Starting phenix.real_space_refine on Sun Sep 29 16:24:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sb3_10134/09_2024/6sb3_10134.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sb3_10134/09_2024/6sb3_10134.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sb3_10134/09_2024/6sb3_10134.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sb3_10134/09_2024/6sb3_10134.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sb3_10134/09_2024/6sb3_10134.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sb3_10134/09_2024/6sb3_10134.cif" } resolution = 3.5 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= 0.004 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 496 5.16 5 C 48080 2.51 5 N 12608 2.21 5 O 14528 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 550 residue(s): 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 75712 Number of models: 1 Model: "" Number of chains: 32 Chain: "A" Number of atoms: 4704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 604, 4704 Classifications: {'peptide': 604} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 571} Chain breaks: 1 Chain: "B" Number of atoms: 4704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 604, 4704 Classifications: {'peptide': 604} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 571} Chain breaks: 1 Chain: "C" Number of atoms: 4704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 604, 4704 Classifications: {'peptide': 604} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 571} Chain breaks: 1 Chain: "D" Number of atoms: 4704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 604, 4704 Classifications: {'peptide': 604} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 571} Chain breaks: 1 Chain: "E" Number of atoms: 4704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 604, 4704 Classifications: {'peptide': 604} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 571} Chain breaks: 1 Chain: "F" Number of atoms: 4704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 604, 4704 Classifications: {'peptide': 604} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 571} Chain breaks: 1 Chain: "G" Number of atoms: 4704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 604, 4704 Classifications: {'peptide': 604} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 571} Chain breaks: 1 Chain: "H" Number of atoms: 4704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 604, 4704 Classifications: {'peptide': 604} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 571} Chain breaks: 1 Chain: "I" Number of atoms: 4704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 604, 4704 Classifications: {'peptide': 604} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 571} Chain breaks: 1 Chain: "J" Number of atoms: 4704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 604, 4704 Classifications: {'peptide': 604} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 571} Chain breaks: 1 Chain: "K" Number of atoms: 4704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 604, 4704 Classifications: {'peptide': 604} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 571} Chain breaks: 1 Chain: "L" Number of atoms: 4704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 604, 4704 Classifications: {'peptide': 604} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 571} Chain breaks: 1 Chain: "M" Number of atoms: 4704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 604, 4704 Classifications: {'peptide': 604} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 571} Chain breaks: 1 Chain: "N" Number of atoms: 4704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 604, 4704 Classifications: {'peptide': 604} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 571} Chain breaks: 1 Chain: "O" Number of atoms: 4704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 604, 4704 Classifications: {'peptide': 604} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 571} Chain breaks: 1 Chain: "P" Number of atoms: 4704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 604, 4704 Classifications: {'peptide': 604} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 571} Chain breaks: 1 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 31.61, per 1000 atoms: 0.42 Number of scatterers: 75712 At special positions: 0 Unit cell: (237.12, 237.12, 100.88, 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 496 16.00 O 14528 8.00 N 12608 7.00 C 48080 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=112, symmetry=0 Simple disulfide: pdb=" SG CYS A 34 " - pdb=" SG CYS A 70 " distance=2.03 Simple disulfide: pdb=" SG CYS A 350 " - pdb=" SG CYS A 369 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 394 " distance=2.05 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 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=2.03 Simple disulfide: pdb=" SG CYS B 350 " - pdb=" SG CYS B 369 " distance=2.03 Simple disulfide: pdb=" SG CYS B 385 " - pdb=" SG CYS B 394 " distance=2.05 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 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 350 " - pdb=" SG CYS C 369 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 394 " distance=2.05 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 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 350 " - pdb=" SG CYS D 369 " distance=2.03 Simple disulfide: pdb=" SG CYS D 385 " - pdb=" SG CYS D 394 " distance=2.05 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 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 350 " - pdb=" SG CYS E 369 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 394 " distance=2.05 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 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=2.03 Simple disulfide: pdb=" SG CYS F 350 " - pdb=" SG CYS F 369 " distance=2.03 Simple disulfide: pdb=" SG CYS F 385 " - pdb=" SG CYS F 394 " distance=2.05 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 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 350 " - pdb=" SG CYS G 369 " distance=2.03 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 394 " distance=2.05 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 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 350 " - pdb=" SG CYS H 369 " distance=2.03 Simple disulfide: pdb=" SG CYS H 385 " - pdb=" SG CYS H 394 " distance=2.05 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 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 350 " - pdb=" SG CYS I 369 " distance=2.03 Simple disulfide: pdb=" SG CYS I 385 " - pdb=" SG CYS I 394 " distance=2.05 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 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=2.03 Simple disulfide: pdb=" SG CYS J 350 " - pdb=" SG CYS J 369 " distance=2.03 Simple disulfide: pdb=" SG CYS J 385 " - pdb=" SG CYS J 394 " distance=2.05 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 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 350 " - pdb=" SG CYS K 369 " distance=2.03 Simple disulfide: pdb=" SG CYS K 385 " - pdb=" SG CYS K 394 " distance=2.05 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 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 350 " - pdb=" SG CYS L 369 " distance=2.03 Simple disulfide: pdb=" SG CYS L 385 " - pdb=" SG CYS L 394 " distance=2.05 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 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 350 " - pdb=" SG CYS M 369 " distance=2.03 Simple disulfide: pdb=" SG CYS M 385 " - pdb=" SG CYS M 394 " distance=2.05 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 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=2.03 Simple disulfide: pdb=" SG CYS N 350 " - pdb=" SG CYS N 369 " distance=2.03 Simple disulfide: pdb=" SG CYS N 385 " - pdb=" SG CYS N 394 " distance=2.05 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 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 350 " - pdb=" SG CYS O 369 " distance=2.03 Simple disulfide: pdb=" SG CYS O 385 " - pdb=" SG CYS O 394 " distance=2.05 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 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 350 " - pdb=" SG CYS P 369 " distance=2.03 Simple disulfide: pdb=" SG CYS P 385 " - pdb=" SG CYS P 394 " distance=2.05 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 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 185 " " NAG A 702 " - " ASN A 269 " " NAG B 701 " - " ASN B 185 " " NAG B 702 " - " ASN B 269 " " NAG C 701 " - " ASN C 185 " " NAG C 702 " - " ASN C 269 " " NAG D 701 " - " ASN D 185 " " NAG D 702 " - " ASN D 269 " " NAG E 701 " - " ASN E 185 " " NAG E 702 " - " ASN E 269 " " NAG F 701 " - " ASN F 185 " " NAG F 702 " - " ASN F 269 " " NAG G 701 " - " ASN G 185 " " NAG G 702 " - " ASN G 269 " " NAG H 701 " - " ASN H 185 " " NAG H 702 " - " ASN H 269 " " NAG I 701 " - " ASN I 185 " " NAG I 702 " - " ASN I 269 " " NAG J 701 " - " ASN J 185 " " NAG J 702 " - " ASN J 269 " " NAG K 701 " - " ASN K 185 " " NAG K 702 " - " ASN K 269 " " NAG L 701 " - " ASN L 185 " " NAG L 702 " - " ASN L 269 " " NAG M 701 " - " ASN M 185 " " NAG M 702 " - " ASN M 269 " " NAG N 701 " - " ASN N 185 " " NAG N 702 " - " ASN N 269 " " NAG O 701 " - " ASN O 185 " " NAG O 702 " - " ASN O 269 " " NAG P 701 " - " ASN P 185 " " NAG P 702 " - " ASN P 269 " Time building additional restraints: 13.70 Conformation dependent library (CDL) restraints added in 7.1 seconds 19200 Ramachandran restraints generated. 9600 Oldfield, 0 Emsley, 9600 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 18048 Finding SS restraints... Secondary structure from input PDB file: 192 helices and 0 sheets defined 24.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.91 Creating SS restraints... Processing helix chain 'A' and resid 31 through 38 Processing helix chain 'A' and resid 130 through 141 removed outlier: 4.100A pdb=" N ARG A 135 " --> pdb=" O THR A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 184 Processing helix chain 'A' and resid 186 through 202 removed outlier: 3.593A pdb=" N THR A 191 " --> pdb=" O THR A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 229 Processing helix chain 'A' and resid 232 through 251 removed outlier: 4.181A pdb=" N LYS A 251 " --> pdb=" O ILE A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 269 Processing helix chain 'A' and resid 288 through 294 Processing helix chain 'A' and resid 310 through 314 Processing helix chain 'A' and resid 323 through 346 Processing helix chain 'A' and resid 393 through 398 removed outlier: 3.952A pdb=" N LEU A 397 " --> pdb=" O LEU A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 642 Processing helix chain 'B' and resid 32 through 38 Processing helix chain 'B' and resid 130 through 141 removed outlier: 4.100A pdb=" N ARG B 135 " --> pdb=" O THR B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 184 Processing helix chain 'B' and resid 186 through 202 removed outlier: 3.592A pdb=" N THR B 191 " --> pdb=" O THR B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 229 Processing helix chain 'B' and resid 232 through 251 removed outlier: 4.182A pdb=" N LYS B 251 " --> pdb=" O ILE B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 269 Processing helix chain 'B' and resid 288 through 294 Processing helix chain 'B' and resid 310 through 314 Processing helix chain 'B' and resid 323 through 346 Processing helix chain 'B' and resid 393 through 398 removed outlier: 3.951A pdb=" N LEU B 397 " --> pdb=" O LEU B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 642 Processing helix chain 'C' and resid 32 through 38 Processing helix chain 'C' and resid 130 through 141 removed outlier: 4.100A pdb=" N ARG C 135 " --> pdb=" O THR C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 184 Processing helix chain 'C' and resid 186 through 202 removed outlier: 3.593A pdb=" N THR C 191 " --> pdb=" O THR C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 229 Processing helix chain 'C' and resid 232 through 251 removed outlier: 4.181A pdb=" N LYS C 251 " --> pdb=" O ILE C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 269 Processing helix chain 'C' and resid 288 through 294 Processing helix chain 'C' and resid 310 through 314 Processing helix chain 'C' and resid 323 through 346 Processing helix chain 'C' and resid 393 through 398 removed outlier: 3.952A pdb=" N LEU C 397 " --> pdb=" O LEU C 393 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 642 Processing helix chain 'D' and resid 32 through 38 Processing helix chain 'D' and resid 130 through 141 removed outlier: 4.100A pdb=" N ARG D 135 " --> pdb=" O THR D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 184 Processing helix chain 'D' and resid 186 through 202 removed outlier: 3.593A pdb=" N THR D 191 " --> pdb=" O THR D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 229 Processing helix chain 'D' and resid 232 through 251 removed outlier: 4.181A pdb=" N LYS D 251 " --> pdb=" O ILE D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 269 Processing helix chain 'D' and resid 288 through 294 Processing helix chain 'D' and resid 310 through 314 Processing helix chain 'D' and resid 323 through 346 Processing helix chain 'D' and resid 393 through 398 removed outlier: 3.951A pdb=" N LEU D 397 " --> pdb=" O LEU D 393 " (cutoff:3.500A) Processing helix chain 'D' and resid 630 through 642 Processing helix chain 'E' and resid 32 through 38 Processing helix chain 'E' and resid 130 through 141 removed outlier: 4.100A pdb=" N ARG E 135 " --> pdb=" O THR E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 168 through 184 Processing helix chain 'E' and resid 186 through 202 removed outlier: 3.593A pdb=" N THR E 191 " --> pdb=" O THR E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 223 through 229 Processing helix chain 'E' and resid 232 through 251 removed outlier: 4.181A pdb=" N LYS E 251 " --> pdb=" O ILE E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 260 through 269 Processing helix chain 'E' and resid 288 through 294 Processing helix chain 'E' and resid 310 through 314 Processing helix chain 'E' and resid 323 through 346 Processing helix chain 'E' and resid 393 through 398 removed outlier: 3.952A pdb=" N LEU E 397 " --> pdb=" O LEU E 393 " (cutoff:3.500A) Processing helix chain 'E' and resid 630 through 642 Processing helix chain 'F' and resid 32 through 38 Processing helix chain 'F' and resid 130 through 141 removed outlier: 4.101A pdb=" N ARG F 135 " --> pdb=" O THR F 131 " (cutoff:3.500A) Processing helix chain 'F' and resid 168 through 184 Processing helix chain 'F' and resid 186 through 202 removed outlier: 3.592A pdb=" N THR F 191 " --> pdb=" O THR F 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 223 through 229 Processing helix chain 'F' and resid 232 through 251 removed outlier: 4.182A pdb=" N LYS F 251 " --> pdb=" O ILE F 247 " (cutoff:3.500A) Processing helix chain 'F' and resid 260 through 269 Processing helix chain 'F' and resid 288 through 294 Processing helix chain 'F' and resid 310 through 314 Processing helix chain 'F' and resid 323 through 346 Processing helix chain 'F' and resid 393 through 398 removed outlier: 3.952A pdb=" N LEU F 397 " --> pdb=" O LEU F 393 " (cutoff:3.500A) Processing helix chain 'F' and resid 630 through 642 Processing helix chain 'G' and resid 32 through 38 Processing helix chain 'G' and resid 130 through 141 removed outlier: 4.100A pdb=" N ARG G 135 " --> pdb=" O THR G 131 " (cutoff:3.500A) Processing helix chain 'G' and resid 168 through 184 Processing helix chain 'G' and resid 186 through 202 removed outlier: 3.593A pdb=" N THR G 191 " --> pdb=" O THR G 187 " (cutoff:3.500A) Processing helix chain 'G' and resid 223 through 229 Processing helix chain 'G' and resid 232 through 251 removed outlier: 4.181A pdb=" N LYS G 251 " --> pdb=" O ILE G 247 " (cutoff:3.500A) Processing helix chain 'G' and resid 260 through 269 Processing helix chain 'G' and resid 288 through 294 Processing helix chain 'G' and resid 310 through 314 Processing helix chain 'G' and resid 323 through 346 Processing helix chain 'G' and resid 393 through 398 removed outlier: 3.952A pdb=" N LEU G 397 " --> pdb=" O LEU G 393 " (cutoff:3.500A) Processing helix chain 'G' and resid 630 through 642 Processing helix chain 'H' and resid 32 through 38 Processing helix chain 'H' and resid 130 through 141 removed outlier: 4.100A pdb=" N ARG H 135 " --> pdb=" O THR H 131 " (cutoff:3.500A) Processing helix chain 'H' and resid 168 through 184 Processing helix chain 'H' and resid 186 through 202 removed outlier: 3.593A pdb=" N THR H 191 " --> pdb=" O THR H 187 " (cutoff:3.500A) Processing helix chain 'H' and resid 223 through 229 Processing helix chain 'H' and resid 232 through 251 removed outlier: 4.181A pdb=" N LYS H 251 " --> pdb=" O ILE H 247 " (cutoff:3.500A) Processing helix chain 'H' and resid 260 through 269 Processing helix chain 'H' and resid 288 through 294 Processing helix chain 'H' and resid 310 through 314 Processing helix chain 'H' and resid 323 through 346 Processing helix chain 'H' and resid 393 through 398 removed outlier: 3.951A pdb=" N LEU H 397 " --> pdb=" O LEU H 393 " (cutoff:3.500A) Processing helix chain 'H' and resid 630 through 642 Processing helix chain 'I' and resid 32 through 38 Processing helix chain 'I' and resid 130 through 141 removed outlier: 4.100A pdb=" N ARG I 135 " --> pdb=" O THR I 131 " (cutoff:3.500A) Processing helix chain 'I' and resid 168 through 184 Processing helix chain 'I' and resid 186 through 202 removed outlier: 3.593A pdb=" N THR I 191 " --> pdb=" O THR I 187 " (cutoff:3.500A) Processing helix chain 'I' and resid 223 through 229 Processing helix chain 'I' and resid 232 through 251 removed outlier: 4.181A pdb=" N LYS I 251 " --> pdb=" O ILE I 247 " (cutoff:3.500A) Processing helix chain 'I' and resid 260 through 269 Processing helix chain 'I' and resid 288 through 294 Processing helix chain 'I' and resid 310 through 314 Processing helix chain 'I' and resid 323 through 346 Processing helix chain 'I' and resid 393 through 398 removed outlier: 3.952A pdb=" N LEU I 397 " --> pdb=" O LEU I 393 " (cutoff:3.500A) Processing helix chain 'I' and resid 630 through 642 Processing helix chain 'J' and resid 32 through 38 Processing helix chain 'J' and resid 130 through 141 removed outlier: 4.100A pdb=" N ARG J 135 " --> pdb=" O THR J 131 " (cutoff:3.500A) Processing helix chain 'J' and resid 168 through 184 Processing helix chain 'J' and resid 186 through 202 removed outlier: 3.593A pdb=" N THR J 191 " --> pdb=" O THR J 187 " (cutoff:3.500A) Processing helix chain 'J' and resid 223 through 229 Processing helix chain 'J' and resid 232 through 251 removed outlier: 4.181A pdb=" N LYS J 251 " --> pdb=" O ILE J 247 " (cutoff:3.500A) Processing helix chain 'J' and resid 260 through 269 Processing helix chain 'J' and resid 288 through 294 Processing helix chain 'J' and resid 310 through 314 Processing helix chain 'J' and resid 323 through 346 Processing helix chain 'J' and resid 393 through 398 removed outlier: 3.952A pdb=" N LEU J 397 " --> pdb=" O LEU J 393 " (cutoff:3.500A) Processing helix chain 'J' and resid 630 through 642 Processing helix chain 'K' and resid 32 through 38 Processing helix chain 'K' and resid 130 through 141 removed outlier: 4.101A pdb=" N ARG K 135 " --> pdb=" O THR K 131 " (cutoff:3.500A) Processing helix chain 'K' and resid 168 through 184 Processing helix chain 'K' and resid 186 through 202 removed outlier: 3.593A pdb=" N THR K 191 " --> pdb=" O THR K 187 " (cutoff:3.500A) Processing helix chain 'K' and resid 223 through 229 Processing helix chain 'K' and resid 232 through 251 removed outlier: 4.182A pdb=" N LYS K 251 " --> pdb=" O ILE K 247 " (cutoff:3.500A) Processing helix chain 'K' and resid 260 through 269 Processing helix chain 'K' and resid 288 through 294 Processing helix chain 'K' and resid 310 through 314 Processing helix chain 'K' and resid 323 through 346 Processing helix chain 'K' and resid 393 through 398 removed outlier: 3.952A pdb=" N LEU K 397 " --> pdb=" O LEU K 393 " (cutoff:3.500A) Processing helix chain 'K' and resid 630 through 642 Processing helix chain 'L' and resid 32 through 38 Processing helix chain 'L' and resid 130 through 141 removed outlier: 4.100A pdb=" N ARG L 135 " --> pdb=" O THR L 131 " (cutoff:3.500A) Processing helix chain 'L' and resid 168 through 184 Processing helix chain 'L' and resid 186 through 202 removed outlier: 3.592A pdb=" N THR L 191 " --> pdb=" O THR L 187 " (cutoff:3.500A) Processing helix chain 'L' and resid 223 through 229 Processing helix chain 'L' and resid 232 through 251 removed outlier: 4.182A pdb=" N LYS L 251 " --> pdb=" O ILE L 247 " (cutoff:3.500A) Processing helix chain 'L' and resid 260 through 269 Processing helix chain 'L' and resid 288 through 294 Processing helix chain 'L' and resid 310 through 314 Processing helix chain 'L' and resid 323 through 346 Processing helix chain 'L' and resid 393 through 398 removed outlier: 3.953A pdb=" N LEU L 397 " --> pdb=" O LEU L 393 " (cutoff:3.500A) Processing helix chain 'L' and resid 630 through 642 Processing helix chain 'M' and resid 32 through 38 Processing helix chain 'M' and resid 130 through 141 removed outlier: 4.101A pdb=" N ARG M 135 " --> pdb=" O THR M 131 " (cutoff:3.500A) Processing helix chain 'M' and resid 168 through 184 Processing helix chain 'M' and resid 186 through 202 removed outlier: 3.593A pdb=" N THR M 191 " --> pdb=" O THR M 187 " (cutoff:3.500A) Processing helix chain 'M' and resid 223 through 229 Processing helix chain 'M' and resid 232 through 251 removed outlier: 4.182A pdb=" N LYS M 251 " --> pdb=" O ILE M 247 " (cutoff:3.500A) Processing helix chain 'M' and resid 260 through 269 Processing helix chain 'M' and resid 288 through 294 Processing helix chain 'M' and resid 310 through 314 Processing helix chain 'M' and resid 323 through 346 Processing helix chain 'M' and resid 393 through 398 removed outlier: 3.953A pdb=" N LEU M 397 " --> pdb=" O LEU M 393 " (cutoff:3.500A) Processing helix chain 'M' and resid 630 through 642 Processing helix chain 'N' and resid 32 through 38 Processing helix chain 'N' and resid 130 through 141 removed outlier: 4.101A pdb=" N ARG N 135 " --> pdb=" O THR N 131 " (cutoff:3.500A) Processing helix chain 'N' and resid 168 through 184 Processing helix chain 'N' and resid 186 through 202 removed outlier: 3.592A pdb=" N THR N 191 " --> pdb=" O THR N 187 " (cutoff:3.500A) Processing helix chain 'N' and resid 223 through 229 Processing helix chain 'N' and resid 232 through 251 removed outlier: 4.181A pdb=" N LYS N 251 " --> pdb=" O ILE N 247 " (cutoff:3.500A) Processing helix chain 'N' and resid 260 through 269 Processing helix chain 'N' and resid 288 through 294 Processing helix chain 'N' and resid 310 through 314 Processing helix chain 'N' and resid 323 through 346 Processing helix chain 'N' and resid 393 through 398 removed outlier: 3.952A pdb=" N LEU N 397 " --> pdb=" O LEU N 393 " (cutoff:3.500A) Processing helix chain 'N' and resid 630 through 642 Processing helix chain 'O' and resid 32 through 38 Processing helix chain 'O' and resid 130 through 141 removed outlier: 4.101A pdb=" N ARG O 135 " --> pdb=" O THR O 131 " (cutoff:3.500A) Processing helix chain 'O' and resid 168 through 184 Processing helix chain 'O' and resid 186 through 202 removed outlier: 3.592A pdb=" N THR O 191 " --> pdb=" O THR O 187 " (cutoff:3.500A) Processing helix chain 'O' and resid 223 through 229 Processing helix chain 'O' and resid 232 through 251 removed outlier: 4.181A pdb=" N LYS O 251 " --> pdb=" O ILE O 247 " (cutoff:3.500A) Processing helix chain 'O' and resid 260 through 269 Processing helix chain 'O' and resid 288 through 294 Processing helix chain 'O' and resid 310 through 314 Processing helix chain 'O' and resid 323 through 346 Processing helix chain 'O' and resid 393 through 398 removed outlier: 3.952A pdb=" N LEU O 397 " --> pdb=" O LEU O 393 " (cutoff:3.500A) Processing helix chain 'O' and resid 630 through 642 Processing helix chain 'P' and resid 32 through 38 Processing helix chain 'P' and resid 130 through 141 removed outlier: 4.100A pdb=" N ARG P 135 " --> pdb=" O THR P 131 " (cutoff:3.500A) Processing helix chain 'P' and resid 168 through 184 Processing helix chain 'P' and resid 186 through 202 removed outlier: 3.593A pdb=" N THR P 191 " --> pdb=" O THR P 187 " (cutoff:3.500A) Processing helix chain 'P' and resid 223 through 229 Processing helix chain 'P' and resid 232 through 251 removed outlier: 4.181A pdb=" N LYS P 251 " --> pdb=" O ILE P 247 " (cutoff:3.500A) Processing helix chain 'P' and resid 260 through 269 Processing helix chain 'P' and resid 288 through 294 Processing helix chain 'P' and resid 310 through 314 Processing helix chain 'P' and resid 323 through 346 Processing helix chain 'P' and resid 393 through 398 removed outlier: 3.951A pdb=" N LEU P 397 " --> pdb=" O LEU P 393 " (cutoff:3.500A) Processing helix chain 'P' and resid 630 through 642 1489 hydrogen bonds defined for protein. 4467 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: 17.24 Time building geometry restraints manager: 16.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 24464 1.34 - 1.46: 17618 1.46 - 1.58: 34574 1.58 - 1.70: 0 1.70 - 1.82: 688 Bond restraints: 77344 Sorted by residual: bond pdb=" C1 NAG N 701 " pdb=" O5 NAG N 701 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.07e+00 bond pdb=" C1 NAG M 701 " pdb=" O5 NAG M 701 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.06e+00 bond pdb=" C1 NAG G 701 " pdb=" O5 NAG G 701 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.06e+00 bond pdb=" C1 NAG D 701 " pdb=" O5 NAG D 701 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.05e+00 bond pdb=" C1 NAG F 701 " pdb=" O5 NAG F 701 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 2.03e+00 ... (remaining 77339 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.09: 99103 1.09 - 2.18: 4796 2.18 - 3.26: 955 3.26 - 4.35: 154 4.35 - 5.44: 96 Bond angle restraints: 105104 Sorted by residual: angle pdb=" N VAL E 125 " pdb=" CA VAL E 125 " pdb=" C VAL E 125 " ideal model delta sigma weight residual 111.91 108.27 3.64 8.90e-01 1.26e+00 1.68e+01 angle pdb=" N VAL D 125 " pdb=" CA VAL D 125 " pdb=" C VAL D 125 " ideal model delta sigma weight residual 111.91 108.27 3.64 8.90e-01 1.26e+00 1.67e+01 angle pdb=" N VAL M 125 " pdb=" CA VAL M 125 " pdb=" C VAL M 125 " ideal model delta sigma weight residual 111.91 108.27 3.64 8.90e-01 1.26e+00 1.67e+01 angle pdb=" N VAL K 125 " pdb=" CA VAL K 125 " pdb=" C VAL K 125 " ideal model delta sigma weight residual 111.91 108.28 3.63 8.90e-01 1.26e+00 1.66e+01 angle pdb=" N VAL F 125 " pdb=" CA VAL F 125 " pdb=" C VAL F 125 " ideal model delta sigma weight residual 111.91 108.29 3.62 8.90e-01 1.26e+00 1.66e+01 ... (remaining 105099 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.83: 42497 16.83 - 33.67: 3775 33.67 - 50.50: 720 50.50 - 67.33: 144 67.33 - 84.17: 48 Dihedral angle restraints: 47184 sinusoidal: 19184 harmonic: 28000 Sorted by residual: dihedral pdb=" CB CYS D 554 " pdb=" SG CYS D 554 " pdb=" SG CYS D 574 " pdb=" CB CYS D 574 " ideal model delta sinusoidal sigma weight residual 93.00 50.95 42.05 1 1.00e+01 1.00e-02 2.47e+01 dihedral pdb=" CB CYS B 554 " pdb=" SG CYS B 554 " pdb=" SG CYS B 574 " pdb=" CB CYS B 574 " ideal model delta sinusoidal sigma weight residual 93.00 50.96 42.04 1 1.00e+01 1.00e-02 2.47e+01 dihedral pdb=" CB CYS E 554 " pdb=" SG CYS E 554 " pdb=" SG CYS E 574 " pdb=" CB CYS E 574 " ideal model delta sinusoidal sigma weight residual 93.00 50.96 42.04 1 1.00e+01 1.00e-02 2.47e+01 ... (remaining 47181 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 7505 0.031 - 0.061: 3136 0.061 - 0.092: 901 0.092 - 0.123: 556 0.123 - 0.153: 62 Chirality restraints: 12160 Sorted by residual: chirality pdb=" CB ILE O 608 " pdb=" CA ILE O 608 " pdb=" CG1 ILE O 608 " pdb=" CG2 ILE O 608 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.87e-01 chirality pdb=" CB ILE P 608 " pdb=" CA ILE P 608 " pdb=" CG1 ILE P 608 " pdb=" CG2 ILE P 608 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.80e-01 chirality pdb=" CB ILE I 608 " pdb=" CA ILE I 608 " pdb=" CG1 ILE I 608 " pdb=" CG2 ILE I 608 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.75e-01 ... (remaining 12157 not shown) Planarity restraints: 13520 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP J 621 " -0.036 5.00e-02 4.00e+02 5.40e-02 4.66e+00 pdb=" N PRO J 622 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO J 622 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO J 622 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP N 621 " 0.036 5.00e-02 4.00e+02 5.39e-02 4.65e+00 pdb=" N PRO N 622 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO N 622 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO N 622 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP D 621 " -0.036 5.00e-02 4.00e+02 5.39e-02 4.65e+00 pdb=" N PRO D 622 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO D 622 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO D 622 " -0.030 5.00e-02 4.00e+02 ... (remaining 13517 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 1347 2.66 - 3.22: 75332 3.22 - 3.78: 124117 3.78 - 4.34: 172734 4.34 - 4.90: 273643 Nonbonded interactions: 647173 Sorted by model distance: nonbonded pdb=" O MET B 59 " pdb=" OH TYR C 85 " model vdw 2.104 3.040 nonbonded pdb=" O MET E 59 " pdb=" OH TYR F 85 " model vdw 2.116 3.040 nonbonded pdb=" O MET G 59 " pdb=" OH TYR H 85 " model vdw 2.165 3.040 nonbonded pdb=" O MET M 59 " pdb=" OH TYR N 85 " model vdw 2.178 3.040 nonbonded pdb=" O MET A 59 " pdb=" OH TYR B 85 " model vdw 2.191 3.040 ... (remaining 647168 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=0.50 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: 2.710 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: 0.090 Extract box with map and model: 2.260 Check model and map are aligned: 0.530 Set scattering table: 0.680 Process input model: 115.230 Find NCS groups from input model: 3.000 Set up NCS constraints: 0.530 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: 0.020 Load rotamer database and sin/cos tables:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 127.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6813 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 : 0.002 0.029 77344 Z= 0.163 Angle : 0.565 5.440 105104 Z= 0.317 Chirality : 0.041 0.153 12160 Planarity : 0.004 0.054 13488 Dihedral : 12.996 84.166 28800 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.84 (0.07), residues: 9600 helix: -1.50 (0.09), residues: 2288 sheet: -1.21 (0.12), residues: 1584 loop : -2.34 (0.07), residues: 5728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 51 HIS 0.002 0.000 HIS L 340 PHE 0.011 0.001 PHE N 133 TYR 0.011 0.001 TYR L 341 ARG 0.005 0.000 ARG J 153 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19200 Ramachandran restraints generated. 9600 Oldfield, 0 Emsley, 9600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19200 Ramachandran restraints generated. 9600 Oldfield, 0 Emsley, 9600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1985 residues out of total 8544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1985 time to evaluate : 6.121 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 43 LEU cc_start: 0.8065 (tp) cc_final: 0.7666 (tp) REVERT: A 492 GLN cc_start: 0.6073 (tt0) cc_final: 0.5748 (mm-40) REVERT: A 516 GLU cc_start: 0.6150 (tp30) cc_final: 0.5893 (tp30) REVERT: A 639 MET cc_start: 0.5102 (ttm) cc_final: 0.4777 (tpp) REVERT: B 43 LEU cc_start: 0.8152 (tp) cc_final: 0.7821 (tp) REVERT: B 154 ASN cc_start: 0.8668 (p0) cc_final: 0.8431 (p0) REVERT: B 303 ILE cc_start: 0.6868 (mm) cc_final: 0.6634 (mm) REVERT: B 335 GLU cc_start: 0.6752 (tp30) cc_final: 0.6546 (tp30) REVERT: B 516 GLU cc_start: 0.6417 (tp30) cc_final: 0.6164 (tp30) REVERT: B 586 LEU cc_start: 0.6999 (mt) cc_final: 0.6777 (mt) REVERT: C 151 GLN cc_start: 0.7207 (pt0) cc_final: 0.6864 (pt0) REVERT: C 154 ASN cc_start: 0.8549 (p0) cc_final: 0.8315 (p0) REVERT: C 492 GLN cc_start: 0.6387 (tt0) cc_final: 0.5715 (mm-40) REVERT: D 151 GLN cc_start: 0.7282 (pt0) cc_final: 0.7033 (pt0) REVERT: D 492 GLN cc_start: 0.6066 (tt0) cc_final: 0.5591 (mm-40) REVERT: E 492 GLN cc_start: 0.6012 (tt0) cc_final: 0.5643 (mm-40) REVERT: E 516 GLU cc_start: 0.5925 (tp30) cc_final: 0.5526 (tp30) REVERT: F 113 LEU cc_start: 0.7116 (tp) cc_final: 0.6458 (mp) REVERT: F 151 GLN cc_start: 0.7086 (pt0) cc_final: 0.6847 (pt0) REVERT: F 236 VAL cc_start: 0.7830 (t) cc_final: 0.7339 (t) REVERT: F 492 GLN cc_start: 0.6610 (tt0) cc_final: 0.5866 (mm-40) REVERT: F 586 LEU cc_start: 0.7150 (mt) cc_final: 0.6724 (mt) REVERT: G 151 GLN cc_start: 0.7170 (pt0) cc_final: 0.6666 (pt0) REVERT: G 154 ASN cc_start: 0.8592 (p0) cc_final: 0.8305 (p0) REVERT: G 236 VAL cc_start: 0.7616 (t) cc_final: 0.7058 (t) REVERT: G 322 LEU cc_start: 0.6987 (mp) cc_final: 0.6760 (mp) REVERT: G 492 GLN cc_start: 0.6460 (tt0) cc_final: 0.5942 (mm-40) REVERT: H 43 LEU cc_start: 0.8305 (tp) cc_final: 0.8104 (tp) REVERT: H 151 GLN cc_start: 0.7265 (pt0) cc_final: 0.6814 (pt0) REVERT: H 154 ASN cc_start: 0.8795 (p0) cc_final: 0.8358 (p0) REVERT: H 236 VAL cc_start: 0.7770 (t) cc_final: 0.7173 (t) REVERT: H 322 LEU cc_start: 0.7205 (mp) cc_final: 0.6912 (mp) REVERT: H 492 GLN cc_start: 0.6342 (tt0) cc_final: 0.5551 (mm-40) REVERT: I 154 ASN cc_start: 0.8689 (p0) cc_final: 0.8407 (p0) REVERT: I 492 GLN cc_start: 0.6677 (tt0) cc_final: 0.5937 (mm-40) REVERT: J 113 LEU cc_start: 0.6998 (tp) cc_final: 0.6367 (mp) REVERT: J 151 GLN cc_start: 0.7027 (pt0) cc_final: 0.6735 (pt0) REVERT: J 154 ASN cc_start: 0.8794 (p0) cc_final: 0.8454 (p0) REVERT: J 236 VAL cc_start: 0.7700 (t) cc_final: 0.7169 (t) REVERT: J 492 GLN cc_start: 0.6087 (tt0) cc_final: 0.5529 (mm-40) REVERT: K 151 GLN cc_start: 0.7159 (pt0) cc_final: 0.6685 (pt0) REVERT: K 154 ASN cc_start: 0.8578 (p0) cc_final: 0.8310 (p0) REVERT: K 492 GLN cc_start: 0.6406 (tt0) cc_final: 0.5733 (mm-40) REVERT: L 151 GLN cc_start: 0.7192 (pt0) cc_final: 0.6803 (pt0) REVERT: L 322 LEU cc_start: 0.7178 (mp) cc_final: 0.6880 (mp) REVERT: L 492 GLN cc_start: 0.6251 (tt0) cc_final: 0.5541 (mm-40) REVERT: M 151 GLN cc_start: 0.6967 (pt0) cc_final: 0.6719 (pt0) REVERT: M 322 LEU cc_start: 0.7410 (mp) cc_final: 0.7082 (mp) REVERT: M 492 GLN cc_start: 0.6489 (tt0) cc_final: 0.5849 (mm-40) REVERT: N 113 LEU cc_start: 0.7068 (tp) cc_final: 0.6436 (mp) REVERT: N 151 GLN cc_start: 0.7040 (pt0) cc_final: 0.6736 (pt0) REVERT: N 236 VAL cc_start: 0.7777 (t) cc_final: 0.7278 (t) REVERT: N 492 GLN cc_start: 0.6391 (tt0) cc_final: 0.5901 (mm-40) REVERT: N 586 LEU cc_start: 0.7221 (mt) cc_final: 0.6852 (mt) REVERT: O 151 GLN cc_start: 0.7163 (pt0) cc_final: 0.6739 (pt0) REVERT: O 154 ASN cc_start: 0.8659 (p0) cc_final: 0.8457 (p0) REVERT: O 236 VAL cc_start: 0.7709 (t) cc_final: 0.7262 (t) REVERT: O 492 GLN cc_start: 0.6289 (tt0) cc_final: 0.5811 (mm-40) REVERT: P 56 ASN cc_start: 0.4679 (t0) cc_final: 0.3691 (t0) REVERT: P 151 GLN cc_start: 0.7153 (pt0) cc_final: 0.6759 (pt0) REVERT: P 154 ASN cc_start: 0.8739 (p0) cc_final: 0.8334 (p0) REVERT: P 236 VAL cc_start: 0.7660 (t) cc_final: 0.7073 (t) REVERT: P 322 LEU cc_start: 0.7165 (mp) cc_final: 0.6851 (mp) REVERT: P 492 GLN cc_start: 0.6451 (tt0) cc_final: 0.5588 (mm-40) outliers start: 0 outliers final: 0 residues processed: 1985 average time/residue: 0.7037 time to fit residues: 2414.6745 Evaluate side-chains 1182 residues out of total 8544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1182 time to evaluate : 6.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 960 random chunks: chunk 810 optimal weight: 6.9990 chunk 727 optimal weight: 0.8980 chunk 403 optimal weight: 8.9990 chunk 248 optimal weight: 0.8980 chunk 490 optimal weight: 3.9990 chunk 388 optimal weight: 0.7980 chunk 752 optimal weight: 0.7980 chunk 291 optimal weight: 0.9990 chunk 457 optimal weight: 0.0670 chunk 560 optimal weight: 0.6980 chunk 871 optimal weight: 0.8980 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 GLN ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 234 ASN A 345 ASN A 357 ASN A 361 GLN A 421 GLN A 561 HIS B 32 GLN ** B 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 345 ASN B 361 GLN B 363 ASN B 421 GLN ** B 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 32 GLN ** C 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 220 HIS C 357 ASN C 421 GLN D 32 GLN ** D 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 220 HIS D 234 ASN D 345 ASN D 357 ASN D 421 GLN D 561 HIS D 625 ASN E 32 GLN E 140 GLN E 186 GLN ** E 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 233 GLN E 234 ASN E 345 ASN E 357 ASN E 421 GLN E 561 HIS E 625 ASN F 32 GLN ** F 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 234 ASN F 357 ASN F 421 GLN F 625 ASN G 32 GLN ** G 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 220 HIS G 234 ASN G 357 ASN G 421 GLN ** G 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 32 GLN ** H 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 220 HIS H 234 ASN H 345 ASN H 357 ASN H 421 GLN H 625 ASN I 32 GLN ** I 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 357 ASN I 361 GLN I 363 ASN I 421 GLN I 625 ASN J 32 GLN ** J 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 357 ASN J 363 ASN J 421 GLN J 625 ASN K 32 GLN ** K 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 220 HIS K 357 ASN K 421 GLN L 32 GLN ** L 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 220 HIS L 234 ASN L 345 ASN L 357 ASN L 421 GLN L 625 ASN M 32 GLN ** M 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 357 ASN M 361 GLN M 363 ASN M 421 GLN N 32 GLN ** N 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 186 GLN ** N 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 234 ASN N 357 ASN N 421 GLN N 625 ASN O 32 GLN ** O 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 234 ASN O 357 ASN O 421 GLN P 32 GLN ** P 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 186 GLN P 220 HIS P 234 ASN P 345 ASN P 357 ASN P 421 GLN P 625 ASN Total number of N/Q/H flips: 96 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6996 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 77344 Z= 0.203 Angle : 0.569 8.569 105104 Z= 0.286 Chirality : 0.043 0.218 12160 Planarity : 0.005 0.050 13488 Dihedral : 4.764 38.105 10928 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.73 % Allowed : 13.67 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.08), residues: 9600 helix: -0.46 (0.10), residues: 2304 sheet: -1.32 (0.12), residues: 1808 loop : -1.85 (0.08), residues: 5488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 461 HIS 0.007 0.001 HIS A 204 PHE 0.030 0.002 PHE E 529 TYR 0.019 0.002 TYR O 593 ARG 0.004 0.001 ARG D 589 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19200 Ramachandran restraints generated. 9600 Oldfield, 0 Emsley, 9600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19200 Ramachandran restraints generated. 9600 Oldfield, 0 Emsley, 9600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1580 residues out of total 8544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 233 poor density : 1347 time to evaluate : 6.103 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: A 59 MET cc_start: 0.6917 (mmm) cc_final: 0.6507 (mmm) REVERT: A 171 PHE cc_start: 0.7779 (t80) cc_final: 0.7143 (t80) REVERT: A 335 GLU cc_start: 0.6905 (tp30) cc_final: 0.6568 (tp30) REVERT: A 492 GLN cc_start: 0.6049 (tt0) cc_final: 0.5553 (mm-40) REVERT: A 516 GLU cc_start: 0.6155 (tp30) cc_final: 0.5895 (tp30) REVERT: A 639 MET cc_start: 0.5200 (ttm) cc_final: 0.4783 (tpp) REVERT: B 303 ILE cc_start: 0.7300 (mm) cc_final: 0.7066 (mm) REVERT: B 516 GLU cc_start: 0.6409 (tp30) cc_final: 0.6109 (tp30) REVERT: C 154 ASN cc_start: 0.8438 (p0) cc_final: 0.8160 (p0) REVERT: C 176 MET cc_start: 0.7692 (OUTLIER) cc_final: 0.7436 (mmp) REVERT: C 322 LEU cc_start: 0.8120 (OUTLIER) cc_final: 0.7824 (tp) REVERT: C 458 ARG cc_start: 0.7212 (mtt90) cc_final: 0.6917 (ptp90) REVERT: C 492 GLN cc_start: 0.6253 (tt0) cc_final: 0.5700 (mm-40) REVERT: D 154 ASN cc_start: 0.8411 (p0) cc_final: 0.8004 (p0) REVERT: D 169 LEU cc_start: 0.7119 (mt) cc_final: 0.6533 (mt) REVERT: D 251 LYS cc_start: 0.6042 (ttmm) cc_final: 0.5699 (ttmm) REVERT: D 308 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8678 (pp) REVERT: D 399 GLN cc_start: 0.7044 (pp30) cc_final: 0.6705 (pp30) REVERT: D 492 GLN cc_start: 0.5959 (tt0) cc_final: 0.5469 (mm-40) REVERT: E 154 ASN cc_start: 0.8444 (p0) cc_final: 0.8243 (p0) REVERT: E 169 LEU cc_start: 0.7006 (mt) cc_final: 0.6381 (mt) REVERT: E 264 LYS cc_start: 0.7012 (mmtm) cc_final: 0.6758 (mmtt) REVERT: E 335 GLU cc_start: 0.7320 (tp30) cc_final: 0.7031 (tp30) REVERT: E 492 GLN cc_start: 0.6011 (tt0) cc_final: 0.5440 (mm-40) REVERT: F 59 MET cc_start: 0.6398 (mmm) cc_final: 0.6004 (mmt) REVERT: F 216 VAL cc_start: 0.8090 (t) cc_final: 0.7869 (t) REVERT: F 364 MET cc_start: 0.7455 (mtp) cc_final: 0.7233 (mtp) REVERT: F 492 GLN cc_start: 0.6524 (tt0) cc_final: 0.5938 (mm-40) REVERT: G 105 MET cc_start: 0.7841 (mmm) cc_final: 0.7501 (mmm) REVERT: G 154 ASN cc_start: 0.8447 (p0) cc_final: 0.8136 (p0) REVERT: G 169 LEU cc_start: 0.7135 (mt) cc_final: 0.6559 (mt) REVERT: G 492 GLN cc_start: 0.6335 (tt0) cc_final: 0.5777 (mm-40) REVERT: H 56 ASN cc_start: 0.5048 (t0) cc_final: 0.4383 (t0) REVERT: H 154 ASN cc_start: 0.8647 (p0) cc_final: 0.8249 (p0) REVERT: H 169 LEU cc_start: 0.7123 (mt) cc_final: 0.6595 (mt) REVERT: H 216 VAL cc_start: 0.8301 (t) cc_final: 0.8049 (t) REVERT: H 236 VAL cc_start: 0.7862 (t) cc_final: 0.7576 (t) REVERT: H 492 GLN cc_start: 0.6296 (tt0) cc_final: 0.5660 (mm-40) REVERT: I 44 GLU cc_start: 0.8130 (tt0) cc_final: 0.7804 (tt0) REVERT: I 59 MET cc_start: 0.6931 (mmm) cc_final: 0.6510 (mmt) REVERT: I 96 MET cc_start: 0.7907 (mpp) cc_final: 0.7566 (mmt) REVERT: I 154 ASN cc_start: 0.8643 (p0) cc_final: 0.8290 (p0) REVERT: I 169 LEU cc_start: 0.7190 (mt) cc_final: 0.6613 (mt) REVERT: I 492 GLN cc_start: 0.6669 (tt0) cc_final: 0.5759 (mm-40) REVERT: I 503 LEU cc_start: 0.7808 (OUTLIER) cc_final: 0.7565 (mm) REVERT: J 59 MET cc_start: 0.6638 (mmm) cc_final: 0.6327 (mmm) REVERT: J 154 ASN cc_start: 0.8529 (p0) cc_final: 0.8165 (p0) REVERT: J 492 GLN cc_start: 0.6329 (tt0) cc_final: 0.5771 (mm-40) REVERT: K 154 ASN cc_start: 0.8453 (p0) cc_final: 0.8147 (p0) REVERT: K 169 LEU cc_start: 0.7267 (mt) cc_final: 0.6644 (mt) REVERT: K 492 GLN cc_start: 0.6287 (tt0) cc_final: 0.5756 (mm-40) REVERT: L 154 ASN cc_start: 0.8611 (p0) cc_final: 0.8397 (p0) REVERT: L 216 VAL cc_start: 0.8334 (t) cc_final: 0.8094 (t) REVERT: L 492 GLN cc_start: 0.6239 (tt0) cc_final: 0.5612 (mm-40) REVERT: M 44 GLU cc_start: 0.7996 (tt0) cc_final: 0.7723 (tt0) REVERT: M 59 MET cc_start: 0.6938 (mmm) cc_final: 0.6490 (mmt) REVERT: M 96 MET cc_start: 0.7943 (mpp) cc_final: 0.7690 (mmt) REVERT: M 154 ASN cc_start: 0.8645 (p0) cc_final: 0.8286 (p0) REVERT: M 335 GLU cc_start: 0.6838 (tp30) cc_final: 0.6358 (tp30) REVERT: M 492 GLN cc_start: 0.6423 (tt0) cc_final: 0.5624 (mm-40) REVERT: M 503 LEU cc_start: 0.7718 (OUTLIER) cc_final: 0.7485 (mm) REVERT: N 216 VAL cc_start: 0.8089 (t) cc_final: 0.7821 (t) REVERT: N 364 MET cc_start: 0.7412 (mtp) cc_final: 0.7194 (mtp) REVERT: N 492 GLN cc_start: 0.6305 (tt0) cc_final: 0.5945 (mm-40) REVERT: N 503 LEU cc_start: 0.7868 (OUTLIER) cc_final: 0.7608 (mm) REVERT: O 169 LEU cc_start: 0.7203 (mt) cc_final: 0.6652 (mt) REVERT: O 176 MET cc_start: 0.7108 (OUTLIER) cc_final: 0.6795 (mmp) REVERT: O 322 LEU cc_start: 0.8017 (OUTLIER) cc_final: 0.7728 (tp) REVERT: O 492 GLN cc_start: 0.6218 (tt0) cc_final: 0.5716 (mm-40) REVERT: P 56 ASN cc_start: 0.5129 (t0) cc_final: 0.4547 (t0) REVERT: P 154 ASN cc_start: 0.8565 (p0) cc_final: 0.8172 (p0) REVERT: P 492 GLN cc_start: 0.6367 (tt0) cc_final: 0.5696 (mm-40) outliers start: 233 outliers final: 115 residues processed: 1481 average time/residue: 0.6848 time to fit residues: 1799.3738 Evaluate side-chains 1243 residues out of total 8544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 1120 time to evaluate : 6.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 366 ASP Chi-restraints excluded: chain C residue 538 VAL Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 234 ASN Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain D residue 281 VAL Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain E residue 277 SER Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 327 VAL Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 538 VAL Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 234 ASN Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 499 ILE Chi-restraints excluded: chain F residue 538 VAL Chi-restraints excluded: chain F residue 610 THR Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 113 LEU Chi-restraints excluded: chain G residue 176 MET Chi-restraints excluded: chain G residue 234 ASN Chi-restraints excluded: chain G residue 333 THR Chi-restraints excluded: chain G residue 503 LEU Chi-restraints excluded: chain G residue 538 VAL Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 113 LEU Chi-restraints excluded: chain H residue 234 ASN Chi-restraints excluded: chain H residue 277 SER Chi-restraints excluded: chain H residue 327 VAL Chi-restraints excluded: chain H residue 333 THR Chi-restraints excluded: chain H residue 366 ASP Chi-restraints excluded: chain H residue 538 VAL Chi-restraints excluded: chain H residue 628 LYS Chi-restraints excluded: chain I residue 277 SER Chi-restraints excluded: chain I residue 327 VAL Chi-restraints excluded: chain I residue 333 THR Chi-restraints excluded: chain I residue 503 LEU Chi-restraints excluded: chain I residue 538 VAL Chi-restraints excluded: chain J residue 277 SER Chi-restraints excluded: chain J residue 333 THR Chi-restraints excluded: chain J residue 499 ILE Chi-restraints excluded: chain J residue 538 VAL Chi-restraints excluded: chain K residue 38 LEU Chi-restraints excluded: chain K residue 84 VAL Chi-restraints excluded: chain K residue 113 LEU Chi-restraints excluded: chain K residue 333 THR Chi-restraints excluded: chain K residue 499 ILE Chi-restraints excluded: chain K residue 503 LEU Chi-restraints excluded: chain K residue 538 VAL Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 84 VAL Chi-restraints excluded: chain L residue 113 LEU Chi-restraints excluded: chain L residue 195 GLU Chi-restraints excluded: chain L residue 234 ASN Chi-restraints excluded: chain L residue 277 SER Chi-restraints excluded: chain L residue 327 VAL Chi-restraints excluded: chain L residue 333 THR Chi-restraints excluded: chain L residue 538 VAL Chi-restraints excluded: chain L residue 628 LYS Chi-restraints excluded: chain M residue 176 MET Chi-restraints excluded: chain M residue 277 SER Chi-restraints excluded: chain M residue 327 VAL Chi-restraints excluded: chain M residue 333 THR Chi-restraints excluded: chain M residue 503 LEU Chi-restraints excluded: chain M residue 538 VAL Chi-restraints excluded: chain N residue 38 LEU Chi-restraints excluded: chain N residue 131 THR Chi-restraints excluded: chain N residue 234 ASN Chi-restraints excluded: chain N residue 277 SER Chi-restraints excluded: chain N residue 333 THR Chi-restraints excluded: chain N residue 503 LEU Chi-restraints excluded: chain N residue 538 VAL Chi-restraints excluded: chain O residue 84 VAL Chi-restraints excluded: chain O residue 113 LEU Chi-restraints excluded: chain O residue 176 MET Chi-restraints excluded: chain O residue 234 ASN Chi-restraints excluded: chain O residue 277 SER Chi-restraints excluded: chain O residue 322 LEU Chi-restraints excluded: chain O residue 333 THR Chi-restraints excluded: chain O residue 366 ASP Chi-restraints excluded: chain O residue 416 VAL Chi-restraints excluded: chain O residue 538 VAL Chi-restraints excluded: chain P residue 84 VAL Chi-restraints excluded: chain P residue 195 GLU Chi-restraints excluded: chain P residue 234 ASN Chi-restraints excluded: chain P residue 277 SER Chi-restraints excluded: chain P residue 327 VAL Chi-restraints excluded: chain P residue 333 THR Chi-restraints excluded: chain P residue 366 ASP Chi-restraints excluded: chain P residue 503 LEU Chi-restraints excluded: chain P residue 538 VAL Chi-restraints excluded: chain P residue 628 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 960 random chunks: chunk 484 optimal weight: 0.7980 chunk 270 optimal weight: 5.9990 chunk 725 optimal weight: 1.9990 chunk 593 optimal weight: 0.8980 chunk 240 optimal weight: 1.9990 chunk 873 optimal weight: 7.9990 chunk 943 optimal weight: 1.9990 chunk 777 optimal weight: 5.9990 chunk 866 optimal weight: 0.1980 chunk 297 optimal weight: 8.9990 chunk 700 optimal weight: 0.6980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 234 ASN A 561 HIS ** B 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 345 ASN ** B 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 561 HIS D 625 ASN ** E 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 186 GLN ** E 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 220 HIS E 345 ASN E 561 HIS E 625 ASN ** F 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 625 ASN ** G 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 625 ASN ** H 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 625 ASN ** I 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 361 GLN I 625 ASN ** J 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 234 ASN ** J 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 625 ASN ** K 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 625 ASN ** M 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 234 ASN ** M 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 361 GLN ** N 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 186 GLN ** N 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 625 ASN ** O 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 220 HIS ** P 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 625 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7100 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 77344 Z= 0.215 Angle : 0.563 10.273 105104 Z= 0.283 Chirality : 0.043 0.212 12160 Planarity : 0.004 0.047 13488 Dihedral : 4.489 28.806 10928 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 3.41 % Allowed : 17.28 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.08), residues: 9600 helix: -0.17 (0.10), residues: 2336 sheet: -1.18 (0.12), residues: 1808 loop : -1.66 (0.08), residues: 5456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 292 HIS 0.006 0.001 HIS A 204 PHE 0.034 0.002 PHE P 225 TYR 0.018 0.002 TYR A 593 ARG 0.005 0.001 ARG D 222 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19200 Ramachandran restraints generated. 9600 Oldfield, 0 Emsley, 9600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19200 Ramachandran restraints generated. 9600 Oldfield, 0 Emsley, 9600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1509 residues out of total 8544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 291 poor density : 1218 time to evaluate : 6.156 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: A 169 LEU cc_start: 0.7112 (mt) cc_final: 0.6645 (mt) REVERT: A 335 GLU cc_start: 0.7085 (tp30) cc_final: 0.6862 (tp30) REVERT: A 492 GLN cc_start: 0.6282 (tt0) cc_final: 0.5516 (mm-40) REVERT: A 516 GLU cc_start: 0.6377 (tp30) cc_final: 0.5958 (tp30) REVERT: B 105 MET cc_start: 0.7925 (mmm) cc_final: 0.7686 (mmm) REVERT: B 135 ARG cc_start: 0.7645 (ttp-110) cc_final: 0.7353 (mtm110) REVERT: B 248 VAL cc_start: 0.7818 (t) cc_final: 0.6861 (m) REVERT: B 265 ASP cc_start: 0.6876 (t0) cc_final: 0.6651 (t0) REVERT: B 303 ILE cc_start: 0.7372 (mm) cc_final: 0.7104 (mm) REVERT: B 322 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.8051 (tp) REVERT: B 364 MET cc_start: 0.7096 (mtp) cc_final: 0.6873 (mtp) REVERT: B 562 LEU cc_start: 0.8405 (tt) cc_final: 0.8202 (tp) REVERT: C 105 MET cc_start: 0.7754 (mmm) cc_final: 0.7439 (mmm) REVERT: C 176 MET cc_start: 0.7691 (OUTLIER) cc_final: 0.7170 (mmp) REVERT: C 492 GLN cc_start: 0.6306 (tt0) cc_final: 0.5738 (mm-40) REVERT: D 154 ASN cc_start: 0.8340 (p0) cc_final: 0.8132 (p0) REVERT: D 169 LEU cc_start: 0.7125 (mt) cc_final: 0.6615 (mt) REVERT: D 308 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8866 (pp) REVERT: D 399 GLN cc_start: 0.7029 (pp30) cc_final: 0.6288 (pp30) REVERT: D 492 GLN cc_start: 0.6224 (tt0) cc_final: 0.5549 (mm-40) REVERT: E 59 MET cc_start: 0.6884 (mmm) cc_final: 0.6436 (mmt) REVERT: E 169 LEU cc_start: 0.7118 (mt) cc_final: 0.6512 (mt) REVERT: E 189 MET cc_start: 0.8411 (tpp) cc_final: 0.8196 (tpp) REVERT: E 492 GLN cc_start: 0.6228 (tt0) cc_final: 0.5560 (mm-40) REVERT: F 59 MET cc_start: 0.6205 (mmm) cc_final: 0.5893 (mmt) REVERT: F 154 ASN cc_start: 0.8438 (p0) cc_final: 0.8198 (p0) REVERT: F 265 ASP cc_start: 0.6931 (t0) cc_final: 0.6713 (t0) REVERT: F 364 MET cc_start: 0.7481 (mtp) cc_final: 0.7272 (mtp) REVERT: F 492 GLN cc_start: 0.6560 (tt0) cc_final: 0.5975 (mm-40) REVERT: G 78 TYR cc_start: 0.8230 (m-80) cc_final: 0.8027 (m-80) REVERT: G 105 MET cc_start: 0.7896 (mmm) cc_final: 0.7580 (mmm) REVERT: G 169 LEU cc_start: 0.7251 (mt) cc_final: 0.6759 (mt) REVERT: G 216 VAL cc_start: 0.8363 (t) cc_final: 0.8143 (t) REVERT: G 265 ASP cc_start: 0.6632 (t0) cc_final: 0.6312 (t0) REVERT: G 492 GLN cc_start: 0.6438 (tt0) cc_final: 0.5835 (mm-40) REVERT: H 105 MET cc_start: 0.7957 (mmm) cc_final: 0.7739 (mmm) REVERT: H 154 ASN cc_start: 0.8520 (p0) cc_final: 0.8143 (p0) REVERT: H 169 LEU cc_start: 0.7170 (mt) cc_final: 0.6686 (mt) REVERT: H 335 GLU cc_start: 0.7224 (tp30) cc_final: 0.6949 (tp30) REVERT: H 492 GLN cc_start: 0.6399 (tt0) cc_final: 0.5782 (mm-40) REVERT: I 44 GLU cc_start: 0.8216 (tt0) cc_final: 0.8002 (tt0) REVERT: I 59 MET cc_start: 0.6844 (mmm) cc_final: 0.6531 (mmt) REVERT: I 169 LEU cc_start: 0.7229 (mt) cc_final: 0.6600 (mt) REVERT: I 492 GLN cc_start: 0.6722 (tt0) cc_final: 0.5780 (mm-40) REVERT: I 510 CYS cc_start: 0.6107 (OUTLIER) cc_final: 0.5353 (m) REVERT: J 57 VAL cc_start: 0.8482 (m) cc_final: 0.8281 (m) REVERT: J 59 MET cc_start: 0.6880 (mmm) cc_final: 0.6469 (mmt) REVERT: J 248 VAL cc_start: 0.7689 (t) cc_final: 0.6594 (m) REVERT: J 492 GLN cc_start: 0.6447 (tt0) cc_final: 0.5877 (mm-40) REVERT: K 169 LEU cc_start: 0.7339 (mt) cc_final: 0.6770 (mt) REVERT: K 216 VAL cc_start: 0.8378 (t) cc_final: 0.8163 (t) REVERT: K 322 LEU cc_start: 0.8237 (tp) cc_final: 0.7981 (tp) REVERT: K 492 GLN cc_start: 0.6177 (tt0) cc_final: 0.5662 (mm-40) REVERT: L 105 MET cc_start: 0.8173 (mmm) cc_final: 0.7883 (mmm) REVERT: L 154 ASN cc_start: 0.8471 (p0) cc_final: 0.8114 (p0) REVERT: L 169 LEU cc_start: 0.7182 (mt) cc_final: 0.6689 (mt) REVERT: L 251 LYS cc_start: 0.6463 (ttmm) cc_final: 0.6233 (ttmm) REVERT: L 335 GLU cc_start: 0.7197 (tp30) cc_final: 0.6924 (tp30) REVERT: L 492 GLN cc_start: 0.6397 (tt0) cc_final: 0.5772 (mm-40) REVERT: M 59 MET cc_start: 0.6894 (mmm) cc_final: 0.6557 (mmt) REVERT: M 96 MET cc_start: 0.8057 (mpp) cc_final: 0.7605 (mmt) REVERT: M 169 LEU cc_start: 0.7127 (mt) cc_final: 0.6588 (mt) REVERT: M 335 GLU cc_start: 0.6974 (tp30) cc_final: 0.6645 (tp30) REVERT: M 492 GLN cc_start: 0.6233 (tt0) cc_final: 0.5404 (mm-40) REVERT: M 503 LEU cc_start: 0.7758 (OUTLIER) cc_final: 0.7545 (mm) REVERT: M 510 CYS cc_start: 0.5837 (OUTLIER) cc_final: 0.5135 (m) REVERT: N 154 ASN cc_start: 0.8355 (p0) cc_final: 0.8101 (p0) REVERT: N 248 VAL cc_start: 0.7689 (t) cc_final: 0.6590 (m) REVERT: N 492 GLN cc_start: 0.6378 (tt0) cc_final: 0.5947 (mm-40) REVERT: N 503 LEU cc_start: 0.7883 (OUTLIER) cc_final: 0.7626 (mm) REVERT: O 78 TYR cc_start: 0.8265 (m-80) cc_final: 0.7967 (m-80) REVERT: O 169 LEU cc_start: 0.7306 (mt) cc_final: 0.6702 (mt) REVERT: O 189 MET cc_start: 0.8539 (tpp) cc_final: 0.8099 (tpp) REVERT: O 492 GLN cc_start: 0.6227 (tt0) cc_final: 0.5681 (mm-40) REVERT: P 154 ASN cc_start: 0.8491 (p0) cc_final: 0.8111 (p0) REVERT: P 189 MET cc_start: 0.8434 (tpp) cc_final: 0.8108 (tpp) REVERT: P 216 VAL cc_start: 0.8391 (t) cc_final: 0.8185 (t) REVERT: P 492 GLN cc_start: 0.6521 (tt0) cc_final: 0.5781 (mm-40) outliers start: 291 outliers final: 179 residues processed: 1392 average time/residue: 0.6686 time to fit residues: 1670.4908 Evaluate side-chains 1279 residues out of total 8544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 1093 time to evaluate : 6.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 499 ILE Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 366 ASP Chi-restraints excluded: chain C residue 538 VAL Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 195 GLU Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 277 SER Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 503 LEU Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 308 LEU Chi-restraints excluded: chain F residue 322 LEU Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 499 ILE Chi-restraints excluded: chain F residue 538 VAL Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain G residue 113 LEU Chi-restraints excluded: chain G residue 131 THR Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain G residue 308 LEU Chi-restraints excluded: chain G residue 333 THR Chi-restraints excluded: chain G residue 366 ASP Chi-restraints excluded: chain G residue 538 VAL Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 113 LEU Chi-restraints excluded: chain H residue 147 THR Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 176 MET Chi-restraints excluded: chain H residue 188 LYS Chi-restraints excluded: chain H residue 195 GLU Chi-restraints excluded: chain H residue 277 SER Chi-restraints excluded: chain H residue 327 VAL Chi-restraints excluded: chain H residue 333 THR Chi-restraints excluded: chain H residue 366 ASP Chi-restraints excluded: chain H residue 416 VAL Chi-restraints excluded: chain H residue 538 VAL Chi-restraints excluded: chain H residue 628 LYS Chi-restraints excluded: chain I residue 38 LEU Chi-restraints excluded: chain I residue 86 THR Chi-restraints excluded: chain I residue 147 THR Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 277 SER Chi-restraints excluded: chain I residue 308 LEU Chi-restraints excluded: chain I residue 327 VAL Chi-restraints excluded: chain I residue 333 THR Chi-restraints excluded: chain I residue 499 ILE Chi-restraints excluded: chain I residue 510 CYS Chi-restraints excluded: chain I residue 538 VAL Chi-restraints excluded: chain J residue 38 LEU Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 131 THR Chi-restraints excluded: chain J residue 159 VAL Chi-restraints excluded: chain J residue 234 ASN Chi-restraints excluded: chain J residue 268 SER Chi-restraints excluded: chain J residue 277 SER Chi-restraints excluded: chain J residue 308 LEU Chi-restraints excluded: chain J residue 322 LEU Chi-restraints excluded: chain J residue 333 THR Chi-restraints excluded: chain J residue 499 ILE Chi-restraints excluded: chain K residue 38 LEU Chi-restraints excluded: chain K residue 84 VAL Chi-restraints excluded: chain K residue 113 LEU Chi-restraints excluded: chain K residue 159 VAL Chi-restraints excluded: chain K residue 308 LEU Chi-restraints excluded: chain K residue 333 THR Chi-restraints excluded: chain K residue 499 ILE Chi-restraints excluded: chain K residue 538 VAL Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 84 VAL Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 113 LEU Chi-restraints excluded: chain L residue 147 THR Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain L residue 176 MET Chi-restraints excluded: chain L residue 188 LYS Chi-restraints excluded: chain L residue 195 GLU Chi-restraints excluded: chain L residue 277 SER Chi-restraints excluded: chain L residue 327 VAL Chi-restraints excluded: chain L residue 333 THR Chi-restraints excluded: chain L residue 416 VAL Chi-restraints excluded: chain L residue 538 VAL Chi-restraints excluded: chain L residue 628 LYS Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 86 THR Chi-restraints excluded: chain M residue 147 THR Chi-restraints excluded: chain M residue 159 VAL Chi-restraints excluded: chain M residue 277 SER Chi-restraints excluded: chain M residue 308 LEU Chi-restraints excluded: chain M residue 322 LEU Chi-restraints excluded: chain M residue 333 THR Chi-restraints excluded: chain M residue 503 LEU Chi-restraints excluded: chain M residue 510 CYS Chi-restraints excluded: chain M residue 538 VAL Chi-restraints excluded: chain N residue 38 LEU Chi-restraints excluded: chain N residue 86 THR Chi-restraints excluded: chain N residue 131 THR Chi-restraints excluded: chain N residue 159 VAL Chi-restraints excluded: chain N residue 277 SER Chi-restraints excluded: chain N residue 308 LEU Chi-restraints excluded: chain N residue 322 LEU Chi-restraints excluded: chain N residue 333 THR Chi-restraints excluded: chain N residue 503 LEU Chi-restraints excluded: chain N residue 538 VAL Chi-restraints excluded: chain O residue 38 LEU Chi-restraints excluded: chain O residue 84 VAL Chi-restraints excluded: chain O residue 86 THR Chi-restraints excluded: chain O residue 113 LEU Chi-restraints excluded: chain O residue 131 THR Chi-restraints excluded: chain O residue 147 THR Chi-restraints excluded: chain O residue 159 VAL Chi-restraints excluded: chain O residue 277 SER Chi-restraints excluded: chain O residue 333 THR Chi-restraints excluded: chain O residue 366 ASP Chi-restraints excluded: chain O residue 416 VAL Chi-restraints excluded: chain O residue 538 VAL Chi-restraints excluded: chain P residue 38 LEU Chi-restraints excluded: chain P residue 84 VAL Chi-restraints excluded: chain P residue 86 THR Chi-restraints excluded: chain P residue 131 THR Chi-restraints excluded: chain P residue 147 THR Chi-restraints excluded: chain P residue 159 VAL Chi-restraints excluded: chain P residue 176 MET Chi-restraints excluded: chain P residue 188 LYS Chi-restraints excluded: chain P residue 195 GLU Chi-restraints excluded: chain P residue 277 SER Chi-restraints excluded: chain P residue 303 ILE Chi-restraints excluded: chain P residue 327 VAL Chi-restraints excluded: chain P residue 333 THR Chi-restraints excluded: chain P residue 366 ASP Chi-restraints excluded: chain P residue 416 VAL Chi-restraints excluded: chain P residue 503 LEU Chi-restraints excluded: chain P residue 538 VAL Chi-restraints excluded: chain P residue 628 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 960 random chunks: chunk 862 optimal weight: 0.9990 chunk 656 optimal weight: 5.9990 chunk 453 optimal weight: 3.9990 chunk 96 optimal weight: 9.9990 chunk 416 optimal weight: 4.9990 chunk 586 optimal weight: 1.9990 chunk 876 optimal weight: 10.0000 chunk 927 optimal weight: 5.9990 chunk 457 optimal weight: 9.9990 chunk 830 optimal weight: 8.9990 chunk 250 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 234 ASN A 345 ASN ** A 561 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 HIS B 234 ASN ** B 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 234 ASN ** D 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 234 ASN D 299 HIS D 345 ASN ** D 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 561 HIS ** E 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 234 ASN E 357 ASN E 561 HIS ** F 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 234 ASN ** F 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 234 ASN G 625 ASN ** H 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 234 ASN H 345 ASN ** H 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 234 ASN ** I 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 361 GLN ** J 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 220 HIS J 230 GLN J 234 ASN ** J 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 234 ASN ** L 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 234 ASN L 345 ASN ** L 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 234 ASN ** M 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 361 GLN ** N 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 234 ASN ** N 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 36 ASN ** O 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 234 ASN P 36 ASN ** P 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 234 ASN P 345 ASN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.3598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.116 77344 Z= 0.468 Angle : 0.735 10.054 105104 Z= 0.376 Chirality : 0.050 0.228 12160 Planarity : 0.006 0.071 13488 Dihedral : 5.196 36.265 10928 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 17.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 5.08 % Allowed : 18.59 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.08), residues: 9600 helix: -0.53 (0.10), residues: 2352 sheet: -1.79 (0.12), residues: 1792 loop : -1.68 (0.08), residues: 5456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP O 51 HIS 0.014 0.002 HIS A 204 PHE 0.035 0.003 PHE F 313 TYR 0.023 0.003 TYR M 593 ARG 0.011 0.001 ARG I 222 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19200 Ramachandran restraints generated. 9600 Oldfield, 0 Emsley, 9600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19200 Ramachandran restraints generated. 9600 Oldfield, 0 Emsley, 9600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1644 residues out of total 8544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 434 poor density : 1210 time to evaluate : 6.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 LEU cc_start: 0.7651 (mt) cc_final: 0.7095 (mt) REVERT: A 458 ARG cc_start: 0.7575 (mtt90) cc_final: 0.7000 (mtt90) REVERT: A 492 GLN cc_start: 0.6543 (tt0) cc_final: 0.6192 (mm-40) REVERT: A 510 CYS cc_start: 0.6904 (m) cc_final: 0.6661 (m) REVERT: B 59 MET cc_start: 0.7375 (mmm) cc_final: 0.7149 (mmt) REVERT: B 135 ARG cc_start: 0.8583 (ttp-110) cc_final: 0.7918 (mtm110) REVERT: B 154 ASN cc_start: 0.8426 (p0) cc_final: 0.8166 (p0) REVERT: B 169 LEU cc_start: 0.7698 (mt) cc_final: 0.7081 (mt) REVERT: B 175 LEU cc_start: 0.7969 (OUTLIER) cc_final: 0.7654 (mt) REVERT: B 189 MET cc_start: 0.8671 (tpp) cc_final: 0.8289 (tpp) REVERT: B 314 ILE cc_start: 0.8542 (OUTLIER) cc_final: 0.7922 (mt) REVERT: B 364 MET cc_start: 0.7978 (mtp) cc_final: 0.7748 (mtp) REVERT: B 593 TYR cc_start: 0.7977 (m-80) cc_final: 0.7756 (m-80) REVERT: C 78 TYR cc_start: 0.8716 (m-80) cc_final: 0.8370 (m-80) REVERT: C 135 ARG cc_start: 0.8371 (ttp-110) cc_final: 0.8047 (ttm170) REVERT: C 189 MET cc_start: 0.8691 (tpp) cc_final: 0.8287 (tpp) REVERT: C 218 GLU cc_start: 0.7517 (mt-10) cc_final: 0.7042 (mp0) REVERT: C 314 ILE cc_start: 0.8739 (OUTLIER) cc_final: 0.8164 (mt) REVERT: C 399 GLN cc_start: 0.6675 (pp30) cc_final: 0.6247 (pp30) REVERT: C 492 GLN cc_start: 0.6541 (tt0) cc_final: 0.6059 (mm-40) REVERT: D 59 MET cc_start: 0.7498 (mmm) cc_final: 0.6765 (mmt) REVERT: D 78 TYR cc_start: 0.8518 (m-80) cc_final: 0.8151 (m-80) REVERT: D 135 ARG cc_start: 0.8371 (ttp-110) cc_final: 0.8045 (mtm110) REVERT: D 169 LEU cc_start: 0.7707 (mt) cc_final: 0.7165 (mt) REVERT: D 218 GLU cc_start: 0.7573 (mt-10) cc_final: 0.7281 (mt-10) REVERT: D 342 TYR cc_start: 0.8475 (m-80) cc_final: 0.8121 (m-80) REVERT: D 399 GLN cc_start: 0.7378 (pp30) cc_final: 0.6755 (pp30) REVERT: D 400 LYS cc_start: 0.5742 (mmtp) cc_final: 0.4860 (mmtp) REVERT: D 492 GLN cc_start: 0.6734 (tt0) cc_final: 0.6154 (mm-40) REVERT: D 533 MET cc_start: 0.6445 (ptm) cc_final: 0.6117 (ptp) REVERT: E 135 ARG cc_start: 0.8538 (ttp-110) cc_final: 0.8087 (mtm110) REVERT: E 169 LEU cc_start: 0.7614 (mt) cc_final: 0.7045 (mt) REVERT: E 218 GLU cc_start: 0.7578 (mt-10) cc_final: 0.7359 (mt-10) REVERT: E 264 LYS cc_start: 0.7299 (mmtm) cc_final: 0.7033 (mptt) REVERT: E 314 ILE cc_start: 0.8455 (OUTLIER) cc_final: 0.7633 (mt) REVERT: E 458 ARG cc_start: 0.7700 (mtt180) cc_final: 0.7498 (mtt90) REVERT: E 492 GLN cc_start: 0.6417 (tt0) cc_final: 0.5968 (mm-40) REVERT: E 502 ASN cc_start: 0.6837 (OUTLIER) cc_final: 0.6457 (p0) REVERT: E 510 CYS cc_start: 0.6979 (m) cc_final: 0.6524 (m) REVERT: F 59 MET cc_start: 0.6881 (mmm) cc_final: 0.6470 (mmt) REVERT: F 105 MET cc_start: 0.8013 (mmm) cc_final: 0.7810 (mmm) REVERT: F 135 ARG cc_start: 0.8570 (ttp-110) cc_final: 0.8058 (mtm110) REVERT: F 175 LEU cc_start: 0.8153 (OUTLIER) cc_final: 0.7865 (mt) REVERT: F 189 MET cc_start: 0.8735 (tpp) cc_final: 0.8449 (tpp) REVERT: F 265 ASP cc_start: 0.7067 (t0) cc_final: 0.6725 (t0) REVERT: F 314 ILE cc_start: 0.8357 (OUTLIER) cc_final: 0.7866 (mt) REVERT: F 400 LYS cc_start: 0.5427 (mmtp) cc_final: 0.5056 (mmtp) REVERT: F 492 GLN cc_start: 0.6520 (tt0) cc_final: 0.6218 (mm-40) REVERT: G 59 MET cc_start: 0.7246 (mmm) cc_final: 0.6907 (mmt) REVERT: G 78 TYR cc_start: 0.8560 (m-80) cc_final: 0.8342 (m-80) REVERT: G 135 ARG cc_start: 0.8375 (ttp-110) cc_final: 0.8132 (ttm170) REVERT: G 189 MET cc_start: 0.8706 (tpp) cc_final: 0.8311 (tpp) REVERT: G 218 GLU cc_start: 0.7469 (mt-10) cc_final: 0.7015 (mp0) REVERT: G 314 ILE cc_start: 0.8808 (OUTLIER) cc_final: 0.8179 (mt) REVERT: G 399 GLN cc_start: 0.6659 (pp30) cc_final: 0.6250 (pp30) REVERT: G 458 ARG cc_start: 0.7168 (ptp90) cc_final: 0.6959 (ptp90) REVERT: G 492 GLN cc_start: 0.6591 (tt0) cc_final: 0.6104 (mm-40) REVERT: H 78 TYR cc_start: 0.8587 (m-80) cc_final: 0.8147 (m-80) REVERT: H 218 GLU cc_start: 0.7599 (mt-10) cc_final: 0.7320 (mt-10) REVERT: H 308 LEU cc_start: 0.9311 (OUTLIER) cc_final: 0.9090 (pp) REVERT: H 399 GLN cc_start: 0.6903 (pp30) cc_final: 0.6533 (pp30) REVERT: H 492 GLN cc_start: 0.6792 (tt0) cc_final: 0.6278 (mm-40) REVERT: I 59 MET cc_start: 0.7218 (mmm) cc_final: 0.6700 (mmt) REVERT: I 169 LEU cc_start: 0.7705 (mt) cc_final: 0.7113 (mt) REVERT: I 492 GLN cc_start: 0.6897 (tt0) cc_final: 0.6144 (mm-40) REVERT: J 135 ARG cc_start: 0.8607 (ttp-110) cc_final: 0.8132 (mtm110) REVERT: J 154 ASN cc_start: 0.8332 (p0) cc_final: 0.8109 (p0) REVERT: J 169 LEU cc_start: 0.7595 (mt) cc_final: 0.7069 (mt) REVERT: J 175 LEU cc_start: 0.8049 (OUTLIER) cc_final: 0.7765 (mt) REVERT: J 218 GLU cc_start: 0.7476 (mt-10) cc_final: 0.7256 (mt-10) REVERT: J 314 ILE cc_start: 0.8315 (OUTLIER) cc_final: 0.7780 (mt) REVERT: J 399 GLN cc_start: 0.6958 (pp30) cc_final: 0.5968 (pp30) REVERT: J 492 GLN cc_start: 0.6648 (tt0) cc_final: 0.6161 (mm-40) REVERT: K 78 TYR cc_start: 0.8677 (m-80) cc_final: 0.8322 (m-80) REVERT: K 135 ARG cc_start: 0.8390 (ttp-110) cc_final: 0.8043 (ttm170) REVERT: K 189 MET cc_start: 0.8796 (tpp) cc_final: 0.8404 (tpp) REVERT: K 218 GLU cc_start: 0.7539 (mt-10) cc_final: 0.7102 (mp0) REVERT: K 458 ARG cc_start: 0.7415 (ptt-90) cc_final: 0.7090 (ptp90) REVERT: K 492 GLN cc_start: 0.6540 (tt0) cc_final: 0.6030 (mm-40) REVERT: L 59 MET cc_start: 0.7411 (mmm) cc_final: 0.6816 (mmt) REVERT: L 78 TYR cc_start: 0.8610 (m-80) cc_final: 0.8386 (m-80) REVERT: L 169 LEU cc_start: 0.7798 (mt) cc_final: 0.7165 (mt) REVERT: L 218 GLU cc_start: 0.7578 (mt-10) cc_final: 0.7357 (mt-10) REVERT: L 274 ARG cc_start: 0.8448 (ptm-80) cc_final: 0.8243 (ptm-80) REVERT: L 399 GLN cc_start: 0.6887 (pp30) cc_final: 0.6527 (pp30) REVERT: L 492 GLN cc_start: 0.6761 (tt0) cc_final: 0.6266 (mm-40) REVERT: M 59 MET cc_start: 0.7265 (mmm) cc_final: 0.6748 (mmt) REVERT: M 169 LEU cc_start: 0.7699 (mt) cc_final: 0.7116 (mt) REVERT: M 314 ILE cc_start: 0.8459 (OUTLIER) cc_final: 0.7868 (mt) REVERT: M 492 GLN cc_start: 0.6802 (tt0) cc_final: 0.6030 (mm-40) REVERT: M 502 ASN cc_start: 0.7080 (OUTLIER) cc_final: 0.6792 (p0) REVERT: N 44 GLU cc_start: 0.8530 (tt0) cc_final: 0.8316 (tt0) REVERT: N 59 MET cc_start: 0.7485 (mmm) cc_final: 0.7272 (mmt) REVERT: N 135 ARG cc_start: 0.8619 (ttp-110) cc_final: 0.8129 (mtm110) REVERT: N 169 LEU cc_start: 0.7620 (mt) cc_final: 0.7094 (mt) REVERT: N 175 LEU cc_start: 0.8079 (OUTLIER) cc_final: 0.7777 (mt) REVERT: N 314 ILE cc_start: 0.8351 (OUTLIER) cc_final: 0.7809 (mt) REVERT: N 492 GLN cc_start: 0.6482 (tt0) cc_final: 0.6103 (mm-40) REVERT: N 503 LEU cc_start: 0.7909 (OUTLIER) cc_final: 0.7701 (mm) REVERT: O 59 MET cc_start: 0.7102 (mmm) cc_final: 0.6830 (mmt) REVERT: O 78 TYR cc_start: 0.8498 (m-80) cc_final: 0.8045 (m-80) REVERT: O 189 MET cc_start: 0.8718 (tpp) cc_final: 0.8322 (tpp) REVERT: O 218 GLU cc_start: 0.7496 (mt-10) cc_final: 0.7285 (mt-10) REVERT: O 399 GLN cc_start: 0.6892 (pp30) cc_final: 0.6540 (pp30) REVERT: O 492 GLN cc_start: 0.6478 (tt0) cc_final: 0.6022 (mm-40) REVERT: P 314 ILE cc_start: 0.8670 (OUTLIER) cc_final: 0.7949 (mt) REVERT: P 335 GLU cc_start: 0.7519 (tp30) cc_final: 0.7068 (tp30) REVERT: P 399 GLN cc_start: 0.6649 (pp30) cc_final: 0.6388 (pp30) REVERT: P 492 GLN cc_start: 0.6659 (tt0) cc_final: 0.6151 (mm-40) outliers start: 434 outliers final: 263 residues processed: 1513 average time/residue: 0.6824 time to fit residues: 1831.4809 Evaluate side-chains 1323 residues out of total 8544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 280 poor density : 1043 time to evaluate : 6.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 151 GLN Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 366 ASP Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 481 THR Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 594 THR Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 366 ASP Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain C residue 422 THR Chi-restraints excluded: chain C residue 481 THR Chi-restraints excluded: chain C residue 538 VAL Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 195 GLU Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 365 ASP Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 481 THR Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 571 VAL Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 277 SER Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain E residue 314 ILE Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 416 VAL Chi-restraints excluded: chain E residue 481 THR Chi-restraints excluded: chain E residue 502 ASN Chi-restraints excluded: chain E residue 538 VAL Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 175 LEU Chi-restraints excluded: chain F residue 268 SER Chi-restraints excluded: chain F residue 277 SER Chi-restraints excluded: chain F residue 303 ILE Chi-restraints excluded: chain F residue 308 LEU Chi-restraints excluded: chain F residue 314 ILE Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain F residue 481 THR Chi-restraints excluded: chain F residue 499 ILE Chi-restraints excluded: chain F residue 538 VAL Chi-restraints excluded: chain F residue 571 VAL Chi-restraints excluded: chain F residue 594 THR Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain G residue 113 LEU Chi-restraints excluded: chain G residue 131 THR Chi-restraints excluded: chain G residue 147 THR Chi-restraints excluded: chain G residue 193 LEU Chi-restraints excluded: chain G residue 277 SER Chi-restraints excluded: chain G residue 314 ILE Chi-restraints excluded: chain G residue 333 THR Chi-restraints excluded: chain G residue 366 ASP Chi-restraints excluded: chain G residue 416 VAL Chi-restraints excluded: chain G residue 481 THR Chi-restraints excluded: chain G residue 538 VAL Chi-restraints excluded: chain G residue 571 VAL Chi-restraints excluded: chain G residue 594 THR Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 113 LEU Chi-restraints excluded: chain H residue 115 ILE Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain H residue 147 THR Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 176 MET Chi-restraints excluded: chain H residue 195 GLU Chi-restraints excluded: chain H residue 239 SER Chi-restraints excluded: chain H residue 277 SER Chi-restraints excluded: chain H residue 308 LEU Chi-restraints excluded: chain H residue 327 VAL Chi-restraints excluded: chain H residue 333 THR Chi-restraints excluded: chain H residue 366 ASP Chi-restraints excluded: chain H residue 416 VAL Chi-restraints excluded: chain H residue 481 THR Chi-restraints excluded: chain H residue 503 LEU Chi-restraints excluded: chain H residue 538 VAL Chi-restraints excluded: chain H residue 571 VAL Chi-restraints excluded: chain I residue 38 LEU Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain I residue 86 THR Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 147 THR Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 277 SER Chi-restraints excluded: chain I residue 308 LEU Chi-restraints excluded: chain I residue 322 LEU Chi-restraints excluded: chain I residue 327 VAL Chi-restraints excluded: chain I residue 333 THR Chi-restraints excluded: chain I residue 481 THR Chi-restraints excluded: chain I residue 538 VAL Chi-restraints excluded: chain I residue 571 VAL Chi-restraints excluded: chain J residue 38 LEU Chi-restraints excluded: chain J residue 45 VAL Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 119 LEU Chi-restraints excluded: chain J residue 131 THR Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 159 VAL Chi-restraints excluded: chain J residue 175 LEU Chi-restraints excluded: chain J residue 268 SER Chi-restraints excluded: chain J residue 277 SER Chi-restraints excluded: chain J residue 308 LEU Chi-restraints excluded: chain J residue 314 ILE Chi-restraints excluded: chain J residue 333 THR Chi-restraints excluded: chain J residue 366 ASP Chi-restraints excluded: chain J residue 416 VAL Chi-restraints excluded: chain J residue 538 VAL Chi-restraints excluded: chain J residue 571 VAL Chi-restraints excluded: chain K residue 38 LEU Chi-restraints excluded: chain K residue 45 VAL Chi-restraints excluded: chain K residue 86 THR Chi-restraints excluded: chain K residue 113 LEU Chi-restraints excluded: chain K residue 147 THR Chi-restraints excluded: chain K residue 176 MET Chi-restraints excluded: chain K residue 277 SER Chi-restraints excluded: chain K residue 308 LEU Chi-restraints excluded: chain K residue 333 THR Chi-restraints excluded: chain K residue 366 ASP Chi-restraints excluded: chain K residue 416 VAL Chi-restraints excluded: chain K residue 481 THR Chi-restraints excluded: chain K residue 499 ILE Chi-restraints excluded: chain K residue 538 VAL Chi-restraints excluded: chain K residue 571 VAL Chi-restraints excluded: chain K residue 594 THR Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 84 VAL Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 113 LEU Chi-restraints excluded: chain L residue 115 ILE Chi-restraints excluded: chain L residue 147 THR Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain L residue 176 MET Chi-restraints excluded: chain L residue 195 GLU Chi-restraints excluded: chain L residue 277 SER Chi-restraints excluded: chain L residue 322 LEU Chi-restraints excluded: chain L residue 327 VAL Chi-restraints excluded: chain L residue 333 THR Chi-restraints excluded: chain L residue 416 VAL Chi-restraints excluded: chain L residue 481 THR Chi-restraints excluded: chain L residue 503 LEU Chi-restraints excluded: chain L residue 538 VAL Chi-restraints excluded: chain L residue 571 VAL Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain M residue 86 THR Chi-restraints excluded: chain M residue 119 LEU Chi-restraints excluded: chain M residue 147 THR Chi-restraints excluded: chain M residue 159 VAL Chi-restraints excluded: chain M residue 193 LEU Chi-restraints excluded: chain M residue 277 SER Chi-restraints excluded: chain M residue 308 LEU Chi-restraints excluded: chain M residue 314 ILE Chi-restraints excluded: chain M residue 322 LEU Chi-restraints excluded: chain M residue 327 VAL Chi-restraints excluded: chain M residue 333 THR Chi-restraints excluded: chain M residue 416 VAL Chi-restraints excluded: chain M residue 481 THR Chi-restraints excluded: chain M residue 502 ASN Chi-restraints excluded: chain M residue 538 VAL Chi-restraints excluded: chain M residue 571 VAL Chi-restraints excluded: chain N residue 38 LEU Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 86 THR Chi-restraints excluded: chain N residue 119 LEU Chi-restraints excluded: chain N residue 131 THR Chi-restraints excluded: chain N residue 147 THR Chi-restraints excluded: chain N residue 159 VAL Chi-restraints excluded: chain N residue 175 LEU Chi-restraints excluded: chain N residue 268 SER Chi-restraints excluded: chain N residue 277 SER Chi-restraints excluded: chain N residue 303 ILE Chi-restraints excluded: chain N residue 308 LEU Chi-restraints excluded: chain N residue 314 ILE Chi-restraints excluded: chain N residue 333 THR Chi-restraints excluded: chain N residue 416 VAL Chi-restraints excluded: chain N residue 481 THR Chi-restraints excluded: chain N residue 503 LEU Chi-restraints excluded: chain N residue 538 VAL Chi-restraints excluded: chain N residue 571 VAL Chi-restraints excluded: chain N residue 594 THR Chi-restraints excluded: chain O residue 38 LEU Chi-restraints excluded: chain O residue 84 VAL Chi-restraints excluded: chain O residue 86 THR Chi-restraints excluded: chain O residue 113 LEU Chi-restraints excluded: chain O residue 119 LEU Chi-restraints excluded: chain O residue 131 THR Chi-restraints excluded: chain O residue 147 THR Chi-restraints excluded: chain O residue 175 LEU Chi-restraints excluded: chain O residue 193 LEU Chi-restraints excluded: chain O residue 277 SER Chi-restraints excluded: chain O residue 333 THR Chi-restraints excluded: chain O residue 366 ASP Chi-restraints excluded: chain O residue 416 VAL Chi-restraints excluded: chain O residue 481 THR Chi-restraints excluded: chain O residue 503 LEU Chi-restraints excluded: chain O residue 509 VAL Chi-restraints excluded: chain O residue 538 VAL Chi-restraints excluded: chain O residue 571 VAL Chi-restraints excluded: chain O residue 594 THR Chi-restraints excluded: chain P residue 38 LEU Chi-restraints excluded: chain P residue 45 VAL Chi-restraints excluded: chain P residue 84 VAL Chi-restraints excluded: chain P residue 86 THR Chi-restraints excluded: chain P residue 113 LEU Chi-restraints excluded: chain P residue 115 ILE Chi-restraints excluded: chain P residue 119 LEU Chi-restraints excluded: chain P residue 131 THR Chi-restraints excluded: chain P residue 147 THR Chi-restraints excluded: chain P residue 159 VAL Chi-restraints excluded: chain P residue 195 GLU Chi-restraints excluded: chain P residue 277 SER Chi-restraints excluded: chain P residue 291 THR Chi-restraints excluded: chain P residue 314 ILE Chi-restraints excluded: chain P residue 322 LEU Chi-restraints excluded: chain P residue 327 VAL Chi-restraints excluded: chain P residue 333 THR Chi-restraints excluded: chain P residue 366 ASP Chi-restraints excluded: chain P residue 416 VAL Chi-restraints excluded: chain P residue 481 THR Chi-restraints excluded: chain P residue 503 LEU Chi-restraints excluded: chain P residue 538 VAL Chi-restraints excluded: chain P residue 571 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 960 random chunks: chunk 772 optimal weight: 1.9990 chunk 526 optimal weight: 7.9990 chunk 13 optimal weight: 0.4980 chunk 690 optimal weight: 0.7980 chunk 382 optimal weight: 0.0770 chunk 791 optimal weight: 0.9980 chunk 641 optimal weight: 20.0000 chunk 1 optimal weight: 0.6980 chunk 473 optimal weight: 0.9990 chunk 832 optimal weight: 2.9990 chunk 234 optimal weight: 0.7980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 234 ASN ** C 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 93 ASN ** D 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 234 ASN D 357 ASN ** D 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 234 ASN E 401 ASN ** F 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 234 ASN ** F 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 234 ASN G 357 ASN ** H 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 401 ASN I 234 ASN ** I 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 53 ASN J 204 HIS ** J 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 361 GLN ** L 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 401 ASN ** M 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 234 ASN ** M 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 401 ASN ** N 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 234 ASN ** N 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 234 ASN ** O 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 401 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.3568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 77344 Z= 0.205 Angle : 0.599 11.061 105104 Z= 0.303 Chirality : 0.044 0.280 12160 Planarity : 0.005 0.070 13488 Dihedral : 4.759 33.317 10928 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 3.77 % Allowed : 21.08 % Favored : 75.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.08), residues: 9600 helix: -0.04 (0.10), residues: 2320 sheet: -1.47 (0.12), residues: 1664 loop : -1.64 (0.08), residues: 5616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP N 292 HIS 0.006 0.001 HIS M 311 PHE 0.026 0.002 PHE E 529 TYR 0.017 0.002 TYR I 78 ARG 0.008 0.001 ARG B 222 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19200 Ramachandran restraints generated. 9600 Oldfield, 0 Emsley, 9600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19200 Ramachandran restraints generated. 9600 Oldfield, 0 Emsley, 9600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1504 residues out of total 8544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 322 poor density : 1182 time to evaluate : 6.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 ASN cc_start: 0.8279 (t0) cc_final: 0.8053 (t0) REVERT: A 169 LEU cc_start: 0.7384 (mt) cc_final: 0.6860 (mt) REVERT: A 492 GLN cc_start: 0.6710 (tt0) cc_final: 0.6020 (mm-40) REVERT: A 510 CYS cc_start: 0.6715 (OUTLIER) cc_final: 0.6310 (m) REVERT: B 189 MET cc_start: 0.8635 (tpp) cc_final: 0.8289 (tpp) REVERT: B 313 PHE cc_start: 0.6531 (t80) cc_final: 0.6241 (t80) REVERT: B 599 MET cc_start: 0.7648 (mtt) cc_final: 0.7428 (mmt) REVERT: C 135 ARG cc_start: 0.7930 (ttp-110) cc_final: 0.7669 (mtm110) REVERT: C 189 MET cc_start: 0.8651 (tpp) cc_final: 0.8315 (tpp) REVERT: C 314 ILE cc_start: 0.8615 (OUTLIER) cc_final: 0.8107 (mt) REVERT: C 492 GLN cc_start: 0.6270 (tt0) cc_final: 0.5780 (mm-40) REVERT: C 639 MET cc_start: 0.5431 (ttm) cc_final: 0.5210 (ttm) REVERT: D 59 MET cc_start: 0.6739 (mmm) cc_final: 0.6477 (mmt) REVERT: D 78 TYR cc_start: 0.8311 (m-80) cc_final: 0.7938 (m-80) REVERT: D 135 ARG cc_start: 0.8092 (ttp-110) cc_final: 0.7828 (mtm110) REVERT: D 154 ASN cc_start: 0.8220 (p0) cc_final: 0.8012 (p0) REVERT: D 169 LEU cc_start: 0.7567 (mt) cc_final: 0.7031 (mt) REVERT: D 492 GLN cc_start: 0.6831 (tt0) cc_final: 0.5995 (mm-40) REVERT: D 503 LEU cc_start: 0.7194 (OUTLIER) cc_final: 0.6766 (mm) REVERT: D 617 SER cc_start: 0.7273 (OUTLIER) cc_final: 0.6885 (p) REVERT: E 126 ASN cc_start: 0.8230 (t0) cc_final: 0.7992 (t0) REVERT: E 135 ARG cc_start: 0.8118 (ttp-110) cc_final: 0.7840 (mtm110) REVERT: E 169 LEU cc_start: 0.7553 (mt) cc_final: 0.7004 (mt) REVERT: E 313 PHE cc_start: 0.6640 (t80) cc_final: 0.6260 (t80) REVERT: E 492 GLN cc_start: 0.6194 (tt0) cc_final: 0.5467 (mm-40) REVERT: E 510 CYS cc_start: 0.6780 (OUTLIER) cc_final: 0.6243 (m) REVERT: F 59 MET cc_start: 0.6229 (mmm) cc_final: 0.6003 (mmt) REVERT: F 135 ARG cc_start: 0.8396 (ttp-110) cc_final: 0.7987 (mtm110) REVERT: F 265 ASP cc_start: 0.7017 (t0) cc_final: 0.6798 (t0) REVERT: F 314 ILE cc_start: 0.8182 (OUTLIER) cc_final: 0.7707 (mt) REVERT: F 458 ARG cc_start: 0.7301 (mtt90) cc_final: 0.7012 (mtt90) REVERT: F 492 GLN cc_start: 0.6677 (tt0) cc_final: 0.6034 (mm-40) REVERT: F 617 SER cc_start: 0.7148 (OUTLIER) cc_final: 0.6677 (p) REVERT: G 59 MET cc_start: 0.6571 (mmm) cc_final: 0.6299 (mmt) REVERT: G 63 MET cc_start: 0.7616 (mmt) cc_final: 0.7408 (mmt) REVERT: G 78 TYR cc_start: 0.8308 (m-80) cc_final: 0.8069 (m-80) REVERT: G 135 ARG cc_start: 0.8139 (ttp-110) cc_final: 0.7786 (mtm110) REVERT: G 189 MET cc_start: 0.8575 (tpp) cc_final: 0.8206 (tpp) REVERT: G 492 GLN cc_start: 0.6367 (tt0) cc_final: 0.5831 (mm-40) REVERT: H 78 TYR cc_start: 0.8429 (m-80) cc_final: 0.8032 (m-80) REVERT: H 267 LEU cc_start: 0.8276 (mm) cc_final: 0.7897 (mt) REVERT: H 492 GLN cc_start: 0.6837 (tt0) cc_final: 0.6063 (mm-40) REVERT: H 593 TYR cc_start: 0.7747 (m-80) cc_final: 0.7535 (m-80) REVERT: I 59 MET cc_start: 0.6637 (mmm) cc_final: 0.6159 (mmt) REVERT: I 169 LEU cc_start: 0.7633 (mt) cc_final: 0.6956 (mt) REVERT: I 265 ASP cc_start: 0.6759 (t0) cc_final: 0.6491 (t0) REVERT: I 313 PHE cc_start: 0.6499 (t80) cc_final: 0.6225 (t80) REVERT: I 492 GLN cc_start: 0.6747 (tt0) cc_final: 0.5852 (mm-40) REVERT: I 510 CYS cc_start: 0.6852 (OUTLIER) cc_final: 0.6215 (m) REVERT: J 135 ARG cc_start: 0.8378 (ttp-110) cc_final: 0.8013 (mtm110) REVERT: J 169 LEU cc_start: 0.7468 (mt) cc_final: 0.6936 (mt) REVERT: J 193 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8515 (mt) REVERT: J 313 PHE cc_start: 0.6460 (t80) cc_final: 0.6240 (t80) REVERT: J 314 ILE cc_start: 0.8215 (OUTLIER) cc_final: 0.7758 (mt) REVERT: J 399 GLN cc_start: 0.6662 (pp30) cc_final: 0.5797 (pp30) REVERT: J 492 GLN cc_start: 0.6573 (tt0) cc_final: 0.6169 (mm-40) REVERT: J 593 TYR cc_start: 0.7976 (m-80) cc_final: 0.7724 (m-80) REVERT: K 135 ARG cc_start: 0.7960 (ttp-110) cc_final: 0.7650 (mtm110) REVERT: K 189 MET cc_start: 0.8803 (tpp) cc_final: 0.8442 (tpp) REVERT: K 492 GLN cc_start: 0.6358 (tt0) cc_final: 0.5739 (mm-40) REVERT: K 510 CYS cc_start: 0.6784 (OUTLIER) cc_final: 0.6519 (m) REVERT: L 59 MET cc_start: 0.6666 (mmm) cc_final: 0.6424 (mmt) REVERT: L 169 LEU cc_start: 0.7650 (mt) cc_final: 0.7005 (mt) REVERT: L 176 MET cc_start: 0.6971 (OUTLIER) cc_final: 0.4749 (mtt) REVERT: L 492 GLN cc_start: 0.6875 (tt0) cc_final: 0.6104 (mm-40) REVERT: M 59 MET cc_start: 0.6582 (mmm) cc_final: 0.6146 (mmt) REVERT: M 169 LEU cc_start: 0.7605 (mt) cc_final: 0.7021 (mt) REVERT: M 314 ILE cc_start: 0.8309 (OUTLIER) cc_final: 0.7776 (mt) REVERT: M 492 GLN cc_start: 0.6363 (tt0) cc_final: 0.5468 (mm-40) REVERT: M 510 CYS cc_start: 0.6707 (OUTLIER) cc_final: 0.6126 (m) REVERT: N 59 MET cc_start: 0.6685 (mmm) cc_final: 0.6400 (mmt) REVERT: N 135 ARG cc_start: 0.8424 (ttp-110) cc_final: 0.8063 (mtm110) REVERT: N 169 LEU cc_start: 0.7543 (mt) cc_final: 0.7001 (mt) REVERT: N 313 PHE cc_start: 0.6518 (t80) cc_final: 0.6252 (t80) REVERT: N 314 ILE cc_start: 0.8222 (OUTLIER) cc_final: 0.7745 (mt) REVERT: N 492 GLN cc_start: 0.6532 (tt0) cc_final: 0.5941 (mm-40) REVERT: O 78 TYR cc_start: 0.8339 (m-80) cc_final: 0.8055 (m-80) REVERT: O 176 MET cc_start: 0.6452 (mmp) cc_final: 0.4686 (mmp) REVERT: O 189 MET cc_start: 0.8598 (tpp) cc_final: 0.8243 (tpp) REVERT: O 492 GLN cc_start: 0.6251 (tt0) cc_final: 0.5725 (mm-40) REVERT: P 176 MET cc_start: 0.6856 (OUTLIER) cc_final: 0.4473 (mtt) REVERT: P 492 GLN cc_start: 0.6779 (tt0) cc_final: 0.6013 (mm-40) REVERT: P 593 TYR cc_start: 0.7818 (m-80) cc_final: 0.7584 (m-80) outliers start: 322 outliers final: 199 residues processed: 1408 average time/residue: 0.6635 time to fit residues: 1674.9906 Evaluate side-chains 1285 residues out of total 8544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 215 poor density : 1070 time to evaluate : 6.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 442 CYS Chi-restraints excluded: chain A residue 510 CYS Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 442 CYS Chi-restraints excluded: chain B residue 499 ILE Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 366 ASP Chi-restraints excluded: chain C residue 376 PHE Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain C residue 442 CYS Chi-restraints excluded: chain C residue 538 VAL Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 195 GLU Chi-restraints excluded: chain D residue 234 ASN Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 462 CYS Chi-restraints excluded: chain D residue 481 THR Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 554 CYS Chi-restraints excluded: chain D residue 617 SER Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain E residue 416 VAL Chi-restraints excluded: chain E residue 503 LEU Chi-restraints excluded: chain E residue 510 CYS Chi-restraints excluded: chain E residue 554 CYS Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 234 ASN Chi-restraints excluded: chain F residue 247 ILE Chi-restraints excluded: chain F residue 303 ILE Chi-restraints excluded: chain F residue 314 ILE Chi-restraints excluded: chain F residue 322 LEU Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain F residue 499 ILE Chi-restraints excluded: chain F residue 538 VAL Chi-restraints excluded: chain F residue 617 SER Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 113 LEU Chi-restraints excluded: chain G residue 147 THR Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain G residue 234 ASN Chi-restraints excluded: chain G residue 366 ASP Chi-restraints excluded: chain G residue 416 VAL Chi-restraints excluded: chain G residue 442 CYS Chi-restraints excluded: chain G residue 538 VAL Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 113 LEU Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 176 MET Chi-restraints excluded: chain H residue 195 GLU Chi-restraints excluded: chain H residue 277 SER Chi-restraints excluded: chain H residue 366 ASP Chi-restraints excluded: chain H residue 416 VAL Chi-restraints excluded: chain H residue 442 CYS Chi-restraints excluded: chain H residue 538 VAL Chi-restraints excluded: chain H residue 554 CYS Chi-restraints excluded: chain I residue 38 LEU Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain I residue 86 THR Chi-restraints excluded: chain I residue 115 ILE Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain I residue 193 LEU Chi-restraints excluded: chain I residue 234 ASN Chi-restraints excluded: chain I residue 247 ILE Chi-restraints excluded: chain I residue 277 SER Chi-restraints excluded: chain I residue 322 LEU Chi-restraints excluded: chain I residue 416 VAL Chi-restraints excluded: chain I residue 510 CYS Chi-restraints excluded: chain I residue 538 VAL Chi-restraints excluded: chain I residue 554 CYS Chi-restraints excluded: chain J residue 38 LEU Chi-restraints excluded: chain J residue 45 VAL Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 159 VAL Chi-restraints excluded: chain J residue 193 LEU Chi-restraints excluded: chain J residue 277 SER Chi-restraints excluded: chain J residue 303 ILE Chi-restraints excluded: chain J residue 314 ILE Chi-restraints excluded: chain J residue 322 LEU Chi-restraints excluded: chain J residue 416 VAL Chi-restraints excluded: chain J residue 442 CYS Chi-restraints excluded: chain J residue 499 ILE Chi-restraints excluded: chain J residue 538 VAL Chi-restraints excluded: chain J residue 594 THR Chi-restraints excluded: chain K residue 38 LEU Chi-restraints excluded: chain K residue 45 VAL Chi-restraints excluded: chain K residue 84 VAL Chi-restraints excluded: chain K residue 86 THR Chi-restraints excluded: chain K residue 113 LEU Chi-restraints excluded: chain K residue 147 THR Chi-restraints excluded: chain K residue 159 VAL Chi-restraints excluded: chain K residue 175 LEU Chi-restraints excluded: chain K residue 234 ASN Chi-restraints excluded: chain K residue 416 VAL Chi-restraints excluded: chain K residue 442 CYS Chi-restraints excluded: chain K residue 499 ILE Chi-restraints excluded: chain K residue 510 CYS Chi-restraints excluded: chain K residue 538 VAL Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 66 THR Chi-restraints excluded: chain L residue 84 VAL Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 113 LEU Chi-restraints excluded: chain L residue 147 THR Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain L residue 176 MET Chi-restraints excluded: chain L residue 234 ASN Chi-restraints excluded: chain L residue 277 SER Chi-restraints excluded: chain L residue 416 VAL Chi-restraints excluded: chain L residue 481 THR Chi-restraints excluded: chain L residue 538 VAL Chi-restraints excluded: chain L residue 554 CYS Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain M residue 86 THR Chi-restraints excluded: chain M residue 115 ILE Chi-restraints excluded: chain M residue 159 VAL Chi-restraints excluded: chain M residue 234 ASN Chi-restraints excluded: chain M residue 247 ILE Chi-restraints excluded: chain M residue 277 SER Chi-restraints excluded: chain M residue 308 LEU Chi-restraints excluded: chain M residue 314 ILE Chi-restraints excluded: chain M residue 322 LEU Chi-restraints excluded: chain M residue 416 VAL Chi-restraints excluded: chain M residue 503 LEU Chi-restraints excluded: chain M residue 510 CYS Chi-restraints excluded: chain M residue 538 VAL Chi-restraints excluded: chain M residue 554 CYS Chi-restraints excluded: chain N residue 38 LEU Chi-restraints excluded: chain N residue 147 THR Chi-restraints excluded: chain N residue 159 VAL Chi-restraints excluded: chain N residue 234 ASN Chi-restraints excluded: chain N residue 277 SER Chi-restraints excluded: chain N residue 303 ILE Chi-restraints excluded: chain N residue 314 ILE Chi-restraints excluded: chain N residue 322 LEU Chi-restraints excluded: chain N residue 416 VAL Chi-restraints excluded: chain N residue 499 ILE Chi-restraints excluded: chain N residue 538 VAL Chi-restraints excluded: chain O residue 38 LEU Chi-restraints excluded: chain O residue 84 VAL Chi-restraints excluded: chain O residue 86 THR Chi-restraints excluded: chain O residue 113 LEU Chi-restraints excluded: chain O residue 147 THR Chi-restraints excluded: chain O residue 159 VAL Chi-restraints excluded: chain O residue 234 ASN Chi-restraints excluded: chain O residue 277 SER Chi-restraints excluded: chain O residue 366 ASP Chi-restraints excluded: chain O residue 416 VAL Chi-restraints excluded: chain O residue 442 CYS Chi-restraints excluded: chain O residue 499 ILE Chi-restraints excluded: chain O residue 538 VAL Chi-restraints excluded: chain P residue 38 LEU Chi-restraints excluded: chain P residue 45 VAL Chi-restraints excluded: chain P residue 66 THR Chi-restraints excluded: chain P residue 84 VAL Chi-restraints excluded: chain P residue 159 VAL Chi-restraints excluded: chain P residue 176 MET Chi-restraints excluded: chain P residue 234 ASN Chi-restraints excluded: chain P residue 303 ILE Chi-restraints excluded: chain P residue 327 VAL Chi-restraints excluded: chain P residue 366 ASP Chi-restraints excluded: chain P residue 416 VAL Chi-restraints excluded: chain P residue 503 LEU Chi-restraints excluded: chain P residue 538 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 960 random chunks: chunk 312 optimal weight: 0.9990 chunk 835 optimal weight: 0.9990 chunk 183 optimal weight: 0.9980 chunk 544 optimal weight: 1.9990 chunk 229 optimal weight: 0.8980 chunk 928 optimal weight: 2.9990 chunk 771 optimal weight: 9.9990 chunk 430 optimal weight: 4.9990 chunk 77 optimal weight: 0.9990 chunk 307 optimal weight: 0.0010 chunk 487 optimal weight: 0.0980 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 401 ASN B 53 ASN B 204 HIS ** B 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 357 ASN ** D 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 401 ASN ** E 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 36 ASN ** G 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 230 GLN ** G 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 234 ASN ** H 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 220 HIS I 230 GLN ** I 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 357 ASN ** K 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 220 HIS M 230 GLN ** M 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 230 GLN N 299 HIS ** N 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 357 ASN P 53 ASN P 204 HIS ** P 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.3655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.097 77344 Z= 0.205 Angle : 0.593 12.091 105104 Z= 0.298 Chirality : 0.044 0.299 12160 Planarity : 0.005 0.069 13488 Dihedral : 4.633 33.681 10928 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 3.87 % Allowed : 21.72 % Favored : 74.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.08), residues: 9600 helix: 0.16 (0.10), residues: 2320 sheet: -1.45 (0.13), residues: 1664 loop : -1.58 (0.08), residues: 5616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP O 627 HIS 0.009 0.001 HIS I 311 PHE 0.024 0.002 PHE E 529 TYR 0.020 0.002 TYR B 593 ARG 0.006 0.001 ARG J 339 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19200 Ramachandran restraints generated. 9600 Oldfield, 0 Emsley, 9600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19200 Ramachandran restraints generated. 9600 Oldfield, 0 Emsley, 9600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1439 residues out of total 8544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 331 poor density : 1108 time to evaluate : 6.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 ASN cc_start: 0.8267 (t0) cc_final: 0.7995 (t0) REVERT: A 169 LEU cc_start: 0.7355 (mt) cc_final: 0.6801 (mt) REVERT: A 189 MET cc_start: 0.8553 (tpt) cc_final: 0.8309 (tpp) REVERT: A 492 GLN cc_start: 0.6619 (tt0) cc_final: 0.5883 (mm-40) REVERT: A 510 CYS cc_start: 0.6671 (OUTLIER) cc_final: 0.6305 (m) REVERT: B 313 PHE cc_start: 0.6406 (t80) cc_final: 0.6152 (t80) REVERT: C 189 MET cc_start: 0.8548 (tpp) cc_final: 0.8221 (tpp) REVERT: C 314 ILE cc_start: 0.8634 (OUTLIER) cc_final: 0.8270 (mt) REVERT: C 335 GLU cc_start: 0.7620 (tp30) cc_final: 0.7402 (tp30) REVERT: C 458 ARG cc_start: 0.6820 (ptp90) cc_final: 0.6590 (ptp90) REVERT: C 492 GLN cc_start: 0.6249 (tt0) cc_final: 0.5750 (mm-40) REVERT: C 639 MET cc_start: 0.5325 (ttm) cc_final: 0.5106 (ttm) REVERT: D 78 TYR cc_start: 0.8319 (m-80) cc_final: 0.7951 (m-80) REVERT: D 135 ARG cc_start: 0.8066 (ttp-110) cc_final: 0.7760 (mtm110) REVERT: D 169 LEU cc_start: 0.7544 (mt) cc_final: 0.6975 (mt) REVERT: D 189 MET cc_start: 0.8423 (tpp) cc_final: 0.7993 (tpp) REVERT: D 492 GLN cc_start: 0.6858 (tt0) cc_final: 0.5953 (mm-40) REVERT: E 126 ASN cc_start: 0.8180 (t0) cc_final: 0.7952 (t0) REVERT: E 169 LEU cc_start: 0.7536 (mt) cc_final: 0.6922 (mt) REVERT: E 313 PHE cc_start: 0.6455 (t80) cc_final: 0.6064 (t80) REVERT: E 492 GLN cc_start: 0.6329 (tt0) cc_final: 0.5400 (mm-40) REVERT: E 510 CYS cc_start: 0.6815 (OUTLIER) cc_final: 0.6264 (m) REVERT: F 59 MET cc_start: 0.6086 (mmm) cc_final: 0.5880 (mmt) REVERT: F 135 ARG cc_start: 0.8348 (ttp-110) cc_final: 0.7961 (mtm110) REVERT: F 265 ASP cc_start: 0.7020 (t0) cc_final: 0.6818 (t0) REVERT: F 313 PHE cc_start: 0.6582 (t80) cc_final: 0.6336 (t80) REVERT: F 492 GLN cc_start: 0.6690 (tt0) cc_final: 0.6003 (mm-40) REVERT: F 599 MET cc_start: 0.7449 (mtt) cc_final: 0.7214 (mmt) REVERT: G 59 MET cc_start: 0.6375 (mmm) cc_final: 0.6062 (mmt) REVERT: G 78 TYR cc_start: 0.8300 (m-80) cc_final: 0.8024 (m-80) REVERT: G 135 ARG cc_start: 0.8060 (ttp-110) cc_final: 0.7648 (mtm110) REVERT: G 189 MET cc_start: 0.8589 (tpp) cc_final: 0.8232 (tpp) REVERT: G 314 ILE cc_start: 0.8593 (OUTLIER) cc_final: 0.8268 (mt) REVERT: G 492 GLN cc_start: 0.6330 (tt0) cc_final: 0.5799 (mm-40) REVERT: H 78 TYR cc_start: 0.8408 (m-80) cc_final: 0.8013 (m-80) REVERT: H 271 THR cc_start: 0.8203 (OUTLIER) cc_final: 0.7983 (t) REVERT: H 492 GLN cc_start: 0.6986 (tt0) cc_final: 0.6038 (mm-40) REVERT: I 59 MET cc_start: 0.6559 (mmm) cc_final: 0.6205 (mmt) REVERT: I 63 MET cc_start: 0.7710 (mmt) cc_final: 0.7380 (mmt) REVERT: I 169 LEU cc_start: 0.7563 (mt) cc_final: 0.6889 (mt) REVERT: I 265 ASP cc_start: 0.6786 (t0) cc_final: 0.6527 (t0) REVERT: I 492 GLN cc_start: 0.6519 (tt0) cc_final: 0.5642 (mm-40) REVERT: I 510 CYS cc_start: 0.6794 (OUTLIER) cc_final: 0.6198 (m) REVERT: J 93 ASN cc_start: 0.7687 (p0) cc_final: 0.7169 (p0) REVERT: J 135 ARG cc_start: 0.8288 (ttp-110) cc_final: 0.7938 (mtm110) REVERT: J 189 MET cc_start: 0.8642 (tpp) cc_final: 0.8225 (tpp) REVERT: J 193 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8525 (mt) REVERT: J 313 PHE cc_start: 0.6528 (t80) cc_final: 0.6290 (t80) REVERT: J 314 ILE cc_start: 0.8204 (OUTLIER) cc_final: 0.7846 (mt) REVERT: J 399 GLN cc_start: 0.6709 (pp30) cc_final: 0.5742 (pp30) REVERT: J 492 GLN cc_start: 0.6458 (tt0) cc_final: 0.6041 (mm-40) REVERT: J 593 TYR cc_start: 0.7906 (m-80) cc_final: 0.7674 (m-80) REVERT: K 189 MET cc_start: 0.8783 (tpp) cc_final: 0.8473 (tpp) REVERT: K 458 ARG cc_start: 0.7410 (ptt-90) cc_final: 0.7132 (ptp90) REVERT: K 492 GLN cc_start: 0.6317 (tt0) cc_final: 0.5729 (mm-40) REVERT: K 510 CYS cc_start: 0.6734 (m) cc_final: 0.6519 (m) REVERT: L 59 MET cc_start: 0.6499 (mmm) cc_final: 0.6277 (mmt) REVERT: L 93 ASN cc_start: 0.7566 (p0) cc_final: 0.7185 (p0) REVERT: L 492 GLN cc_start: 0.6816 (tt0) cc_final: 0.6068 (mm-40) REVERT: L 593 TYR cc_start: 0.7845 (m-80) cc_final: 0.7621 (m-80) REVERT: M 59 MET cc_start: 0.6556 (mmm) cc_final: 0.6215 (mmt) REVERT: M 96 MET cc_start: 0.8189 (mpp) cc_final: 0.7950 (mmt) REVERT: M 169 LEU cc_start: 0.7544 (mt) cc_final: 0.6977 (mt) REVERT: M 314 ILE cc_start: 0.8337 (OUTLIER) cc_final: 0.7866 (mt) REVERT: M 492 GLN cc_start: 0.6381 (tt0) cc_final: 0.5512 (mm-40) REVERT: M 510 CYS cc_start: 0.6558 (OUTLIER) cc_final: 0.5995 (m) REVERT: N 59 MET cc_start: 0.6628 (mmm) cc_final: 0.6363 (mmt) REVERT: N 135 ARG cc_start: 0.8394 (ttp-110) cc_final: 0.8030 (mtm110) REVERT: N 189 MET cc_start: 0.8626 (tpp) cc_final: 0.8302 (tpp) REVERT: N 313 PHE cc_start: 0.6575 (t80) cc_final: 0.6338 (t80) REVERT: N 492 GLN cc_start: 0.6607 (tt0) cc_final: 0.5904 (mm-40) REVERT: O 135 ARG cc_start: 0.8010 (ttp-110) cc_final: 0.7740 (ttp-170) REVERT: O 169 LEU cc_start: 0.7659 (mt) cc_final: 0.7174 (mt) REVERT: O 176 MET cc_start: 0.6483 (mmp) cc_final: 0.4580 (mmp) REVERT: O 189 MET cc_start: 0.8629 (tpp) cc_final: 0.8224 (tpp) REVERT: O 492 GLN cc_start: 0.6273 (tt0) cc_final: 0.5751 (mm-40) REVERT: P 267 LEU cc_start: 0.8370 (mm) cc_final: 0.7971 (mt) REVERT: P 314 ILE cc_start: 0.8431 (OUTLIER) cc_final: 0.8007 (mt) REVERT: P 492 GLN cc_start: 0.6781 (tt0) cc_final: 0.6041 (mm-40) outliers start: 331 outliers final: 261 residues processed: 1325 average time/residue: 0.6415 time to fit residues: 1535.6350 Evaluate side-chains 1315 residues out of total 8544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 272 poor density : 1043 time to evaluate : 6.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 442 CYS Chi-restraints excluded: chain A residue 462 CYS Chi-restraints excluded: chain A residue 499 ILE Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 510 CYS Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 247 ILE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 442 CYS Chi-restraints excluded: chain B residue 462 CYS Chi-restraints excluded: chain B residue 499 ILE Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 366 ASP Chi-restraints excluded: chain C residue 376 PHE Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain C residue 442 CYS Chi-restraints excluded: chain C residue 538 VAL Chi-restraints excluded: chain C residue 554 CYS Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 195 GLU Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 442 CYS Chi-restraints excluded: chain D residue 481 THR Chi-restraints excluded: chain D residue 499 ILE Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 554 CYS Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 63 MET Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain E residue 277 SER Chi-restraints excluded: chain E residue 416 VAL Chi-restraints excluded: chain E residue 442 CYS Chi-restraints excluded: chain E residue 503 LEU Chi-restraints excluded: chain E residue 510 CYS Chi-restraints excluded: chain E residue 554 CYS Chi-restraints excluded: chain E residue 590 LEU Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 115 ILE Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 247 ILE Chi-restraints excluded: chain F residue 303 ILE Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain F residue 442 CYS Chi-restraints excluded: chain F residue 499 ILE Chi-restraints excluded: chain F residue 538 VAL Chi-restraints excluded: chain F residue 554 CYS Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 113 LEU Chi-restraints excluded: chain G residue 147 THR Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain G residue 314 ILE Chi-restraints excluded: chain G residue 322 LEU Chi-restraints excluded: chain G residue 366 ASP Chi-restraints excluded: chain G residue 416 VAL Chi-restraints excluded: chain G residue 442 CYS Chi-restraints excluded: chain G residue 462 CYS Chi-restraints excluded: chain G residue 499 ILE Chi-restraints excluded: chain G residue 503 LEU Chi-restraints excluded: chain G residue 538 VAL Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 113 LEU Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain H residue 147 THR Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 176 MET Chi-restraints excluded: chain H residue 195 GLU Chi-restraints excluded: chain H residue 234 ASN Chi-restraints excluded: chain H residue 271 THR Chi-restraints excluded: chain H residue 277 SER Chi-restraints excluded: chain H residue 322 LEU Chi-restraints excluded: chain H residue 366 ASP Chi-restraints excluded: chain H residue 416 VAL Chi-restraints excluded: chain H residue 442 CYS Chi-restraints excluded: chain H residue 462 CYS Chi-restraints excluded: chain H residue 499 ILE Chi-restraints excluded: chain H residue 503 LEU Chi-restraints excluded: chain H residue 538 VAL Chi-restraints excluded: chain H residue 554 CYS Chi-restraints excluded: chain I residue 38 LEU Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain I residue 86 THR Chi-restraints excluded: chain I residue 115 ILE Chi-restraints excluded: chain I residue 147 THR Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain I residue 193 LEU Chi-restraints excluded: chain I residue 247 ILE Chi-restraints excluded: chain I residue 277 SER Chi-restraints excluded: chain I residue 322 LEU Chi-restraints excluded: chain I residue 416 VAL Chi-restraints excluded: chain I residue 442 CYS Chi-restraints excluded: chain I residue 499 ILE Chi-restraints excluded: chain I residue 503 LEU Chi-restraints excluded: chain I residue 510 CYS Chi-restraints excluded: chain I residue 538 VAL Chi-restraints excluded: chain I residue 554 CYS Chi-restraints excluded: chain I residue 586 LEU Chi-restraints excluded: chain J residue 38 LEU Chi-restraints excluded: chain J residue 45 VAL Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 115 ILE Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 159 VAL Chi-restraints excluded: chain J residue 193 LEU Chi-restraints excluded: chain J residue 247 ILE Chi-restraints excluded: chain J residue 277 SER Chi-restraints excluded: chain J residue 303 ILE Chi-restraints excluded: chain J residue 314 ILE Chi-restraints excluded: chain J residue 416 VAL Chi-restraints excluded: chain J residue 442 CYS Chi-restraints excluded: chain J residue 499 ILE Chi-restraints excluded: chain J residue 503 LEU Chi-restraints excluded: chain J residue 538 VAL Chi-restraints excluded: chain J residue 554 CYS Chi-restraints excluded: chain J residue 586 LEU Chi-restraints excluded: chain K residue 38 LEU Chi-restraints excluded: chain K residue 45 VAL Chi-restraints excluded: chain K residue 84 VAL Chi-restraints excluded: chain K residue 86 THR Chi-restraints excluded: chain K residue 113 LEU Chi-restraints excluded: chain K residue 115 ILE Chi-restraints excluded: chain K residue 147 THR Chi-restraints excluded: chain K residue 159 VAL Chi-restraints excluded: chain K residue 176 MET Chi-restraints excluded: chain K residue 365 ASP Chi-restraints excluded: chain K residue 366 ASP Chi-restraints excluded: chain K residue 416 VAL Chi-restraints excluded: chain K residue 442 CYS Chi-restraints excluded: chain K residue 499 ILE Chi-restraints excluded: chain K residue 503 LEU Chi-restraints excluded: chain K residue 538 VAL Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 66 THR Chi-restraints excluded: chain L residue 84 VAL Chi-restraints excluded: chain L residue 113 LEU Chi-restraints excluded: chain L residue 147 THR Chi-restraints excluded: chain L residue 148 THR Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain L residue 175 LEU Chi-restraints excluded: chain L residue 176 MET Chi-restraints excluded: chain L residue 195 GLU Chi-restraints excluded: chain L residue 234 ASN Chi-restraints excluded: chain L residue 277 SER Chi-restraints excluded: chain L residue 322 LEU Chi-restraints excluded: chain L residue 416 VAL Chi-restraints excluded: chain L residue 462 CYS Chi-restraints excluded: chain L residue 481 THR Chi-restraints excluded: chain L residue 499 ILE Chi-restraints excluded: chain L residue 538 VAL Chi-restraints excluded: chain L residue 554 CYS Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 63 MET Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain M residue 86 THR Chi-restraints excluded: chain M residue 147 THR Chi-restraints excluded: chain M residue 159 VAL Chi-restraints excluded: chain M residue 193 LEU Chi-restraints excluded: chain M residue 247 ILE Chi-restraints excluded: chain M residue 277 SER Chi-restraints excluded: chain M residue 314 ILE Chi-restraints excluded: chain M residue 322 LEU Chi-restraints excluded: chain M residue 416 VAL Chi-restraints excluded: chain M residue 442 CYS Chi-restraints excluded: chain M residue 462 CYS Chi-restraints excluded: chain M residue 503 LEU Chi-restraints excluded: chain M residue 510 CYS Chi-restraints excluded: chain M residue 538 VAL Chi-restraints excluded: chain M residue 554 CYS Chi-restraints excluded: chain M residue 590 LEU Chi-restraints excluded: chain N residue 38 LEU Chi-restraints excluded: chain N residue 113 LEU Chi-restraints excluded: chain N residue 115 ILE Chi-restraints excluded: chain N residue 147 THR Chi-restraints excluded: chain N residue 159 VAL Chi-restraints excluded: chain N residue 247 ILE Chi-restraints excluded: chain N residue 277 SER Chi-restraints excluded: chain N residue 416 VAL Chi-restraints excluded: chain N residue 442 CYS Chi-restraints excluded: chain N residue 499 ILE Chi-restraints excluded: chain N residue 538 VAL Chi-restraints excluded: chain N residue 554 CYS Chi-restraints excluded: chain O residue 38 LEU Chi-restraints excluded: chain O residue 84 VAL Chi-restraints excluded: chain O residue 86 THR Chi-restraints excluded: chain O residue 113 LEU Chi-restraints excluded: chain O residue 131 THR Chi-restraints excluded: chain O residue 147 THR Chi-restraints excluded: chain O residue 159 VAL Chi-restraints excluded: chain O residue 247 ILE Chi-restraints excluded: chain O residue 277 SER Chi-restraints excluded: chain O residue 366 ASP Chi-restraints excluded: chain O residue 416 VAL Chi-restraints excluded: chain O residue 442 CYS Chi-restraints excluded: chain O residue 499 ILE Chi-restraints excluded: chain O residue 538 VAL Chi-restraints excluded: chain O residue 554 CYS Chi-restraints excluded: chain P residue 38 LEU Chi-restraints excluded: chain P residue 45 VAL Chi-restraints excluded: chain P residue 66 THR Chi-restraints excluded: chain P residue 84 VAL Chi-restraints excluded: chain P residue 86 THR Chi-restraints excluded: chain P residue 119 LEU Chi-restraints excluded: chain P residue 147 THR Chi-restraints excluded: chain P residue 159 VAL Chi-restraints excluded: chain P residue 176 MET Chi-restraints excluded: chain P residue 234 ASN Chi-restraints excluded: chain P residue 277 SER Chi-restraints excluded: chain P residue 303 ILE Chi-restraints excluded: chain P residue 314 ILE Chi-restraints excluded: chain P residue 322 LEU Chi-restraints excluded: chain P residue 366 ASP Chi-restraints excluded: chain P residue 416 VAL Chi-restraints excluded: chain P residue 462 CYS Chi-restraints excluded: chain P residue 499 ILE Chi-restraints excluded: chain P residue 503 LEU Chi-restraints excluded: chain P residue 538 VAL Chi-restraints excluded: chain P residue 554 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 960 random chunks: chunk 895 optimal weight: 0.0010 chunk 104 optimal weight: 0.0060 chunk 529 optimal weight: 7.9990 chunk 678 optimal weight: 4.9990 chunk 525 optimal weight: 4.9990 chunk 781 optimal weight: 0.0370 chunk 518 optimal weight: 6.9990 chunk 925 optimal weight: 0.0170 chunk 579 optimal weight: 3.9990 chunk 564 optimal weight: 2.9990 chunk 427 optimal weight: 1.9990 overall best weight: 0.4120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 ASN ** B 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 234 ASN F 357 ASN G 36 ASN G 126 ASN G 204 HIS ** G 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 53 ASN H 204 HIS H 230 GLN H 357 ASN I 53 ASN I 234 ASN I 311 HIS I 357 ASN ** K 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 234 ASN ** K 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 357 ASN ** M 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 234 ASN M 311 HIS M 357 ASN N 126 ASN N 204 HIS N 357 ASN ** N 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 357 ASN ** P 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 357 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.3718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 77344 Z= 0.174 Angle : 0.575 12.805 105104 Z= 0.287 Chirality : 0.043 0.243 12160 Planarity : 0.005 0.069 13488 Dihedral : 4.518 34.846 10928 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 4.45 % Allowed : 21.61 % Favored : 73.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.08), residues: 9600 helix: 0.29 (0.10), residues: 2336 sheet: -1.17 (0.13), residues: 1584 loop : -1.50 (0.08), residues: 5680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 627 HIS 0.008 0.001 HIS M 311 PHE 0.022 0.002 PHE E 529 TYR 0.024 0.001 TYR N 593 ARG 0.006 0.000 ARG J 339 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19200 Ramachandran restraints generated. 9600 Oldfield, 0 Emsley, 9600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19200 Ramachandran restraints generated. 9600 Oldfield, 0 Emsley, 9600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1482 residues out of total 8544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 380 poor density : 1102 time to evaluate : 6.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 LEU cc_start: 0.7330 (mt) cc_final: 0.6699 (mt) REVERT: A 492 GLN cc_start: 0.6555 (tt0) cc_final: 0.5766 (mm-40) REVERT: A 510 CYS cc_start: 0.6583 (OUTLIER) cc_final: 0.6229 (m) REVERT: B 189 MET cc_start: 0.8724 (tpp) cc_final: 0.8288 (tpp) REVERT: B 313 PHE cc_start: 0.6346 (t80) cc_final: 0.6114 (t80) REVERT: C 169 LEU cc_start: 0.7554 (mt) cc_final: 0.7137 (mt) REVERT: C 189 MET cc_start: 0.8551 (tpp) cc_final: 0.8219 (tpp) REVERT: C 314 ILE cc_start: 0.8568 (OUTLIER) cc_final: 0.8344 (mt) REVERT: C 384 GLU cc_start: 0.6398 (mt-10) cc_final: 0.6024 (mm-30) REVERT: C 458 ARG cc_start: 0.6913 (ptp90) cc_final: 0.6679 (ptp90) REVERT: C 492 GLN cc_start: 0.6191 (tt0) cc_final: 0.5706 (mm-40) REVERT: C 639 MET cc_start: 0.5344 (ttm) cc_final: 0.5128 (ttm) REVERT: D 75 ASP cc_start: 0.7225 (p0) cc_final: 0.6978 (p0) REVERT: D 78 TYR cc_start: 0.8282 (m-80) cc_final: 0.7921 (m-80) REVERT: D 135 ARG cc_start: 0.7936 (ttp-110) cc_final: 0.7692 (mtm110) REVERT: D 169 LEU cc_start: 0.7474 (mt) cc_final: 0.6901 (mt) REVERT: D 189 MET cc_start: 0.8503 (tpp) cc_final: 0.8092 (tpp) REVERT: D 492 GLN cc_start: 0.6880 (tt0) cc_final: 0.5965 (mm-40) REVERT: E 126 ASN cc_start: 0.8252 (t0) cc_final: 0.8029 (t0) REVERT: E 169 LEU cc_start: 0.7437 (mt) cc_final: 0.6867 (mt) REVERT: E 189 MET cc_start: 0.8401 (tpp) cc_final: 0.8162 (tpp) REVERT: E 271 THR cc_start: 0.8180 (OUTLIER) cc_final: 0.7876 (t) REVERT: E 313 PHE cc_start: 0.6475 (t80) cc_final: 0.6099 (t80) REVERT: E 492 GLN cc_start: 0.6315 (tt0) cc_final: 0.5344 (mm-40) REVERT: E 510 CYS cc_start: 0.6855 (OUTLIER) cc_final: 0.6304 (m) REVERT: F 59 MET cc_start: 0.6045 (mmm) cc_final: 0.5843 (mmt) REVERT: F 135 ARG cc_start: 0.8270 (ttp-110) cc_final: 0.7898 (mtm110) REVERT: F 169 LEU cc_start: 0.7404 (mt) cc_final: 0.6955 (mt) REVERT: F 265 ASP cc_start: 0.6968 (t0) cc_final: 0.6748 (t0) REVERT: F 313 PHE cc_start: 0.6477 (t80) cc_final: 0.6176 (t80) REVERT: F 492 GLN cc_start: 0.6723 (tt0) cc_final: 0.5990 (mm-40) REVERT: G 59 MET cc_start: 0.6230 (mmm) cc_final: 0.5951 (mmt) REVERT: G 78 TYR cc_start: 0.8238 (m-80) cc_final: 0.7968 (m-80) REVERT: G 135 ARG cc_start: 0.7914 (ttp-110) cc_final: 0.7548 (mtm110) REVERT: G 169 LEU cc_start: 0.7520 (mt) cc_final: 0.7110 (mt) REVERT: G 189 MET cc_start: 0.8579 (tpp) cc_final: 0.8211 (tpp) REVERT: G 314 ILE cc_start: 0.8521 (OUTLIER) cc_final: 0.8308 (mt) REVERT: G 458 ARG cc_start: 0.7326 (ptp90) cc_final: 0.7119 (ptp90) REVERT: G 492 GLN cc_start: 0.6279 (tt0) cc_final: 0.5739 (mm-40) REVERT: H 78 TYR cc_start: 0.8338 (m-80) cc_final: 0.7925 (m-80) REVERT: H 93 ASN cc_start: 0.7474 (p0) cc_final: 0.7086 (p0) REVERT: H 189 MET cc_start: 0.8451 (tpp) cc_final: 0.8021 (tpp) REVERT: H 492 GLN cc_start: 0.6886 (tt0) cc_final: 0.5987 (mm-40) REVERT: I 59 MET cc_start: 0.6423 (mmm) cc_final: 0.6155 (mmt) REVERT: I 169 LEU cc_start: 0.7481 (mt) cc_final: 0.6838 (mt) REVERT: I 265 ASP cc_start: 0.6823 (t0) cc_final: 0.6540 (t0) REVERT: I 492 GLN cc_start: 0.6443 (tt0) cc_final: 0.5568 (mm-40) REVERT: J 135 ARG cc_start: 0.8186 (ttp-110) cc_final: 0.7871 (mtm110) REVERT: J 189 MET cc_start: 0.8666 (tpp) cc_final: 0.8280 (tpp) REVERT: J 313 PHE cc_start: 0.6433 (t80) cc_final: 0.6171 (t80) REVERT: J 492 GLN cc_start: 0.6573 (tt0) cc_final: 0.6005 (mm-40) REVERT: J 593 TYR cc_start: 0.7798 (m-80) cc_final: 0.7596 (m-80) REVERT: J 599 MET cc_start: 0.7614 (mmt) cc_final: 0.7138 (mmt) REVERT: K 169 LEU cc_start: 0.7501 (mt) cc_final: 0.7119 (mt) REVERT: K 189 MET cc_start: 0.8775 (tpp) cc_final: 0.8461 (tpp) REVERT: K 458 ARG cc_start: 0.7378 (ptt-90) cc_final: 0.7059 (ptp90) REVERT: K 492 GLN cc_start: 0.6300 (tt0) cc_final: 0.5683 (mm-40) REVERT: K 599 MET cc_start: 0.7316 (mtt) cc_final: 0.7114 (mmt) REVERT: L 59 MET cc_start: 0.6235 (mmm) cc_final: 0.6008 (mmt) REVERT: L 93 ASN cc_start: 0.7553 (p0) cc_final: 0.7173 (p0) REVERT: L 492 GLN cc_start: 0.6806 (tt0) cc_final: 0.6035 (mm-40) REVERT: M 59 MET cc_start: 0.6401 (mmm) cc_final: 0.6086 (mmt) REVERT: M 96 MET cc_start: 0.8171 (mpp) cc_final: 0.7915 (mmt) REVERT: M 169 LEU cc_start: 0.7316 (mt) cc_final: 0.6699 (mt) REVERT: M 314 ILE cc_start: 0.8204 (OUTLIER) cc_final: 0.7755 (mt) REVERT: M 492 GLN cc_start: 0.6462 (tt0) cc_final: 0.5425 (mm-40) REVERT: M 510 CYS cc_start: 0.6482 (OUTLIER) cc_final: 0.5954 (m) REVERT: N 59 MET cc_start: 0.6509 (mmm) cc_final: 0.6294 (mmt) REVERT: N 135 ARG cc_start: 0.8224 (ttp-110) cc_final: 0.7934 (mtm110) REVERT: N 169 LEU cc_start: 0.7377 (mt) cc_final: 0.6930 (mt) REVERT: N 313 PHE cc_start: 0.6443 (t80) cc_final: 0.6161 (t80) REVERT: N 492 GLN cc_start: 0.6697 (tt0) cc_final: 0.5924 (mm-40) REVERT: O 59 MET cc_start: 0.6196 (mmm) cc_final: 0.5917 (mmt) REVERT: O 135 ARG cc_start: 0.7923 (ttp-110) cc_final: 0.7460 (mtm110) REVERT: O 169 LEU cc_start: 0.7617 (mt) cc_final: 0.7093 (mt) REVERT: O 176 MET cc_start: 0.6506 (mmp) cc_final: 0.4568 (mmp) REVERT: O 189 MET cc_start: 0.8668 (tpp) cc_final: 0.8323 (tpp) REVERT: O 265 ASP cc_start: 0.6724 (t0) cc_final: 0.6519 (t0) REVERT: O 492 GLN cc_start: 0.6276 (tt0) cc_final: 0.5733 (mm-40) REVERT: P 56 ASN cc_start: 0.7287 (OUTLIER) cc_final: 0.6708 (m-40) REVERT: P 75 ASP cc_start: 0.7464 (p0) cc_final: 0.7184 (p0) REVERT: P 169 LEU cc_start: 0.7465 (mt) cc_final: 0.7056 (mt) REVERT: P 267 LEU cc_start: 0.8319 (mm) cc_final: 0.7933 (mt) REVERT: P 314 ILE cc_start: 0.8318 (OUTLIER) cc_final: 0.8027 (mt) REVERT: P 492 GLN cc_start: 0.6833 (tt0) cc_final: 0.5925 (mm-40) outliers start: 380 outliers final: 269 residues processed: 1374 average time/residue: 0.6453 time to fit residues: 1603.7538 Evaluate side-chains 1319 residues out of total 8544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 278 poor density : 1041 time to evaluate : 6.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 93 ASN Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 442 CYS Chi-restraints excluded: chain A residue 462 CYS Chi-restraints excluded: chain A residue 499 ILE Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 510 CYS Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 247 ILE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 442 CYS Chi-restraints excluded: chain B residue 462 CYS Chi-restraints excluded: chain B residue 499 ILE Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 366 ASP Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain C residue 442 CYS Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 538 VAL Chi-restraints excluded: chain C residue 554 CYS Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 442 CYS Chi-restraints excluded: chain D residue 462 CYS Chi-restraints excluded: chain D residue 481 THR Chi-restraints excluded: chain D residue 499 ILE Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 554 CYS Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 63 MET Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 199 LEU Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain E residue 271 THR Chi-restraints excluded: chain E residue 277 SER Chi-restraints excluded: chain E residue 416 VAL Chi-restraints excluded: chain E residue 442 CYS Chi-restraints excluded: chain E residue 462 CYS Chi-restraints excluded: chain E residue 481 THR Chi-restraints excluded: chain E residue 503 LEU Chi-restraints excluded: chain E residue 510 CYS Chi-restraints excluded: chain E residue 554 CYS Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 115 ILE Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 303 ILE Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain F residue 420 SER Chi-restraints excluded: chain F residue 442 CYS Chi-restraints excluded: chain F residue 499 ILE Chi-restraints excluded: chain F residue 503 LEU Chi-restraints excluded: chain F residue 538 VAL Chi-restraints excluded: chain F residue 554 CYS Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 113 LEU Chi-restraints excluded: chain G residue 131 THR Chi-restraints excluded: chain G residue 147 THR Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain G residue 247 ILE Chi-restraints excluded: chain G residue 314 ILE Chi-restraints excluded: chain G residue 322 LEU Chi-restraints excluded: chain G residue 366 ASP Chi-restraints excluded: chain G residue 416 VAL Chi-restraints excluded: chain G residue 442 CYS Chi-restraints excluded: chain G residue 499 ILE Chi-restraints excluded: chain G residue 503 LEU Chi-restraints excluded: chain G residue 538 VAL Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 147 THR Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 176 MET Chi-restraints excluded: chain H residue 195 GLU Chi-restraints excluded: chain H residue 234 ASN Chi-restraints excluded: chain H residue 247 ILE Chi-restraints excluded: chain H residue 277 SER Chi-restraints excluded: chain H residue 322 LEU Chi-restraints excluded: chain H residue 366 ASP Chi-restraints excluded: chain H residue 416 VAL Chi-restraints excluded: chain H residue 442 CYS Chi-restraints excluded: chain H residue 462 CYS Chi-restraints excluded: chain H residue 499 ILE Chi-restraints excluded: chain H residue 503 LEU Chi-restraints excluded: chain H residue 538 VAL Chi-restraints excluded: chain H residue 554 CYS Chi-restraints excluded: chain H residue 594 THR Chi-restraints excluded: chain I residue 38 LEU Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain I residue 115 ILE Chi-restraints excluded: chain I residue 147 THR Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain I residue 193 LEU Chi-restraints excluded: chain I residue 247 ILE Chi-restraints excluded: chain I residue 277 SER Chi-restraints excluded: chain I residue 322 LEU Chi-restraints excluded: chain I residue 416 VAL Chi-restraints excluded: chain I residue 442 CYS Chi-restraints excluded: chain I residue 462 CYS Chi-restraints excluded: chain I residue 499 ILE Chi-restraints excluded: chain I residue 503 LEU Chi-restraints excluded: chain I residue 554 CYS Chi-restraints excluded: chain I residue 586 LEU Chi-restraints excluded: chain J residue 38 LEU Chi-restraints excluded: chain J residue 45 VAL Chi-restraints excluded: chain J residue 115 ILE Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 159 VAL Chi-restraints excluded: chain J residue 247 ILE Chi-restraints excluded: chain J residue 277 SER Chi-restraints excluded: chain J residue 290 GLU Chi-restraints excluded: chain J residue 481 THR Chi-restraints excluded: chain J residue 499 ILE Chi-restraints excluded: chain J residue 503 LEU Chi-restraints excluded: chain J residue 538 VAL Chi-restraints excluded: chain J residue 554 CYS Chi-restraints excluded: chain K residue 38 LEU Chi-restraints excluded: chain K residue 45 VAL Chi-restraints excluded: chain K residue 84 VAL Chi-restraints excluded: chain K residue 86 THR Chi-restraints excluded: chain K residue 113 LEU Chi-restraints excluded: chain K residue 147 THR Chi-restraints excluded: chain K residue 159 VAL Chi-restraints excluded: chain K residue 175 LEU Chi-restraints excluded: chain K residue 234 ASN Chi-restraints excluded: chain K residue 247 ILE Chi-restraints excluded: chain K residue 365 ASP Chi-restraints excluded: chain K residue 366 ASP Chi-restraints excluded: chain K residue 416 VAL Chi-restraints excluded: chain K residue 462 CYS Chi-restraints excluded: chain K residue 499 ILE Chi-restraints excluded: chain K residue 503 LEU Chi-restraints excluded: chain K residue 538 VAL Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 66 THR Chi-restraints excluded: chain L residue 84 VAL Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 113 LEU Chi-restraints excluded: chain L residue 147 THR Chi-restraints excluded: chain L residue 148 THR Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain L residue 175 LEU Chi-restraints excluded: chain L residue 176 MET Chi-restraints excluded: chain L residue 234 ASN Chi-restraints excluded: chain L residue 277 SER Chi-restraints excluded: chain L residue 322 LEU Chi-restraints excluded: chain L residue 416 VAL Chi-restraints excluded: chain L residue 462 CYS Chi-restraints excluded: chain L residue 481 THR Chi-restraints excluded: chain L residue 503 LEU Chi-restraints excluded: chain L residue 538 VAL Chi-restraints excluded: chain L residue 554 CYS Chi-restraints excluded: chain L residue 594 THR Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 63 MET Chi-restraints excluded: chain M residue 115 ILE Chi-restraints excluded: chain M residue 147 THR Chi-restraints excluded: chain M residue 159 VAL Chi-restraints excluded: chain M residue 193 LEU Chi-restraints excluded: chain M residue 247 ILE Chi-restraints excluded: chain M residue 277 SER Chi-restraints excluded: chain M residue 314 ILE Chi-restraints excluded: chain M residue 322 LEU Chi-restraints excluded: chain M residue 416 VAL Chi-restraints excluded: chain M residue 442 CYS Chi-restraints excluded: chain M residue 462 CYS Chi-restraints excluded: chain M residue 499 ILE Chi-restraints excluded: chain M residue 503 LEU Chi-restraints excluded: chain M residue 510 CYS Chi-restraints excluded: chain M residue 538 VAL Chi-restraints excluded: chain M residue 554 CYS Chi-restraints excluded: chain N residue 38 LEU Chi-restraints excluded: chain N residue 86 THR Chi-restraints excluded: chain N residue 147 THR Chi-restraints excluded: chain N residue 159 VAL Chi-restraints excluded: chain N residue 277 SER Chi-restraints excluded: chain N residue 416 VAL Chi-restraints excluded: chain N residue 442 CYS Chi-restraints excluded: chain N residue 499 ILE Chi-restraints excluded: chain N residue 503 LEU Chi-restraints excluded: chain N residue 538 VAL Chi-restraints excluded: chain N residue 554 CYS Chi-restraints excluded: chain N residue 594 THR Chi-restraints excluded: chain O residue 38 LEU Chi-restraints excluded: chain O residue 84 VAL Chi-restraints excluded: chain O residue 86 THR Chi-restraints excluded: chain O residue 113 LEU Chi-restraints excluded: chain O residue 131 THR Chi-restraints excluded: chain O residue 147 THR Chi-restraints excluded: chain O residue 159 VAL Chi-restraints excluded: chain O residue 247 ILE Chi-restraints excluded: chain O residue 277 SER Chi-restraints excluded: chain O residue 365 ASP Chi-restraints excluded: chain O residue 366 ASP Chi-restraints excluded: chain O residue 416 VAL Chi-restraints excluded: chain O residue 442 CYS Chi-restraints excluded: chain O residue 462 CYS Chi-restraints excluded: chain O residue 499 ILE Chi-restraints excluded: chain O residue 503 LEU Chi-restraints excluded: chain O residue 538 VAL Chi-restraints excluded: chain O residue 554 CYS Chi-restraints excluded: chain P residue 38 LEU Chi-restraints excluded: chain P residue 45 VAL Chi-restraints excluded: chain P residue 56 ASN Chi-restraints excluded: chain P residue 66 THR Chi-restraints excluded: chain P residue 84 VAL Chi-restraints excluded: chain P residue 86 THR Chi-restraints excluded: chain P residue 147 THR Chi-restraints excluded: chain P residue 159 VAL Chi-restraints excluded: chain P residue 176 MET Chi-restraints excluded: chain P residue 234 ASN Chi-restraints excluded: chain P residue 277 SER Chi-restraints excluded: chain P residue 314 ILE Chi-restraints excluded: chain P residue 322 LEU Chi-restraints excluded: chain P residue 366 ASP Chi-restraints excluded: chain P residue 416 VAL Chi-restraints excluded: chain P residue 462 CYS Chi-restraints excluded: chain P residue 499 ILE Chi-restraints excluded: chain P residue 503 LEU Chi-restraints excluded: chain P residue 538 VAL Chi-restraints excluded: chain P residue 554 CYS Chi-restraints excluded: chain P residue 594 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 960 random chunks: chunk 572 optimal weight: 8.9990 chunk 369 optimal weight: 3.9990 chunk 552 optimal weight: 2.9990 chunk 278 optimal weight: 7.9990 chunk 181 optimal weight: 0.7980 chunk 179 optimal weight: 3.9990 chunk 588 optimal weight: 0.0670 chunk 630 optimal weight: 0.9990 chunk 457 optimal weight: 10.0000 chunk 86 optimal weight: 0.9980 chunk 727 optimal weight: 4.9990 overall best weight: 1.1722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 GLN ** A 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 234 ASN ** D 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 234 ASN ** E 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 234 ASN ** F 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 36 ASN ** G 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 234 ASN H 234 ASN I 234 ASN ** K 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 234 ASN N 53 ASN N 234 ASN ** N 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 36 ASN ** O 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 234 ASN ** P 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.3932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 77344 Z= 0.249 Angle : 0.595 13.032 105104 Z= 0.299 Chirality : 0.044 0.263 12160 Planarity : 0.005 0.068 13488 Dihedral : 4.531 32.671 10928 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 4.46 % Allowed : 21.89 % Favored : 73.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.08), residues: 9600 helix: 0.28 (0.10), residues: 2336 sheet: -1.17 (0.13), residues: 1584 loop : -1.49 (0.08), residues: 5680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP N 292 HIS 0.006 0.001 HIS A 311 PHE 0.024 0.002 PHE H 313 TYR 0.021 0.002 TYR N 593 ARG 0.007 0.000 ARG A 305 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19200 Ramachandran restraints generated. 9600 Oldfield, 0 Emsley, 9600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19200 Ramachandran restraints generated. 9600 Oldfield, 0 Emsley, 9600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1450 residues out of total 8544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 381 poor density : 1069 time to evaluate : 6.282 Fit side-chains revert: symmetry clash REVERT: A 169 LEU cc_start: 0.7470 (mt) cc_final: 0.6840 (mt) REVERT: A 492 GLN cc_start: 0.6691 (tt0) cc_final: 0.6013 (mm-40) REVERT: A 510 CYS cc_start: 0.6730 (OUTLIER) cc_final: 0.6515 (m) REVERT: B 305 ARG cc_start: 0.8384 (OUTLIER) cc_final: 0.7611 (ptp90) REVERT: B 599 MET cc_start: 0.7719 (mmt) cc_final: 0.7123 (mmt) REVERT: C 169 LEU cc_start: 0.7648 (mt) cc_final: 0.7253 (mt) REVERT: C 189 MET cc_start: 0.8683 (tpp) cc_final: 0.8297 (tpp) REVERT: C 308 LEU cc_start: 0.7182 (pt) cc_final: 0.6341 (mp) REVERT: C 314 ILE cc_start: 0.8729 (OUTLIER) cc_final: 0.8395 (mt) REVERT: C 384 GLU cc_start: 0.6573 (mt-10) cc_final: 0.6071 (mm-30) REVERT: C 399 GLN cc_start: 0.6285 (pp30) cc_final: 0.5457 (pp30) REVERT: C 492 GLN cc_start: 0.6487 (tt0) cc_final: 0.5924 (mm-40) REVERT: D 75 ASP cc_start: 0.7345 (p0) cc_final: 0.7064 (p0) REVERT: D 135 ARG cc_start: 0.8101 (ttp-110) cc_final: 0.7836 (mtm110) REVERT: D 189 MET cc_start: 0.8571 (tpp) cc_final: 0.8199 (tpp) REVERT: D 492 GLN cc_start: 0.6752 (tt0) cc_final: 0.6041 (mm-40) REVERT: E 169 LEU cc_start: 0.7476 (mt) cc_final: 0.6915 (mt) REVERT: E 189 MET cc_start: 0.8445 (tpp) cc_final: 0.8206 (tpp) REVERT: E 313 PHE cc_start: 0.6642 (t80) cc_final: 0.6289 (t80) REVERT: E 492 GLN cc_start: 0.6397 (tt0) cc_final: 0.5564 (mm-40) REVERT: E 510 CYS cc_start: 0.6825 (OUTLIER) cc_final: 0.6208 (m) REVERT: F 59 MET cc_start: 0.6268 (mmm) cc_final: 0.6022 (mmt) REVERT: F 169 LEU cc_start: 0.7446 (mt) cc_final: 0.6988 (mt) REVERT: F 265 ASP cc_start: 0.6906 (t0) cc_final: 0.6670 (t0) REVERT: F 305 ARG cc_start: 0.8449 (OUTLIER) cc_final: 0.7542 (ptp90) REVERT: F 492 GLN cc_start: 0.6781 (tt0) cc_final: 0.6067 (mm-40) REVERT: F 599 MET cc_start: 0.7659 (mmt) cc_final: 0.7014 (mmt) REVERT: G 78 TYR cc_start: 0.8337 (m-80) cc_final: 0.8028 (m-80) REVERT: G 93 ASN cc_start: 0.7794 (OUTLIER) cc_final: 0.7393 (p0) REVERT: G 135 ARG cc_start: 0.7998 (ttp-110) cc_final: 0.7655 (mtm110) REVERT: G 169 LEU cc_start: 0.7595 (mt) cc_final: 0.7173 (mt) REVERT: G 189 MET cc_start: 0.8619 (tpp) cc_final: 0.8222 (tpp) REVERT: G 308 LEU cc_start: 0.7064 (pt) cc_final: 0.6434 (mp) REVERT: G 314 ILE cc_start: 0.8721 (OUTLIER) cc_final: 0.8430 (mt) REVERT: G 458 ARG cc_start: 0.7348 (ptp90) cc_final: 0.7102 (ptp90) REVERT: G 492 GLN cc_start: 0.6580 (tt0) cc_final: 0.5954 (mm-40) REVERT: H 78 TYR cc_start: 0.8374 (m-80) cc_final: 0.7944 (m-80) REVERT: H 93 ASN cc_start: 0.7532 (p0) cc_final: 0.7198 (p0) REVERT: H 169 LEU cc_start: 0.7480 (mt) cc_final: 0.7109 (mt) REVERT: H 176 MET cc_start: 0.7074 (OUTLIER) cc_final: 0.4716 (mtt) REVERT: H 189 MET cc_start: 0.8540 (tpp) cc_final: 0.8201 (tpp) REVERT: H 313 PHE cc_start: 0.6991 (t80) cc_final: 0.6674 (m-80) REVERT: H 399 GLN cc_start: 0.6465 (pp30) cc_final: 0.6027 (pp30) REVERT: H 492 GLN cc_start: 0.6744 (tt0) cc_final: 0.5995 (mm-40) REVERT: I 59 MET cc_start: 0.6701 (mmm) cc_final: 0.6359 (mmt) REVERT: I 63 MET cc_start: 0.7895 (mmt) cc_final: 0.7543 (mmt) REVERT: I 169 LEU cc_start: 0.7525 (mt) cc_final: 0.6874 (mt) REVERT: I 492 GLN cc_start: 0.6797 (tt0) cc_final: 0.5733 (mm-40) REVERT: I 510 CYS cc_start: 0.6788 (OUTLIER) cc_final: 0.6256 (m) REVERT: J 93 ASN cc_start: 0.7773 (p0) cc_final: 0.7253 (p0) REVERT: J 135 ARG cc_start: 0.8338 (ttp-110) cc_final: 0.8017 (mtm110) REVERT: J 169 LEU cc_start: 0.7454 (mt) cc_final: 0.6996 (mt) REVERT: J 492 GLN cc_start: 0.6623 (tt0) cc_final: 0.6090 (mm-40) REVERT: J 599 MET cc_start: 0.7696 (mmt) cc_final: 0.7049 (mmt) REVERT: K 59 MET cc_start: 0.6691 (mmm) cc_final: 0.6432 (mmt) REVERT: K 169 LEU cc_start: 0.7559 (mt) cc_final: 0.7160 (mt) REVERT: K 189 MET cc_start: 0.8782 (tpp) cc_final: 0.8493 (tpp) REVERT: K 313 PHE cc_start: 0.7389 (t80) cc_final: 0.7145 (m-80) REVERT: K 492 GLN cc_start: 0.6568 (tt0) cc_final: 0.5933 (mm-40) REVERT: L 78 TYR cc_start: 0.8367 (m-80) cc_final: 0.7985 (m-80) REVERT: L 169 LEU cc_start: 0.7520 (mt) cc_final: 0.7094 (mt) REVERT: L 399 GLN cc_start: 0.6452 (pp30) cc_final: 0.6019 (pp30) REVERT: L 492 GLN cc_start: 0.6701 (tt0) cc_final: 0.6124 (mm-40) REVERT: M 59 MET cc_start: 0.6670 (mmm) cc_final: 0.6299 (mmt) REVERT: M 169 LEU cc_start: 0.7483 (mt) cc_final: 0.6886 (mt) REVERT: M 314 ILE cc_start: 0.8322 (OUTLIER) cc_final: 0.7872 (mt) REVERT: M 399 GLN cc_start: 0.6373 (pp30) cc_final: 0.5767 (pp30) REVERT: M 492 GLN cc_start: 0.6629 (tt0) cc_final: 0.5584 (mm-40) REVERT: N 59 MET cc_start: 0.6838 (mmm) cc_final: 0.6465 (mmt) REVERT: N 169 LEU cc_start: 0.7417 (mt) cc_final: 0.6954 (mt) REVERT: N 313 PHE cc_start: 0.6668 (t80) cc_final: 0.6464 (t80) REVERT: N 492 GLN cc_start: 0.6721 (tt0) cc_final: 0.5971 (mm-40) REVERT: O 78 TYR cc_start: 0.8289 (m-80) cc_final: 0.7996 (m-80) REVERT: O 169 LEU cc_start: 0.7696 (mt) cc_final: 0.7256 (mt) REVERT: O 189 MET cc_start: 0.8700 (tpp) cc_final: 0.8394 (tpp) REVERT: O 492 GLN cc_start: 0.6542 (tt0) cc_final: 0.5937 (mm-40) REVERT: P 169 LEU cc_start: 0.7644 (mt) cc_final: 0.7247 (mt) REVERT: P 176 MET cc_start: 0.6977 (OUTLIER) cc_final: 0.4462 (mtt) REVERT: P 267 LEU cc_start: 0.8485 (mm) cc_final: 0.8073 (mt) REVERT: P 314 ILE cc_start: 0.8434 (OUTLIER) cc_final: 0.8125 (mt) REVERT: P 399 GLN cc_start: 0.6448 (pp30) cc_final: 0.5969 (pp30) REVERT: P 492 GLN cc_start: 0.7001 (tt0) cc_final: 0.6158 (mm-40) outliers start: 381 outliers final: 317 residues processed: 1340 average time/residue: 0.6395 time to fit residues: 1558.5406 Evaluate side-chains 1352 residues out of total 8544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 329 poor density : 1023 time to evaluate : 6.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 442 CYS Chi-restraints excluded: chain A residue 462 CYS Chi-restraints excluded: chain A residue 499 ILE Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 510 CYS Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 63 MET Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 247 ILE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 305 ARG Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 442 CYS Chi-restraints excluded: chain B residue 462 CYS Chi-restraints excluded: chain B residue 499 ILE Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 554 CYS Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain B residue 594 THR Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 366 ASP Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain C residue 442 CYS Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 538 VAL Chi-restraints excluded: chain C residue 586 LEU Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 442 CYS Chi-restraints excluded: chain D residue 462 CYS Chi-restraints excluded: chain D residue 499 ILE Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 554 CYS Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 63 MET Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 199 LEU Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain E residue 277 SER Chi-restraints excluded: chain E residue 303 ILE Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 416 VAL Chi-restraints excluded: chain E residue 442 CYS Chi-restraints excluded: chain E residue 462 CYS Chi-restraints excluded: chain E residue 481 THR Chi-restraints excluded: chain E residue 499 ILE Chi-restraints excluded: chain E residue 503 LEU Chi-restraints excluded: chain E residue 510 CYS Chi-restraints excluded: chain E residue 538 VAL Chi-restraints excluded: chain E residue 554 CYS Chi-restraints excluded: chain E residue 590 LEU Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 115 ILE Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 247 ILE Chi-restraints excluded: chain F residue 303 ILE Chi-restraints excluded: chain F residue 305 ARG Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain F residue 420 SER Chi-restraints excluded: chain F residue 442 CYS Chi-restraints excluded: chain F residue 499 ILE Chi-restraints excluded: chain F residue 503 LEU Chi-restraints excluded: chain F residue 538 VAL Chi-restraints excluded: chain F residue 554 CYS Chi-restraints excluded: chain F residue 594 THR Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 93 ASN Chi-restraints excluded: chain G residue 113 LEU Chi-restraints excluded: chain G residue 131 THR Chi-restraints excluded: chain G residue 147 THR Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain G residue 234 ASN Chi-restraints excluded: chain G residue 247 ILE Chi-restraints excluded: chain G residue 314 ILE Chi-restraints excluded: chain G residue 322 LEU Chi-restraints excluded: chain G residue 333 THR Chi-restraints excluded: chain G residue 366 ASP Chi-restraints excluded: chain G residue 416 VAL Chi-restraints excluded: chain G residue 442 CYS Chi-restraints excluded: chain G residue 499 ILE Chi-restraints excluded: chain G residue 503 LEU Chi-restraints excluded: chain G residue 538 VAL Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain H residue 147 THR Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 176 MET Chi-restraints excluded: chain H residue 195 GLU Chi-restraints excluded: chain H residue 234 ASN Chi-restraints excluded: chain H residue 247 ILE Chi-restraints excluded: chain H residue 277 SER Chi-restraints excluded: chain H residue 322 LEU Chi-restraints excluded: chain H residue 333 THR Chi-restraints excluded: chain H residue 366 ASP Chi-restraints excluded: chain H residue 416 VAL Chi-restraints excluded: chain H residue 442 CYS Chi-restraints excluded: chain H residue 462 CYS Chi-restraints excluded: chain H residue 481 THR Chi-restraints excluded: chain H residue 503 LEU Chi-restraints excluded: chain H residue 538 VAL Chi-restraints excluded: chain H residue 554 CYS Chi-restraints excluded: chain H residue 594 THR Chi-restraints excluded: chain I residue 38 LEU Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain I residue 86 THR Chi-restraints excluded: chain I residue 115 ILE Chi-restraints excluded: chain I residue 147 THR Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 193 LEU Chi-restraints excluded: chain I residue 234 ASN Chi-restraints excluded: chain I residue 247 ILE Chi-restraints excluded: chain I residue 277 SER Chi-restraints excluded: chain I residue 322 LEU Chi-restraints excluded: chain I residue 416 VAL Chi-restraints excluded: chain I residue 442 CYS Chi-restraints excluded: chain I residue 462 CYS Chi-restraints excluded: chain I residue 499 ILE Chi-restraints excluded: chain I residue 503 LEU Chi-restraints excluded: chain I residue 510 CYS Chi-restraints excluded: chain I residue 586 LEU Chi-restraints excluded: chain J residue 38 LEU Chi-restraints excluded: chain J residue 45 VAL Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 115 ILE Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 159 VAL Chi-restraints excluded: chain J residue 247 ILE Chi-restraints excluded: chain J residue 267 LEU Chi-restraints excluded: chain J residue 277 SER Chi-restraints excluded: chain J residue 290 GLU Chi-restraints excluded: chain J residue 416 VAL Chi-restraints excluded: chain J residue 420 SER Chi-restraints excluded: chain J residue 442 CYS Chi-restraints excluded: chain J residue 481 THR Chi-restraints excluded: chain J residue 499 ILE Chi-restraints excluded: chain J residue 503 LEU Chi-restraints excluded: chain J residue 538 VAL Chi-restraints excluded: chain J residue 554 CYS Chi-restraints excluded: chain K residue 38 LEU Chi-restraints excluded: chain K residue 45 VAL Chi-restraints excluded: chain K residue 84 VAL Chi-restraints excluded: chain K residue 86 THR Chi-restraints excluded: chain K residue 113 LEU Chi-restraints excluded: chain K residue 115 ILE Chi-restraints excluded: chain K residue 119 LEU Chi-restraints excluded: chain K residue 139 LEU Chi-restraints excluded: chain K residue 147 THR Chi-restraints excluded: chain K residue 159 VAL Chi-restraints excluded: chain K residue 175 LEU Chi-restraints excluded: chain K residue 234 ASN Chi-restraints excluded: chain K residue 247 ILE Chi-restraints excluded: chain K residue 333 THR Chi-restraints excluded: chain K residue 365 ASP Chi-restraints excluded: chain K residue 366 ASP Chi-restraints excluded: chain K residue 416 VAL Chi-restraints excluded: chain K residue 442 CYS Chi-restraints excluded: chain K residue 462 CYS Chi-restraints excluded: chain K residue 499 ILE Chi-restraints excluded: chain K residue 503 LEU Chi-restraints excluded: chain K residue 538 VAL Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 66 THR Chi-restraints excluded: chain L residue 84 VAL Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 113 LEU Chi-restraints excluded: chain L residue 147 THR Chi-restraints excluded: chain L residue 148 THR Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain L residue 175 LEU Chi-restraints excluded: chain L residue 176 MET Chi-restraints excluded: chain L residue 195 GLU Chi-restraints excluded: chain L residue 234 ASN Chi-restraints excluded: chain L residue 247 ILE Chi-restraints excluded: chain L residue 277 SER Chi-restraints excluded: chain L residue 322 LEU Chi-restraints excluded: chain L residue 333 THR Chi-restraints excluded: chain L residue 416 VAL Chi-restraints excluded: chain L residue 462 CYS Chi-restraints excluded: chain L residue 481 THR Chi-restraints excluded: chain L residue 503 LEU Chi-restraints excluded: chain L residue 538 VAL Chi-restraints excluded: chain L residue 554 CYS Chi-restraints excluded: chain L residue 594 THR Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 63 MET Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain M residue 86 THR Chi-restraints excluded: chain M residue 115 ILE Chi-restraints excluded: chain M residue 147 THR Chi-restraints excluded: chain M residue 159 VAL Chi-restraints excluded: chain M residue 193 LEU Chi-restraints excluded: chain M residue 234 ASN Chi-restraints excluded: chain M residue 247 ILE Chi-restraints excluded: chain M residue 277 SER Chi-restraints excluded: chain M residue 314 ILE Chi-restraints excluded: chain M residue 322 LEU Chi-restraints excluded: chain M residue 416 VAL Chi-restraints excluded: chain M residue 442 CYS Chi-restraints excluded: chain M residue 462 CYS Chi-restraints excluded: chain M residue 481 THR Chi-restraints excluded: chain M residue 499 ILE Chi-restraints excluded: chain M residue 503 LEU Chi-restraints excluded: chain M residue 538 VAL Chi-restraints excluded: chain M residue 554 CYS Chi-restraints excluded: chain M residue 590 LEU Chi-restraints excluded: chain N residue 38 LEU Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 86 THR Chi-restraints excluded: chain N residue 113 LEU Chi-restraints excluded: chain N residue 115 ILE Chi-restraints excluded: chain N residue 147 THR Chi-restraints excluded: chain N residue 159 VAL Chi-restraints excluded: chain N residue 199 LEU Chi-restraints excluded: chain N residue 247 ILE Chi-restraints excluded: chain N residue 268 SER Chi-restraints excluded: chain N residue 277 SER Chi-restraints excluded: chain N residue 416 VAL Chi-restraints excluded: chain N residue 442 CYS Chi-restraints excluded: chain N residue 499 ILE Chi-restraints excluded: chain N residue 503 LEU Chi-restraints excluded: chain N residue 538 VAL Chi-restraints excluded: chain N residue 554 CYS Chi-restraints excluded: chain N residue 594 THR Chi-restraints excluded: chain O residue 38 LEU Chi-restraints excluded: chain O residue 84 VAL Chi-restraints excluded: chain O residue 86 THR Chi-restraints excluded: chain O residue 113 LEU Chi-restraints excluded: chain O residue 131 THR Chi-restraints excluded: chain O residue 147 THR Chi-restraints excluded: chain O residue 159 VAL Chi-restraints excluded: chain O residue 193 LEU Chi-restraints excluded: chain O residue 247 ILE Chi-restraints excluded: chain O residue 277 SER Chi-restraints excluded: chain O residue 333 THR Chi-restraints excluded: chain O residue 365 ASP Chi-restraints excluded: chain O residue 366 ASP Chi-restraints excluded: chain O residue 416 VAL Chi-restraints excluded: chain O residue 442 CYS Chi-restraints excluded: chain O residue 462 CYS Chi-restraints excluded: chain O residue 499 ILE Chi-restraints excluded: chain O residue 503 LEU Chi-restraints excluded: chain O residue 538 VAL Chi-restraints excluded: chain O residue 554 CYS Chi-restraints excluded: chain P residue 38 LEU Chi-restraints excluded: chain P residue 45 VAL Chi-restraints excluded: chain P residue 66 THR Chi-restraints excluded: chain P residue 84 VAL Chi-restraints excluded: chain P residue 86 THR Chi-restraints excluded: chain P residue 119 LEU Chi-restraints excluded: chain P residue 147 THR Chi-restraints excluded: chain P residue 159 VAL Chi-restraints excluded: chain P residue 176 MET Chi-restraints excluded: chain P residue 234 ASN Chi-restraints excluded: chain P residue 277 SER Chi-restraints excluded: chain P residue 314 ILE Chi-restraints excluded: chain P residue 322 LEU Chi-restraints excluded: chain P residue 333 THR Chi-restraints excluded: chain P residue 366 ASP Chi-restraints excluded: chain P residue 416 VAL Chi-restraints excluded: chain P residue 462 CYS Chi-restraints excluded: chain P residue 503 LEU Chi-restraints excluded: chain P residue 538 VAL Chi-restraints excluded: chain P residue 554 CYS Chi-restraints excluded: chain P residue 594 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 960 random chunks: chunk 841 optimal weight: 0.0000 chunk 886 optimal weight: 3.9990 chunk 808 optimal weight: 0.5980 chunk 862 optimal weight: 6.9990 chunk 518 optimal weight: 8.9990 chunk 375 optimal weight: 7.9990 chunk 677 optimal weight: 0.1980 chunk 264 optimal weight: 0.9990 chunk 779 optimal weight: 8.9990 chunk 815 optimal weight: 5.9990 chunk 859 optimal weight: 7.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 ASN A 311 HIS ** B 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 234 ASN ** E 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 234 ASN ** E 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 234 ASN G 36 ASN ** G 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 230 GLN I 234 ASN J 234 ASN K 36 ASN ** K 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 234 ASN ** L 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 36 ASN ** O 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.4036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 77344 Z= 0.246 Angle : 0.596 11.342 105104 Z= 0.300 Chirality : 0.044 0.283 12160 Planarity : 0.005 0.069 13488 Dihedral : 4.546 31.992 10928 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 4.52 % Allowed : 22.06 % Favored : 73.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.08), residues: 9600 helix: 0.30 (0.10), residues: 2336 sheet: -1.17 (0.13), residues: 1600 loop : -1.47 (0.08), residues: 5664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 51 HIS 0.008 0.001 HIS A 311 PHE 0.031 0.002 PHE P 376 TYR 0.024 0.002 TYR A 573 ARG 0.009 0.000 ARG N 339 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19200 Ramachandran restraints generated. 9600 Oldfield, 0 Emsley, 9600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19200 Ramachandran restraints generated. 9600 Oldfield, 0 Emsley, 9600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1454 residues out of total 8544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 386 poor density : 1068 time to evaluate : 6.230 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 169 LEU cc_start: 0.7538 (mt) cc_final: 0.6916 (mt) REVERT: A 492 GLN cc_start: 0.6799 (tt0) cc_final: 0.6073 (mm-40) REVERT: A 510 CYS cc_start: 0.6764 (m) cc_final: 0.6536 (m) REVERT: B 189 MET cc_start: 0.8727 (tpp) cc_final: 0.8290 (tpp) REVERT: B 305 ARG cc_start: 0.8396 (OUTLIER) cc_final: 0.7602 (ptp90) REVERT: B 335 GLU cc_start: 0.7490 (tp30) cc_final: 0.7093 (tp30) REVERT: B 599 MET cc_start: 0.7797 (mmt) cc_final: 0.7129 (mmt) REVERT: C 169 LEU cc_start: 0.7687 (mt) cc_final: 0.7265 (mt) REVERT: C 189 MET cc_start: 0.8684 (tpp) cc_final: 0.8296 (tpp) REVERT: C 308 LEU cc_start: 0.7144 (pt) cc_final: 0.6391 (mp) REVERT: C 314 ILE cc_start: 0.8753 (OUTLIER) cc_final: 0.8389 (mt) REVERT: C 399 GLN cc_start: 0.6301 (pp30) cc_final: 0.5487 (pp30) REVERT: C 492 GLN cc_start: 0.6580 (tt0) cc_final: 0.6045 (mm-40) REVERT: C 507 LEU cc_start: 0.6076 (tp) cc_final: 0.5873 (tp) REVERT: D 75 ASP cc_start: 0.7365 (p0) cc_final: 0.7085 (p0) REVERT: D 78 TYR cc_start: 0.8342 (m-80) cc_final: 0.7997 (m-80) REVERT: D 135 ARG cc_start: 0.8118 (ttp-110) cc_final: 0.7865 (mtm110) REVERT: D 169 LEU cc_start: 0.7557 (mt) cc_final: 0.7006 (mt) REVERT: D 189 MET cc_start: 0.8562 (tpp) cc_final: 0.8159 (tpp) REVERT: D 492 GLN cc_start: 0.6551 (tt0) cc_final: 0.6000 (mm-40) REVERT: E 169 LEU cc_start: 0.7536 (mt) cc_final: 0.6943 (mt) REVERT: E 189 MET cc_start: 0.8418 (tpp) cc_final: 0.8192 (tpp) REVERT: E 313 PHE cc_start: 0.6646 (t80) cc_final: 0.6288 (t80) REVERT: E 492 GLN cc_start: 0.6443 (tt0) cc_final: 0.5587 (mm-40) REVERT: F 59 MET cc_start: 0.6316 (mmm) cc_final: 0.6049 (mmt) REVERT: F 169 LEU cc_start: 0.7450 (mt) cc_final: 0.7011 (mt) REVERT: F 265 ASP cc_start: 0.6913 (t0) cc_final: 0.6699 (t0) REVERT: F 271 THR cc_start: 0.8407 (OUTLIER) cc_final: 0.8151 (t) REVERT: F 492 GLN cc_start: 0.6813 (tt0) cc_final: 0.6088 (mm-40) REVERT: F 599 MET cc_start: 0.7739 (mmt) cc_final: 0.7011 (mmt) REVERT: G 63 MET cc_start: 0.7796 (mmt) cc_final: 0.7575 (mmt) REVERT: G 78 TYR cc_start: 0.8334 (m-80) cc_final: 0.8043 (m-80) REVERT: G 135 ARG cc_start: 0.8026 (ttp-110) cc_final: 0.7661 (mtm110) REVERT: G 169 LEU cc_start: 0.7647 (mt) cc_final: 0.7216 (mt) REVERT: G 189 MET cc_start: 0.8623 (tpp) cc_final: 0.8226 (tpp) REVERT: G 308 LEU cc_start: 0.7142 (pt) cc_final: 0.6459 (mp) REVERT: G 314 ILE cc_start: 0.8692 (OUTLIER) cc_final: 0.8387 (mt) REVERT: G 458 ARG cc_start: 0.7379 (ptp90) cc_final: 0.7168 (ptp90) REVERT: G 492 GLN cc_start: 0.6594 (tt0) cc_final: 0.5975 (mm-40) REVERT: H 75 ASP cc_start: 0.7264 (p0) cc_final: 0.7064 (p0) REVERT: H 78 TYR cc_start: 0.8436 (m-80) cc_final: 0.7989 (m-80) REVERT: H 93 ASN cc_start: 0.7586 (p0) cc_final: 0.7212 (p0) REVERT: H 169 LEU cc_start: 0.7460 (mt) cc_final: 0.7089 (mt) REVERT: H 176 MET cc_start: 0.7093 (OUTLIER) cc_final: 0.4682 (mtt) REVERT: H 189 MET cc_start: 0.8541 (tpp) cc_final: 0.8145 (tpp) REVERT: H 399 GLN cc_start: 0.6477 (pp30) cc_final: 0.5946 (pp30) REVERT: H 492 GLN cc_start: 0.6788 (tt0) cc_final: 0.5987 (mm-40) REVERT: I 59 MET cc_start: 0.6706 (mmm) cc_final: 0.6366 (mmt) REVERT: I 63 MET cc_start: 0.7922 (mmt) cc_final: 0.7515 (mmt) REVERT: I 169 LEU cc_start: 0.7545 (mt) cc_final: 0.7013 (mt) REVERT: I 492 GLN cc_start: 0.6870 (tt0) cc_final: 0.5772 (mm-40) REVERT: I 510 CYS cc_start: 0.6791 (OUTLIER) cc_final: 0.6238 (m) REVERT: J 93 ASN cc_start: 0.7816 (p0) cc_final: 0.7258 (p0) REVERT: J 135 ARG cc_start: 0.8397 (ttp-110) cc_final: 0.8044 (mtm110) REVERT: J 169 LEU cc_start: 0.7472 (mt) cc_final: 0.7025 (mt) REVERT: J 313 PHE cc_start: 0.6620 (t80) cc_final: 0.6367 (t80) REVERT: J 399 GLN cc_start: 0.6844 (pp30) cc_final: 0.5687 (pp30) REVERT: J 400 LYS cc_start: 0.4774 (mmtp) cc_final: 0.3565 (mmtt) REVERT: J 492 GLN cc_start: 0.6792 (tt0) cc_final: 0.6107 (mm-40) REVERT: J 599 MET cc_start: 0.7787 (mmt) cc_final: 0.7173 (mmt) REVERT: K 59 MET cc_start: 0.6657 (mmm) cc_final: 0.6419 (mmt) REVERT: K 169 LEU cc_start: 0.7625 (mt) cc_final: 0.7207 (mt) REVERT: K 189 MET cc_start: 0.8715 (tpp) cc_final: 0.8462 (tpp) REVERT: K 313 PHE cc_start: 0.7428 (t80) cc_final: 0.7136 (m-80) REVERT: K 458 ARG cc_start: 0.7608 (ptt-90) cc_final: 0.7383 (ptp90) REVERT: K 492 GLN cc_start: 0.6630 (tt0) cc_final: 0.5994 (mm-40) REVERT: L 78 TYR cc_start: 0.8381 (m-80) cc_final: 0.7972 (m-80) REVERT: L 169 LEU cc_start: 0.7655 (mt) cc_final: 0.7261 (mt) REVERT: L 399 GLN cc_start: 0.6499 (pp30) cc_final: 0.5991 (pp30) REVERT: L 492 GLN cc_start: 0.6740 (tt0) cc_final: 0.6141 (mm-40) REVERT: M 59 MET cc_start: 0.6742 (mmm) cc_final: 0.6368 (mmt) REVERT: M 169 LEU cc_start: 0.7476 (mt) cc_final: 0.6890 (mt) REVERT: M 314 ILE cc_start: 0.8345 (OUTLIER) cc_final: 0.7917 (mt) REVERT: M 399 GLN cc_start: 0.6521 (pp30) cc_final: 0.5923 (pp30) REVERT: M 492 GLN cc_start: 0.6621 (tt0) cc_final: 0.5578 (mm-40) REVERT: N 59 MET cc_start: 0.6936 (mmm) cc_final: 0.6600 (mmt) REVERT: N 169 LEU cc_start: 0.7490 (mt) cc_final: 0.7022 (mt) REVERT: N 271 THR cc_start: 0.8475 (OUTLIER) cc_final: 0.8184 (t) REVERT: N 492 GLN cc_start: 0.6777 (tt0) cc_final: 0.6036 (mm-40) REVERT: O 78 TYR cc_start: 0.8289 (m-80) cc_final: 0.8038 (m-80) REVERT: O 169 LEU cc_start: 0.7731 (mt) cc_final: 0.7292 (mt) REVERT: O 189 MET cc_start: 0.8720 (tpp) cc_final: 0.8433 (tpp) REVERT: O 492 GLN cc_start: 0.6530 (tt0) cc_final: 0.5910 (mm-40) REVERT: P 169 LEU cc_start: 0.7623 (mt) cc_final: 0.7231 (mt) REVERT: P 176 MET cc_start: 0.7017 (OUTLIER) cc_final: 0.4565 (mtt) REVERT: P 267 LEU cc_start: 0.8461 (mm) cc_final: 0.8063 (mt) REVERT: P 314 ILE cc_start: 0.8435 (OUTLIER) cc_final: 0.8172 (mt) REVERT: P 399 GLN cc_start: 0.6511 (pp30) cc_final: 0.5973 (pp30) REVERT: P 492 GLN cc_start: 0.6870 (tt0) cc_final: 0.6112 (mm-40) outliers start: 386 outliers final: 338 residues processed: 1343 average time/residue: 0.6303 time to fit residues: 1535.3845 Evaluate side-chains 1388 residues out of total 8544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 348 poor density : 1040 time to evaluate : 6.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 93 ASN Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 442 CYS Chi-restraints excluded: chain A residue 462 CYS Chi-restraints excluded: chain A residue 499 ILE Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 63 MET Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 247 ILE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 305 ARG Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 442 CYS Chi-restraints excluded: chain B residue 462 CYS Chi-restraints excluded: chain B residue 499 ILE Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain B residue 594 THR Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 366 ASP Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain C residue 442 CYS Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 538 VAL Chi-restraints excluded: chain C residue 554 CYS Chi-restraints excluded: chain C residue 586 LEU Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 234 ASN Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 442 CYS Chi-restraints excluded: chain D residue 462 CYS Chi-restraints excluded: chain D residue 499 ILE Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 63 MET Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 199 LEU Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain E residue 277 SER Chi-restraints excluded: chain E residue 303 ILE Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 416 VAL Chi-restraints excluded: chain E residue 442 CYS Chi-restraints excluded: chain E residue 462 CYS Chi-restraints excluded: chain E residue 481 THR Chi-restraints excluded: chain E residue 499 ILE Chi-restraints excluded: chain E residue 503 LEU Chi-restraints excluded: chain E residue 554 CYS Chi-restraints excluded: chain E residue 590 LEU Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 115 ILE Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 234 ASN Chi-restraints excluded: chain F residue 247 ILE Chi-restraints excluded: chain F residue 271 THR Chi-restraints excluded: chain F residue 303 ILE Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 420 SER Chi-restraints excluded: chain F residue 442 CYS Chi-restraints excluded: chain F residue 499 ILE Chi-restraints excluded: chain F residue 503 LEU Chi-restraints excluded: chain F residue 538 VAL Chi-restraints excluded: chain F residue 554 CYS Chi-restraints excluded: chain F residue 594 THR Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain G residue 113 LEU Chi-restraints excluded: chain G residue 115 ILE Chi-restraints excluded: chain G residue 131 THR Chi-restraints excluded: chain G residue 147 THR Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain G residue 247 ILE Chi-restraints excluded: chain G residue 314 ILE Chi-restraints excluded: chain G residue 322 LEU Chi-restraints excluded: chain G residue 333 THR Chi-restraints excluded: chain G residue 366 ASP Chi-restraints excluded: chain G residue 416 VAL Chi-restraints excluded: chain G residue 442 CYS Chi-restraints excluded: chain G residue 462 CYS Chi-restraints excluded: chain G residue 499 ILE Chi-restraints excluded: chain G residue 503 LEU Chi-restraints excluded: chain G residue 538 VAL Chi-restraints excluded: chain G residue 554 CYS Chi-restraints excluded: chain G residue 586 LEU Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain H residue 147 THR Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 176 MET Chi-restraints excluded: chain H residue 188 LYS Chi-restraints excluded: chain H residue 195 GLU Chi-restraints excluded: chain H residue 277 SER Chi-restraints excluded: chain H residue 322 LEU Chi-restraints excluded: chain H residue 333 THR Chi-restraints excluded: chain H residue 366 ASP Chi-restraints excluded: chain H residue 416 VAL Chi-restraints excluded: chain H residue 442 CYS Chi-restraints excluded: chain H residue 462 CYS Chi-restraints excluded: chain H residue 481 THR Chi-restraints excluded: chain H residue 499 ILE Chi-restraints excluded: chain H residue 503 LEU Chi-restraints excluded: chain H residue 538 VAL Chi-restraints excluded: chain H residue 554 CYS Chi-restraints excluded: chain H residue 594 THR Chi-restraints excluded: chain I residue 38 LEU Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain I residue 86 THR Chi-restraints excluded: chain I residue 115 ILE Chi-restraints excluded: chain I residue 147 THR Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 193 LEU Chi-restraints excluded: chain I residue 234 ASN Chi-restraints excluded: chain I residue 247 ILE Chi-restraints excluded: chain I residue 277 SER Chi-restraints excluded: chain I residue 322 LEU Chi-restraints excluded: chain I residue 333 THR Chi-restraints excluded: chain I residue 416 VAL Chi-restraints excluded: chain I residue 442 CYS Chi-restraints excluded: chain I residue 462 CYS Chi-restraints excluded: chain I residue 481 THR Chi-restraints excluded: chain I residue 499 ILE Chi-restraints excluded: chain I residue 503 LEU Chi-restraints excluded: chain I residue 510 CYS Chi-restraints excluded: chain I residue 554 CYS Chi-restraints excluded: chain J residue 38 LEU Chi-restraints excluded: chain J residue 45 VAL Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 115 ILE Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 159 VAL Chi-restraints excluded: chain J residue 247 ILE Chi-restraints excluded: chain J residue 267 LEU Chi-restraints excluded: chain J residue 277 SER Chi-restraints excluded: chain J residue 290 GLU Chi-restraints excluded: chain J residue 303 ILE Chi-restraints excluded: chain J residue 333 THR Chi-restraints excluded: chain J residue 416 VAL Chi-restraints excluded: chain J residue 420 SER Chi-restraints excluded: chain J residue 442 CYS Chi-restraints excluded: chain J residue 462 CYS Chi-restraints excluded: chain J residue 481 THR Chi-restraints excluded: chain J residue 499 ILE Chi-restraints excluded: chain J residue 503 LEU Chi-restraints excluded: chain J residue 538 VAL Chi-restraints excluded: chain J residue 554 CYS Chi-restraints excluded: chain K residue 38 LEU Chi-restraints excluded: chain K residue 45 VAL Chi-restraints excluded: chain K residue 84 VAL Chi-restraints excluded: chain K residue 86 THR Chi-restraints excluded: chain K residue 113 LEU Chi-restraints excluded: chain K residue 115 ILE Chi-restraints excluded: chain K residue 119 LEU Chi-restraints excluded: chain K residue 139 LEU Chi-restraints excluded: chain K residue 147 THR Chi-restraints excluded: chain K residue 159 VAL Chi-restraints excluded: chain K residue 175 LEU Chi-restraints excluded: chain K residue 234 ASN Chi-restraints excluded: chain K residue 247 ILE Chi-restraints excluded: chain K residue 333 THR Chi-restraints excluded: chain K residue 365 ASP Chi-restraints excluded: chain K residue 366 ASP Chi-restraints excluded: chain K residue 416 VAL Chi-restraints excluded: chain K residue 442 CYS Chi-restraints excluded: chain K residue 462 CYS Chi-restraints excluded: chain K residue 499 ILE Chi-restraints excluded: chain K residue 503 LEU Chi-restraints excluded: chain K residue 538 VAL Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 66 THR Chi-restraints excluded: chain L residue 84 VAL Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 113 LEU Chi-restraints excluded: chain L residue 147 THR Chi-restraints excluded: chain L residue 148 THR Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain L residue 175 LEU Chi-restraints excluded: chain L residue 176 MET Chi-restraints excluded: chain L residue 195 GLU Chi-restraints excluded: chain L residue 247 ILE Chi-restraints excluded: chain L residue 277 SER Chi-restraints excluded: chain L residue 322 LEU Chi-restraints excluded: chain L residue 333 THR Chi-restraints excluded: chain L residue 416 VAL Chi-restraints excluded: chain L residue 462 CYS Chi-restraints excluded: chain L residue 481 THR Chi-restraints excluded: chain L residue 499 ILE Chi-restraints excluded: chain L residue 503 LEU Chi-restraints excluded: chain L residue 538 VAL Chi-restraints excluded: chain L residue 554 CYS Chi-restraints excluded: chain L residue 586 LEU Chi-restraints excluded: chain L residue 594 THR Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 63 MET Chi-restraints excluded: chain M residue 86 THR Chi-restraints excluded: chain M residue 115 ILE Chi-restraints excluded: chain M residue 147 THR Chi-restraints excluded: chain M residue 159 VAL Chi-restraints excluded: chain M residue 193 LEU Chi-restraints excluded: chain M residue 234 ASN Chi-restraints excluded: chain M residue 247 ILE Chi-restraints excluded: chain M residue 277 SER Chi-restraints excluded: chain M residue 314 ILE Chi-restraints excluded: chain M residue 322 LEU Chi-restraints excluded: chain M residue 416 VAL Chi-restraints excluded: chain M residue 442 CYS Chi-restraints excluded: chain M residue 462 CYS Chi-restraints excluded: chain M residue 481 THR Chi-restraints excluded: chain M residue 499 ILE Chi-restraints excluded: chain M residue 503 LEU Chi-restraints excluded: chain M residue 538 VAL Chi-restraints excluded: chain M residue 554 CYS Chi-restraints excluded: chain M residue 590 LEU Chi-restraints excluded: chain N residue 38 LEU Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 86 THR Chi-restraints excluded: chain N residue 113 LEU Chi-restraints excluded: chain N residue 115 ILE Chi-restraints excluded: chain N residue 147 THR Chi-restraints excluded: chain N residue 159 VAL Chi-restraints excluded: chain N residue 199 LEU Chi-restraints excluded: chain N residue 234 ASN Chi-restraints excluded: chain N residue 247 ILE Chi-restraints excluded: chain N residue 271 THR Chi-restraints excluded: chain N residue 277 SER Chi-restraints excluded: chain N residue 333 THR Chi-restraints excluded: chain N residue 416 VAL Chi-restraints excluded: chain N residue 420 SER Chi-restraints excluded: chain N residue 442 CYS Chi-restraints excluded: chain N residue 499 ILE Chi-restraints excluded: chain N residue 503 LEU Chi-restraints excluded: chain N residue 538 VAL Chi-restraints excluded: chain N residue 554 CYS Chi-restraints excluded: chain N residue 590 LEU Chi-restraints excluded: chain N residue 594 THR Chi-restraints excluded: chain O residue 38 LEU Chi-restraints excluded: chain O residue 84 VAL Chi-restraints excluded: chain O residue 86 THR Chi-restraints excluded: chain O residue 113 LEU Chi-restraints excluded: chain O residue 131 THR Chi-restraints excluded: chain O residue 147 THR Chi-restraints excluded: chain O residue 159 VAL Chi-restraints excluded: chain O residue 234 ASN Chi-restraints excluded: chain O residue 247 ILE Chi-restraints excluded: chain O residue 277 SER Chi-restraints excluded: chain O residue 308 LEU Chi-restraints excluded: chain O residue 333 THR Chi-restraints excluded: chain O residue 365 ASP Chi-restraints excluded: chain O residue 366 ASP Chi-restraints excluded: chain O residue 416 VAL Chi-restraints excluded: chain O residue 442 CYS Chi-restraints excluded: chain O residue 462 CYS Chi-restraints excluded: chain O residue 499 ILE Chi-restraints excluded: chain O residue 503 LEU Chi-restraints excluded: chain O residue 538 VAL Chi-restraints excluded: chain O residue 554 CYS Chi-restraints excluded: chain P residue 38 LEU Chi-restraints excluded: chain P residue 45 VAL Chi-restraints excluded: chain P residue 66 THR Chi-restraints excluded: chain P residue 84 VAL Chi-restraints excluded: chain P residue 86 THR Chi-restraints excluded: chain P residue 119 LEU Chi-restraints excluded: chain P residue 147 THR Chi-restraints excluded: chain P residue 159 VAL Chi-restraints excluded: chain P residue 176 MET Chi-restraints excluded: chain P residue 234 ASN Chi-restraints excluded: chain P residue 247 ILE Chi-restraints excluded: chain P residue 277 SER Chi-restraints excluded: chain P residue 314 ILE Chi-restraints excluded: chain P residue 322 LEU Chi-restraints excluded: chain P residue 333 THR Chi-restraints excluded: chain P residue 366 ASP Chi-restraints excluded: chain P residue 416 VAL Chi-restraints excluded: chain P residue 462 CYS Chi-restraints excluded: chain P residue 503 LEU Chi-restraints excluded: chain P residue 538 VAL Chi-restraints excluded: chain P residue 554 CYS Chi-restraints excluded: chain P residue 594 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 960 random chunks: chunk 566 optimal weight: 2.9990 chunk 911 optimal weight: 1.9990 chunk 556 optimal weight: 1.9990 chunk 432 optimal weight: 1.9990 chunk 633 optimal weight: 1.9990 chunk 956 optimal weight: 7.9990 chunk 880 optimal weight: 8.9990 chunk 761 optimal weight: 9.9990 chunk 79 optimal weight: 3.9990 chunk 588 optimal weight: 8.9990 chunk 466 optimal weight: 20.0000 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 36 ASN ** G 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 36 ASN ** K 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 36 ASN ** O 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.4061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.318 77344 Z= 0.411 Angle : 0.782 59.199 105104 Z= 0.440 Chirality : 0.048 0.622 12160 Planarity : 0.005 0.168 13488 Dihedral : 4.558 31.924 10928 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 14.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 4.15 % Allowed : 22.37 % Favored : 73.48 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.08), residues: 9600 helix: 0.26 (0.10), residues: 2336 sheet: -1.17 (0.13), residues: 1600 loop : -1.47 (0.08), residues: 5664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 51 HIS 0.005 0.001 HIS J 311 PHE 0.031 0.002 PHE P 376 TYR 0.037 0.002 TYR D 573 ARG 0.015 0.000 ARG C 458 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19200 Ramachandran restraints generated. 9600 Oldfield, 0 Emsley, 9600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19200 Ramachandran restraints generated. 9600 Oldfield, 0 Emsley, 9600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1402 residues out of total 8544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 355 poor density : 1047 time to evaluate : 6.250 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 169 LEU cc_start: 0.7535 (mt) cc_final: 0.6916 (mt) REVERT: A 492 GLN cc_start: 0.6796 (tt0) cc_final: 0.6080 (mm-40) REVERT: A 510 CYS cc_start: 0.6783 (m) cc_final: 0.6514 (m) REVERT: A 562 LEU cc_start: 0.8637 (tt) cc_final: 0.8435 (tt) REVERT: B 169 LEU cc_start: 0.7489 (mt) cc_final: 0.7004 (mt) REVERT: B 189 MET cc_start: 0.8725 (tpp) cc_final: 0.8290 (tpp) REVERT: B 305 ARG cc_start: 0.8395 (OUTLIER) cc_final: 0.7585 (ptp90) REVERT: B 335 GLU cc_start: 0.7499 (tp30) cc_final: 0.7095 (tp30) REVERT: B 599 MET cc_start: 0.7802 (mmt) cc_final: 0.7134 (mmt) REVERT: C 169 LEU cc_start: 0.7696 (mt) cc_final: 0.7275 (mt) REVERT: C 189 MET cc_start: 0.8686 (tpp) cc_final: 0.8298 (tpp) REVERT: C 308 LEU cc_start: 0.7169 (pt) cc_final: 0.6430 (mp) REVERT: C 314 ILE cc_start: 0.8762 (OUTLIER) cc_final: 0.8395 (mt) REVERT: C 399 GLN cc_start: 0.6320 (pp30) cc_final: 0.5499 (pp30) REVERT: C 492 GLN cc_start: 0.6583 (tt0) cc_final: 0.6049 (mm-40) REVERT: C 507 LEU cc_start: 0.6081 (tp) cc_final: 0.5879 (tp) REVERT: D 75 ASP cc_start: 0.7390 (p0) cc_final: 0.7101 (p0) REVERT: D 135 ARG cc_start: 0.8138 (ttp-110) cc_final: 0.7877 (mtm110) REVERT: D 169 LEU cc_start: 0.7569 (mt) cc_final: 0.7015 (mt) REVERT: D 189 MET cc_start: 0.8564 (tpp) cc_final: 0.8156 (tpp) REVERT: D 492 GLN cc_start: 0.6558 (tt0) cc_final: 0.6007 (mm-40) REVERT: E 169 LEU cc_start: 0.7536 (mt) cc_final: 0.6937 (mt) REVERT: E 189 MET cc_start: 0.8422 (tpp) cc_final: 0.8196 (tpp) REVERT: E 313 PHE cc_start: 0.6670 (t80) cc_final: 0.6309 (t80) REVERT: E 492 GLN cc_start: 0.6438 (tt0) cc_final: 0.5597 (mm-40) REVERT: F 59 MET cc_start: 0.6343 (mmm) cc_final: 0.6079 (mmt) REVERT: F 169 LEU cc_start: 0.7462 (mt) cc_final: 0.7020 (mt) REVERT: F 265 ASP cc_start: 0.6914 (t0) cc_final: 0.6698 (t0) REVERT: F 271 THR cc_start: 0.8417 (OUTLIER) cc_final: 0.8177 (t) REVERT: F 492 GLN cc_start: 0.6824 (tt0) cc_final: 0.6097 (mm-40) REVERT: F 599 MET cc_start: 0.7725 (mmt) cc_final: 0.7006 (mmt) REVERT: G 63 MET cc_start: 0.7819 (mmt) cc_final: 0.7602 (mmt) REVERT: G 78 TYR cc_start: 0.8346 (m-80) cc_final: 0.8056 (m-80) REVERT: G 135 ARG cc_start: 0.8034 (ttp-110) cc_final: 0.7677 (mtm110) REVERT: G 169 LEU cc_start: 0.7653 (mt) cc_final: 0.7230 (mt) REVERT: G 189 MET cc_start: 0.8630 (tpp) cc_final: 0.8229 (tpp) REVERT: G 308 LEU cc_start: 0.7154 (pt) cc_final: 0.6478 (mp) REVERT: G 314 ILE cc_start: 0.8684 (OUTLIER) cc_final: 0.8389 (mt) REVERT: G 458 ARG cc_start: 0.7398 (ptp90) cc_final: 0.7167 (ptp90) REVERT: G 492 GLN cc_start: 0.6591 (tt0) cc_final: 0.5979 (mm-40) REVERT: H 78 TYR cc_start: 0.8441 (m-80) cc_final: 0.8003 (m-80) REVERT: H 93 ASN cc_start: 0.7585 (p0) cc_final: 0.7216 (p0) REVERT: H 169 LEU cc_start: 0.7471 (mt) cc_final: 0.7100 (mt) REVERT: H 176 MET cc_start: 0.7102 (OUTLIER) cc_final: 0.4686 (mtt) REVERT: H 189 MET cc_start: 0.8521 (tpp) cc_final: 0.8147 (tpp) REVERT: H 399 GLN cc_start: 0.6499 (pp30) cc_final: 0.6026 (pp30) REVERT: H 492 GLN cc_start: 0.6803 (tt0) cc_final: 0.5995 (mm-40) REVERT: I 59 MET cc_start: 0.6715 (mmm) cc_final: 0.6385 (mmt) REVERT: I 63 MET cc_start: 0.7936 (mmt) cc_final: 0.7532 (mmt) REVERT: I 169 LEU cc_start: 0.7557 (mt) cc_final: 0.7022 (mt) REVERT: I 492 GLN cc_start: 0.6869 (tt0) cc_final: 0.5783 (mm-40) REVERT: J 93 ASN cc_start: 0.7839 (p0) cc_final: 0.7273 (p0) REVERT: J 135 ARG cc_start: 0.8413 (ttp-110) cc_final: 0.8055 (mtm110) REVERT: J 169 LEU cc_start: 0.7477 (mt) cc_final: 0.7035 (mt) REVERT: J 313 PHE cc_start: 0.6632 (t80) cc_final: 0.6383 (t80) REVERT: J 399 GLN cc_start: 0.6846 (pp30) cc_final: 0.5697 (pp30) REVERT: J 400 LYS cc_start: 0.4785 (mmtp) cc_final: 0.3570 (mmtt) REVERT: J 492 GLN cc_start: 0.6813 (tt0) cc_final: 0.6115 (mm-40) REVERT: J 599 MET cc_start: 0.7786 (mmt) cc_final: 0.7175 (mmt) REVERT: K 59 MET cc_start: 0.6676 (mmm) cc_final: 0.6441 (mmt) REVERT: K 169 LEU cc_start: 0.7592 (mt) cc_final: 0.7178 (mt) REVERT: K 189 MET cc_start: 0.8730 (tpp) cc_final: 0.8458 (tpp) REVERT: K 313 PHE cc_start: 0.7437 (t80) cc_final: 0.7140 (m-80) REVERT: K 458 ARG cc_start: 0.7598 (ptt-90) cc_final: 0.7385 (ptp90) REVERT: K 492 GLN cc_start: 0.6647 (tt0) cc_final: 0.5996 (mm-40) REVERT: L 78 TYR cc_start: 0.8373 (m-80) cc_final: 0.7985 (m-80) REVERT: L 169 LEU cc_start: 0.7672 (mt) cc_final: 0.7271 (mt) REVERT: L 399 GLN cc_start: 0.6503 (pp30) cc_final: 0.5989 (pp30) REVERT: L 492 GLN cc_start: 0.6745 (tt0) cc_final: 0.6148 (mm-40) REVERT: M 59 MET cc_start: 0.6716 (mmm) cc_final: 0.6345 (mmt) REVERT: M 169 LEU cc_start: 0.7488 (mt) cc_final: 0.6897 (mt) REVERT: M 314 ILE cc_start: 0.8359 (OUTLIER) cc_final: 0.7924 (mt) REVERT: M 399 GLN cc_start: 0.6538 (pp30) cc_final: 0.5892 (pp30) REVERT: M 492 GLN cc_start: 0.6622 (tt0) cc_final: 0.5585 (mm-40) REVERT: N 59 MET cc_start: 0.6962 (mmm) cc_final: 0.6619 (mmt) REVERT: N 169 LEU cc_start: 0.7494 (mt) cc_final: 0.7030 (mt) REVERT: N 271 THR cc_start: 0.8488 (OUTLIER) cc_final: 0.8202 (t) REVERT: N 492 GLN cc_start: 0.6764 (tt0) cc_final: 0.6030 (mm-40) REVERT: O 78 TYR cc_start: 0.8294 (m-80) cc_final: 0.8048 (m-80) REVERT: O 169 LEU cc_start: 0.7738 (mt) cc_final: 0.7307 (mt) REVERT: O 189 MET cc_start: 0.8727 (tpp) cc_final: 0.8434 (tpp) REVERT: O 218 GLU cc_start: 0.7457 (mt-10) cc_final: 0.7182 (mt-10) REVERT: O 492 GLN cc_start: 0.6527 (tt0) cc_final: 0.5917 (mm-40) REVERT: P 169 LEU cc_start: 0.7632 (mt) cc_final: 0.7239 (mt) REVERT: P 176 MET cc_start: 0.7000 (OUTLIER) cc_final: 0.4659 (mtt) REVERT: P 267 LEU cc_start: 0.8452 (mm) cc_final: 0.8066 (mt) REVERT: P 314 ILE cc_start: 0.8444 (OUTLIER) cc_final: 0.8180 (mt) REVERT: P 399 GLN cc_start: 0.6512 (pp30) cc_final: 0.5984 (pp30) REVERT: P 492 GLN cc_start: 0.6879 (tt0) cc_final: 0.6120 (mm-40) REVERT: P 598 LEU cc_start: 0.7708 (mt) cc_final: 0.7250 (mt) outliers start: 355 outliers final: 339 residues processed: 1296 average time/residue: 0.6356 time to fit residues: 1497.3601 Evaluate side-chains 1394 residues out of total 8544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 348 poor density : 1046 time to evaluate : 6.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 93 ASN Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 442 CYS Chi-restraints excluded: chain A residue 462 CYS Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 499 ILE Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 63 MET Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 247 ILE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 305 ARG Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 442 CYS Chi-restraints excluded: chain B residue 462 CYS Chi-restraints excluded: chain B residue 499 ILE Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain B residue 594 THR Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 365 ASP Chi-restraints excluded: chain C residue 366 ASP Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain C residue 442 CYS Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 538 VAL Chi-restraints excluded: chain C residue 554 CYS Chi-restraints excluded: chain C residue 586 LEU Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 442 CYS Chi-restraints excluded: chain D residue 462 CYS Chi-restraints excluded: chain D residue 499 ILE Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 63 MET Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 199 LEU Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain E residue 277 SER Chi-restraints excluded: chain E residue 303 ILE Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 416 VAL Chi-restraints excluded: chain E residue 442 CYS Chi-restraints excluded: chain E residue 462 CYS Chi-restraints excluded: chain E residue 481 THR Chi-restraints excluded: chain E residue 499 ILE Chi-restraints excluded: chain E residue 503 LEU Chi-restraints excluded: chain E residue 554 CYS Chi-restraints excluded: chain E residue 590 LEU Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 115 ILE Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 247 ILE Chi-restraints excluded: chain F residue 271 THR Chi-restraints excluded: chain F residue 303 ILE Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 420 SER Chi-restraints excluded: chain F residue 442 CYS Chi-restraints excluded: chain F residue 499 ILE Chi-restraints excluded: chain F residue 503 LEU Chi-restraints excluded: chain F residue 538 VAL Chi-restraints excluded: chain F residue 594 THR Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain G residue 113 LEU Chi-restraints excluded: chain G residue 115 ILE Chi-restraints excluded: chain G residue 131 THR Chi-restraints excluded: chain G residue 147 THR Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain G residue 247 ILE Chi-restraints excluded: chain G residue 314 ILE Chi-restraints excluded: chain G residue 322 LEU Chi-restraints excluded: chain G residue 333 THR Chi-restraints excluded: chain G residue 366 ASP Chi-restraints excluded: chain G residue 416 VAL Chi-restraints excluded: chain G residue 442 CYS Chi-restraints excluded: chain G residue 462 CYS Chi-restraints excluded: chain G residue 499 ILE Chi-restraints excluded: chain G residue 503 LEU Chi-restraints excluded: chain G residue 538 VAL Chi-restraints excluded: chain G residue 554 CYS Chi-restraints excluded: chain G residue 586 LEU Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain H residue 147 THR Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 176 MET Chi-restraints excluded: chain H residue 188 LYS Chi-restraints excluded: chain H residue 195 GLU Chi-restraints excluded: chain H residue 247 ILE Chi-restraints excluded: chain H residue 277 SER Chi-restraints excluded: chain H residue 322 LEU Chi-restraints excluded: chain H residue 333 THR Chi-restraints excluded: chain H residue 366 ASP Chi-restraints excluded: chain H residue 416 VAL Chi-restraints excluded: chain H residue 442 CYS Chi-restraints excluded: chain H residue 462 CYS Chi-restraints excluded: chain H residue 481 THR Chi-restraints excluded: chain H residue 499 ILE Chi-restraints excluded: chain H residue 503 LEU Chi-restraints excluded: chain H residue 538 VAL Chi-restraints excluded: chain H residue 554 CYS Chi-restraints excluded: chain H residue 594 THR Chi-restraints excluded: chain I residue 38 LEU Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain I residue 86 THR Chi-restraints excluded: chain I residue 115 ILE Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 147 THR Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 193 LEU Chi-restraints excluded: chain I residue 234 ASN Chi-restraints excluded: chain I residue 247 ILE Chi-restraints excluded: chain I residue 277 SER Chi-restraints excluded: chain I residue 322 LEU Chi-restraints excluded: chain I residue 333 THR Chi-restraints excluded: chain I residue 416 VAL Chi-restraints excluded: chain I residue 442 CYS Chi-restraints excluded: chain I residue 462 CYS Chi-restraints excluded: chain I residue 481 THR Chi-restraints excluded: chain I residue 499 ILE Chi-restraints excluded: chain I residue 503 LEU Chi-restraints excluded: chain I residue 554 CYS Chi-restraints excluded: chain J residue 38 LEU Chi-restraints excluded: chain J residue 45 VAL Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 113 LEU Chi-restraints excluded: chain J residue 115 ILE Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 159 VAL Chi-restraints excluded: chain J residue 247 ILE Chi-restraints excluded: chain J residue 277 SER Chi-restraints excluded: chain J residue 303 ILE Chi-restraints excluded: chain J residue 333 THR Chi-restraints excluded: chain J residue 416 VAL Chi-restraints excluded: chain J residue 420 SER Chi-restraints excluded: chain J residue 442 CYS Chi-restraints excluded: chain J residue 462 CYS Chi-restraints excluded: chain J residue 481 THR Chi-restraints excluded: chain J residue 499 ILE Chi-restraints excluded: chain J residue 503 LEU Chi-restraints excluded: chain J residue 538 VAL Chi-restraints excluded: chain J residue 554 CYS Chi-restraints excluded: chain K residue 38 LEU Chi-restraints excluded: chain K residue 45 VAL Chi-restraints excluded: chain K residue 84 VAL Chi-restraints excluded: chain K residue 86 THR Chi-restraints excluded: chain K residue 113 LEU Chi-restraints excluded: chain K residue 115 ILE Chi-restraints excluded: chain K residue 119 LEU Chi-restraints excluded: chain K residue 139 LEU Chi-restraints excluded: chain K residue 147 THR Chi-restraints excluded: chain K residue 159 VAL Chi-restraints excluded: chain K residue 175 LEU Chi-restraints excluded: chain K residue 247 ILE Chi-restraints excluded: chain K residue 333 THR Chi-restraints excluded: chain K residue 365 ASP Chi-restraints excluded: chain K residue 366 ASP Chi-restraints excluded: chain K residue 416 VAL Chi-restraints excluded: chain K residue 442 CYS Chi-restraints excluded: chain K residue 462 CYS Chi-restraints excluded: chain K residue 499 ILE Chi-restraints excluded: chain K residue 503 LEU Chi-restraints excluded: chain K residue 538 VAL Chi-restraints excluded: chain K residue 586 LEU Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 66 THR Chi-restraints excluded: chain L residue 84 VAL Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 113 LEU Chi-restraints excluded: chain L residue 147 THR Chi-restraints excluded: chain L residue 148 THR Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain L residue 175 LEU Chi-restraints excluded: chain L residue 176 MET Chi-restraints excluded: chain L residue 195 GLU Chi-restraints excluded: chain L residue 234 ASN Chi-restraints excluded: chain L residue 247 ILE Chi-restraints excluded: chain L residue 277 SER Chi-restraints excluded: chain L residue 322 LEU Chi-restraints excluded: chain L residue 333 THR Chi-restraints excluded: chain L residue 416 VAL Chi-restraints excluded: chain L residue 462 CYS Chi-restraints excluded: chain L residue 481 THR Chi-restraints excluded: chain L residue 499 ILE Chi-restraints excluded: chain L residue 503 LEU Chi-restraints excluded: chain L residue 538 VAL Chi-restraints excluded: chain L residue 554 CYS Chi-restraints excluded: chain L residue 586 LEU Chi-restraints excluded: chain L residue 594 THR Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 63 MET Chi-restraints excluded: chain M residue 86 THR Chi-restraints excluded: chain M residue 115 ILE Chi-restraints excluded: chain M residue 147 THR Chi-restraints excluded: chain M residue 159 VAL Chi-restraints excluded: chain M residue 193 LEU Chi-restraints excluded: chain M residue 234 ASN Chi-restraints excluded: chain M residue 247 ILE Chi-restraints excluded: chain M residue 277 SER Chi-restraints excluded: chain M residue 314 ILE Chi-restraints excluded: chain M residue 322 LEU Chi-restraints excluded: chain M residue 416 VAL Chi-restraints excluded: chain M residue 442 CYS Chi-restraints excluded: chain M residue 462 CYS Chi-restraints excluded: chain M residue 481 THR Chi-restraints excluded: chain M residue 499 ILE Chi-restraints excluded: chain M residue 503 LEU Chi-restraints excluded: chain M residue 538 VAL Chi-restraints excluded: chain M residue 554 CYS Chi-restraints excluded: chain M residue 590 LEU Chi-restraints excluded: chain N residue 38 LEU Chi-restraints excluded: chain N residue 86 THR Chi-restraints excluded: chain N residue 113 LEU Chi-restraints excluded: chain N residue 115 ILE Chi-restraints excluded: chain N residue 147 THR Chi-restraints excluded: chain N residue 159 VAL Chi-restraints excluded: chain N residue 199 LEU Chi-restraints excluded: chain N residue 234 ASN Chi-restraints excluded: chain N residue 247 ILE Chi-restraints excluded: chain N residue 271 THR Chi-restraints excluded: chain N residue 277 SER Chi-restraints excluded: chain N residue 333 THR Chi-restraints excluded: chain N residue 416 VAL Chi-restraints excluded: chain N residue 420 SER Chi-restraints excluded: chain N residue 442 CYS Chi-restraints excluded: chain N residue 499 ILE Chi-restraints excluded: chain N residue 503 LEU Chi-restraints excluded: chain N residue 538 VAL Chi-restraints excluded: chain N residue 590 LEU Chi-restraints excluded: chain N residue 594 THR Chi-restraints excluded: chain O residue 38 LEU Chi-restraints excluded: chain O residue 84 VAL Chi-restraints excluded: chain O residue 86 THR Chi-restraints excluded: chain O residue 113 LEU Chi-restraints excluded: chain O residue 131 THR Chi-restraints excluded: chain O residue 147 THR Chi-restraints excluded: chain O residue 159 VAL Chi-restraints excluded: chain O residue 234 ASN Chi-restraints excluded: chain O residue 247 ILE Chi-restraints excluded: chain O residue 277 SER Chi-restraints excluded: chain O residue 308 LEU Chi-restraints excluded: chain O residue 333 THR Chi-restraints excluded: chain O residue 365 ASP Chi-restraints excluded: chain O residue 366 ASP Chi-restraints excluded: chain O residue 416 VAL Chi-restraints excluded: chain O residue 442 CYS Chi-restraints excluded: chain O residue 462 CYS Chi-restraints excluded: chain O residue 499 ILE Chi-restraints excluded: chain O residue 503 LEU Chi-restraints excluded: chain O residue 538 VAL Chi-restraints excluded: chain O residue 554 CYS Chi-restraints excluded: chain P residue 38 LEU Chi-restraints excluded: chain P residue 45 VAL Chi-restraints excluded: chain P residue 66 THR Chi-restraints excluded: chain P residue 84 VAL Chi-restraints excluded: chain P residue 86 THR Chi-restraints excluded: chain P residue 119 LEU Chi-restraints excluded: chain P residue 147 THR Chi-restraints excluded: chain P residue 159 VAL Chi-restraints excluded: chain P residue 176 MET Chi-restraints excluded: chain P residue 234 ASN Chi-restraints excluded: chain P residue 247 ILE Chi-restraints excluded: chain P residue 277 SER Chi-restraints excluded: chain P residue 314 ILE Chi-restraints excluded: chain P residue 322 LEU Chi-restraints excluded: chain P residue 333 THR Chi-restraints excluded: chain P residue 366 ASP Chi-restraints excluded: chain P residue 416 VAL Chi-restraints excluded: chain P residue 462 CYS Chi-restraints excluded: chain P residue 481 THR Chi-restraints excluded: chain P residue 503 LEU Chi-restraints excluded: chain P residue 533 MET Chi-restraints excluded: chain P residue 538 VAL Chi-restraints excluded: chain P residue 554 CYS Chi-restraints excluded: chain P residue 594 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 960 random chunks: chunk 604 optimal weight: 0.8980 chunk 811 optimal weight: 0.8980 chunk 233 optimal weight: 9.9990 chunk 702 optimal weight: 6.9990 chunk 112 optimal weight: 0.6980 chunk 211 optimal weight: 0.9990 chunk 762 optimal weight: 1.9990 chunk 319 optimal weight: 0.8980 chunk 783 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 140 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 36 ASN ** G 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 36 ASN ** K 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 36 ASN ** O 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.211961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.169405 restraints weight = 81899.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.171398 restraints weight = 80201.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.173843 restraints weight = 52423.847| |-----------------------------------------------------------------------------| r_work (final): 0.3940 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3939 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3939 r_free = 0.3939 target_work(ls_wunit_k1) = 0.173 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3938 r_free = 0.3938 target_work(ls_wunit_k1) = 0.173 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3938 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.4063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.318 77344 Z= 0.411 Angle : 0.782 59.199 105104 Z= 0.440 Chirality : 0.048 0.622 12160 Planarity : 0.005 0.168 13488 Dihedral : 4.558 31.924 10928 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 15.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 4.07 % Allowed : 22.46 % Favored : 73.47 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.08), residues: 9600 helix: 0.26 (0.10), residues: 2336 sheet: -1.17 (0.13), residues: 1600 loop : -1.47 (0.08), residues: 5664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 51 HIS 0.005 0.001 HIS J 311 PHE 0.031 0.002 PHE P 376 TYR 0.037 0.002 TYR D 573 ARG 0.015 0.000 ARG C 458 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 22905.49 seconds wall clock time: 395 minutes 13.14 seconds (23713.14 seconds total)