E 500 " pdb=" CG PRO E 500 " ideal model delta sigma weight residual 1.492 1.634 -0.142 5.00e-02 4.00e+02 8.07e+00 bond pdb=" CB PRO M 500 " pdb=" CG PRO M 500 " ideal model delta sigma weight residual 1.492 1.634 -0.142 5.00e-02 4.00e+02 8.02e+00 bond pdb=" CA ILE E 499 " pdb=" C ILE E 499 " ideal model delta sigma weight residual 1.524 1.543 -0.019 8.30e-03 1.45e+04 5.27e+00 bond pdb=" CB PRO H 592 " pdb=" CG PRO H 592 " ideal model delta sigma weight residual 1.506 1.586 -0.080 3.90e-02 6.57e+02 4.22e+00 bond pdb=" CB PRO P 592 " pdb=" CG PRO P 592 " ideal model delta sigma weight residual 1.506 1.586 -0.080 3.90e-02 6.57e+02 4.19e+00 ... (remaining 68619 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.51: 91915 2.51 - 5.02: 1052 5.02 - 7.54: 109 7.54 - 10.05: 41 10.05 - 12.56: 19 Bond angle restraints: 93136 Sorted by residual: angle pdb=" N VAL O 588 " pdb=" CA VAL O 588 " pdb=" C VAL O 588 " ideal model delta sigma weight residual 111.91 103.63 8.28 8.90e-01 1.26e+00 8.65e+01 angle pdb=" CA PRO E 500 " pdb=" N PRO E 500 " pdb=" CD PRO E 500 " ideal model delta sigma weight residual 112.00 100.43 11.57 1.40e+00 5.10e-01 6.83e+01 angle pdb=" CA PRO M 500 " pdb=" N PRO M 500 " pdb=" CD PRO M 500 " ideal model delta sigma weight residual 112.00 100.74 11.26 1.40e+00 5.10e-01 6.47e+01 angle pdb=" CA PRO P 592 " pdb=" N PRO P 592 " pdb=" CD PRO P 592 " ideal model delta sigma weight residual 111.50 103.16 8.34 1.40e+00 5.10e-01 3.55e+01 angle pdb=" CA PRO H 592 " pdb=" N PRO H 592 " pdb=" CD PRO H 592 " ideal model delta sigma weight residual 111.50 103.18 8.32 1.40e+00 5.10e-01 3.53e+01 ... (remaining 93131 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.69: 40800 24.69 - 49.38: 1079 49.38 - 74.07: 293 74.07 - 98.76: 22 98.76 - 123.46: 174 Dihedral angle restraints: 42368 sinusoidal: 17760 harmonic: 24608 Sorted by residual: dihedral pdb=" CA MET F 533 " pdb=" C MET F 533 " pdb=" N GLY F 534 " pdb=" CA GLY F 534 " ideal model delta harmonic sigma weight residual 180.00 151.19 28.81 0 5.00e+00 4.00e-02 3.32e+01 dihedral pdb=" CA MET N 533 " pdb=" C MET N 533 " pdb=" N GLY N 534 " pdb=" CA GLY N 534 " ideal model delta harmonic sigma weight residual 180.00 153.77 26.23 0 5.00e+00 4.00e-02 2.75e+01 dihedral pdb=" CA LEU G 590 " pdb=" C LEU G 590 " pdb=" N PRO G 591 " pdb=" CA PRO G 591 " ideal model delta harmonic sigma weight residual 180.00 156.30 23.70 0 5.00e+00 4.00e-02 2.25e+01 ... (remaining 42365 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 8336 0.049 - 0.099: 1944 0.099 - 0.148: 500 0.148 - 0.197: 5 0.197 - 0.247: 31 Chirality restraints: 10816 Sorted by residual: chirality pdb=" C1 NAG I 701 " pdb=" ND2 ASN I 269 " pdb=" C2 NAG I 701 " pdb=" O5 NAG I 701 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" C1 NAG A 701 " pdb=" ND2 ASN A 269 " pdb=" C2 NAG A 701 " pdb=" O5 NAG A 701 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" C1 NAG D 701 " pdb=" ND2 ASN D 269 " pdb=" C2 NAG D 701 " pdb=" O5 NAG D 701 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.44e+00 ... (remaining 10813 not shown) Planarity restraints: 11808 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE M 499 " 0.071 5.00e-02 4.00e+02 9.95e-02 1.58e+01 pdb=" N PRO M 500 " -0.172 5.00e-02 4.00e+02 pdb=" CA PRO M 500 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO M 500 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE E 499 " 0.071 5.00e-02 4.00e+02 9.94e-02 1.58e+01 pdb=" N PRO E 500 " -0.171 5.00e-02 4.00e+02 pdb=" CA PRO E 500 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO E 500 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 590 " 0.044 5.00e-02 4.00e+02 6.60e-02 6.97e+00 pdb=" N PRO D 591 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO D 591 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 591 " 0.037 5.00e-02 4.00e+02 ... (remaining 11805 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 680 2.57 - 3.15: 53890 3.15 - 3.74: 100890 3.74 - 4.32: 145575 4.32 - 4.90: 245449 Nonbonded interactions: 546484 Sorted by model distance: nonbonded pdb=" OD1 ASN M 345 " pdb=" OH TYR M 593 " model vdw 1.988 3.040 nonbonded pdb=" O MET A 59 " pdb=" OH TYR B 85 " model vdw 1.999 3.040 nonbonded pdb=" OD1 ASN E 345 " pdb=" OH TYR E 593 " model vdw 2.001 3.040 nonbonded pdb=" O MET J 59 " pdb=" OH TYR K 85 " model vdw 2.005 3.040 nonbonded pdb=" O MET N 59 " pdb=" OH TYR O 85 " model vdw 2.013 3.040 ... (remaining 546479 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' } 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 group one per residue 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: 2.060 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: 0.040 Extract box with map and model: 2.080 Check model and map are aligned: 0.390 Set scattering table: 0.500 Process input model: 108.300 Find NCS groups from input model: 2.570 Set up NCS constraints: 0.340 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:2.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 118.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: -0.0024 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 : 0.008 0.142 68624 Z= 0.500 Angle : 0.739 12.560 93136 Z= 0.392 Chirality : 0.046 0.247 10816 Planarity : 0.004 0.100 11792 Dihedral : 14.734 123.456 26176 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.87 % Favored : 95.96 % Rotamer: Outliers : 0.97 % Allowed : 8.93 % Favored : 90.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.20 % 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: -0.24 (0.09), residues: 8432 helix: 1.59 (0.15), residues: 1232 sheet: -0.02 (0.09), residues: 3744 loop : -0.85 (0.11), residues: 3456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 104 HIS 0.006 0.001 HIS A 220 PHE 0.020 0.002 PHE L 313 TYR 0.037 0.002 TYR C 593 ARG 0.004 0.001 ARG G 589 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16864 Ramachandran restraints generated. 8432 Oldfield, 0 Emsley, 8432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16864 Ramachandran restraints generated. 8432 Oldfield, 0 Emsley, 8432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 761 residues out of total 7504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 688 time to evaluate : 5.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.1922 (mtm) cc_final: 0.1158 (ptt) REVERT: A 106 ASN cc_start: 0.5456 (t0) cc_final: 0.5039 (t0) REVERT: B 304 ASP cc_start: 0.4766 (t0) cc_final: 0.4419 (t0) REVERT: C 193 LEU cc_start: 0.8555 (tp) cc_final: 0.8180 (mm) REVERT: D 247 ILE cc_start: -0.2509 (OUTLIER) cc_final: -0.2867 (tp) REVERT: E 105 MET cc_start: -0.3613 (ttm) cc_final: -0.4346 (mmt) REVERT: G 176 MET cc_start: 0.6586 (mtt) cc_final: 0.6306 (mtt) REVERT: G 406 ASP cc_start: 0.6261 (t0) cc_final: 0.5473 (m-30) REVERT: G 533 MET cc_start: -0.3595 (ptp) cc_final: -0.5450 (mmt) REVERT: H 47 PRO cc_start: 0.2973 (Cg_endo) cc_final: 0.2763 (Cg_exo) REVERT: H 176 MET cc_start: 0.7337 (mtt) cc_final: 0.7029 (mmp) REVERT: H 196 LEU cc_start: 0.7370 (mm) cc_final: 0.6914 (tp) REVERT: H 205 VAL cc_start: 0.7166 (t) cc_final: 0.6881 (t) REVERT: H 529 PHE cc_start: 0.5513 (p90) cc_final: 0.5124 (p90) REVERT: H 599 MET cc_start: -0.0446 (mmp) cc_final: -0.0795 (tpt) REVERT: I 154 ASN cc_start: 0.5363 (m-40) cc_final: 0.4800 (p0) REVERT: I 599 MET cc_start: 0.4755 (mmt) cc_final: 0.1540 (mtm) REVERT: J 180 ASP cc_start: 0.5855 (m-30) cc_final: 0.5192 (t0) REVERT: K 153 ARG cc_start: 0.1519 (ttt-90) cc_final: 0.0716 (mtt180) REVERT: K 176 MET cc_start: 0.3980 (mtt) cc_final: 0.3469 (ttp) REVERT: K 196 LEU cc_start: -0.0659 (OUTLIER) cc_final: -0.1001 (tt) REVERT: K 442 CYS cc_start: 0.1497 (m) cc_final: 0.1184 (m) REVERT: K 599 MET cc_start: 0.1760 (mmt) cc_final: 0.0176 (mtt) REVERT: L 136 MET cc_start: 0.2996 (ptt) cc_final: 0.2590 (ptm) REVERT: L 304 ASP cc_start: 0.0847 (t0) cc_final: 0.0112 (t0) REVERT: L 322 LEU cc_start: -0.0118 (mt) cc_final: -0.0686 (mm) REVERT: L 443 LYS cc_start: 0.0376 (pttt) cc_final: -0.0211 (mttp) REVERT: M 181 GLN cc_start: -0.4238 (OUTLIER) cc_final: -0.4775 (tt0) REVERT: M 528 PHE cc_start: 0.3284 (m-80) cc_final: 0.2189 (m-80) REVERT: M 529 PHE cc_start: 0.6328 (p90) cc_final: 0.6120 (p90) REVERT: M 576 LYS cc_start: -0.0515 (mttt) cc_final: -0.0789 (tttt) REVERT: N 116 ASN cc_start: 0.5302 (m-40) cc_final: 0.5102 (t0) REVERT: N 171 PHE cc_start: 0.2157 (t80) cc_final: 0.1623 (t80) REVERT: N 233 GLN cc_start: 0.6883 (tt0) cc_final: 0.6260 (mp10) REVERT: N 408 SER cc_start: 0.2190 (p) cc_final: 0.1917 (t) REVERT: N 585 LEU cc_start: -0.1191 (OUTLIER) cc_final: -0.1667 (mt) REVERT: O 154 ASN cc_start: 0.1213 (m-40) cc_final: 0.0304 (m-40) REVERT: O 160 LYS cc_start: 0.3507 (mttm) cc_final: 0.3264 (tptm) REVERT: O 176 MET cc_start: 0.4309 (mtt) cc_final: 0.3697 (tpt) REVERT: O 406 ASP cc_start: 0.2565 (t0) cc_final: 0.2072 (m-30) REVERT: O 407 PHE cc_start: 0.2639 (m-80) cc_final: 0.1814 (m-10) REVERT: O 488 MET cc_start: -0.0280 (tmt) cc_final: -0.1699 (ttm) REVERT: P 96 MET cc_start: -0.1935 (mtt) cc_final: -0.3621 (ttt) outliers start: 73 outliers final: 17 residues processed: 752 average time/residue: 0.6476 time to fit residues: 829.4314 Evaluate side-chains 460 residues out of total 7504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 439 time to evaluate : 5.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain E residue 585 LEU Chi-restraints excluded: chain F residue 247 ILE Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 242 ILE Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 247 ILE Chi-restraints excluded: chain K residue 45 VAL Chi-restraints excluded: chain K residue 196 LEU Chi-restraints excluded: chain L residue 515 TYR Chi-restraints excluded: chain M residue 181 GLN Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 430 LEU Chi-restraints excluded: chain N residue 585 LEU Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain P residue 45 VAL Chi-restraints excluded: chain P residue 196 LEU Chi-restraints excluded: chain P residue 247 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 848 random chunks: chunk 716 optimal weight: 0.9980 chunk 642 optimal weight: 0.5980 chunk 356 optimal weight: 4.9990 chunk 219 optimal weight: 10.0000 chunk 433 optimal weight: 40.0000 chunk 343 optimal weight: 6.9990 chunk 664 optimal weight: 0.0670 chunk 257 optimal weight: 6.9990 chunk 404 optimal weight: 7.9990 chunk 494 optimal weight: 0.8980 chunk 770 optimal weight: 2.9990 overall best weight: 1.1120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 ASN A 276 GLN A 383 GLN B 32 GLN ** B 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 234 ASN B 299 HIS B 467 GLN ** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 276 GLN C 311 HIS C 383 GLN C 467 GLN D 276 GLN D 311 HIS D 383 GLN D 467 GLN E 276 GLN E 467 GLN F 217 GLN F 259 GLN F 276 GLN F 311 HIS F 340 HIS F 383 GLN F 401 ASN F 467 GLN ** G 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 276 GLN G 383 GLN G 467 GLN H 181 GLN H 186 GLN ** H 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 234 ASN H 276 GLN H 299 HIS H 311 HIS H 345 ASN H 383 GLN H 467 GLN I 276 GLN I 299 HIS J 89 GLN J 181 GLN ** J 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 220 HIS J 234 ASN J 311 HIS J 467 GLN J 490 ASN ** K 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 276 GLN K 311 HIS K 383 GLN K 467 GLN ** K 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 181 GLN ** L 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 276 GLN L 299 HIS L 311 HIS L 383 GLN L 401 ASN L 467 GLN L 561 HIS M 276 GLN M 311 HIS ** M 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 204 HIS N 276 GLN N 299 HIS N 311 HIS N 399 GLN ** N 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 467 GLN ** N 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 69 ASN O 108 GLN O 233 GLN O 276 GLN O 383 GLN O 467 GLN O 561 HIS P 77 GLN P 181 GLN P 276 GLN P 299 HIS P 467 GLN P 490 ASN Total number of N/Q/H flips: 79 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0329 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 68624 Z= 0.195 Angle : 0.667 13.619 93136 Z= 0.326 Chirality : 0.046 0.224 10816 Planarity : 0.005 0.052 11792 Dihedral : 10.191 93.268 10484 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.81 % Favored : 97.01 % Rotamer: Outliers : 2.00 % Allowed : 8.54 % Favored : 89.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.20 % 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: -0.24 (0.09), residues: 8432 helix: 1.11 (0.14), residues: 1328 sheet: 0.16 (0.09), residues: 3680 loop : -0.95 (0.11), residues: 3424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 51 HIS 0.012 0.001 HIS L 220 PHE 0.037 0.002 PHE C 225 TYR 0.026 0.002 TYR N 593 ARG 0.008 0.001 ARG K 270 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16864 Ramachandran restraints generated. 8432 Oldfield, 0 Emsley, 8432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16864 Ramachandran restraints generated. 8432 Oldfield, 0 Emsley, 8432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 643 residues out of total 7504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 493 time to evaluate : 5.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 ILE cc_start: 0.3639 (mp) cc_final: 0.3425 (mm) REVERT: A 96 MET cc_start: 0.1814 (mtm) cc_final: 0.1084 (ptt) REVERT: A 341 TYR cc_start: 0.0821 (OUTLIER) cc_final: 0.0322 (t80) REVERT: A 503 LEU cc_start: 0.1375 (OUTLIER) cc_final: 0.1107 (mm) REVERT: B 488 MET cc_start: -0.3423 (mmt) cc_final: -0.4106 (mmt) REVERT: C 533 MET cc_start: 0.3582 (ppp) cc_final: 0.3314 (ppp) REVERT: D 63 MET cc_start: -0.5107 (mmt) cc_final: -0.6287 (mmt) REVERT: E 59 MET cc_start: -0.3307 (mmp) cc_final: -0.3542 (mmt) REVERT: E 105 MET cc_start: -0.3569 (ttm) cc_final: -0.4201 (mmt) REVERT: F 96 MET cc_start: 0.1947 (tmm) cc_final: -0.0266 (mmt) REVERT: F 533 MET cc_start: -0.0251 (OUTLIER) cc_final: -0.1109 (tmm) REVERT: G 176 MET cc_start: 0.6489 (mtt) cc_final: 0.6210 (mtt) REVERT: G 233 GLN cc_start: 0.5484 (mp10) cc_final: 0.5277 (mp10) REVERT: G 406 ASP cc_start: 0.6396 (t0) cc_final: 0.5890 (m-30) REVERT: G 430 LEU cc_start: -0.1303 (OUTLIER) cc_final: -0.1528 (tt) REVERT: G 533 MET cc_start: -0.4560 (ptp) cc_final: -0.5403 (mmt) REVERT: H 149 ARG cc_start: 0.0593 (ttt90) cc_final: -0.0995 (mtt180) REVERT: H 176 MET cc_start: 0.7515 (mtt) cc_final: 0.7096 (mmp) REVERT: H 430 LEU cc_start: -0.1509 (OUTLIER) cc_final: -0.2757 (tp) REVERT: H 503 LEU cc_start: -0.4740 (OUTLIER) cc_final: -0.5193 (tp) REVERT: H 529 PHE cc_start: 0.5381 (p90) cc_final: 0.5084 (p90) REVERT: I 63 MET cc_start: 0.1808 (ttt) cc_final: 0.1265 (ttm) REVERT: I 154 ASN cc_start: 0.5927 (m-40) cc_final: 0.5215 (p0) REVERT: I 488 MET cc_start: 0.0989 (mmp) cc_final: 0.0406 (mtp) REVERT: I 599 MET cc_start: 0.3505 (mmt) cc_final: 0.1633 (mtm) REVERT: J 155 ARG cc_start: 0.2141 (ttp-170) cc_final: 0.1435 (ttp-170) REVERT: J 180 ASP cc_start: 0.5705 (m-30) cc_final: 0.5269 (t0) REVERT: J 488 MET cc_start: 0.3605 (mmt) cc_final: 0.2574 (mmt) REVERT: J 525 PHE cc_start: 0.2742 (OUTLIER) cc_final: 0.2023 (p90) REVERT: J 580 PHE cc_start: -0.1887 (OUTLIER) cc_final: -0.4425 (m-80) REVERT: K 97 ASN cc_start: 0.3911 (m110) cc_final: 0.2674 (t0) REVERT: K 442 CYS cc_start: 0.1869 (m) cc_final: 0.1390 (m) REVERT: K 599 MET cc_start: -0.0349 (mmp) cc_final: -0.1246 (mtt) REVERT: L 403 LEU cc_start: -0.0319 (OUTLIER) cc_final: -0.0900 (mp) REVERT: L 430 LEU cc_start: -0.3848 (OUTLIER) cc_final: -0.5427 (mt) REVERT: L 443 LYS cc_start: 0.0779 (pttt) cc_final: 0.0112 (mttp) REVERT: M 188 LYS cc_start: 0.2066 (mppt) cc_final: 0.0917 (tptt) REVERT: M 196 LEU cc_start: -0.4581 (OUTLIER) cc_final: -0.4890 (tt) REVERT: M 528 PHE cc_start: 0.3207 (m-80) cc_final: 0.2286 (m-10) REVERT: M 576 LYS cc_start: -0.0956 (mttt) cc_final: -0.1293 (tttt) REVERT: N 89 GLN cc_start: 0.2109 (mt0) cc_final: 0.1190 (tm-30) REVERT: N 119 LEU cc_start: 0.5270 (OUTLIER) cc_final: 0.4787 (mp) REVERT: O 136 MET cc_start: 0.8464 (mpp) cc_final: 0.6194 (tmm) REVERT: O 160 LYS cc_start: 0.4096 (mttm) cc_final: 0.2936 (tptm) REVERT: O 179 CYS cc_start: 0.5604 (t) cc_final: 0.5381 (m) REVERT: O 488 MET cc_start: -0.0016 (tmt) cc_final: -0.1500 (ttm) REVERT: P 108 GLN cc_start: 0.7098 (pp30) cc_final: 0.6743 (pp30) REVERT: P 176 MET cc_start: 0.5840 (mmp) cc_final: 0.5582 (mmp) REVERT: P 181 GLN cc_start: -0.6731 (OUTLIER) cc_final: -0.7528 (mt0) REVERT: P 394 CYS cc_start: 0.3664 (OUTLIER) cc_final: 0.3016 (p) REVERT: P 430 LEU cc_start: 0.2691 (OUTLIER) cc_final: 0.2313 (tp) REVERT: P 461 TRP cc_start: -0.3139 (p-90) cc_final: -0.3949 (p-90) REVERT: P 488 MET cc_start: 0.1320 (mmt) cc_final: -0.0648 (mtp) REVERT: P 599 MET cc_start: -0.0963 (OUTLIER) cc_final: -0.2068 (tpt) outliers start: 150 outliers final: 54 residues processed: 617 average time/residue: 0.6531 time to fit residues: 697.8972 Evaluate side-chains 480 residues out of total 7504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 410 time to evaluate : 5.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 341 TYR Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 247 ILE Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain D residue 181 GLN Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain E residue 343 THR Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 247 ILE Chi-restraints excluded: chain F residue 533 MET Chi-restraints excluded: chain G residue 430 LEU Chi-restraints excluded: chain H residue 216 VAL Chi-restraints excluded: chain H residue 229 ASN Chi-restraints excluded: chain H residue 409 CYS Chi-restraints excluded: chain H residue 430 LEU Chi-restraints excluded: chain H residue 503 LEU Chi-restraints excluded: chain I residue 105 MET Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 263 THR Chi-restraints excluded: chain J residue 162 THR Chi-restraints excluded: chain J residue 196 LEU Chi-restraints excluded: chain J residue 199 LEU Chi-restraints excluded: chain J residue 513 LEU Chi-restraints excluded: chain J residue 525 PHE Chi-restraints excluded: chain J residue 570 GLN Chi-restraints excluded: chain J residue 580 PHE Chi-restraints excluded: chain J residue 588 VAL Chi-restraints excluded: chain J residue 594 THR Chi-restraints excluded: chain J residue 599 MET Chi-restraints excluded: chain K residue 45 VAL Chi-restraints excluded: chain K residue 94 LEU Chi-restraints excluded: chain K residue 95 GLU Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 87 ILE Chi-restraints excluded: chain L residue 231 ASN Chi-restraints excluded: chain L residue 403 LEU Chi-restraints excluded: chain L residue 430 LEU Chi-restraints excluded: chain L residue 515 TYR Chi-restraints excluded: chain M residue 189 MET Chi-restraints excluded: chain M residue 196 LEU Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 119 LEU Chi-restraints excluded: chain N residue 326 LEU Chi-restraints excluded: chain N residue 437 THR Chi-restraints excluded: chain N residue 445 VAL Chi-restraints excluded: chain N residue 585 LEU Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain O residue 69 ASN Chi-restraints excluded: chain O residue 392 VAL Chi-restraints excluded: chain O residue 561 HIS Chi-restraints excluded: chain P residue 45 VAL Chi-restraints excluded: chain P residue 175 LEU Chi-restraints excluded: chain P residue 181 GLN Chi-restraints excluded: chain P residue 196 LEU Chi-restraints excluded: chain P residue 247 ILE Chi-restraints excluded: chain P residue 281 VAL Chi-restraints excluded: chain P residue 394 CYS Chi-restraints excluded: chain P residue 430 LEU Chi-restraints excluded: chain P residue 484 THR Chi-restraints excluded: chain P residue 574 CYS Chi-restraints excluded: chain P residue 599 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 848 random chunks: chunk 427 optimal weight: 20.0000 chunk 238 optimal weight: 9.9990 chunk 640 optimal weight: 1.9990 chunk 524 optimal weight: 0.0170 chunk 212 optimal weight: 110.0000 chunk 771 optimal weight: 0.0980 chunk 833 optimal weight: 10.0000 chunk 687 optimal weight: 4.9990 chunk 765 optimal weight: 5.9990 chunk 263 optimal weight: 0.5980 chunk 618 optimal weight: 0.6980 overall best weight: 0.6820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 108 GLN D 561 HIS E 560 GLN F 561 HIS ** G 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 GLN H 229 ASN H 231 ASN H 401 ASN I 144 GLN ** J 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 217 GLN K 204 HIS ** K 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 345 ASN M 220 HIS M 249 ASN ** M 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 401 ASN ** N 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 220 HIS N 560 GLN O 116 ASN O 217 GLN O 561 HIS P 144 GLN P 231 ASN P 399 GLN ** P 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 539 ASN P 560 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0399 moved from start: 0.3059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.069 68624 Z= 0.147 Angle : 0.581 11.286 93136 Z= 0.284 Chirality : 0.044 0.312 10816 Planarity : 0.004 0.061 11792 Dihedral : 7.491 73.435 10466 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.69 % Favored : 97.13 % Rotamer: Outliers : 1.71 % Allowed : 9.12 % Favored : 89.18 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.20 % Twisted Proline : 0.22 % 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: -0.17 (0.09), residues: 8432 helix: 0.80 (0.14), residues: 1392 sheet: 0.35 (0.09), residues: 3536 loop : -0.92 (0.11), residues: 3504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP M 104 HIS 0.024 0.001 HIS O 561 PHE 0.018 0.001 PHE D 528 TYR 0.016 0.001 TYR C 593 ARG 0.005 0.000 ARG D 124 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16864 Ramachandran restraints generated. 8432 Oldfield, 0 Emsley, 8432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16864 Ramachandran restraints generated. 8432 Oldfield, 0 Emsley, 8432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 7504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 438 time to evaluate : 5.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.1955 (mtm) cc_final: 0.1018 (ptt) REVERT: A 533 MET cc_start: 0.7166 (ppp) cc_final: 0.6953 (ppp) REVERT: B 488 MET cc_start: -0.4348 (mmt) cc_final: -0.4627 (mmt) REVERT: C 99 GLU cc_start: -0.4610 (OUTLIER) cc_final: -0.5454 (tt0) REVERT: C 251 LYS cc_start: 0.4721 (OUTLIER) cc_final: 0.4483 (tmmt) REVERT: D 63 MET cc_start: -0.5459 (mmt) cc_final: -0.6220 (mmt) REVERT: E 105 MET cc_start: -0.3650 (ttm) cc_final: -0.4288 (mmt) REVERT: F 59 MET cc_start: -0.1581 (mmm) cc_final: -0.2198 (mtt) REVERT: F 96 MET cc_start: 0.1887 (tmm) cc_final: -0.0193 (mmt) REVERT: F 593 TYR cc_start: -0.2605 (OUTLIER) cc_final: -0.3149 (t80) REVERT: G 176 MET cc_start: 0.6550 (mtt) cc_final: 0.6233 (mtt) REVERT: G 189 MET cc_start: -0.0656 (OUTLIER) cc_final: -0.1300 (mmm) REVERT: G 406 ASP cc_start: 0.6498 (t0) cc_final: 0.6076 (m-30) REVERT: G 430 LEU cc_start: -0.1220 (OUTLIER) cc_final: -0.1430 (tt) REVERT: G 533 MET cc_start: -0.4455 (ptp) cc_final: -0.5378 (mmt) REVERT: H 176 MET cc_start: 0.7421 (mtt) cc_final: 0.7064 (mmp) REVERT: H 503 LEU cc_start: -0.4492 (OUTLIER) cc_final: -0.4973 (tp) REVERT: I 63 MET cc_start: 0.1417 (ttt) cc_final: 0.1177 (ttm) REVERT: I 154 ASN cc_start: 0.5805 (m-40) cc_final: 0.5391 (p0) REVERT: I 181 GLN cc_start: 0.4536 (mm-40) cc_final: 0.4213 (pt0) REVERT: I 189 MET cc_start: 0.1632 (mmm) cc_final: 0.0829 (mmm) REVERT: I 488 MET cc_start: 0.1169 (mmp) cc_final: 0.0362 (mtp) REVERT: I 599 MET cc_start: 0.3617 (mmt) cc_final: 0.1995 (mtm) REVERT: J 155 ARG cc_start: 0.2080 (ttp-170) cc_final: 0.1656 (ttp-170) REVERT: J 180 ASP cc_start: 0.6052 (m-30) cc_final: 0.5650 (t0) REVERT: J 488 MET cc_start: 0.3512 (mmt) cc_final: 0.2493 (mmt) REVERT: J 525 PHE cc_start: 0.3501 (t80) cc_final: 0.2567 (p90) REVERT: J 580 PHE cc_start: -0.2078 (OUTLIER) cc_final: -0.4479 (m-80) REVERT: K 70 CYS cc_start: 0.3140 (m) cc_final: 0.2846 (m) REVERT: K 97 ASN cc_start: 0.4100 (m110) cc_final: 0.3532 (m110) REVERT: K 442 CYS cc_start: 0.2071 (m) cc_final: 0.1582 (m) REVERT: K 599 MET cc_start: 0.0712 (mmp) cc_final: -0.0439 (mtt) REVERT: L 189 MET cc_start: -0.5428 (tpt) cc_final: -0.5657 (tpt) REVERT: L 403 LEU cc_start: -0.0101 (OUTLIER) cc_final: -0.0903 (mp) REVERT: L 443 LYS cc_start: 0.0693 (pttt) cc_final: 0.0137 (mptt) REVERT: L 598 LEU cc_start: -0.0037 (OUTLIER) cc_final: -0.0242 (tp) REVERT: M 188 LYS cc_start: 0.1973 (mppt) cc_final: 0.0796 (tptt) REVERT: M 196 LEU cc_start: -0.4646 (OUTLIER) cc_final: -0.4950 (tt) REVERT: M 528 PHE cc_start: 0.3344 (m-80) cc_final: 0.2378 (m-10) REVERT: M 529 PHE cc_start: 0.5691 (p90) cc_final: 0.5377 (p90) REVERT: M 576 LYS cc_start: -0.1009 (mttt) cc_final: -0.1308 (tttt) REVERT: M 598 LEU cc_start: 0.2950 (mt) cc_final: 0.2119 (pp) REVERT: N 119 LEU cc_start: 0.5288 (OUTLIER) cc_final: 0.4559 (mp) REVERT: O 63 MET cc_start: 0.2264 (mtt) cc_final: 0.1943 (tmm) REVERT: O 136 MET cc_start: 0.8728 (mpp) cc_final: 0.6075 (tmm) REVERT: O 160 LYS cc_start: 0.4014 (mttm) cc_final: 0.2528 (tptm) REVERT: O 179 CYS cc_start: 0.5999 (t) cc_final: 0.5522 (m) REVERT: O 274 ARG cc_start: 0.1260 (ttp-170) cc_final: -0.1346 (mmt90) REVERT: O 488 MET cc_start: -0.0045 (tmt) cc_final: -0.1506 (ttm) REVERT: P 95 GLU cc_start: -0.2973 (OUTLIER) cc_final: -0.4381 (tt0) REVERT: P 96 MET cc_start: -0.1292 (mpp) cc_final: -0.2824 (ttt) REVERT: P 159 VAL cc_start: 0.0100 (OUTLIER) cc_final: -0.0143 (p) REVERT: P 181 GLN cc_start: -0.7057 (OUTLIER) cc_final: -0.7338 (mt0) REVERT: P 385 CYS cc_start: 0.1945 (OUTLIER) cc_final: 0.0034 (p) REVERT: P 394 CYS cc_start: 0.3806 (OUTLIER) cc_final: 0.3307 (p) REVERT: P 430 LEU cc_start: 0.2417 (OUTLIER) cc_final: 0.2168 (tp) REVERT: P 461 TRP cc_start: -0.3225 (p-90) cc_final: -0.3680 (p-90) REVERT: P 488 MET cc_start: 0.1064 (mmt) cc_final: -0.0392 (mtp) REVERT: P 523 VAL cc_start: -0.0302 (OUTLIER) cc_final: -0.1043 (t) REVERT: P 533 MET cc_start: 0.6942 (mtp) cc_final: 0.6541 (ttt) outliers start: 128 outliers final: 66 residues processed: 546 average time/residue: 0.6136 time to fit residues: 582.6732 Evaluate side-chains 483 residues out of total 7504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 399 time to evaluate : 5.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 247 ILE Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 494 CYS Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 251 LYS Chi-restraints excluded: chain C residue 342 TYR Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 181 GLN Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain D residue 403 LEU Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain E residue 394 CYS Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 247 ILE Chi-restraints excluded: chain F residue 533 MET Chi-restraints excluded: chain F residue 593 TYR Chi-restraints excluded: chain G residue 189 MET Chi-restraints excluded: chain G residue 430 LEU Chi-restraints excluded: chain G residue 589 ARG Chi-restraints excluded: chain G residue 590 LEU Chi-restraints excluded: chain H residue 229 ASN Chi-restraints excluded: chain H residue 503 LEU Chi-restraints excluded: chain H residue 594 THR Chi-restraints excluded: chain I residue 105 MET Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 263 THR Chi-restraints excluded: chain I residue 594 THR Chi-restraints excluded: chain J residue 216 VAL Chi-restraints excluded: chain J residue 402 LEU Chi-restraints excluded: chain J residue 513 LEU Chi-restraints excluded: chain J residue 570 GLN Chi-restraints excluded: chain J residue 580 PHE Chi-restraints excluded: chain J residue 586 LEU Chi-restraints excluded: chain K residue 45 VAL Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain L residue 175 LEU Chi-restraints excluded: chain L residue 193 LEU Chi-restraints excluded: chain L residue 403 LEU Chi-restraints excluded: chain L residue 515 TYR Chi-restraints excluded: chain L residue 598 LEU Chi-restraints excluded: chain M residue 189 MET Chi-restraints excluded: chain M residue 196 LEU Chi-restraints excluded: chain M residue 303 ILE Chi-restraints excluded: chain M residue 588 VAL Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 119 LEU Chi-restraints excluded: chain N residue 209 VAL Chi-restraints excluded: chain N residue 275 VAL Chi-restraints excluded: chain N residue 303 ILE Chi-restraints excluded: chain N residue 326 LEU Chi-restraints excluded: chain N residue 437 THR Chi-restraints excluded: chain N residue 533 MET Chi-restraints excluded: chain N residue 585 LEU Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain O residue 87 ILE Chi-restraints excluded: chain O residue 110 THR Chi-restraints excluded: chain O residue 133 PHE Chi-restraints excluded: chain P residue 45 VAL Chi-restraints excluded: chain P residue 95 GLU Chi-restraints excluded: chain P residue 159 VAL Chi-restraints excluded: chain P residue 175 LEU Chi-restraints excluded: chain P residue 181 GLN Chi-restraints excluded: chain P residue 196 LEU Chi-restraints excluded: chain P residue 209 VAL Chi-restraints excluded: chain P residue 247 ILE Chi-restraints excluded: chain P residue 281 VAL Chi-restraints excluded: chain P residue 385 CYS Chi-restraints excluded: chain P residue 394 CYS Chi-restraints excluded: chain P residue 417 HIS Chi-restraints excluded: chain P residue 430 LEU Chi-restraints excluded: chain P residue 484 THR Chi-restraints excluded: chain P residue 523 VAL Chi-restraints excluded: chain P residue 574 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 848 random chunks: chunk 762 optimal weight: 10.0000 chunk 580 optimal weight: 7.9990 chunk 400 optimal weight: 0.6980 chunk 85 optimal weight: 50.0000 chunk 368 optimal weight: 20.0000 chunk 518 optimal weight: 10.0000 chunk 774 optimal weight: 0.7980 chunk 819 optimal weight: 2.9990 chunk 404 optimal weight: 20.0000 chunk 733 optimal weight: 1.9990 chunk 220 optimal weight: 20.0000 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 ASN ** A 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 186 GLN A 230 GLN A 340 HIS A 401 ASN ** A 561 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 GLN ** B 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 570 GLN ** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 299 HIS ** C 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 108 GLN E 89 GLN E 561 HIS F 116 ASN F 220 HIS ** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 181 GLN H 144 GLN H 154 ASN H 293 GLN H 311 HIS H 401 ASN H 561 HIS I 272 ASN I 311 HIS ** I 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 186 GLN J 299 HIS J 399 GLN K 32 GLN K 401 ASN K 421 GLN ** K 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 77 GLN L 97 ASN L 108 GLN ** L 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 234 ASN ** L 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 561 HIS ** L 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 97 ASN ** M 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 93 ASN ** N 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 217 GLN ** N 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 399 GLN ** N 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 69 ASN O 116 ASN ** O 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 561 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 154 ASN P 293 GLN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0978 moved from start: 0.5073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.120 68624 Z= 0.300 Angle : 0.810 15.517 93136 Z= 0.412 Chirality : 0.051 0.386 10816 Planarity : 0.007 0.143 11792 Dihedral : 7.565 59.934 10466 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.35 % Favored : 95.43 % Rotamer: Outliers : 2.67 % Allowed : 9.58 % Favored : 87.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.76 (0.09), residues: 8432 helix: 0.23 (0.13), residues: 1389 sheet: 0.06 (0.09), residues: 3484 loop : -1.32 (0.10), residues: 3559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP N 292 HIS 0.021 0.002 HIS L 204 PHE 0.065 0.002 PHE K 278 TYR 0.035 0.002 TYR M 382 ARG 0.017 0.001 ARG H 305 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16864 Ramachandran restraints generated. 8432 Oldfield, 0 Emsley, 8432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16864 Ramachandran restraints generated. 8432 Oldfield, 0 Emsley, 8432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 715 residues out of total 7504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 200 poor density : 515 time to evaluate : 5.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.1098 (mtm) cc_final: 0.0249 (ptt) REVERT: A 173 LYS cc_start: 0.4491 (mmtt) cc_final: 0.4266 (mmtt) REVERT: A 503 LEU cc_start: 0.1938 (OUTLIER) cc_final: 0.1387 (mm) REVERT: B 209 VAL cc_start: -0.0698 (m) cc_final: -0.1741 (p) REVERT: B 488 MET cc_start: -0.4396 (mmt) cc_final: -0.4600 (mmt) REVERT: C 99 GLU cc_start: -0.4597 (OUTLIER) cc_final: -0.5421 (tt0) REVERT: D 63 MET cc_start: -0.5748 (mmt) cc_final: -0.6221 (mmt) REVERT: E 105 MET cc_start: -0.3435 (ttm) cc_final: -0.4038 (mmt) REVERT: F 59 MET cc_start: -0.0953 (mmm) cc_final: -0.1736 (mmt) REVERT: F 96 MET cc_start: 0.1973 (tmm) cc_final: -0.0178 (mmt) REVERT: F 593 TYR cc_start: -0.2174 (OUTLIER) cc_final: -0.2538 (t80) REVERT: G 176 MET cc_start: 0.6615 (mtt) cc_final: 0.6342 (mtt) REVERT: G 189 MET cc_start: -0.0411 (OUTLIER) cc_final: -0.0808 (mmm) REVERT: G 406 ASP cc_start: 0.6524 (t0) cc_final: 0.6096 (m-30) REVERT: G 533 MET cc_start: -0.4953 (ptp) cc_final: -0.5813 (mmt) REVERT: H 153 ARG cc_start: 0.3118 (ttt-90) cc_final: 0.1729 (mtp180) REVERT: H 176 MET cc_start: 0.7455 (mtt) cc_final: 0.7027 (mmp) REVERT: H 196 LEU cc_start: 0.7742 (mt) cc_final: 0.7400 (tp) REVERT: H 229 ASN cc_start: 0.7317 (OUTLIER) cc_final: 0.6784 (t0) REVERT: H 430 LEU cc_start: -0.0868 (OUTLIER) cc_final: -0.1911 (tp) REVERT: H 503 LEU cc_start: -0.3592 (OUTLIER) cc_final: -0.3986 (tp) REVERT: H 592 PRO cc_start: 0.5006 (Cg_exo) cc_final: 0.4503 (Cg_endo) REVERT: I 96 MET cc_start: 0.1175 (tpt) cc_final: -0.0494 (tpt) REVERT: I 192 TYR cc_start: 0.1366 (t80) cc_final: 0.0854 (t80) REVERT: I 488 MET cc_start: 0.1199 (mmp) cc_final: 0.0822 (mtp) REVERT: I 599 MET cc_start: 0.3291 (mmt) cc_final: 0.1519 (mtm) REVERT: J 95 GLU cc_start: 0.0430 (OUTLIER) cc_final: -0.0564 (mt-10) REVERT: J 189 MET cc_start: 0.4197 (mmm) cc_final: 0.3716 (mmm) REVERT: J 222 ARG cc_start: -0.0856 (OUTLIER) cc_final: -0.4136 (mtp180) REVERT: J 448 ASP cc_start: -0.0709 (OUTLIER) cc_final: -0.2211 (t0) REVERT: J 599 MET cc_start: 0.1130 (mpt) cc_final: -0.1592 (mtt) REVERT: K 77 GLN cc_start: -0.0153 (mt0) cc_final: -0.0634 (tt0) REVERT: K 599 MET cc_start: 0.1107 (mmp) cc_final: -0.1184 (mtt) REVERT: L 52 ASP cc_start: 0.6933 (t0) cc_final: 0.6116 (t70) REVERT: L 63 MET cc_start: 0.1686 (mmt) cc_final: 0.0765 (tpp) REVERT: L 95 GLU cc_start: 0.1833 (OUTLIER) cc_final: -0.1194 (tt0) REVERT: L 124 ARG cc_start: -0.0617 (ttp-170) cc_final: -0.3655 (ptt90) REVERT: L 219 ASP cc_start: 0.2218 (m-30) cc_final: 0.1630 (p0) REVERT: L 430 LEU cc_start: -0.3217 (OUTLIER) cc_final: -0.3535 (tp) REVERT: M 101 LEU cc_start: -0.1111 (OUTLIER) cc_final: -0.1772 (tt) REVERT: M 176 MET cc_start: -0.4308 (OUTLIER) cc_final: -0.4514 (mmp) REVERT: M 276 GLN cc_start: -0.1217 (tt0) cc_final: -0.1613 (tt0) REVERT: M 528 PHE cc_start: 0.4262 (m-80) cc_final: 0.3247 (m-10) REVERT: M 598 LEU cc_start: 0.3884 (mt) cc_final: 0.3256 (pp) REVERT: N 119 LEU cc_start: 0.5328 (OUTLIER) cc_final: 0.4977 (mp) REVERT: N 136 MET cc_start: 0.7306 (ttp) cc_final: 0.7058 (ttp) REVERT: N 161 THR cc_start: 0.4357 (p) cc_final: 0.3071 (m) REVERT: N 391 ASP cc_start: 0.5462 (p0) cc_final: 0.4784 (t70) REVERT: O 63 MET cc_start: 0.1783 (mtt) cc_final: 0.1092 (ptt) REVERT: O 179 CYS cc_start: 0.6192 (t) cc_final: 0.5699 (m) REVERT: O 222 ARG cc_start: 0.0365 (mtt180) cc_final: 0.0010 (ptm-80) REVERT: O 488 MET cc_start: -0.0994 (tmt) cc_final: -0.2187 (ttm) REVERT: P 95 GLU cc_start: -0.2113 (OUTLIER) cc_final: -0.3386 (tt0) REVERT: P 96 MET cc_start: 0.0558 (mpp) cc_final: -0.0923 (ttt) REVERT: P 107 TYR cc_start: 0.3314 (m-80) cc_final: 0.2523 (m-80) REVERT: P 159 VAL cc_start: 0.1433 (OUTLIER) cc_final: 0.1182 (p) REVERT: P 181 GLN cc_start: -0.7202 (OUTLIER) cc_final: -0.8070 (mt0) REVERT: P 385 CYS cc_start: 0.1396 (OUTLIER) cc_final: 0.0276 (p) REVERT: P 418 LEU cc_start: 0.3253 (mt) cc_final: 0.2613 (mt) REVERT: P 533 MET cc_start: 0.6221 (mtp) cc_final: 0.6014 (ttt) outliers start: 200 outliers final: 96 residues processed: 680 average time/residue: 0.6385 time to fit residues: 748.7987 Evaluate side-chains 553 residues out of total 7504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 438 time to evaluate : 5.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 259 GLN Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 247 ILE Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 181 GLN Chi-restraints excluded: chain D residue 403 LEU Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain E residue 61 ARG Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain E residue 394 CYS Chi-restraints excluded: chain E residue 463 VAL Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 247 ILE Chi-restraints excluded: chain F residue 533 MET Chi-restraints excluded: chain F residue 593 TYR Chi-restraints excluded: chain G residue 39 LYS Chi-restraints excluded: chain G residue 189 MET Chi-restraints excluded: chain G residue 589 ARG Chi-restraints excluded: chain H residue 95 GLU Chi-restraints excluded: chain H residue 216 VAL Chi-restraints excluded: chain H residue 229 ASN Chi-restraints excluded: chain H residue 378 PHE Chi-restraints excluded: chain H residue 430 LEU Chi-restraints excluded: chain H residue 503 LEU Chi-restraints excluded: chain H residue 564 VAL Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 209 VAL Chi-restraints excluded: chain I residue 263 THR Chi-restraints excluded: chain J residue 95 GLU Chi-restraints excluded: chain J residue 152 VAL Chi-restraints excluded: chain J residue 162 THR Chi-restraints excluded: chain J residue 199 LEU Chi-restraints excluded: chain J residue 222 ARG Chi-restraints excluded: chain J residue 268 SER Chi-restraints excluded: chain J residue 402 LEU Chi-restraints excluded: chain J residue 430 LEU Chi-restraints excluded: chain J residue 448 ASP Chi-restraints excluded: chain J residue 523 VAL Chi-restraints excluded: chain J residue 564 VAL Chi-restraints excluded: chain J residue 570 GLN Chi-restraints excluded: chain K residue 44 GLU Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 94 LEU Chi-restraints excluded: chain K residue 95 GLU Chi-restraints excluded: chain K residue 165 SER Chi-restraints excluded: chain K residue 430 LEU Chi-restraints excluded: chain L residue 31 PHE Chi-restraints excluded: chain L residue 87 ILE Chi-restraints excluded: chain L residue 90 LYS Chi-restraints excluded: chain L residue 95 GLU Chi-restraints excluded: chain L residue 155 ARG Chi-restraints excluded: chain L residue 175 LEU Chi-restraints excluded: chain L residue 204 HIS Chi-restraints excluded: chain L residue 303 ILE Chi-restraints excluded: chain L residue 430 LEU Chi-restraints excluded: chain L residue 515 TYR Chi-restraints excluded: chain M residue 101 LEU Chi-restraints excluded: chain M residue 176 MET Chi-restraints excluded: chain M residue 189 MET Chi-restraints excluded: chain M residue 266 TYR Chi-restraints excluded: chain M residue 303 ILE Chi-restraints excluded: chain M residue 539 ASN Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 68 THR Chi-restraints excluded: chain N residue 87 ILE Chi-restraints excluded: chain N residue 112 SER Chi-restraints excluded: chain N residue 119 LEU Chi-restraints excluded: chain N residue 209 VAL Chi-restraints excluded: chain N residue 263 THR Chi-restraints excluded: chain N residue 275 VAL Chi-restraints excluded: chain N residue 303 ILE Chi-restraints excluded: chain N residue 308 LEU Chi-restraints excluded: chain N residue 310 LEU Chi-restraints excluded: chain N residue 406 ASP Chi-restraints excluded: chain N residue 437 THR Chi-restraints excluded: chain N residue 533 MET Chi-restraints excluded: chain N residue 585 LEU Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain O residue 84 VAL Chi-restraints excluded: chain O residue 94 LEU Chi-restraints excluded: chain O residue 110 THR Chi-restraints excluded: chain O residue 206 ILE Chi-restraints excluded: chain O residue 376 PHE Chi-restraints excluded: chain O residue 561 HIS Chi-restraints excluded: chain O residue 570 GLN Chi-restraints excluded: chain P residue 45 VAL Chi-restraints excluded: chain P residue 63 MET Chi-restraints excluded: chain P residue 95 GLU Chi-restraints excluded: chain P residue 159 VAL Chi-restraints excluded: chain P residue 175 LEU Chi-restraints excluded: chain P residue 181 GLN Chi-restraints excluded: chain P residue 196 LEU Chi-restraints excluded: chain P residue 209 VAL Chi-restraints excluded: chain P residue 242 ILE Chi-restraints excluded: chain P residue 247 ILE Chi-restraints excluded: chain P residue 385 CYS Chi-restraints excluded: chain P residue 417 HIS Chi-restraints excluded: chain P residue 423 HIS Chi-restraints excluded: chain P residue 484 THR Chi-restraints excluded: chain P residue 574 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 848 random chunks: chunk 682 optimal weight: 0.9990 chunk 465 optimal weight: 0.9990 chunk 11 optimal weight: 30.0000 chunk 610 optimal weight: 0.9980 chunk 338 optimal weight: 10.0000 chunk 699 optimal weight: 7.9990 chunk 566 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 418 optimal weight: 6.9990 chunk 735 optimal weight: 0.8980 chunk 206 optimal weight: 0.0470 overall best weight: 0.7882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 186 GLN B 108 GLN B 181 GLN ** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 186 GLN C 570 GLN ** E 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 299 HIS ** H 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 230 GLN H 231 ASN H 401 ASN H 561 HIS ** I 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 217 GLN K 293 GLN K 401 ASN K 560 GLN ** L 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 69 ASN P 217 GLN ** P 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 345 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0863 moved from start: 0.5204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.105 68624 Z= 0.161 Angle : 0.584 13.070 93136 Z= 0.294 Chirality : 0.044 0.426 10816 Planarity : 0.005 0.093 11792 Dihedral : 6.410 59.819 10463 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.61 % Favored : 97.20 % Rotamer: Outliers : 1.92 % Allowed : 10.98 % Favored : 87.10 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.20 % 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: -0.52 (0.09), residues: 8432 helix: 0.55 (0.14), residues: 1392 sheet: 0.13 (0.09), residues: 3552 loop : -1.15 (0.10), residues: 3488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP J 51 HIS 0.010 0.001 HIS L 204 PHE 0.031 0.001 PHE G 283 TYR 0.022 0.001 TYR N 67 ARG 0.005 0.000 ARG L 274 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16864 Ramachandran restraints generated. 8432 Oldfield, 0 Emsley, 8432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16864 Ramachandran restraints generated. 8432 Oldfield, 0 Emsley, 8432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 594 residues out of total 7504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 450 time to evaluate : 5.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.1341 (mtm) cc_final: 0.0241 (ptt) REVERT: A 176 MET cc_start: -0.0832 (mmp) cc_final: -0.1516 (mpp) REVERT: A 503 LEU cc_start: 0.1964 (OUTLIER) cc_final: 0.1404 (mm) REVERT: B 488 MET cc_start: -0.4349 (mmt) cc_final: -0.4911 (mmt) REVERT: C 99 GLU cc_start: -0.4662 (OUTLIER) cc_final: -0.5138 (tt0) REVERT: C 488 MET cc_start: -0.2592 (mtt) cc_final: -0.4677 (mmt) REVERT: D 63 MET cc_start: -0.5934 (mmt) cc_final: -0.6308 (mmt) REVERT: E 105 MET cc_start: -0.3430 (ttm) cc_final: -0.3998 (mmp) REVERT: E 599 MET cc_start: 0.1125 (mmp) cc_final: -0.0487 (mmp) REVERT: F 59 MET cc_start: -0.0711 (mmm) cc_final: -0.2100 (mmt) REVERT: F 96 MET cc_start: 0.1792 (tmm) cc_final: -0.0204 (mmt) REVERT: F 593 TYR cc_start: -0.2176 (OUTLIER) cc_final: -0.2530 (t80) REVERT: G 176 MET cc_start: 0.6461 (mtt) cc_final: 0.6172 (mtt) REVERT: G 189 MET cc_start: 0.0736 (OUTLIER) cc_final: -0.0049 (mmm) REVERT: G 533 MET cc_start: -0.4989 (ptp) cc_final: -0.5828 (mmt) REVERT: H 104 TRP cc_start: 0.4249 (t60) cc_final: 0.2830 (m-90) REVERT: H 153 ARG cc_start: 0.3147 (ttt-90) cc_final: 0.1595 (mtm180) REVERT: H 176 MET cc_start: 0.7412 (mtt) cc_final: 0.6962 (mmp) REVERT: H 196 LEU cc_start: 0.7716 (mt) cc_final: 0.7368 (tp) REVERT: H 430 LEU cc_start: -0.1085 (OUTLIER) cc_final: -0.1910 (tp) REVERT: H 503 LEU cc_start: -0.3887 (OUTLIER) cc_final: -0.4246 (tp) REVERT: I 96 MET cc_start: 0.0911 (tpt) cc_final: -0.0722 (tpt) REVERT: I 481 THR cc_start: 0.1422 (p) cc_final: 0.0769 (t) REVERT: I 599 MET cc_start: 0.3350 (mmt) cc_final: 0.1660 (mtm) REVERT: J 63 MET cc_start: 0.0338 (mmt) cc_final: -0.1238 (mmt) REVERT: J 95 GLU cc_start: 0.0343 (OUTLIER) cc_final: -0.0372 (mt-10) REVERT: J 180 ASP cc_start: 0.6328 (m-30) cc_final: 0.5542 (t0) REVERT: J 402 LEU cc_start: 0.7943 (tp) cc_final: 0.7300 (pt) REVERT: K 70 CYS cc_start: 0.3199 (m) cc_final: 0.2829 (m) REVERT: K 217 GLN cc_start: 0.1329 (OUTLIER) cc_final: -0.0070 (tm-30) REVERT: K 303 ILE cc_start: -0.1471 (OUTLIER) cc_final: -0.1775 (tt) REVERT: K 589 ARG cc_start: 0.1847 (ptp90) cc_final: 0.1019 (ptt-90) REVERT: K 599 MET cc_start: 0.1118 (mmp) cc_final: -0.1046 (mtt) REVERT: L 63 MET cc_start: 0.1111 (mmt) cc_final: 0.0477 (tpp) REVERT: L 95 GLU cc_start: 0.2362 (OUTLIER) cc_final: -0.0375 (tt0) REVERT: L 124 ARG cc_start: -0.0743 (ttp-170) cc_final: -0.3373 (ptt-90) REVERT: L 219 ASP cc_start: 0.2403 (m-30) cc_final: 0.1752 (p0) REVERT: M 528 PHE cc_start: 0.4465 (m-80) cc_final: 0.3521 (m-10) REVERT: M 529 PHE cc_start: 0.5948 (p90) cc_final: 0.5476 (p90) REVERT: M 598 LEU cc_start: 0.3655 (mt) cc_final: 0.3191 (pp) REVERT: N 116 ASN cc_start: 0.8013 (t0) cc_final: 0.7734 (t0) REVERT: N 119 LEU cc_start: 0.5868 (OUTLIER) cc_final: 0.5649 (tt) REVERT: N 121 LEU cc_start: 0.4630 (OUTLIER) cc_final: 0.4286 (tp) REVERT: N 136 MET cc_start: 0.7247 (ttp) cc_final: 0.6997 (ttp) REVERT: N 161 THR cc_start: 0.4372 (p) cc_final: 0.2680 (m) REVERT: N 176 MET cc_start: -0.2309 (OUTLIER) cc_final: -0.2613 (ppp) REVERT: N 391 ASP cc_start: 0.5322 (p0) cc_final: 0.4765 (t70) REVERT: O 72 THR cc_start: 0.0087 (OUTLIER) cc_final: -0.0142 (p) REVERT: O 204 HIS cc_start: 0.0948 (OUTLIER) cc_final: -0.2144 (m-70) REVERT: O 431 GLU cc_start: 0.1365 (mm-30) cc_final: 0.0797 (mm-30) REVERT: O 488 MET cc_start: -0.0933 (tmt) cc_final: -0.2174 (ttm) REVERT: P 95 GLU cc_start: -0.2133 (OUTLIER) cc_final: -0.3794 (tt0) REVERT: P 96 MET cc_start: 0.0797 (mpp) cc_final: -0.0350 (ttt) REVERT: P 107 TYR cc_start: 0.3635 (m-80) cc_final: 0.2791 (m-80) REVERT: P 181 GLN cc_start: -0.6908 (OUTLIER) cc_final: -0.7871 (mt0) REVERT: P 418 LEU cc_start: 0.2809 (mt) cc_final: 0.2309 (mt) REVERT: P 461 TRP cc_start: -0.2504 (p-90) cc_final: -0.2825 (p-90) REVERT: P 533 MET cc_start: 0.6411 (mtp) cc_final: 0.6145 (ttt) outliers start: 144 outliers final: 82 residues processed: 571 average time/residue: 0.6328 time to fit residues: 622.1139 Evaluate side-chains 514 residues out of total 7504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 415 time to evaluate : 5.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 341 TYR Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 247 ILE Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 494 CYS Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 181 GLN Chi-restraints excluded: chain D residue 403 LEU Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain E residue 394 CYS Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 189 MET Chi-restraints excluded: chain F residue 247 ILE Chi-restraints excluded: chain F residue 533 MET Chi-restraints excluded: chain F residue 593 TYR Chi-restraints excluded: chain G residue 39 LYS Chi-restraints excluded: chain G residue 189 MET Chi-restraints excluded: chain G residue 216 VAL Chi-restraints excluded: chain G residue 589 ARG Chi-restraints excluded: chain G residue 590 LEU Chi-restraints excluded: chain H residue 216 VAL Chi-restraints excluded: chain H residue 409 CYS Chi-restraints excluded: chain H residue 430 LEU Chi-restraints excluded: chain H residue 503 LEU Chi-restraints excluded: chain H residue 562 LEU Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 263 THR Chi-restraints excluded: chain I residue 523 VAL Chi-restraints excluded: chain J residue 95 GLU Chi-restraints excluded: chain J residue 162 THR Chi-restraints excluded: chain J residue 268 SER Chi-restraints excluded: chain J residue 570 GLN Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 206 ILE Chi-restraints excluded: chain K residue 217 GLN Chi-restraints excluded: chain K residue 303 ILE Chi-restraints excluded: chain K residue 512 SER Chi-restraints excluded: chain K residue 513 LEU Chi-restraints excluded: chain L residue 87 ILE Chi-restraints excluded: chain L residue 90 LYS Chi-restraints excluded: chain L residue 95 GLU Chi-restraints excluded: chain L residue 155 ARG Chi-restraints excluded: chain L residue 157 TYR Chi-restraints excluded: chain L residue 175 LEU Chi-restraints excluded: chain L residue 193 LEU Chi-restraints excluded: chain L residue 403 LEU Chi-restraints excluded: chain L residue 463 VAL Chi-restraints excluded: chain L residue 479 VAL Chi-restraints excluded: chain L residue 515 TYR Chi-restraints excluded: chain M residue 189 MET Chi-restraints excluded: chain M residue 303 ILE Chi-restraints excluded: chain M residue 523 VAL Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 68 THR Chi-restraints excluded: chain N residue 119 LEU Chi-restraints excluded: chain N residue 121 LEU Chi-restraints excluded: chain N residue 176 MET Chi-restraints excluded: chain N residue 209 VAL Chi-restraints excluded: chain N residue 275 VAL Chi-restraints excluded: chain N residue 303 ILE Chi-restraints excluded: chain N residue 308 LEU Chi-restraints excluded: chain N residue 310 LEU Chi-restraints excluded: chain N residue 315 LYS Chi-restraints excluded: chain N residue 437 THR Chi-restraints excluded: chain N residue 445 VAL Chi-restraints excluded: chain N residue 533 MET Chi-restraints excluded: chain N residue 585 LEU Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain O residue 72 THR Chi-restraints excluded: chain O residue 84 VAL Chi-restraints excluded: chain O residue 110 THR Chi-restraints excluded: chain O residue 204 HIS Chi-restraints excluded: chain O residue 236 VAL Chi-restraints excluded: chain O residue 392 VAL Chi-restraints excluded: chain O residue 418 LEU Chi-restraints excluded: chain O residue 570 GLN Chi-restraints excluded: chain O residue 588 VAL Chi-restraints excluded: chain P residue 95 GLU Chi-restraints excluded: chain P residue 175 LEU Chi-restraints excluded: chain P residue 181 GLN Chi-restraints excluded: chain P residue 196 LEU Chi-restraints excluded: chain P residue 209 VAL Chi-restraints excluded: chain P residue 247 ILE Chi-restraints excluded: chain P residue 417 HIS Chi-restraints excluded: chain P residue 484 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 848 random chunks: chunk 275 optimal weight: 10.0000 chunk 738 optimal weight: 5.9990 chunk 162 optimal weight: 50.0000 chunk 481 optimal weight: 0.9980 chunk 202 optimal weight: 40.0000 chunk 820 optimal weight: 0.6980 chunk 681 optimal weight: 6.9990 chunk 379 optimal weight: 7.9990 chunk 68 optimal weight: 0.5980 chunk 271 optimal weight: 9.9990 chunk 430 optimal weight: 3.9990 overall best weight: 2.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 311 HIS A 561 HIS ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 186 GLN ** C 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 140 GLN E 89 GLN E 423 HIS F 220 HIS ** F 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 229 ASN H 230 GLN H 401 ASN H 417 HIS I 144 GLN ** I 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 53 ASN J 181 GLN J 311 HIS ** J 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 77 GLN K 217 GLN ** K 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 401 ASN K 570 GLN ** L 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 116 ASN ** L 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 399 GLN ** L 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 97 ASN ** M 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 186 GLN ** M 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 154 ASN ** N 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 234 ASN N 383 GLN N 401 ASN ** N 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 69 ASN O 144 GLN ** O 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 311 HIS ** P 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 293 GLN ** P 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1163 moved from start: 0.6266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 68624 Z= 0.263 Angle : 0.728 17.394 93136 Z= 0.370 Chirality : 0.048 0.372 10816 Planarity : 0.006 0.126 11792 Dihedral : 7.010 59.863 10462 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.65 % Favored : 95.13 % Rotamer: Outliers : 2.39 % Allowed : 11.57 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.93 (0.09), residues: 8432 helix: 0.08 (0.13), residues: 1467 sheet: 0.02 (0.09), residues: 3420 loop : -1.52 (0.10), residues: 3545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP J 51 HIS 0.019 0.002 HIS L 204 PHE 0.051 0.002 PHE K 278 TYR 0.028 0.002 TYR M 382 ARG 0.014 0.001 ARG J 305 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16864 Ramachandran restraints generated. 8432 Oldfield, 0 Emsley, 8432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16864 Ramachandran restraints generated. 8432 Oldfield, 0 Emsley, 8432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 638 residues out of total 7504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 459 time to evaluate : 5.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.1166 (mtm) cc_final: 0.0028 (ptt) REVERT: A 503 LEU cc_start: 0.2028 (OUTLIER) cc_final: 0.1441 (mm) REVERT: B 142 LYS cc_start: 0.6536 (tptp) cc_final: 0.6336 (tptp) REVERT: B 488 MET cc_start: -0.4454 (mmt) cc_final: -0.4735 (mmt) REVERT: C 99 GLU cc_start: -0.4575 (OUTLIER) cc_final: -0.5713 (mm-30) REVERT: C 488 MET cc_start: -0.2690 (mtt) cc_final: -0.4024 (mmt) REVERT: D 63 MET cc_start: -0.5764 (mmt) cc_final: -0.6462 (mmt) REVERT: D 105 MET cc_start: 0.0729 (ppp) cc_final: 0.0216 (pmm) REVERT: E 105 MET cc_start: -0.3464 (ttm) cc_final: -0.3926 (mmp) REVERT: E 599 MET cc_start: 0.1170 (mmp) cc_final: -0.0385 (mmp) REVERT: F 59 MET cc_start: -0.0650 (mmm) cc_final: -0.1964 (mmt) REVERT: F 96 MET cc_start: 0.1738 (tmm) cc_final: -0.0294 (mmt) REVERT: F 593 TYR cc_start: -0.1515 (OUTLIER) cc_final: -0.1828 (t80) REVERT: G 176 MET cc_start: 0.6414 (mtt) cc_final: 0.6125 (mtt) REVERT: G 189 MET cc_start: 0.1282 (OUTLIER) cc_final: 0.0733 (mmm) REVERT: G 533 MET cc_start: -0.4901 (ptp) cc_final: -0.5855 (mmt) REVERT: H 104 TRP cc_start: 0.4103 (t60) cc_final: 0.2800 (m-90) REVERT: H 153 ARG cc_start: 0.3482 (ttt-90) cc_final: 0.1717 (mtp180) REVERT: H 176 MET cc_start: 0.7461 (mtt) cc_final: 0.6956 (mmp) REVERT: H 196 LEU cc_start: 0.8193 (mt) cc_final: 0.7536 (tp) REVERT: H 430 LEU cc_start: -0.0638 (OUTLIER) cc_final: -0.1831 (tp) REVERT: H 503 LEU cc_start: -0.3546 (OUTLIER) cc_final: -0.3748 (tp) REVERT: I 95 GLU cc_start: 0.0341 (OUTLIER) cc_final: -0.1062 (tt0) REVERT: I 96 MET cc_start: 0.1547 (tpt) cc_final: -0.0502 (tpt) REVERT: I 105 MET cc_start: -0.1112 (OUTLIER) cc_final: -0.2011 (mpp) REVERT: I 599 MET cc_start: 0.3670 (mmt) cc_final: 0.1550 (mtm) REVERT: J 95 GLU cc_start: 0.0750 (OUTLIER) cc_final: 0.0518 (mt-10) REVERT: J 222 ARG cc_start: -0.1091 (OUTLIER) cc_final: -0.4861 (ptm160) REVERT: J 599 MET cc_start: 0.0578 (mpt) cc_final: -0.2457 (mtt) REVERT: K 217 GLN cc_start: 0.1800 (OUTLIER) cc_final: 0.0214 (tm-30) REVERT: K 303 ILE cc_start: -0.1635 (OUTLIER) cc_final: -0.2127 (tt) REVERT: K 551 LEU cc_start: 0.0355 (mt) cc_final: 0.0102 (tp) REVERT: K 599 MET cc_start: 0.0953 (mmp) cc_final: -0.1243 (mtt) REVERT: L 85 TYR cc_start: 0.2881 (OUTLIER) cc_final: -0.0202 (p90) REVERT: L 95 GLU cc_start: 0.2848 (OUTLIER) cc_final: 0.1013 (mt-10) REVERT: L 96 MET cc_start: 0.2265 (mtm) cc_final: 0.0339 (tpt) REVERT: L 97 ASN cc_start: 0.3049 (OUTLIER) cc_final: 0.0170 (t0) REVERT: L 124 ARG cc_start: -0.0323 (ttp-170) cc_final: -0.3211 (ptt-90) REVERT: L 234 ASN cc_start: 0.0813 (OUTLIER) cc_final: 0.0612 (m-40) REVERT: L 303 ILE cc_start: 0.3180 (OUTLIER) cc_final: 0.2875 (tt) REVERT: M 259 GLN cc_start: 0.7497 (tm-30) cc_final: 0.6795 (tm-30) REVERT: M 399 GLN cc_start: 0.5015 (mp-120) cc_final: 0.4522 (mp-120) REVERT: M 533 MET cc_start: 0.0457 (tpt) cc_final: 0.0009 (tpt) REVERT: M 598 LEU cc_start: 0.4738 (mt) cc_final: 0.4357 (pp) REVERT: N 121 LEU cc_start: 0.4713 (OUTLIER) cc_final: 0.4362 (tp) REVERT: N 134 GLN cc_start: 0.6678 (tm-30) cc_final: 0.6242 (tm-30) REVERT: N 136 MET cc_start: 0.7481 (ttp) cc_final: 0.7085 (ttp) REVERT: N 176 MET cc_start: -0.2411 (mmt) cc_final: -0.2734 (tpp) REVERT: N 391 ASP cc_start: 0.5469 (p0) cc_final: 0.4936 (t70) REVERT: O 136 MET cc_start: 0.8760 (mpp) cc_final: 0.8233 (mpp) REVERT: O 179 CYS cc_start: 0.5644 (OUTLIER) cc_final: 0.5352 (m) REVERT: O 204 HIS cc_start: 0.2026 (OUTLIER) cc_final: -0.1488 (m-70) REVERT: O 431 GLU cc_start: 0.1429 (mm-30) cc_final: 0.0992 (mm-30) REVERT: O 488 MET cc_start: -0.1738 (tmt) cc_final: -0.2643 (ttm) REVERT: P 95 GLU cc_start: -0.0753 (OUTLIER) cc_final: -0.2504 (tt0) REVERT: P 96 MET cc_start: 0.2139 (mpp) cc_final: 0.1392 (ttt) REVERT: P 115 ILE cc_start: 0.6478 (mm) cc_final: 0.6036 (tp) REVERT: P 181 GLN cc_start: -0.6794 (OUTLIER) cc_final: -0.7820 (mt0) REVERT: P 418 LEU cc_start: 0.3449 (mt) cc_final: 0.2596 (mt) REVERT: P 533 MET cc_start: 0.6100 (mtp) cc_final: 0.5850 (ttt) outliers start: 179 outliers final: 111 residues processed: 600 average time/residue: 0.6748 time to fit residues: 708.2298 Evaluate side-chains 554 residues out of total 7504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 421 time to evaluate : 5.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 259 GLN Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 247 ILE Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 181 GLN Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain D residue 403 LEU Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain E residue 394 CYS Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 189 MET Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 247 ILE Chi-restraints excluded: chain F residue 593 TYR Chi-restraints excluded: chain G residue 39 LYS Chi-restraints excluded: chain G residue 189 MET Chi-restraints excluded: chain G residue 216 VAL Chi-restraints excluded: chain G residue 257 ILE Chi-restraints excluded: chain G residue 402 LEU Chi-restraints excluded: chain G residue 589 ARG Chi-restraints excluded: chain H residue 216 VAL Chi-restraints excluded: chain H residue 378 PHE Chi-restraints excluded: chain H residue 409 CYS Chi-restraints excluded: chain H residue 430 LEU Chi-restraints excluded: chain H residue 503 LEU Chi-restraints excluded: chain H residue 562 LEU Chi-restraints excluded: chain H residue 594 THR Chi-restraints excluded: chain I residue 95 GLU Chi-restraints excluded: chain I residue 105 MET Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 263 THR Chi-restraints excluded: chain I residue 463 VAL Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 87 ILE Chi-restraints excluded: chain J residue 95 GLU Chi-restraints excluded: chain J residue 162 THR Chi-restraints excluded: chain J residue 199 LEU Chi-restraints excluded: chain J residue 220 HIS Chi-restraints excluded: chain J residue 222 ARG Chi-restraints excluded: chain J residue 268 SER Chi-restraints excluded: chain J residue 430 LEU Chi-restraints excluded: chain J residue 448 ASP Chi-restraints excluded: chain J residue 523 VAL Chi-restraints excluded: chain J residue 533 MET Chi-restraints excluded: chain J residue 564 VAL Chi-restraints excluded: chain J residue 570 GLN Chi-restraints excluded: chain K residue 31 PHE Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 84 VAL Chi-restraints excluded: chain K residue 192 TYR Chi-restraints excluded: chain K residue 217 GLN Chi-restraints excluded: chain K residue 237 THR Chi-restraints excluded: chain K residue 303 ILE Chi-restraints excluded: chain K residue 430 LEU Chi-restraints excluded: chain K residue 512 SER Chi-restraints excluded: chain L residue 31 PHE Chi-restraints excluded: chain L residue 85 TYR Chi-restraints excluded: chain L residue 87 ILE Chi-restraints excluded: chain L residue 90 LYS Chi-restraints excluded: chain L residue 95 GLU Chi-restraints excluded: chain L residue 97 ASN Chi-restraints excluded: chain L residue 155 ARG Chi-restraints excluded: chain L residue 157 TYR Chi-restraints excluded: chain L residue 175 LEU Chi-restraints excluded: chain L residue 204 HIS Chi-restraints excluded: chain L residue 234 ASN Chi-restraints excluded: chain L residue 303 ILE Chi-restraints excluded: chain L residue 403 LEU Chi-restraints excluded: chain L residue 440 ILE Chi-restraints excluded: chain L residue 479 VAL Chi-restraints excluded: chain L residue 538 VAL Chi-restraints excluded: chain L residue 589 ARG Chi-restraints excluded: chain L residue 590 LEU Chi-restraints excluded: chain L residue 598 LEU Chi-restraints excluded: chain M residue 167 LEU Chi-restraints excluded: chain M residue 303 ILE Chi-restraints excluded: chain M residue 436 CYS Chi-restraints excluded: chain M residue 523 VAL Chi-restraints excluded: chain M residue 574 CYS Chi-restraints excluded: chain M residue 594 THR Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 58 ASP Chi-restraints excluded: chain N residue 68 THR Chi-restraints excluded: chain N residue 121 LEU Chi-restraints excluded: chain N residue 209 VAL Chi-restraints excluded: chain N residue 262 LEU Chi-restraints excluded: chain N residue 275 VAL Chi-restraints excluded: chain N residue 303 ILE Chi-restraints excluded: chain N residue 308 LEU Chi-restraints excluded: chain N residue 310 LEU Chi-restraints excluded: chain N residue 437 THR Chi-restraints excluded: chain N residue 445 VAL Chi-restraints excluded: chain N residue 533 MET Chi-restraints excluded: chain N residue 585 LEU Chi-restraints excluded: chain O residue 84 VAL Chi-restraints excluded: chain O residue 110 THR Chi-restraints excluded: chain O residue 179 CYS Chi-restraints excluded: chain O residue 204 HIS Chi-restraints excluded: chain O residue 206 ILE Chi-restraints excluded: chain O residue 308 LEU Chi-restraints excluded: chain O residue 376 PHE Chi-restraints excluded: chain O residue 392 VAL Chi-restraints excluded: chain O residue 418 LEU Chi-restraints excluded: chain O residue 588 VAL Chi-restraints excluded: chain P residue 95 GLU Chi-restraints excluded: chain P residue 141 VAL Chi-restraints excluded: chain P residue 175 LEU Chi-restraints excluded: chain P residue 181 GLN Chi-restraints excluded: chain P residue 196 LEU Chi-restraints excluded: chain P residue 209 VAL Chi-restraints excluded: chain P residue 247 ILE Chi-restraints excluded: chain P residue 338 VAL Chi-restraints excluded: chain P residue 423 HIS Chi-restraints excluded: chain P residue 484 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 848 random chunks: chunk 791 optimal weight: 10.0000 chunk 92 optimal weight: 50.0000 chunk 467 optimal weight: 30.0000 chunk 599 optimal weight: 1.9990 chunk 464 optimal weight: 2.9990 chunk 690 optimal weight: 1.9990 chunk 458 optimal weight: 0.0870 chunk 817 optimal weight: 10.0000 chunk 511 optimal weight: 0.8980 chunk 498 optimal weight: 20.0000 chunk 377 optimal weight: 8.9990 overall best weight: 1.5964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 GLN ** C 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 230 GLN ** F 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 200 ASN I 154 ASN ** I 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 561 HIS J 134 GLN J 276 GLN ** J 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 421 GLN K 490 ASN ** K 561 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 GLN ** L 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 186 GLN ** M 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 93 ASN ** N 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 560 GLN O 417 HIS P 234 ASN P 293 GLN ** P 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1138 moved from start: 0.6571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 68624 Z= 0.188 Angle : 0.622 14.578 93136 Z= 0.312 Chirality : 0.045 0.337 10816 Planarity : 0.005 0.066 11792 Dihedral : 6.531 59.324 10459 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.46 % Favored : 96.36 % Rotamer: Outliers : 2.07 % Allowed : 12.35 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.20 % 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: -0.79 (0.09), residues: 8432 helix: 0.38 (0.14), residues: 1397 sheet: 0.00 (0.09), residues: 3452 loop : -1.38 (0.10), residues: 3583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP L 51 HIS 0.012 0.001 HIS L 204 PHE 0.043 0.002 PHE J 476 TYR 0.028 0.002 TYR L 413 ARG 0.006 0.001 ARG P 124 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16864 Ramachandran restraints generated. 8432 Oldfield, 0 Emsley, 8432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16864 Ramachandran restraints generated. 8432 Oldfield, 0 Emsley, 8432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 586 residues out of total 7504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 431 time to evaluate : 5.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.1552 (mtm) cc_final: 0.0103 (ptt) REVERT: A 503 LEU cc_start: 0.1927 (OUTLIER) cc_final: 0.1306 (mm) REVERT: B 96 MET cc_start: -0.1905 (mpp) cc_final: -0.2193 (mpp) REVERT: B 176 MET cc_start: 0.5868 (mmp) cc_final: 0.5568 (mmp) REVERT: B 488 MET cc_start: -0.4420 (mmt) cc_final: -0.4796 (mmt) REVERT: C 99 GLU cc_start: -0.4523 (OUTLIER) cc_final: -0.5566 (mm-30) REVERT: C 189 MET cc_start: 0.7648 (mmp) cc_final: 0.7001 (mtt) REVERT: C 488 MET cc_start: -0.2756 (mtt) cc_final: -0.4090 (mmt) REVERT: D 63 MET cc_start: -0.5994 (mmt) cc_final: -0.6515 (mmt) REVERT: D 105 MET cc_start: 0.0903 (ppp) cc_final: 0.0396 (pmm) REVERT: E 105 MET cc_start: -0.3957 (ttm) cc_final: -0.4207 (mpp) REVERT: E 599 MET cc_start: 0.1030 (mmp) cc_final: -0.0213 (mmp) REVERT: F 59 MET cc_start: -0.0673 (mmm) cc_final: -0.1978 (mmt) REVERT: F 96 MET cc_start: 0.1675 (tmm) cc_final: -0.0303 (mmt) REVERT: F 593 TYR cc_start: -0.1586 (OUTLIER) cc_final: -0.1887 (t80) REVERT: G 176 MET cc_start: 0.6407 (mtt) cc_final: 0.6124 (mtt) REVERT: G 189 MET cc_start: 0.1425 (OUTLIER) cc_final: 0.0992 (mmm) REVERT: G 533 MET cc_start: -0.4940 (ptp) cc_final: -0.5873 (mmt) REVERT: H 95 GLU cc_start: 0.2114 (OUTLIER) cc_final: 0.1671 (mt-10) REVERT: H 104 TRP cc_start: 0.4287 (t60) cc_final: 0.3010 (m-90) REVERT: H 153 ARG cc_start: 0.3463 (ttt-90) cc_final: 0.1653 (mtp180) REVERT: H 176 MET cc_start: 0.7488 (mtt) cc_final: 0.7011 (mmp) REVERT: H 196 LEU cc_start: 0.7967 (mt) cc_final: 0.7699 (tp) REVERT: H 430 LEU cc_start: -0.0789 (OUTLIER) cc_final: -0.2013 (tp) REVERT: H 503 LEU cc_start: -0.3591 (OUTLIER) cc_final: -0.3887 (tp) REVERT: I 95 GLU cc_start: 0.0332 (OUTLIER) cc_final: -0.0966 (tt0) REVERT: I 96 MET cc_start: 0.1479 (tpt) cc_final: -0.0688 (tpt) REVERT: I 105 MET cc_start: -0.0994 (OUTLIER) cc_final: -0.1693 (mpp) REVERT: I 189 MET cc_start: 0.1395 (mmm) cc_final: 0.1154 (mmm) REVERT: I 522 SER cc_start: 0.5243 (p) cc_final: 0.5001 (m) REVERT: I 599 MET cc_start: 0.3490 (mmt) cc_final: 0.1486 (mtm) REVERT: J 63 MET cc_start: 0.0590 (mmt) cc_final: -0.1815 (mmm) REVERT: J 189 MET cc_start: 0.3686 (mmm) cc_final: 0.2408 (mmm) REVERT: J 222 ARG cc_start: -0.0884 (OUTLIER) cc_final: -0.3857 (ttt-90) REVERT: J 599 MET cc_start: 0.0576 (mpt) cc_final: -0.2629 (mtt) REVERT: K 217 GLN cc_start: 0.1298 (OUTLIER) cc_final: 0.0156 (tm-30) REVERT: K 303 ILE cc_start: -0.1574 (OUTLIER) cc_final: -0.1864 (tt) REVERT: K 551 LEU cc_start: 0.0637 (mt) cc_final: 0.0432 (tp) REVERT: K 599 MET cc_start: 0.0779 (mmp) cc_final: -0.1376 (mtt) REVERT: L 63 MET cc_start: 0.1218 (mmt) cc_final: 0.0231 (tpp) REVERT: L 85 TYR cc_start: 0.2704 (OUTLIER) cc_final: -0.0255 (p90) REVERT: L 87 ILE cc_start: 0.5528 (OUTLIER) cc_final: 0.4984 (tp) REVERT: L 95 GLU cc_start: 0.3092 (OUTLIER) cc_final: 0.0558 (tt0) REVERT: L 97 ASN cc_start: 0.2882 (OUTLIER) cc_final: 0.0577 (t0) REVERT: L 461 TRP cc_start: 0.4076 (p-90) cc_final: 0.3868 (p-90) REVERT: M 128 LYS cc_start: 0.5067 (tmmt) cc_final: 0.4602 (tmmt) REVERT: M 259 GLN cc_start: 0.7723 (tm-30) cc_final: 0.6869 (tm-30) REVERT: M 533 MET cc_start: 0.0634 (tpt) cc_final: 0.0324 (tpt) REVERT: M 598 LEU cc_start: 0.5142 (mt) cc_final: 0.4841 (pp) REVERT: N 121 LEU cc_start: 0.4487 (OUTLIER) cc_final: 0.4261 (tp) REVERT: N 134 GLN cc_start: 0.6843 (tm-30) cc_final: 0.6410 (tm-30) REVERT: N 136 MET cc_start: 0.7464 (ttp) cc_final: 0.7006 (ttp) REVERT: N 176 MET cc_start: -0.2492 (mmt) cc_final: -0.2706 (tpp) REVERT: N 233 GLN cc_start: 0.7501 (tt0) cc_final: 0.6856 (tm-30) REVERT: N 391 ASP cc_start: 0.5347 (p0) cc_final: 0.4835 (t70) REVERT: O 94 LEU cc_start: 0.0537 (OUTLIER) cc_final: -0.0299 (mt) REVERT: O 135 ARG cc_start: 0.7206 (ptt180) cc_final: 0.6886 (ptt180) REVERT: O 136 MET cc_start: 0.8603 (mpp) cc_final: 0.8314 (mpp) REVERT: O 204 HIS cc_start: 0.1773 (OUTLIER) cc_final: -0.1562 (m-70) REVERT: O 251 LYS cc_start: 0.1086 (OUTLIER) cc_final: -0.0534 (tptt) REVERT: O 488 MET cc_start: -0.1716 (tmt) cc_final: -0.2625 (ttm) REVERT: P 89 GLN cc_start: 0.0065 (OUTLIER) cc_final: -0.0815 (mt0) REVERT: P 95 GLU cc_start: -0.0153 (OUTLIER) cc_final: -0.2499 (tt0) REVERT: P 96 MET cc_start: 0.3001 (mpp) cc_final: 0.2217 (ttt) REVERT: P 115 ILE cc_start: 0.6477 (mm) cc_final: 0.6223 (tp) REVERT: P 181 GLN cc_start: -0.6491 (OUTLIER) cc_final: -0.7709 (mt0) REVERT: P 418 LEU cc_start: 0.3232 (mt) cc_final: 0.2530 (mt) REVERT: P 533 MET cc_start: 0.6099 (mtp) cc_final: 0.5837 (ttt) outliers start: 155 outliers final: 104 residues processed: 554 average time/residue: 0.6102 time to fit residues: 584.7422 Evaluate side-chains 538 residues out of total 7504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 411 time to evaluate : 5.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 259 GLN Chi-restraints excluded: chain A residue 341 TYR Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 247 ILE Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 181 GLN Chi-restraints excluded: chain D residue 403 LEU Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain E residue 394 CYS Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 189 MET Chi-restraints excluded: chain F residue 247 ILE Chi-restraints excluded: chain F residue 593 TYR Chi-restraints excluded: chain G residue 39 LYS Chi-restraints excluded: chain G residue 105 MET Chi-restraints excluded: chain G residue 189 MET Chi-restraints excluded: chain G residue 216 VAL Chi-restraints excluded: chain G residue 257 ILE Chi-restraints excluded: chain G residue 402 LEU Chi-restraints excluded: chain G residue 417 HIS Chi-restraints excluded: chain G residue 589 ARG Chi-restraints excluded: chain G residue 590 LEU Chi-restraints excluded: chain H residue 95 GLU Chi-restraints excluded: chain H residue 216 VAL Chi-restraints excluded: chain H residue 409 CYS Chi-restraints excluded: chain H residue 430 LEU Chi-restraints excluded: chain H residue 503 LEU Chi-restraints excluded: chain H residue 562 LEU Chi-restraints excluded: chain H residue 594 THR Chi-restraints excluded: chain I residue 95 GLU Chi-restraints excluded: chain I residue 105 MET Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 263 THR Chi-restraints excluded: chain I residue 463 VAL Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 162 THR Chi-restraints excluded: chain J residue 209 VAL Chi-restraints excluded: chain J residue 220 HIS Chi-restraints excluded: chain J residue 222 ARG Chi-restraints excluded: chain J residue 268 SER Chi-restraints excluded: chain J residue 430 LEU Chi-restraints excluded: chain J residue 523 VAL Chi-restraints excluded: chain J residue 570 GLN Chi-restraints excluded: chain K residue 44 GLU Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 159 VAL Chi-restraints excluded: chain K residue 192 TYR Chi-restraints excluded: chain K residue 197 LEU Chi-restraints excluded: chain K residue 217 GLN Chi-restraints excluded: chain K residue 218 GLU Chi-restraints excluded: chain K residue 293 GLN Chi-restraints excluded: chain K residue 303 ILE Chi-restraints excluded: chain K residue 430 LEU Chi-restraints excluded: chain K residue 441 PHE Chi-restraints excluded: chain K residue 512 SER Chi-restraints excluded: chain L residue 85 TYR Chi-restraints excluded: chain L residue 87 ILE Chi-restraints excluded: chain L residue 90 LYS Chi-restraints excluded: chain L residue 95 GLU Chi-restraints excluded: chain L residue 97 ASN Chi-restraints excluded: chain L residue 155 ARG Chi-restraints excluded: chain L residue 157 TYR Chi-restraints excluded: chain L residue 175 LEU Chi-restraints excluded: chain L residue 403 LEU Chi-restraints excluded: chain L residue 479 VAL Chi-restraints excluded: chain L residue 538 VAL Chi-restraints excluded: chain L residue 589 ARG Chi-restraints excluded: chain L residue 598 LEU Chi-restraints excluded: chain M residue 167 LEU Chi-restraints excluded: chain M residue 296 ILE Chi-restraints excluded: chain M residue 303 ILE Chi-restraints excluded: chain M residue 436 CYS Chi-restraints excluded: chain M residue 529 PHE Chi-restraints excluded: chain N residue 68 THR Chi-restraints excluded: chain N residue 87 ILE Chi-restraints excluded: chain N residue 95 GLU Chi-restraints excluded: chain N residue 105 MET Chi-restraints excluded: chain N residue 119 LEU Chi-restraints excluded: chain N residue 121 LEU Chi-restraints excluded: chain N residue 131 THR Chi-restraints excluded: chain N residue 209 VAL Chi-restraints excluded: chain N residue 262 LEU Chi-restraints excluded: chain N residue 275 VAL Chi-restraints excluded: chain N residue 303 ILE Chi-restraints excluded: chain N residue 308 LEU Chi-restraints excluded: chain N residue 310 LEU Chi-restraints excluded: chain N residue 437 THR Chi-restraints excluded: chain N residue 445 VAL Chi-restraints excluded: chain N residue 533 MET Chi-restraints excluded: chain N residue 585 LEU Chi-restraints excluded: chain O residue 84 VAL Chi-restraints excluded: chain O residue 94 LEU Chi-restraints excluded: chain O residue 110 THR Chi-restraints excluded: chain O residue 204 HIS Chi-restraints excluded: chain O residue 251 LYS Chi-restraints excluded: chain O residue 392 VAL Chi-restraints excluded: chain O residue 575 VAL Chi-restraints excluded: chain O residue 588 VAL Chi-restraints excluded: chain P residue 89 GLN Chi-restraints excluded: chain P residue 95 GLU Chi-restraints excluded: chain P residue 141 VAL Chi-restraints excluded: chain P residue 175 LEU Chi-restraints excluded: chain P residue 181 GLN Chi-restraints excluded: chain P residue 196 LEU Chi-restraints excluded: chain P residue 209 VAL Chi-restraints excluded: chain P residue 247 ILE Chi-restraints excluded: chain P residue 338 VAL Chi-restraints excluded: chain P residue 417 HIS Chi-restraints excluded: chain P residue 484 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 848 random chunks: chunk 505 optimal weight: 0.4980 chunk 326 optimal weight: 20.0000 chunk 488 optimal weight: 9.9990 chunk 246 optimal weight: 20.0000 chunk 160 optimal weight: 20.0000 chunk 158 optimal weight: 50.0000 chunk 519 optimal weight: 5.9990 chunk 556 optimal weight: 2.9990 chunk 404 optimal weight: 1.9990 chunk 76 optimal weight: 50.0000 chunk 642 optimal weight: 0.7980 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 ASN ** A 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 144 GLN B 108 GLN C 186 GLN ** C 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 217 GLN ** F 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 53 ASN H 417 HIS ** I 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 220 HIS ** K 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 560 GLN ** K 561 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 186 GLN M 234 ASN ** M 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 423 HIS M 471 ASN N 93 ASN ** N 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 383 GLN ** O 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1334 moved from start: 0.7434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 68624 Z= 0.263 Angle : 0.733 16.543 93136 Z= 0.370 Chirality : 0.048 0.399 10816 Planarity : 0.006 0.145 11792 Dihedral : 7.004 58.844 10458 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.47 % Favored : 94.35 % Rotamer: Outliers : 2.29 % Allowed : 12.45 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.02 (0.09), residues: 8432 helix: 0.37 (0.14), residues: 1363 sheet: -0.11 (0.09), residues: 3329 loop : -1.57 (0.10), residues: 3740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP L 51 HIS 0.019 0.002 HIS L 204 PHE 0.046 0.002 PHE N 278 TYR 0.029 0.002 TYR L 341 ARG 0.026 0.001 ARG H 305 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16864 Ramachandran restraints generated. 8432 Oldfield, 0 Emsley, 8432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16864 Ramachandran restraints generated. 8432 Oldfield, 0 Emsley, 8432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 653 residues out of total 7504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 481 time to evaluate : 6.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 MET cc_start: -0.3298 (mmt) cc_final: -0.4010 (mmt) REVERT: A 96 MET cc_start: 0.1362 (mtm) cc_final: -0.0065 (ptt) REVERT: A 431 GLU cc_start: 0.0377 (pp20) cc_final: 0.0066 (pp20) REVERT: A 503 LEU cc_start: 0.2038 (OUTLIER) cc_final: 0.1365 (mm) REVERT: A 533 MET cc_start: 0.6815 (ppp) cc_final: 0.6558 (ppp) REVERT: B 105 MET cc_start: 0.2929 (mmt) cc_final: 0.2477 (mmt) REVERT: B 209 VAL cc_start: -0.0438 (OUTLIER) cc_final: -0.1287 (p) REVERT: B 488 MET cc_start: -0.4255 (mmt) cc_final: -0.4594 (mmt) REVERT: C 488 MET cc_start: -0.2529 (mtt) cc_final: -0.3762 (mmt) REVERT: D 63 MET cc_start: -0.6002 (mmt) cc_final: -0.6638 (mmt) REVERT: D 105 MET cc_start: 0.1247 (ppp) cc_final: 0.0820 (pmm) REVERT: E 105 MET cc_start: -0.4153 (ttm) cc_final: -0.4364 (mmt) REVERT: E 599 MET cc_start: 0.1356 (mmp) cc_final: -0.0266 (mmp) REVERT: F 96 MET cc_start: 0.1702 (tmm) cc_final: -0.0119 (mmt) REVERT: G 176 MET cc_start: 0.6405 (mtt) cc_final: 0.6117 (mtt) REVERT: G 189 MET cc_start: 0.1565 (OUTLIER) cc_final: 0.1056 (mmm) REVERT: G 533 MET cc_start: -0.5306 (ptp) cc_final: -0.6299 (mmt) REVERT: H 95 GLU cc_start: 0.2222 (OUTLIER) cc_final: -0.0840 (tt0) REVERT: H 104 TRP cc_start: 0.3949 (t60) cc_final: 0.2724 (m-90) REVERT: H 176 MET cc_start: 0.7525 (mtt) cc_final: 0.6972 (mmp) REVERT: H 430 LEU cc_start: -0.0636 (OUTLIER) cc_final: -0.1853 (tp) REVERT: H 503 LEU cc_start: -0.3301 (OUTLIER) cc_final: -0.3628 (tp) REVERT: I 59 MET cc_start: -0.0021 (mmm) cc_final: -0.0344 (mtt) REVERT: I 95 GLU cc_start: 0.0927 (OUTLIER) cc_final: -0.0657 (tt0) REVERT: I 96 MET cc_start: 0.1557 (tpt) cc_final: -0.0453 (tpt) REVERT: I 105 MET cc_start: -0.1143 (OUTLIER) cc_final: -0.1548 (mpp) REVERT: I 522 SER cc_start: 0.5127 (p) cc_final: 0.4891 (m) REVERT: I 599 MET cc_start: 0.4112 (mmt) cc_final: 0.1663 (mtm) REVERT: J 186 GLN cc_start: 0.5485 (tt0) cc_final: 0.4797 (tp40) REVERT: J 222 ARG cc_start: -0.1115 (OUTLIER) cc_final: -0.4846 (ptm160) REVERT: J 599 MET cc_start: 0.0264 (mpt) cc_final: -0.3454 (mtt) REVERT: K 176 MET cc_start: 0.4794 (mmt) cc_final: 0.4589 (mmp) REVERT: K 551 LEU cc_start: 0.1131 (mt) cc_final: 0.0899 (tp) REVERT: K 599 MET cc_start: 0.0967 (mmp) cc_final: -0.1189 (mtt) REVERT: L 52 ASP cc_start: 0.6973 (t0) cc_final: 0.6634 (t0) REVERT: L 63 MET cc_start: 0.1413 (mmt) cc_final: 0.0658 (tpp) REVERT: L 85 TYR cc_start: 0.2902 (OUTLIER) cc_final: 0.2222 (p90) REVERT: L 97 ASN cc_start: 0.2816 (OUTLIER) cc_final: 0.0322 (t0) REVERT: L 124 ARG cc_start: 0.0403 (ttp-170) cc_final: -0.2509 (ptt-90) REVERT: L 234 ASN cc_start: 0.1787 (OUTLIER) cc_final: 0.1466 (m-40) REVERT: L 251 LYS cc_start: 0.7546 (tttt) cc_final: 0.7195 (tmtt) REVERT: L 272 ASN cc_start: -0.1371 (OUTLIER) cc_final: -0.3264 (t0) REVERT: M 96 MET cc_start: 0.3484 (mmt) cc_final: 0.3274 (mmt) REVERT: M 128 LYS cc_start: 0.5433 (tmmt) cc_final: 0.5077 (tmmt) REVERT: M 259 GLN cc_start: 0.7791 (tm-30) cc_final: 0.7391 (tm-30) REVERT: M 430 LEU cc_start: -0.3299 (OUTLIER) cc_final: -0.3522 (tp) REVERT: M 599 MET cc_start: 0.7986 (mmp) cc_final: 0.7615 (mmp) REVERT: N 112 SER cc_start: 0.8013 (m) cc_final: 0.7728 (t) REVERT: N 121 LEU cc_start: 0.4526 (OUTLIER) cc_final: 0.4310 (tp) REVERT: N 134 GLN cc_start: 0.6815 (tm-30) cc_final: 0.6353 (tm-30) REVERT: N 136 MET cc_start: 0.7642 (ttp) cc_final: 0.7168 (ttp) REVERT: N 233 GLN cc_start: 0.7573 (tt0) cc_final: 0.6798 (tm-30) REVERT: N 234 ASN cc_start: 0.7019 (m-40) cc_final: 0.6406 (t0) REVERT: N 391 ASP cc_start: 0.5457 (p0) cc_final: 0.4852 (t70) REVERT: N 599 MET cc_start: -0.2520 (ptt) cc_final: -0.3220 (tpt) REVERT: O 85 TYR cc_start: 0.5513 (p90) cc_final: 0.3308 (p90) REVERT: O 96 MET cc_start: 0.1410 (ptt) cc_final: -0.0654 (mtp) REVERT: O 108 GLN cc_start: 0.8634 (tm-30) cc_final: 0.8074 (tm-30) REVERT: O 226 LEU cc_start: 0.3757 (OUTLIER) cc_final: 0.2956 (mp) REVERT: O 251 LYS cc_start: 0.0122 (OUTLIER) cc_final: -0.1660 (tptt) REVERT: O 431 GLU cc_start: 0.1331 (mm-30) cc_final: 0.0897 (mm-30) REVERT: O 488 MET cc_start: -0.1700 (tmt) cc_final: -0.2530 (ttm) REVERT: P 89 GLN cc_start: 0.0898 (OUTLIER) cc_final: -0.0712 (mm-40) REVERT: P 95 GLU cc_start: 0.0887 (OUTLIER) cc_final: -0.2466 (tm-30) REVERT: P 118 GLU cc_start: 0.2188 (mp0) cc_final: 0.1432 (mp0) REVERT: P 140 GLN cc_start: 0.6771 (tp40) cc_final: 0.6555 (mp10) REVERT: P 181 GLN cc_start: -0.6736 (OUTLIER) cc_final: -0.7899 (mt0) REVERT: P 196 LEU cc_start: 0.0672 (OUTLIER) cc_final: 0.0350 (tp) REVERT: P 418 LEU cc_start: 0.3648 (mt) cc_final: 0.2864 (mt) REVERT: P 533 MET cc_start: 0.6124 (mtp) cc_final: 0.5853 (ttt) outliers start: 172 outliers final: 115 residues processed: 617 average time/residue: 0.6298 time to fit residues: 678.8107 Evaluate side-chains 587 residues out of total 7504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 451 time to evaluate : 5.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 259 GLN Chi-restraints excluded: chain A residue 341 TYR Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 108 GLN Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 247 ILE Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 181 GLN Chi-restraints excluded: chain D residue 403 LEU Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain E residue 394 CYS Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 189 MET Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 247 ILE Chi-restraints excluded: chain F residue 533 MET Chi-restraints excluded: chain G residue 39 LYS Chi-restraints excluded: chain G residue 189 MET Chi-restraints excluded: chain G residue 216 VAL Chi-restraints excluded: chain G residue 257 ILE Chi-restraints excluded: chain G residue 589 ARG Chi-restraints excluded: chain G residue 590 LEU Chi-restraints excluded: chain H residue 95 GLU Chi-restraints excluded: chain H residue 216 VAL Chi-restraints excluded: chain H residue 409 CYS Chi-restraints excluded: chain H residue 430 LEU Chi-restraints excluded: chain H residue 503 LEU Chi-restraints excluded: chain H residue 508 LYS Chi-restraints excluded: chain H residue 562 LEU Chi-restraints excluded: chain I residue 95 GLU Chi-restraints excluded: chain I residue 104 TRP Chi-restraints excluded: chain I residue 105 MET Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 263 THR Chi-restraints excluded: chain I residue 452 VAL Chi-restraints excluded: chain I residue 463 VAL Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 162 THR Chi-restraints excluded: chain J residue 220 HIS Chi-restraints excluded: chain J residue 222 ARG Chi-restraints excluded: chain J residue 268 SER Chi-restraints excluded: chain J residue 430 LEU Chi-restraints excluded: chain J residue 523 VAL Chi-restraints excluded: chain J residue 533 MET Chi-restraints excluded: chain J residue 564 VAL Chi-restraints excluded: chain J residue 570 GLN Chi-restraints excluded: chain K residue 44 GLU Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 94 LEU Chi-restraints excluded: chain K residue 159 VAL Chi-restraints excluded: chain K residue 165 SER Chi-restraints excluded: chain K residue 192 TYR Chi-restraints excluded: chain K residue 278 PHE Chi-restraints excluded: chain K residue 293 GLN Chi-restraints excluded: chain K residue 299 HIS Chi-restraints excluded: chain K residue 430 LEU Chi-restraints excluded: chain K residue 512 SER Chi-restraints excluded: chain L residue 85 TYR Chi-restraints excluded: chain L residue 90 LYS Chi-restraints excluded: chain L residue 95 GLU Chi-restraints excluded: chain L residue 97 ASN Chi-restraints excluded: chain L residue 155 ARG Chi-restraints excluded: chain L residue 157 TYR Chi-restraints excluded: chain L residue 175 LEU Chi-restraints excluded: chain L residue 193 LEU Chi-restraints excluded: chain L residue 204 HIS Chi-restraints excluded: chain L residue 234 ASN Chi-restraints excluded: chain L residue 272 ASN Chi-restraints excluded: chain L residue 403 LEU Chi-restraints excluded: chain L residue 463 VAL Chi-restraints excluded: chain L residue 479 VAL Chi-restraints excluded: chain L residue 538 VAL Chi-restraints excluded: chain L residue 598 LEU Chi-restraints excluded: chain M residue 167 LEU Chi-restraints excluded: chain M residue 296 ILE Chi-restraints excluded: chain M residue 301 VAL Chi-restraints excluded: chain M residue 303 ILE Chi-restraints excluded: chain M residue 421 GLN Chi-restraints excluded: chain M residue 430 LEU Chi-restraints excluded: chain M residue 436 CYS Chi-restraints excluded: chain M residue 529 PHE Chi-restraints excluded: chain M residue 539 ASN Chi-restraints excluded: chain M residue 574 CYS Chi-restraints excluded: chain N residue 58 ASP Chi-restraints excluded: chain N residue 68 THR Chi-restraints excluded: chain N residue 87 ILE Chi-restraints excluded: chain N residue 95 GLU Chi-restraints excluded: chain N residue 105 MET Chi-restraints excluded: chain N residue 121 LEU Chi-restraints excluded: chain N residue 131 THR Chi-restraints excluded: chain N residue 209 VAL Chi-restraints excluded: chain N residue 262 LEU Chi-restraints excluded: chain N residue 263 THR Chi-restraints excluded: chain N residue 292 TRP Chi-restraints excluded: chain N residue 303 ILE Chi-restraints excluded: chain N residue 308 LEU Chi-restraints excluded: chain N residue 310 LEU Chi-restraints excluded: chain N residue 437 THR Chi-restraints excluded: chain N residue 445 VAL Chi-restraints excluded: chain N residue 533 MET Chi-restraints excluded: chain N residue 585 LEU Chi-restraints excluded: chain O residue 84 VAL Chi-restraints excluded: chain O residue 110 THR Chi-restraints excluded: chain O residue 156 ILE Chi-restraints excluded: chain O residue 204 HIS Chi-restraints excluded: chain O residue 206 ILE Chi-restraints excluded: chain O residue 226 LEU Chi-restraints excluded: chain O residue 251 LYS Chi-restraints excluded: chain O residue 259 GLN Chi-restraints excluded: chain O residue 392 VAL Chi-restraints excluded: chain O residue 575 VAL Chi-restraints excluded: chain O residue 588 VAL Chi-restraints excluded: chain P residue 89 GLN Chi-restraints excluded: chain P residue 95 GLU Chi-restraints excluded: chain P residue 175 LEU Chi-restraints excluded: chain P residue 181 GLN Chi-restraints excluded: chain P residue 196 LEU Chi-restraints excluded: chain P residue 209 VAL Chi-restraints excluded: chain P residue 247 ILE Chi-restraints excluded: chain P residue 484 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 848 random chunks: chunk 743 optimal weight: 0.8980 chunk 783 optimal weight: 9.9990 chunk 714 optimal weight: 0.5980 chunk 761 optimal weight: 0.9980 chunk 782 optimal weight: 3.9990 chunk 458 optimal weight: 10.0000 chunk 331 optimal weight: 7.9990 chunk 598 optimal weight: 8.9990 chunk 233 optimal weight: 20.0000 chunk 688 optimal weight: 0.0770 chunk 720 optimal weight: 0.7980 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 144 GLN B 108 GLN B 204 HIS C 234 ASN ** C 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 53 ASN H 231 ASN H 417 HIS I 97 ASN ** I 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 272 ASN J 134 GLN J 154 ASN ** J 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 561 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 144 GLN ** L 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 259 GLN ** P 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1211 moved from start: 0.7440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.079 68624 Z= 0.157 Angle : 0.598 13.084 93136 Z= 0.299 Chirality : 0.044 0.352 10816 Planarity : 0.005 0.064 11792 Dihedral : 6.496 59.488 10458 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.33 % Favored : 96.49 % Rotamer: Outliers : 1.73 % Allowed : 13.35 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.20 % 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 (0.09), residues: 8432 helix: 0.49 (0.14), residues: 1393 sheet: -0.09 (0.09), residues: 3414 loop : -1.41 (0.10), residues: 3625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP L 51 HIS 0.010 0.001 HIS L 204 PHE 0.037 0.001 PHE K 476 TYR 0.028 0.001 TYR D 498 ARG 0.008 0.000 ARG J 305 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16864 Ramachandran restraints generated. 8432 Oldfield, 0 Emsley, 8432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16864 Ramachandran restraints generated. 8432 Oldfield, 0 Emsley, 8432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 591 residues out of total 7504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 461 time to evaluate : 5.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.1552 (mtm) cc_final: -0.0089 (ptt) REVERT: A 431 GLU cc_start: 0.0552 (pp20) cc_final: 0.0308 (pp20) REVERT: A 503 LEU cc_start: 0.2006 (OUTLIER) cc_final: 0.1372 (mm) REVERT: B 209 VAL cc_start: -0.0653 (OUTLIER) cc_final: -0.1164 (p) REVERT: B 488 MET cc_start: -0.4265 (mmt) cc_final: -0.4573 (mmt) REVERT: C 488 MET cc_start: -0.2778 (mtt) cc_final: -0.3983 (mmt) REVERT: D 63 MET cc_start: -0.6070 (mmt) cc_final: -0.6635 (mmt) REVERT: D 105 MET cc_start: 0.1202 (ppp) cc_final: 0.0482 (pmm) REVERT: E 105 MET cc_start: -0.4251 (ttm) cc_final: -0.4464 (mmt) REVERT: E 599 MET cc_start: 0.1281 (mmp) cc_final: -0.0301 (mmp) REVERT: F 96 MET cc_start: 0.1613 (tmm) cc_final: -0.0137 (mmt) REVERT: G 176 MET cc_start: 0.6438 (mtt) cc_final: 0.6157 (mtt) REVERT: G 189 MET cc_start: 0.1471 (OUTLIER) cc_final: 0.0959 (mmm) REVERT: G 533 MET cc_start: -0.5267 (ptp) cc_final: -0.6205 (mmm) REVERT: H 95 GLU cc_start: 0.2159 (OUTLIER) cc_final: -0.0781 (tt0) REVERT: H 104 TRP cc_start: 0.3831 (t60) cc_final: 0.2720 (m-90) REVERT: H 176 MET cc_start: 0.7531 (mtt) cc_final: 0.6999 (mmp) REVERT: H 430 LEU cc_start: -0.0944 (OUTLIER) cc_final: -0.1860 (tp) REVERT: H 503 LEU cc_start: -0.3320 (OUTLIER) cc_final: -0.3596 (tp) REVERT: I 96 MET cc_start: 0.0942 (tpt) cc_final: -0.0926 (tpt) REVERT: I 105 MET cc_start: -0.0753 (OUTLIER) cc_final: -0.1173 (mpp) REVERT: I 522 SER cc_start: 0.5213 (p) cc_final: 0.4942 (m) REVERT: I 599 MET cc_start: 0.3402 (mmt) cc_final: 0.1520 (mtm) REVERT: J 136 MET cc_start: 0.5547 (mmp) cc_final: 0.5098 (tpt) REVERT: J 222 ARG cc_start: -0.0614 (OUTLIER) cc_final: -0.3894 (ttt-90) REVERT: J 599 MET cc_start: 0.0273 (mpt) cc_final: -0.2911 (mtt) REVERT: K 551 LEU cc_start: 0.1354 (mt) cc_final: 0.1116 (tp) REVERT: K 599 MET cc_start: 0.0810 (mmp) cc_final: -0.1308 (mtt) REVERT: L 63 MET cc_start: 0.1161 (mmt) cc_final: 0.0099 (tpp) REVERT: L 124 ARG cc_start: 0.0364 (ttp-170) cc_final: -0.2488 (ptt-90) REVERT: L 161 THR cc_start: 0.2078 (p) cc_final: 0.1694 (p) REVERT: M 51 TRP cc_start: 0.4419 (t-100) cc_final: 0.4193 (t-100) REVERT: M 96 MET cc_start: 0.3466 (mmt) cc_final: 0.3264 (mmt) REVERT: M 128 LYS cc_start: 0.5463 (tmmt) cc_final: 0.5171 (tmmt) REVERT: M 130 SER cc_start: 0.7622 (m) cc_final: 0.6834 (p) REVERT: M 259 GLN cc_start: 0.7822 (tm-30) cc_final: 0.7450 (tm-30) REVERT: M 430 LEU cc_start: -0.3265 (OUTLIER) cc_final: -0.3481 (tp) REVERT: N 121 LEU cc_start: 0.4528 (OUTLIER) cc_final: 0.4327 (tp) REVERT: N 136 MET cc_start: 0.7397 (ttp) cc_final: 0.6993 (ttp) REVERT: N 176 MET cc_start: 0.1903 (tpt) cc_final: 0.1657 (ppp) REVERT: N 234 ASN cc_start: 0.6914 (m-40) cc_final: 0.6154 (t0) REVERT: N 391 ASP cc_start: 0.5316 (p0) cc_final: 0.4668 (t70) REVERT: N 520 LYS cc_start: 0.3933 (tptp) cc_final: 0.3375 (mtpt) REVERT: N 599 MET cc_start: -0.2544 (ptt) cc_final: -0.3028 (tpt) REVERT: O 63 MET cc_start: 0.1917 (tpp) cc_final: 0.1102 (ttm) REVERT: O 96 MET cc_start: 0.0950 (ptt) cc_final: -0.0490 (mtp) REVERT: O 108 GLN cc_start: 0.8600 (tm-30) cc_final: 0.8126 (tm-30) REVERT: O 136 MET cc_start: 0.8237 (mpp) cc_final: 0.5977 (tmm) REVERT: O 204 HIS cc_start: 0.2102 (OUTLIER) cc_final: -0.1176 (m-70) REVERT: O 251 LYS cc_start: 0.0602 (OUTLIER) cc_final: -0.0596 (tptt) REVERT: O 488 MET cc_start: -0.1651 (tmt) cc_final: -0.2335 (ttm) REVERT: O 533 MET cc_start: -0.0766 (mpp) cc_final: -0.1035 (tpp) REVERT: P 95 GLU cc_start: 0.0960 (OUTLIER) cc_final: -0.0707 (mt-10) REVERT: P 118 GLU cc_start: 0.2157 (mp0) cc_final: 0.1570 (mp0) REVERT: P 181 GLN cc_start: -0.6289 (OUTLIER) cc_final: -0.7519 (mt0) REVERT: P 196 LEU cc_start: 0.0699 (OUTLIER) cc_final: 0.0413 (tp) REVERT: P 533 MET cc_start: 0.6070 (mtp) cc_final: 0.5799 (ttt) outliers start: 130 outliers final: 91 residues processed: 565 average time/residue: 0.6313 time to fit residues: 616.7288 Evaluate side-chains 545 residues out of total 7504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 439 time to evaluate : 5.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 259 GLN Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 341 TYR Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 108 GLN Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 247 ILE Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 181 GLN Chi-restraints excluded: chain D residue 403 LEU Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain E residue 394 CYS Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 189 MET Chi-restraints excluded: chain F residue 225 PHE Chi-restraints excluded: chain F residue 247 ILE Chi-restraints excluded: chain F residue 533 MET Chi-restraints excluded: chain G residue 39 LYS Chi-restraints excluded: chain G residue 189 MET Chi-restraints excluded: chain G residue 216 VAL Chi-restraints excluded: chain G residue 257 ILE Chi-restraints excluded: chain G residue 402 LEU Chi-restraints excluded: chain G residue 589 ARG Chi-restraints excluded: chain G residue 590 LEU Chi-restraints excluded: chain H residue 95 GLU Chi-restraints excluded: chain H residue 216 VAL Chi-restraints excluded: chain H residue 409 CYS Chi-restraints excluded: chain H residue 430 LEU Chi-restraints excluded: chain H residue 503 LEU Chi-restraints excluded: chain H residue 562 LEU Chi-restraints excluded: chain I residue 105 MET Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 209 VAL Chi-restraints excluded: chain J residue 162 THR Chi-restraints excluded: chain J residue 209 VAL Chi-restraints excluded: chain J residue 220 HIS Chi-restraints excluded: chain J residue 222 ARG Chi-restraints excluded: chain J residue 268 SER Chi-restraints excluded: chain J residue 523 VAL Chi-restraints excluded: chain J residue 570 GLN Chi-restraints excluded: chain K residue 44 GLU Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 159 VAL Chi-restraints excluded: chain K residue 192 TYR Chi-restraints excluded: chain K residue 197 LEU Chi-restraints excluded: chain K residue 293 GLN Chi-restraints excluded: chain K residue 430 LEU Chi-restraints excluded: chain K residue 512 SER Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 90 LYS Chi-restraints excluded: chain L residue 95 GLU Chi-restraints excluded: chain L residue 97 ASN Chi-restraints excluded: chain L residue 155 ARG Chi-restraints excluded: chain L residue 157 TYR Chi-restraints excluded: chain L residue 175 LEU Chi-restraints excluded: chain L residue 193 LEU Chi-restraints excluded: chain L residue 403 LEU Chi-restraints excluded: chain L residue 479 VAL Chi-restraints excluded: chain L residue 598 LEU Chi-restraints excluded: chain M residue 167 LEU Chi-restraints excluded: chain M residue 301 VAL Chi-restraints excluded: chain M residue 430 LEU Chi-restraints excluded: chain M residue 436 CYS Chi-restraints excluded: chain M residue 529 PHE Chi-restraints excluded: chain N residue 58 ASP Chi-restraints excluded: chain N residue 121 LEU Chi-restraints excluded: chain N residue 131 THR Chi-restraints excluded: chain N residue 209 VAL Chi-restraints excluded: chain N residue 262 LEU Chi-restraints excluded: chain N residue 263 THR Chi-restraints excluded: chain N residue 292 TRP Chi-restraints excluded: chain N residue 303 ILE Chi-restraints excluded: chain N residue 437 THR Chi-restraints excluded: chain N residue 445 VAL Chi-restraints excluded: chain N residue 533 MET Chi-restraints excluded: chain O residue 84 VAL Chi-restraints excluded: chain O residue 110 THR Chi-restraints excluded: chain O residue 204 HIS Chi-restraints excluded: chain O residue 206 ILE Chi-restraints excluded: chain O residue 251 LYS Chi-restraints excluded: chain O residue 259 GLN Chi-restraints excluded: chain O residue 392 VAL Chi-restraints excluded: chain O residue 575 VAL Chi-restraints excluded: chain O residue 588 VAL Chi-restraints excluded: chain P residue 95 GLU Chi-restraints excluded: chain P residue 175 LEU Chi-restraints excluded: chain P residue 181 GLN Chi-restraints excluded: chain P residue 196 LEU Chi-restraints excluded: chain P residue 209 VAL Chi-restraints excluded: chain P residue 247 ILE Chi-restraints excluded: chain P residue 484 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 848 random chunks: chunk 758 optimal weight: 0.6980 chunk 500 optimal weight: 10.0000 chunk 805 optimal weight: 6.9990 chunk 491 optimal weight: 6.9990 chunk 382 optimal weight: 0.9980 chunk 559 optimal weight: 1.9990 chunk 844 optimal weight: 6.9990 chunk 777 optimal weight: 6.9990 chunk 672 optimal weight: 6.9990 chunk 69 optimal weight: 4.9990 chunk 519 optimal weight: 3.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 144 GLN A 217 GLN A 299 HIS B 108 GLN B 154 ASN C 570 GLN E 490 ASN ** F 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 53 ASN H 144 GLN H 417 HIS ** I 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 423 HIS J 276 GLN ** J 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 561 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 561 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 220 HIS ** M 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 298 ASN ** N 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 204 HIS ** O 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 311 HIS ** P 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 560 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1446 moved from start: 0.8267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.237 68624 Z= 0.262 Angle : 0.750 15.544 93136 Z= 0.381 Chirality : 0.049 0.444 10816 Planarity : 0.006 0.131 11792 Dihedral : 7.050 59.476 10456 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 15.14 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.21 % Favored : 93.62 % Rotamer: Outliers : 1.80 % Allowed : 13.53 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.13 (0.09), residues: 8432 helix: 0.38 (0.14), residues: 1355 sheet: -0.24 (0.09), residues: 3340 loop : -1.62 (0.10), residues: 3737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.003 TRP K 461 HIS 0.019 0.002 HIS L 204 PHE 0.038 0.002 PHE N 278 TYR 0.058 0.002 TYR K 413 ARG 0.011 0.001 ARG B 135 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16864 Ramachandran restraints generated. 8432 Oldfield, 0 Emsley, 8432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16864 Ramachandran restraints generated. 8432 Oldfield, 0 Emsley, 8432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 612 residues out of total 7504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 477 time to evaluate : 5.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 MET cc_start: -0.3319 (mmt) cc_final: -0.4125 (mmt) REVERT: A 96 MET cc_start: 0.1363 (mtm) cc_final: 0.0017 (ptt) REVERT: A 265 ASP cc_start: 0.4006 (p0) cc_final: 0.3663 (p0) REVERT: A 431 GLU cc_start: 0.0282 (pp20) cc_final: 0.0060 (pp20) REVERT: A 503 LEU cc_start: 0.2099 (OUTLIER) cc_final: 0.1399 (mm) REVERT: A 599 MET cc_start: -0.2441 (pmm) cc_final: -0.5060 (ptt) REVERT: B 209 VAL cc_start: -0.0261 (OUTLIER) cc_final: -0.0859 (p) REVERT: B 488 MET cc_start: -0.4055 (mmt) cc_final: -0.4382 (mmt) REVERT: C 283 PHE cc_start: -0.0855 (t80) cc_final: -0.1465 (t80) REVERT: D 63 MET cc_start: -0.6005 (mmt) cc_final: -0.6548 (mmt) REVERT: D 488 MET cc_start: 0.6018 (ppp) cc_final: 0.5521 (pmm) REVERT: E 105 MET cc_start: -0.4132 (ttm) cc_final: -0.4362 (mmt) REVERT: E 599 MET cc_start: 0.1314 (mmp) cc_final: -0.0324 (mmp) REVERT: F 96 MET cc_start: 0.1729 (tmm) cc_final: -0.0126 (mmt) REVERT: G 176 MET cc_start: 0.6465 (mtt) cc_final: 0.6158 (mtt) REVERT: G 189 MET cc_start: 0.1637 (OUTLIER) cc_final: 0.1153 (mmm) REVERT: G 533 MET cc_start: -0.5462 (ptp) cc_final: -0.6384 (mmm) REVERT: H 95 GLU cc_start: 0.2148 (OUTLIER) cc_final: -0.0647 (tt0) REVERT: H 104 TRP cc_start: 0.3675 (t60) cc_final: 0.2621 (m-90) REVERT: H 176 MET cc_start: 0.7558 (mtt) cc_final: 0.7009 (mmp) REVERT: H 430 LEU cc_start: -0.0813 (OUTLIER) cc_final: -0.1705 (tp) REVERT: H 503 LEU cc_start: -0.3018 (OUTLIER) cc_final: -0.3318 (tp) REVERT: H 589 ARG cc_start: 0.3493 (tpm170) cc_final: 0.2798 (ptm160) REVERT: I 96 MET cc_start: 0.1337 (tpt) cc_final: -0.0577 (tpt) REVERT: I 391 ASP cc_start: 0.0307 (p0) cc_final: -0.1424 (t70) REVERT: I 599 MET cc_start: 0.3235 (mmt) cc_final: 0.1129 (mtm) REVERT: J 55 ARG cc_start: 0.3660 (mpt90) cc_final: 0.3013 (mtt90) REVERT: J 136 MET cc_start: 0.5373 (mmp) cc_final: 0.4920 (tpt) REVERT: J 222 ARG cc_start: -0.0928 (OUTLIER) cc_final: -0.4677 (ptm160) REVERT: J 429 ARG cc_start: -0.2035 (ttm170) cc_final: -0.3575 (tpt170) REVERT: J 599 MET cc_start: 0.0095 (mpt) cc_final: -0.3368 (mtm) REVERT: K 456 GLU cc_start: -0.0746 (pt0) cc_final: -0.1224 (tp30) REVERT: K 599 MET cc_start: 0.1220 (mmp) cc_final: -0.0959 (mtt) REVERT: L 52 ASP cc_start: 0.6661 (t0) cc_final: 0.6405 (t70) REVERT: L 63 MET cc_start: 0.1337 (mmt) cc_final: 0.0377 (tpp) REVERT: L 85 TYR cc_start: 0.2438 (OUTLIER) cc_final: 0.1460 (p90) REVERT: L 124 ARG cc_start: 0.1420 (ttp-170) cc_final: -0.1655 (ptt-90) REVERT: L 251 LYS cc_start: 0.7401 (tttt) cc_final: 0.7034 (tppt) REVERT: M 73 THR cc_start: -0.3112 (OUTLIER) cc_final: -0.3331 (p) REVERT: M 114 SER cc_start: 0.7747 (m) cc_final: 0.7140 (t) REVERT: M 128 LYS cc_start: 0.5937 (tmmt) cc_final: 0.5573 (tmmt) REVERT: M 130 SER cc_start: 0.7695 (m) cc_final: 0.6833 (p) REVERT: M 186 GLN cc_start: 0.3532 (tt0) cc_final: 0.3325 (mt0) REVERT: M 259 GLN cc_start: 0.7635 (tm-30) cc_final: 0.7256 (tm-30) REVERT: M 274 ARG cc_start: 0.1418 (OUTLIER) cc_final: -0.0317 (ttp-170) REVERT: M 430 LEU cc_start: -0.2899 (OUTLIER) cc_final: -0.3154 (tp) REVERT: M 599 MET cc_start: 0.7979 (mmp) cc_final: 0.7749 (mmp) REVERT: N 59 MET cc_start: 0.3592 (tpt) cc_final: 0.2756 (tpp) REVERT: N 108 GLN cc_start: 0.6740 (mt0) cc_final: 0.5839 (mp10) REVERT: N 121 LEU cc_start: 0.5001 (OUTLIER) cc_final: 0.4733 (tp) REVERT: N 176 MET cc_start: 0.2328 (tpt) cc_final: 0.1883 (ppp) REVERT: N 233 GLN cc_start: 0.7450 (tt0) cc_final: 0.6822 (tm-30) REVERT: N 234 ASN cc_start: 0.7008 (m-40) cc_final: 0.6431 (t0) REVERT: N 391 ASP cc_start: 0.5346 (p0) cc_final: 0.4649 (t70) REVERT: N 399 GLN cc_start: 0.3944 (tp40) cc_final: 0.3406 (tp40) REVERT: N 520 LYS cc_start: 0.4078 (tptp) cc_final: 0.3421 (mmmm) REVERT: O 85 TYR cc_start: 0.5718 (p90) cc_final: 0.3788 (p90) REVERT: O 96 MET cc_start: 0.2065 (ptt) cc_final: 0.0074 (mtp) REVERT: O 108 GLN cc_start: 0.8817 (tm-30) cc_final: 0.8149 (tm-30) REVERT: O 136 MET cc_start: 0.8170 (mpp) cc_final: 0.7519 (mpp) REVERT: O 176 MET cc_start: 0.3445 (mtp) cc_final: 0.3238 (mtp) REVERT: O 204 HIS cc_start: 0.2636 (OUTLIER) cc_final: -0.1174 (m-70) REVERT: O 251 LYS cc_start: 0.0507 (OUTLIER) cc_final: -0.0628 (tptt) REVERT: O 431 GLU cc_start: 0.1291 (mm-30) cc_final: 0.1083 (mm-30) REVERT: O 488 MET cc_start: -0.1503 (tmt) cc_final: -0.2357 (ttm) REVERT: O 533 MET cc_start: -0.0689 (mpp) cc_final: -0.0970 (tpp) REVERT: P 96 MET cc_start: 0.4886 (mpp) cc_final: 0.4598 (ttm) REVERT: P 118 GLU cc_start: 0.2131 (mp0) cc_final: 0.1524 (mp0) REVERT: P 181 GLN cc_start: -0.6369 (OUTLIER) cc_final: -0.7767 (mt0) REVERT: P 196 LEU cc_start: 0.0568 (OUTLIER) cc_final: 0.0315 (tp) REVERT: P 533 MET cc_start: 0.6121 (mtp) cc_final: 0.5864 (ttt) outliers start: 135 outliers final: 98 residues processed: 582 average time/residue: 0.6338 time to fit residues: 638.1375 Evaluate side-chains 572 residues out of total 7504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 458 time to evaluate : 5.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 108 GLN Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 247 ILE Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 181 GLN Chi-restraints excluded: chain D residue 403 LEU Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain E residue 394 CYS Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 189 MET Chi-restraints excluded: chain F residue 225 PHE Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 247 ILE Chi-restraints excluded: chain F residue 533 MET Chi-restraints excluded: chain G residue 39 LYS Chi-restraints excluded: chain G residue 189 MET Chi-restraints excluded: chain G residue 216 VAL Chi-restraints excluded: chain G residue 257 ILE Chi-restraints excluded: chain G residue 589 ARG Chi-restraints excluded: chain G residue 590 LEU Chi-restraints excluded: chain H residue 95 GLU Chi-restraints excluded: chain H residue 216 VAL Chi-restraints excluded: chain H residue 409 CYS Chi-restraints excluded: chain H residue 430 LEU Chi-restraints excluded: chain H residue 503 LEU Chi-restraints excluded: chain H residue 562 LEU Chi-restraints excluded: chain I residue 104 TRP Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 209 VAL Chi-restraints excluded: chain I residue 452 VAL Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 162 THR Chi-restraints excluded: chain J residue 220 HIS Chi-restraints excluded: chain J residue 222 ARG Chi-restraints excluded: chain J residue 268 SER Chi-restraints excluded: chain J residue 430 LEU Chi-restraints excluded: chain J residue 523 VAL Chi-restraints excluded: chain J residue 570 GLN Chi-restraints excluded: chain K residue 31 PHE Chi-restraints excluded: chain K residue 44 GLU Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 84 VAL Chi-restraints excluded: chain K residue 159 VAL Chi-restraints excluded: chain K residue 161 THR Chi-restraints excluded: chain K residue 192 TYR Chi-restraints excluded: chain K residue 197 LEU Chi-restraints excluded: chain K residue 293 GLN Chi-restraints excluded: chain K residue 430 LEU Chi-restraints excluded: chain K residue 441 PHE Chi-restraints excluded: chain K residue 479 VAL Chi-restraints excluded: chain K residue 512 SER Chi-restraints excluded: chain L residue 85 TYR Chi-restraints excluded: chain L residue 90 LYS Chi-restraints excluded: chain L residue 95 GLU Chi-restraints excluded: chain L residue 97 ASN Chi-restraints excluded: chain L residue 175 LEU Chi-restraints excluded: chain L residue 193 LEU Chi-restraints excluded: chain L residue 197 LEU Chi-restraints excluded: chain L residue 234 ASN Chi-restraints excluded: chain L residue 403 LEU Chi-restraints excluded: chain L residue 479 VAL Chi-restraints excluded: chain L residue 531 CYS Chi-restraints excluded: chain L residue 538 VAL Chi-restraints excluded: chain L residue 598 LEU Chi-restraints excluded: chain M residue 73 THR Chi-restraints excluded: chain M residue 167 LEU Chi-restraints excluded: chain M residue 220 HIS Chi-restraints excluded: chain M residue 274 ARG Chi-restraints excluded: chain M residue 301 VAL Chi-restraints excluded: chain M residue 430 LEU Chi-restraints excluded: chain M residue 436 CYS Chi-restraints excluded: chain M residue 529 PHE Chi-restraints excluded: chain N residue 58 ASP Chi-restraints excluded: chain N residue 121 LEU Chi-restraints excluded: chain N residue 131 THR Chi-restraints excluded: chain N residue 209 VAL Chi-restraints excluded: chain N residue 262 LEU Chi-restraints excluded: chain N residue 263 THR Chi-restraints excluded: chain N residue 292 TRP Chi-restraints excluded: chain N residue 303 ILE Chi-restraints excluded: chain N residue 437 THR Chi-restraints excluded: chain N residue 445 VAL Chi-restraints excluded: chain N residue 528 PHE Chi-restraints excluded: chain N residue 533 MET Chi-restraints excluded: chain O residue 84 VAL Chi-restraints excluded: chain O residue 110 THR Chi-restraints excluded: chain O residue 156 ILE Chi-restraints excluded: chain O residue 204 HIS Chi-restraints excluded: chain O residue 251 LYS Chi-restraints excluded: chain O residue 259 GLN Chi-restraints excluded: chain O residue 392 VAL Chi-restraints excluded: chain O residue 575 VAL Chi-restraints excluded: chain O residue 588 VAL Chi-restraints excluded: chain P residue 45 VAL Chi-restraints excluded: chain P residue 175 LEU Chi-restraints excluded: chain P residue 181 GLN Chi-restraints excluded: chain P residue 196 LEU Chi-restraints excluded: chain P residue 209 VAL Chi-restraints excluded: chain P residue 484 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 848 random chunks: chunk 412 optimal weight: 0.0770 chunk 534 optimal weight: 0.5980 chunk 716 optimal weight: 0.7980 chunk 206 optimal weight: 40.0000 chunk 620 optimal weight: 2.9990 chunk 99 optimal weight: 20.0000 chunk 186 optimal weight: 20.0000 chunk 673 optimal weight: 0.0020 chunk 281 optimal weight: 40.0000 chunk 691 optimal weight: 0.7980 chunk 85 optimal weight: 9.9990 overall best weight: 0.4546 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 144 GLN B 154 ASN ** C 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 108 GLN D 471 ASN E 383 GLN ** F 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 53 ASN H 144 GLN H 345 ASN J 134 GLN ** J 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 561 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 181 GLN ** K 561 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 154 ASN ** L 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 299 HIS L 401 ASN ** L 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 298 ASN N 97 ASN ** N 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 299 HIS ** N 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 116 ASN ** O 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 204 HIS ** P 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 423 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5623 r_free = 0.5623 target = 0.369733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.5595 r_free = 0.5595 target = 0.362047 restraints weight = 112303.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.5593 r_free = 0.5593 target = 0.361529 restraints weight = 108929.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.5591 r_free = 0.5591 target = 0.360489 restraints weight = 84919.352| |-----------------------------------------------------------------------------| r_work (final): 0.5590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1715 moved from start: 0.8157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.078 68624 Z= 0.162 Angle : 0.620 13.641 93136 Z= 0.310 Chirality : 0.045 0.364 10816 Planarity : 0.005 0.085 11792 Dihedral : 6.468 59.508 10454 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.21 % Favored : 96.61 % Rotamer: Outliers : 1.35 % Allowed : 14.21 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.20 % 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: -0.88 (0.09), residues: 8432 helix: 0.62 (0.14), residues: 1352 sheet: -0.14 (0.09), residues: 3399 loop : -1.43 (0.10), residues: 3681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP B 104 HIS 0.031 0.001 HIS O 204 PHE 0.030 0.001 PHE O 378 TYR 0.043 0.001 TYR L 78 ARG 0.018 0.001 ARG M 222 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11831.56 seconds wall clock time: 208 minutes 32.08 seconds (12512.08 seconds total)