Starting phenix.real_space_refine on Wed Apr 10 19:03:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x5b_22048/04_2024/6x5b_22048_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x5b_22048/04_2024/6x5b_22048.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x5b_22048/04_2024/6x5b_22048_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x5b_22048/04_2024/6x5b_22048_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x5b_22048/04_2024/6x5b_22048_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x5b_22048/04_2024/6x5b_22048.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x5b_22048/04_2024/6x5b_22048.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x5b_22048/04_2024/6x5b_22048_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x5b_22048/04_2024/6x5b_22048_updated.pdb" } resolution = 3.6 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 108 5.16 5 C 12723 2.51 5 N 3456 2.21 5 O 3945 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 20232 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 2769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2769 Classifications: {'peptide': 353} Link IDs: {'PTRANS': 21, 'TRANS': 331} Chain breaks: 5 Chain: "B" Number of atoms: 1184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1184 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 2, 'TRANS': 146} Chain: "L" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 812 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 98} Chain: "C" Number of atoms: 768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 768 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "H" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 971 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "D" Number of atoms: 2769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2769 Classifications: {'peptide': 353} Link IDs: {'PTRANS': 21, 'TRANS': 331} Chain breaks: 5 Chain: "E" Number of atoms: 1184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1184 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 2, 'TRANS': 146} Chain: "F" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 812 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 98} Chain: "G" Number of atoms: 768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 768 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "I" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 971 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "J" Number of atoms: 2769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2769 Classifications: {'peptide': 353} Link IDs: {'PTRANS': 21, 'TRANS': 331} Chain breaks: 5 Chain: "K" Number of atoms: 1184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1184 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 2, 'TRANS': 146} Chain: "M" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 812 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 98} Chain: "N" Number of atoms: 768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 768 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "O" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 971 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} 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 Chain: "Q" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "R" 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: "S" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "T" 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: "U" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'NAG': 1, 'UOV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'NAG': 1, 'UOV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "J" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'NAG': 1, 'UOV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 10.31, per 1000 atoms: 0.51 Number of scatterers: 20232 At special positions: 0 Unit cell: (150.65, 156.4, 140.3, 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 108 16.00 O 3945 8.00 N 3456 7.00 C 12723 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.08 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.04 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.02 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.07 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 16 " - pdb=" SG CYS C 84 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.02 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 74 " distance=2.08 Simple disulfide: pdb=" SG CYS D 119 " - pdb=" SG CYS D 205 " distance=2.04 Simple disulfide: pdb=" SG CYS D 218 " - pdb=" SG CYS D 247 " distance=2.03 Simple disulfide: pdb=" SG CYS D 228 " - pdb=" SG CYS D 239 " distance=2.03 Simple disulfide: pdb=" SG CYS D 296 " - pdb=" SG CYS D 331 " distance=2.02 Simple disulfide: pdb=" SG CYS D 385 " - pdb=" SG CYS D 418 " distance=2.03 Simple disulfide: pdb=" SG CYS D 501 " - pdb=" SG CYS E 605 " distance=2.07 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.02 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.03 Simple disulfide: pdb=" SG CYS G 16 " - pdb=" SG CYS G 84 " distance=2.02 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.02 Simple disulfide: pdb=" SG CYS J 54 " - pdb=" SG CYS J 74 " distance=2.08 Simple disulfide: pdb=" SG CYS J 119 " - pdb=" SG CYS J 205 " distance=2.04 Simple disulfide: pdb=" SG CYS J 218 " - pdb=" SG CYS J 247 " distance=2.03 Simple disulfide: pdb=" SG CYS J 228 " - pdb=" SG CYS J 239 " distance=2.03 Simple disulfide: pdb=" SG CYS J 296 " - pdb=" SG CYS J 331 " distance=2.02 Simple disulfide: pdb=" SG CYS J 385 " - pdb=" SG CYS J 418 " distance=2.03 Simple disulfide: pdb=" SG CYS J 501 " - pdb=" SG CYS K 605 " distance=2.07 Simple disulfide: pdb=" SG CYS K 598 " - pdb=" SG CYS K 604 " distance=2.02 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.03 Simple disulfide: pdb=" SG CYS N 16 " - pdb=" SG CYS N 84 " distance=2.02 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 92 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN Q 4 " - " MAN Q 5 " " MAN S 4 " - " MAN S 5 " " MAN U 4 " - " MAN U 5 " ALPHA1-3 " BMA Q 3 " - " MAN Q 4 " " BMA S 3 " - " MAN S 4 " " BMA U 3 " - " MAN U 4 " BETA1-4 " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " NAG-ASN " NAG A 607 " - " ASN A 276 " " NAG A 608 " - " ASN A 295 " " NAG A 609 " - " ASN A 332 " " NAG A 610 " - " ASN A 362 " " NAG A 611 " - " ASN A 386 " " NAG A 612 " - " ASN A 392 " " NAG A 613 " - " ASN A 413 " " NAG A 614 " - " ASN A 448 " " NAG B 701 " - " ASN B 611 " " NAG D 607 " - " ASN D 276 " " NAG D 608 " - " ASN D 295 " " NAG D 609 " - " ASN D 332 " " NAG D 610 " - " ASN D 362 " " NAG D 611 " - " ASN D 386 " " NAG D 612 " - " ASN D 392 " " NAG D 613 " - " ASN D 413 " " NAG D 614 " - " ASN D 448 " " NAG E 701 " - " ASN E 611 " " NAG J 607 " - " ASN J 276 " " NAG J 608 " - " ASN J 295 " " NAG J 609 " - " ASN J 332 " " NAG J 610 " - " ASN J 362 " " NAG J 611 " - " ASN J 386 " " NAG J 612 " - " ASN J 392 " " NAG J 613 " - " ASN J 413 " " NAG J 614 " - " ASN J 448 " " NAG K 701 " - " ASN K 611 " " NAG P 1 " - " ASN A 241 " " NAG Q 1 " - " ASN A 262 " " NAG R 1 " - " ASN D 241 " " NAG S 1 " - " ASN D 262 " " NAG T 1 " - " ASN J 241 " " NAG U 1 " - " ASN J 262 " Time building additional restraints: 7.89 Conformation dependent library (CDL) restraints added in 3.4 seconds 4854 Ramachandran restraints generated. 2427 Oldfield, 0 Emsley, 2427 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4614 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 57 helices and 39 sheets defined 21.4% alpha, 24.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.72 Creating SS restraints... Processing helix chain 'A' and resid 66 through 68 No H-bonds generated for 'chain 'A' and resid 66 through 68' Processing helix chain 'A' and resid 70 through 73 No H-bonds generated for 'chain 'A' and resid 70 through 73' Processing helix chain 'A' and resid 100 through 113 Processing helix chain 'A' and resid 335 through 352 removed outlier: 3.730A pdb=" N GLU A 351 " --> pdb=" O ALA A 347 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLN A 352 " --> pdb=" O LYS A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 372 No H-bonds generated for 'chain 'A' and resid 369 through 372' Processing helix chain 'A' and resid 475 through 485 removed outlier: 4.973A pdb=" N TYR A 484 " --> pdb=" O SER A 481 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N LYS A 485 " --> pdb=" O GLU A 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 517 through 527 removed outlier: 3.843A pdb=" N PHE B 522 " --> pdb=" O PHE B 518 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLY B 524 " --> pdb=" O LEU B 520 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N ALA B 525 " --> pdb=" O GLY B 521 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ALA B 526 " --> pdb=" O PHE B 522 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N GLY B 527 " --> pdb=" O LEU B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 530 through 545 Processing helix chain 'B' and resid 562 through 596 removed outlier: 5.485A pdb=" N LEU B 566 " --> pdb=" O GLN B 563 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N VAL B 570 " --> pdb=" O GLN B 567 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N TRP B 571 " --> pdb=" O LEU B 568 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY B 572 " --> pdb=" O THR B 569 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE B 573 " --> pdb=" O VAL B 570 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU B 581 " --> pdb=" O ALA B 578 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N LEU B 593 " --> pdb=" O GLN B 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 624 Processing helix chain 'B' and resid 628 through 634 removed outlier: 4.142A pdb=" N LYS B 633 " --> pdb=" O MET B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 659 removed outlier: 5.206A pdb=" N GLN B 640 " --> pdb=" O ASN B 637 " (cutoff:3.500A) Processing helix chain 'L' and resid 80 through 82 No H-bonds generated for 'chain 'L' and resid 80 through 82' Processing helix chain 'C' and resid 59 through 64 removed outlier: 4.461A pdb=" N ASP C 63 " --> pdb=" O SER C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 78 No H-bonds generated for 'chain 'C' and resid 76 through 78' Processing helix chain 'H' and resid 29 through 31 No H-bonds generated for 'chain 'H' and resid 29 through 31' Processing helix chain 'H' and resid 61 through 63 No H-bonds generated for 'chain 'H' and resid 61 through 63' Processing helix chain 'H' and resid 84 through 86 No H-bonds generated for 'chain 'H' and resid 84 through 86' Processing helix chain 'H' and resid 100 through 100B No H-bonds generated for 'chain 'H' and resid 100 through 100B' Processing helix chain 'D' and resid 66 through 68 No H-bonds generated for 'chain 'D' and resid 66 through 68' Processing helix chain 'D' and resid 70 through 73 No H-bonds generated for 'chain 'D' and resid 70 through 73' Processing helix chain 'D' and resid 100 through 113 Processing helix chain 'D' and resid 335 through 352 removed outlier: 3.729A pdb=" N GLU D 351 " --> pdb=" O ALA D 347 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN D 352 " --> pdb=" O LYS D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 369 through 372 No H-bonds generated for 'chain 'D' and resid 369 through 372' Processing helix chain 'D' and resid 475 through 485 removed outlier: 4.973A pdb=" N TYR D 484 " --> pdb=" O SER D 481 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N LYS D 485 " --> pdb=" O GLU D 482 " (cutoff:3.500A) Processing helix chain 'E' and resid 517 through 527 removed outlier: 3.843A pdb=" N PHE E 522 " --> pdb=" O PHE E 518 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLY E 524 " --> pdb=" O LEU E 520 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N ALA E 525 " --> pdb=" O GLY E 521 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ALA E 526 " --> pdb=" O PHE E 522 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N GLY E 527 " --> pdb=" O LEU E 523 " (cutoff:3.500A) Processing helix chain 'E' and resid 530 through 545 Processing helix chain 'E' and resid 562 through 596 removed outlier: 5.485A pdb=" N LEU E 566 " --> pdb=" O GLN E 563 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N VAL E 570 " --> pdb=" O GLN E 567 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N TRP E 571 " --> pdb=" O LEU E 568 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY E 572 " --> pdb=" O THR E 569 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE E 573 " --> pdb=" O VAL E 570 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU E 581 " --> pdb=" O ALA E 578 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N LEU E 593 " --> pdb=" O GLN E 590 " (cutoff:3.500A) Processing helix chain 'E' and resid 619 through 624 Processing helix chain 'E' and resid 628 through 634 removed outlier: 4.142A pdb=" N LYS E 633 " --> pdb=" O MET E 629 " (cutoff:3.500A) Processing helix chain 'E' and resid 636 through 659 removed outlier: 5.205A pdb=" N GLN E 640 " --> pdb=" O ASN E 637 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 82 No H-bonds generated for 'chain 'F' and resid 80 through 82' Processing helix chain 'G' and resid 59 through 64 removed outlier: 4.461A pdb=" N ASP G 63 " --> pdb=" O SER G 60 " (cutoff:3.500A) Processing helix chain 'G' and resid 76 through 78 No H-bonds generated for 'chain 'G' and resid 76 through 78' Processing helix chain 'I' and resid 29 through 31 No H-bonds generated for 'chain 'I' and resid 29 through 31' Processing helix chain 'I' and resid 61 through 63 No H-bonds generated for 'chain 'I' and resid 61 through 63' Processing helix chain 'I' and resid 84 through 86 No H-bonds generated for 'chain 'I' and resid 84 through 86' Processing helix chain 'I' and resid 100 through 100B No H-bonds generated for 'chain 'I' and resid 100 through 100B' Processing helix chain 'J' and resid 66 through 68 No H-bonds generated for 'chain 'J' and resid 66 through 68' Processing helix chain 'J' and resid 70 through 73 No H-bonds generated for 'chain 'J' and resid 70 through 73' Processing helix chain 'J' and resid 100 through 113 Processing helix chain 'J' and resid 335 through 352 removed outlier: 3.729A pdb=" N GLU J 351 " --> pdb=" O ALA J 347 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLN J 352 " --> pdb=" O LYS J 348 " (cutoff:3.500A) Processing helix chain 'J' and resid 369 through 372 No H-bonds generated for 'chain 'J' and resid 369 through 372' Processing helix chain 'J' and resid 475 through 485 removed outlier: 4.973A pdb=" N TYR J 484 " --> pdb=" O SER J 481 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N LYS J 485 " --> pdb=" O GLU J 482 " (cutoff:3.500A) Processing helix chain 'K' and resid 517 through 527 removed outlier: 3.843A pdb=" N PHE K 522 " --> pdb=" O PHE K 518 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLY K 524 " --> pdb=" O LEU K 520 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N ALA K 525 " --> pdb=" O GLY K 521 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ALA K 526 " --> pdb=" O PHE K 522 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N GLY K 527 " --> pdb=" O LEU K 523 " (cutoff:3.500A) Processing helix chain 'K' and resid 530 through 545 Processing helix chain 'K' and resid 562 through 596 removed outlier: 5.485A pdb=" N LEU K 566 " --> pdb=" O GLN K 563 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N VAL K 570 " --> pdb=" O GLN K 567 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N TRP K 571 " --> pdb=" O LEU K 568 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY K 572 " --> pdb=" O THR K 569 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE K 573 " --> pdb=" O VAL K 570 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU K 581 " --> pdb=" O ALA K 578 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N LEU K 593 " --> pdb=" O GLN K 590 " (cutoff:3.500A) Processing helix chain 'K' and resid 619 through 624 Processing helix chain 'K' and resid 628 through 634 removed outlier: 4.142A pdb=" N LYS K 633 " --> pdb=" O MET K 629 " (cutoff:3.500A) Processing helix chain 'K' and resid 636 through 659 removed outlier: 5.205A pdb=" N GLN K 640 " --> pdb=" O ASN K 637 " (cutoff:3.500A) Processing helix chain 'M' and resid 80 through 82 No H-bonds generated for 'chain 'M' and resid 80 through 82' Processing helix chain 'N' and resid 59 through 64 removed outlier: 4.462A pdb=" N ASP N 63 " --> pdb=" O SER N 60 " (cutoff:3.500A) Processing helix chain 'N' and resid 76 through 78 No H-bonds generated for 'chain 'N' and resid 76 through 78' Processing helix chain 'O' and resid 29 through 31 No H-bonds generated for 'chain 'O' and resid 29 through 31' Processing helix chain 'O' and resid 61 through 63 No H-bonds generated for 'chain 'O' and resid 61 through 63' Processing helix chain 'O' and resid 84 through 86 No H-bonds generated for 'chain 'O' and resid 84 through 86' Processing helix chain 'O' and resid 100 through 100B No H-bonds generated for 'chain 'O' and resid 100 through 100B' Processing sheet with id= A, first strand: chain 'A' and resid 35 through 40 Processing sheet with id= B, first strand: chain 'A' and resid 45 through 47 Processing sheet with id= C, first strand: chain 'A' and resid 53 through 56 Processing sheet with id= D, first strand: chain 'A' and resid 91 through 94 Processing sheet with id= E, first strand: chain 'A' and resid 199 through 202 Processing sheet with id= F, first strand: chain 'A' and resid 271 through 273 removed outlier: 6.773A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 443 through 449 removed outlier: 4.622A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'L' and resid 4 through 6 Processing sheet with id= I, first strand: chain 'L' and resid 85 through 90 removed outlier: 6.413A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 2 through 5 removed outlier: 4.767A pdb=" N PHE C 26 " --> pdb=" O ASN C 39 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU C 37 " --> pdb=" O TRP C 28 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N ASN C 30 " --> pdb=" O LYS C 35 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LYS C 35 " --> pdb=" O ASN C 30 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLY C 38 " --> pdb=" O THR C 45 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 12 through 17 Processing sheet with id= L, first strand: chain 'H' and resid 3 through 6 Processing sheet with id= M, first strand: chain 'H' and resid 107 through 109 removed outlier: 3.505A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL H 56 " --> pdb=" O ILE H 52 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 35 through 40 Processing sheet with id= O, first strand: chain 'D' and resid 45 through 47 Processing sheet with id= P, first strand: chain 'D' and resid 53 through 56 Processing sheet with id= Q, first strand: chain 'D' and resid 91 through 94 Processing sheet with id= R, first strand: chain 'D' and resid 199 through 202 Processing sheet with id= S, first strand: chain 'D' and resid 271 through 273 removed outlier: 6.773A pdb=" N LEU D 260 " --> pdb=" O THR D 450 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 443 through 449 removed outlier: 4.621A pdb=" N PHE D 382 " --> pdb=" O LYS D 421 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'F' and resid 4 through 6 Processing sheet with id= V, first strand: chain 'F' and resid 85 through 90 removed outlier: 6.414A pdb=" N GLN F 37 " --> pdb=" O LEU F 46 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N LEU F 46 " --> pdb=" O GLN F 37 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'G' and resid 2 through 5 removed outlier: 4.767A pdb=" N PHE G 26 " --> pdb=" O ASN G 39 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU G 37 " --> pdb=" O TRP G 28 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ASN G 30 " --> pdb=" O LYS G 35 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LYS G 35 " --> pdb=" O ASN G 30 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLY G 38 " --> pdb=" O THR G 45 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'G' and resid 12 through 17 Processing sheet with id= Y, first strand: chain 'I' and resid 3 through 6 Processing sheet with id= Z, first strand: chain 'I' and resid 107 through 109 removed outlier: 3.505A pdb=" N GLY I 49 " --> pdb=" O TRP I 36 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL I 56 " --> pdb=" O ILE I 52 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'J' and resid 35 through 40 Processing sheet with id= AB, first strand: chain 'J' and resid 45 through 47 Processing sheet with id= AC, first strand: chain 'J' and resid 53 through 56 Processing sheet with id= AD, first strand: chain 'J' and resid 91 through 94 Processing sheet with id= AE, first strand: chain 'J' and resid 199 through 202 Processing sheet with id= AF, first strand: chain 'J' and resid 271 through 273 removed outlier: 6.773A pdb=" N LEU J 260 " --> pdb=" O THR J 450 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'J' and resid 443 through 449 removed outlier: 4.621A pdb=" N PHE J 382 " --> pdb=" O LYS J 421 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'M' and resid 4 through 6 Processing sheet with id= AI, first strand: chain 'M' and resid 85 through 90 removed outlier: 6.412A pdb=" N GLN M 37 " --> pdb=" O LEU M 46 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N LEU M 46 " --> pdb=" O GLN M 37 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'N' and resid 2 through 5 removed outlier: 4.766A pdb=" N PHE N 26 " --> pdb=" O ASN N 39 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU N 37 " --> pdb=" O TRP N 28 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N ASN N 30 " --> pdb=" O LYS N 35 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LYS N 35 " --> pdb=" O ASN N 30 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLY N 38 " --> pdb=" O THR N 45 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'N' and resid 12 through 17 Processing sheet with id= AL, first strand: chain 'O' and resid 3 through 6 Processing sheet with id= AM, first strand: chain 'O' and resid 107 through 109 removed outlier: 3.506A pdb=" N GLY O 49 " --> pdb=" O TRP O 36 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N ARG O 38 " --> pdb=" O TRP O 47 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N TRP O 47 " --> pdb=" O ARG O 38 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL O 56 " --> pdb=" O ILE O 52 " (cutoff:3.500A) 720 hydrogen bonds defined for protein. 1476 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: 6.56 Time building geometry restraints manager: 8.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3689 1.31 - 1.45: 6397 1.45 - 1.59: 10290 1.59 - 1.73: 120 1.73 - 1.86: 141 Bond restraints: 20637 Sorted by residual: bond pdb=" NE ARG A 504 " pdb=" CZ ARG A 504 " ideal model delta sigma weight residual 1.326 1.402 -0.076 1.10e-02 8.26e+03 4.82e+01 bond pdb=" NE ARG D 504 " pdb=" CZ ARG D 504 " ideal model delta sigma weight residual 1.326 1.402 -0.076 1.10e-02 8.26e+03 4.77e+01 bond pdb=" NE ARG J 504 " pdb=" CZ ARG J 504 " ideal model delta sigma weight residual 1.326 1.402 -0.076 1.10e-02 8.26e+03 4.74e+01 bond pdb=" CG HIS D 374 " pdb=" CD2 HIS D 374 " ideal model delta sigma weight residual 1.354 1.283 0.071 1.10e-02 8.26e+03 4.15e+01 bond pdb=" CG HIS A 374 " pdb=" CD2 HIS A 374 " ideal model delta sigma weight residual 1.354 1.283 0.071 1.10e-02 8.26e+03 4.11e+01 ... (remaining 20632 not shown) Histogram of bond angle deviations from ideal: 84.65 - 94.57: 9 94.57 - 104.50: 351 104.50 - 114.43: 12228 114.43 - 124.35: 14512 124.35 - 134.28: 896 Bond angle restraints: 27996 Sorted by residual: angle pdb=" C08 UOV E 702 " pdb=" C09 UOV E 702 " pdb=" N10 UOV E 702 " ideal model delta sigma weight residual 97.96 123.30 -25.34 3.00e+00 1.11e-01 7.13e+01 angle pdb=" C08 UOV B 702 " pdb=" C09 UOV B 702 " pdb=" N10 UOV B 702 " ideal model delta sigma weight residual 97.96 123.27 -25.31 3.00e+00 1.11e-01 7.12e+01 angle pdb=" C08 UOV K 702 " pdb=" C09 UOV K 702 " pdb=" N10 UOV K 702 " ideal model delta sigma weight residual 97.96 123.26 -25.30 3.00e+00 1.11e-01 7.11e+01 angle pdb=" C15 UOV B 702 " pdb=" C16 UOV B 702 " pdb=" O19 UOV B 702 " ideal model delta sigma weight residual 96.48 121.54 -25.06 3.00e+00 1.11e-01 6.98e+01 angle pdb=" C15 UOV E 702 " pdb=" C16 UOV E 702 " pdb=" O19 UOV E 702 " ideal model delta sigma weight residual 96.48 121.53 -25.05 3.00e+00 1.11e-01 6.97e+01 ... (remaining 27991 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.66: 12642 23.66 - 47.31: 225 47.31 - 70.97: 90 70.97 - 94.63: 18 94.63 - 118.28: 27 Dihedral angle restraints: 13002 sinusoidal: 5859 harmonic: 7143 Sorted by residual: dihedral pdb=" CB CYS A 119 " pdb=" SG CYS A 119 " pdb=" SG CYS A 205 " pdb=" CB CYS A 205 " ideal model delta sinusoidal sigma weight residual -86.00 -166.17 80.17 1 1.00e+01 1.00e-02 7.96e+01 dihedral pdb=" CB CYS D 119 " pdb=" SG CYS D 119 " pdb=" SG CYS D 205 " pdb=" CB CYS D 205 " ideal model delta sinusoidal sigma weight residual -86.00 -166.16 80.16 1 1.00e+01 1.00e-02 7.96e+01 dihedral pdb=" CB CYS J 119 " pdb=" SG CYS J 119 " pdb=" SG CYS J 205 " pdb=" CB CYS J 205 " ideal model delta sinusoidal sigma weight residual -86.00 -166.13 80.13 1 1.00e+01 1.00e-02 7.95e+01 ... (remaining 12999 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 2230 0.104 - 0.207: 757 0.207 - 0.311: 142 0.311 - 0.414: 90 0.414 - 0.518: 42 Chirality restraints: 3261 Sorted by residual: chirality pdb=" C1 NAG R 2 " pdb=" O4 NAG R 1 " pdb=" C2 NAG R 2 " pdb=" O5 NAG R 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.25e+02 chirality pdb=" C1 NAG T 2 " pdb=" O4 NAG T 1 " pdb=" C2 NAG T 2 " pdb=" O5 NAG T 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.23e+02 chirality pdb=" C1 NAG P 2 " pdb=" O4 NAG P 1 " pdb=" C2 NAG P 2 " pdb=" O5 NAG P 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.22e+02 ... (remaining 3258 not shown) Planarity restraints: 3552 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN K 611 " -0.095 2.00e-02 2.50e+03 9.97e-02 1.24e+02 pdb=" CG ASN K 611 " 0.038 2.00e-02 2.50e+03 pdb=" OD1 ASN K 611 " 0.023 2.00e-02 2.50e+03 pdb=" ND2 ASN K 611 " 0.155 2.00e-02 2.50e+03 pdb=" C1 NAG K 701 " -0.121 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 611 " -0.095 2.00e-02 2.50e+03 9.97e-02 1.24e+02 pdb=" CG ASN E 611 " 0.038 2.00e-02 2.50e+03 pdb=" OD1 ASN E 611 " 0.023 2.00e-02 2.50e+03 pdb=" ND2 ASN E 611 " 0.155 2.00e-02 2.50e+03 pdb=" C1 NAG E 701 " -0.121 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 611 " -0.095 2.00e-02 2.50e+03 9.96e-02 1.24e+02 pdb=" CG ASN B 611 " 0.038 2.00e-02 2.50e+03 pdb=" OD1 ASN B 611 " 0.023 2.00e-02 2.50e+03 pdb=" ND2 ASN B 611 " 0.155 2.00e-02 2.50e+03 pdb=" C1 NAG B 701 " -0.121 2.00e-02 2.50e+03 ... (remaining 3549 not shown) Histogram of nonbonded interaction distances: 2.43 - 2.93: 8822 2.93 - 3.42: 18237 3.42 - 3.91: 34916 3.91 - 4.41: 39810 4.41 - 4.90: 63677 Nonbonded interactions: 165462 Sorted by model distance: nonbonded pdb=" N ASN D 301 " pdb=" N ASN D 302 " model vdw 2.434 2.560 nonbonded pdb=" N ASN A 301 " pdb=" N ASN A 302 " model vdw 2.435 2.560 nonbonded pdb=" N ASN J 301 " pdb=" N ASN J 302 " model vdw 2.435 2.560 nonbonded pdb=" N ASN G 39 " pdb=" OD1 ASN G 39 " model vdw 2.446 2.520 nonbonded pdb=" N ASN C 39 " pdb=" OD1 ASN C 39 " model vdw 2.446 2.520 ... (remaining 165457 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'J' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'K' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'N' } ncs_group { reference = chain 'F' selection = chain 'L' selection = chain 'M' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'O' } ncs_group { reference = chain 'P' selection = chain 'R' selection = chain 'T' } ncs_group { reference = chain 'Q' selection = chain 'S' selection = chain 'U' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.420 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: 0.020 Extract box with map and model: 6.210 Check model and map are aligned: 0.280 Set scattering table: 0.170 Process input model: 53.730 Find NCS groups from input model: 1.180 Set up NCS constraints: 0.230 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 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 : 0.021 0.122 20637 Z= 1.389 Angle : 1.787 25.340 27996 Z= 1.144 Chirality : 0.126 0.518 3261 Planarity : 0.009 0.055 3519 Dihedral : 12.104 118.283 8289 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 0.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.17), residues: 2427 helix: -0.36 (0.22), residues: 444 sheet: 0.77 (0.20), residues: 687 loop : 0.48 (0.17), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.010 TRP N 28 HIS 0.008 0.002 HIS J 374 PHE 0.029 0.007 PHE K 522 TYR 0.068 0.010 TYR F 91 ARG 0.006 0.001 ARG G 59 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4854 Ramachandran restraints generated. 2427 Oldfield, 0 Emsley, 2427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4854 Ramachandran restraints generated. 2427 Oldfield, 0 Emsley, 2427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 700 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 700 time to evaluate : 2.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 428 GLN cc_start: 0.7463 (mp10) cc_final: 0.6898 (mt0) REVERT: A 446 SER cc_start: 0.8579 (m) cc_final: 0.8068 (p) REVERT: A 475 MET cc_start: 0.7946 (mmp) cc_final: 0.7640 (tpp) REVERT: B 638 TYR cc_start: 0.7099 (m-80) cc_final: 0.6885 (m-10) REVERT: L 52 SER cc_start: 0.7491 (p) cc_final: 0.7282 (t) REVERT: C 74 LEU cc_start: 0.7327 (tp) cc_final: 0.6422 (tp) REVERT: H 81 GLU cc_start: 0.6204 (tt0) cc_final: 0.5926 (tt0) REVERT: H 111 VAL cc_start: 0.5893 (t) cc_final: 0.5347 (t) REVERT: D 446 SER cc_start: 0.8450 (m) cc_final: 0.7985 (p) REVERT: E 638 TYR cc_start: 0.6894 (m-80) cc_final: 0.6657 (m-10) REVERT: G 60 SER cc_start: 0.9055 (p) cc_final: 0.8830 (p) REVERT: G 74 LEU cc_start: 0.7418 (tp) cc_final: 0.6622 (tp) REVERT: G 86 VAL cc_start: 0.8044 (t) cc_final: 0.7637 (t) REVERT: I 12 LYS cc_start: 0.7676 (mmtt) cc_final: 0.7110 (mmtt) REVERT: I 36 TRP cc_start: 0.7482 (m100) cc_final: 0.7117 (m100) REVERT: I 111 VAL cc_start: 0.6246 (t) cc_final: 0.5462 (t) REVERT: J 116 LEU cc_start: 0.8745 (mt) cc_final: 0.8519 (mp) REVERT: J 428 GLN cc_start: 0.7638 (mp10) cc_final: 0.7174 (mt0) REVERT: J 446 SER cc_start: 0.8557 (m) cc_final: 0.8232 (p) REVERT: J 475 MET cc_start: 0.7925 (mmp) cc_final: 0.7708 (mmm) REVERT: J 482 GLU cc_start: 0.6800 (mm-30) cc_final: 0.6581 (mm-30) REVERT: K 627 THR cc_start: 0.8250 (p) cc_final: 0.7938 (p) REVERT: K 629 MET cc_start: 0.7935 (mmm) cc_final: 0.7626 (mmm) REVERT: K 638 TYR cc_start: 0.6863 (m-80) cc_final: 0.6572 (m-10) REVERT: O 108 LEU cc_start: 0.8688 (tp) cc_final: 0.8471 (tt) REVERT: O 111 VAL cc_start: 0.6308 (t) cc_final: 0.5383 (t) outliers start: 0 outliers final: 0 residues processed: 700 average time/residue: 0.3417 time to fit residues: 356.4546 Evaluate side-chains 362 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 362 time to evaluate : 2.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 202 optimal weight: 0.6980 chunk 181 optimal weight: 4.9990 chunk 100 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 chunk 97 optimal weight: 5.9990 chunk 188 optimal weight: 0.7980 chunk 72 optimal weight: 5.9990 chunk 114 optimal weight: 1.9990 chunk 140 optimal weight: 0.9980 chunk 217 optimal weight: 5.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 72 HIS ** A 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 249 HIS A 355 ASN A 363 HIS ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 620 ASN L 37 GLN L 42 GLN L 93 ASN C 94 GLN H 58 HIS H 62 HIS ** D 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 72 HIS ** D 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 203 GLN ** D 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 249 HIS D 325 ASN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 428 GLN E 554 ASN E 607 ASN E 620 ASN F 37 GLN F 93 ASN G 25 GLN I 58 HIS ** J 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 72 HIS ** J 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 249 HIS J 363 HIS ** J 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 564 HIS K 620 ASN M 37 GLN O 39 GLN O 58 HIS Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.3179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 20637 Z= 0.247 Angle : 0.769 12.980 27996 Z= 0.396 Chirality : 0.049 0.228 3261 Planarity : 0.006 0.044 3519 Dihedral : 10.368 111.277 3651 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.93 % Allowed : 10.01 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.17), residues: 2427 helix: -0.42 (0.23), residues: 435 sheet: 0.75 (0.22), residues: 600 loop : 0.09 (0.17), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP F 94 HIS 0.010 0.002 HIS D 66 PHE 0.019 0.002 PHE A 53 TYR 0.029 0.003 TYR A 435 ARG 0.007 0.001 ARG I 50 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4854 Ramachandran restraints generated. 2427 Oldfield, 0 Emsley, 2427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4854 Ramachandran restraints generated. 2427 Oldfield, 0 Emsley, 2427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 406 time to evaluate : 2.219 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: A 426 MET cc_start: 0.7485 (mtp) cc_final: 0.7213 (mtp) REVERT: A 428 GLN cc_start: 0.8002 (mp10) cc_final: 0.7047 (mt0) REVERT: A 446 SER cc_start: 0.8581 (m) cc_final: 0.8049 (p) REVERT: B 620 ASN cc_start: 0.7137 (m-40) cc_final: 0.6820 (m110) REVERT: L 2 LEU cc_start: 0.4934 (OUTLIER) cc_final: 0.4405 (mt) REVERT: L 36 TYR cc_start: 0.6998 (m-80) cc_final: 0.6714 (m-80) REVERT: H 12 LYS cc_start: 0.6619 (mptt) cc_final: 0.5807 (mttp) REVERT: D 64 GLU cc_start: 0.7791 (tm-30) cc_final: 0.6878 (tt0) REVERT: D 74 CYS cc_start: 0.5379 (m) cc_final: 0.5117 (m) REVERT: D 446 SER cc_start: 0.8413 (m) cc_final: 0.7927 (p) REVERT: D 475 MET cc_start: 0.7963 (mmm) cc_final: 0.7580 (mmm) REVERT: E 565 MET cc_start: 0.7432 (ptm) cc_final: 0.7143 (ptm) REVERT: I 12 LYS cc_start: 0.7479 (mmtt) cc_final: 0.7066 (mmtm) REVERT: J 64 GLU cc_start: 0.7492 (tm-30) cc_final: 0.6619 (tt0) REVERT: J 428 GLN cc_start: 0.7860 (mp10) cc_final: 0.7064 (mt0) REVERT: J 446 SER cc_start: 0.8535 (m) cc_final: 0.8112 (p) REVERT: J 482 GLU cc_start: 0.6917 (mm-30) cc_final: 0.6644 (mm-30) REVERT: N 58 ARG cc_start: 0.8363 (mtp85) cc_final: 0.8153 (ttt90) REVERT: O 12 LYS cc_start: 0.6280 (mptt) cc_final: 0.4843 (mttt) outliers start: 63 outliers final: 41 residues processed: 445 average time/residue: 0.3635 time to fit residues: 246.9739 Evaluate side-chains 364 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 322 time to evaluate : 2.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 325 ASN Chi-restraints excluded: chain A residue 485 LYS Chi-restraints excluded: chain B residue 563 GLN Chi-restraints excluded: chain B residue 564 HIS Chi-restraints excluded: chain L residue 2 LEU Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 54 LEU Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 325 ASN Chi-restraints excluded: chain D residue 485 LYS Chi-restraints excluded: chain E residue 564 HIS Chi-restraints excluded: chain E residue 629 MET Chi-restraints excluded: chain F residue 82 ASP Chi-restraints excluded: chain G residue 53 ASP Chi-restraints excluded: chain G residue 88 ASP Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 232 THR Chi-restraints excluded: chain J residue 325 ASN Chi-restraints excluded: chain K residue 563 GLN Chi-restraints excluded: chain K residue 565 MET Chi-restraints excluded: chain K residue 646 LEU Chi-restraints excluded: chain M residue 82 ASP Chi-restraints excluded: chain N residue 53 ASP Chi-restraints excluded: chain N residue 88 ASP Chi-restraints excluded: chain O residue 35 THR Chi-restraints excluded: chain O residue 45 LEU Chi-restraints excluded: chain O residue 54 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 121 optimal weight: 1.9990 chunk 67 optimal weight: 7.9990 chunk 181 optimal weight: 0.9980 chunk 148 optimal weight: 9.9990 chunk 60 optimal weight: 5.9990 chunk 218 optimal weight: 5.9990 chunk 235 optimal weight: 20.0000 chunk 194 optimal weight: 0.8980 chunk 216 optimal weight: 9.9990 chunk 74 optimal weight: 8.9990 chunk 175 optimal weight: 0.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 ASN A 363 HIS ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 ASN D 82 GLN D 229 ASN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 564 HIS F 42 GLN F 79 GLN J 80 ASN J 229 ASN J 363 HIS ** J 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 564 HIS K 620 ASN M 93 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 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 : 0.005 0.048 20637 Z= 0.308 Angle : 0.726 13.305 27996 Z= 0.368 Chirality : 0.048 0.204 3261 Planarity : 0.005 0.056 3519 Dihedral : 9.515 114.197 3651 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.26 % Allowed : 12.57 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.17), residues: 2427 helix: -0.93 (0.23), residues: 432 sheet: 0.66 (0.21), residues: 645 loop : -0.37 (0.17), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP H 36 HIS 0.006 0.001 HIS J 66 PHE 0.019 0.002 PHE D 53 TYR 0.025 0.003 TYR O 100E ARG 0.006 0.001 ARG H 50 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4854 Ramachandran restraints generated. 2427 Oldfield, 0 Emsley, 2427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4854 Ramachandran restraints generated. 2427 Oldfield, 0 Emsley, 2427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 380 time to evaluate : 2.317 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 381 GLU cc_start: 0.8006 (mm-30) cc_final: 0.7779 (mm-30) REVERT: A 446 SER cc_start: 0.8702 (m) cc_final: 0.8114 (p) REVERT: L 36 TYR cc_start: 0.7222 (m-80) cc_final: 0.6871 (m-80) REVERT: C 94 GLN cc_start: 0.7115 (tp-100) cc_final: 0.6487 (tp40) REVERT: H 18 VAL cc_start: 0.7198 (t) cc_final: 0.6210 (m) REVERT: H 19 LYS cc_start: 0.8088 (OUTLIER) cc_final: 0.7220 (tmtt) REVERT: D 446 SER cc_start: 0.8601 (m) cc_final: 0.8029 (p) REVERT: D 475 MET cc_start: 0.8048 (mmm) cc_final: 0.7787 (mmm) REVERT: J 446 SER cc_start: 0.8724 (m) cc_final: 0.8376 (p) REVERT: K 627 THR cc_start: 0.8282 (p) cc_final: 0.7957 (p) REVERT: M 24 ARG cc_start: 0.6529 (ttm110) cc_final: 0.6284 (ttm-80) REVERT: N 74 LEU cc_start: 0.6775 (tp) cc_final: 0.6284 (tp) REVERT: O 12 LYS cc_start: 0.6380 (tptt) cc_final: 0.6151 (mttp) outliers start: 70 outliers final: 50 residues processed: 417 average time/residue: 0.3071 time to fit residues: 200.0781 Evaluate side-chains 359 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 308 time to evaluate : 2.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 325 ASN Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 485 LYS Chi-restraints excluded: chain B residue 563 GLN Chi-restraints excluded: chain B residue 564 HIS Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain H residue 19 LYS Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 54 LEU Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 485 LYS Chi-restraints excluded: chain E residue 564 HIS Chi-restraints excluded: chain E residue 615 SER Chi-restraints excluded: chain E residue 644 THR Chi-restraints excluded: chain F residue 82 ASP Chi-restraints excluded: chain G residue 34 ILE Chi-restraints excluded: chain G residue 53 ASP Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 88 ASP Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain J residue 232 THR Chi-restraints excluded: chain J residue 325 ASN Chi-restraints excluded: chain J residue 373 THR Chi-restraints excluded: chain K residue 563 GLN Chi-restraints excluded: chain K residue 565 MET Chi-restraints excluded: chain K residue 615 SER Chi-restraints excluded: chain K residue 618 THR Chi-restraints excluded: chain K residue 644 THR Chi-restraints excluded: chain K residue 646 LEU Chi-restraints excluded: chain M residue 82 ASP Chi-restraints excluded: chain N residue 60 SER Chi-restraints excluded: chain N residue 88 ASP Chi-restraints excluded: chain O residue 35 THR Chi-restraints excluded: chain O residue 45 LEU Chi-restraints excluded: chain O residue 54 LEU Chi-restraints excluded: chain O residue 68 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 215 optimal weight: 20.0000 chunk 164 optimal weight: 0.0370 chunk 113 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 104 optimal weight: 0.4980 chunk 146 optimal weight: 7.9990 chunk 219 optimal weight: 0.0040 chunk 231 optimal weight: 3.9990 chunk 114 optimal weight: 0.8980 chunk 207 optimal weight: 4.9990 chunk 62 optimal weight: 0.7980 overall best weight: 0.4470 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 GLN A 363 HIS ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 ASN J 363 HIS ** J 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 620 ASN M 93 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.4321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20637 Z= 0.173 Angle : 0.637 12.830 27996 Z= 0.320 Chirality : 0.045 0.168 3261 Planarity : 0.005 0.055 3519 Dihedral : 8.602 113.279 3651 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.08 % Favored : 95.88 % Rotamer: Outliers : 2.84 % Allowed : 13.87 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.17), residues: 2427 helix: -1.08 (0.23), residues: 432 sheet: 0.75 (0.22), residues: 603 loop : -0.53 (0.17), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP H 36 HIS 0.014 0.001 HIS E 564 PHE 0.016 0.002 PHE J 53 TYR 0.030 0.002 TYR M 49 ARG 0.004 0.000 ARG I 50 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4854 Ramachandran restraints generated. 2427 Oldfield, 0 Emsley, 2427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4854 Ramachandran restraints generated. 2427 Oldfield, 0 Emsley, 2427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 365 time to evaluate : 2.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 TRP cc_start: 0.7771 (m100) cc_final: 0.7527 (m100) REVERT: A 446 SER cc_start: 0.8627 (m) cc_final: 0.8124 (p) REVERT: B 657 GLU cc_start: 0.7648 (tp30) cc_final: 0.7419 (tt0) REVERT: L 36 TYR cc_start: 0.7076 (m-80) cc_final: 0.6784 (m-80) REVERT: L 38 GLN cc_start: 0.5968 (OUTLIER) cc_final: 0.5649 (tp40) REVERT: C 94 GLN cc_start: 0.7022 (tp-100) cc_final: 0.6604 (tp40) REVERT: H 12 LYS cc_start: 0.6964 (tptt) cc_final: 0.6161 (ttmm) REVERT: H 91 PHE cc_start: 0.6200 (OUTLIER) cc_final: 0.5590 (p90) REVERT: D 64 GLU cc_start: 0.7797 (tm-30) cc_final: 0.6853 (tt0) REVERT: D 446 SER cc_start: 0.8570 (m) cc_final: 0.8113 (p) REVERT: F 70 GLU cc_start: 0.6838 (mp0) cc_final: 0.6494 (mp0) REVERT: I 43 GLN cc_start: 0.8011 (tp-100) cc_final: 0.7622 (tp-100) REVERT: I 91 PHE cc_start: 0.6333 (OUTLIER) cc_final: 0.5412 (p90) REVERT: J 345 ILE cc_start: 0.7745 (mp) cc_final: 0.7517 (mp) REVERT: J 446 SER cc_start: 0.8603 (m) cc_final: 0.8134 (p) REVERT: M 24 ARG cc_start: 0.6466 (ttm110) cc_final: 0.6240 (ttm-80) REVERT: N 54 ARG cc_start: 0.8300 (mtp-110) cc_final: 0.7880 (mtp180) REVERT: N 74 LEU cc_start: 0.6741 (tp) cc_final: 0.6004 (tp) REVERT: O 91 PHE cc_start: 0.6400 (OUTLIER) cc_final: 0.6134 (p90) outliers start: 61 outliers final: 34 residues processed: 399 average time/residue: 0.2983 time to fit residues: 189.3378 Evaluate side-chains 348 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 310 time to evaluate : 2.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 485 LYS Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 54 LEU Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 91 PHE Chi-restraints excluded: chain D residue 325 ASN Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain D residue 485 LYS Chi-restraints excluded: chain E residue 618 THR Chi-restraints excluded: chain F residue 82 ASP Chi-restraints excluded: chain G residue 53 ASP Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 88 ASP Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain I residue 91 PHE Chi-restraints excluded: chain I residue 108 LEU Chi-restraints excluded: chain J residue 57 ASP Chi-restraints excluded: chain K residue 563 GLN Chi-restraints excluded: chain K residue 564 HIS Chi-restraints excluded: chain K residue 646 LEU Chi-restraints excluded: chain M residue 82 ASP Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 53 ASP Chi-restraints excluded: chain N residue 88 ASP Chi-restraints excluded: chain O residue 35 THR Chi-restraints excluded: chain O residue 45 LEU Chi-restraints excluded: chain O residue 54 LEU Chi-restraints excluded: chain O residue 68 THR Chi-restraints excluded: chain O residue 91 PHE Chi-restraints excluded: chain O residue 107 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 193 optimal weight: 2.9990 chunk 131 optimal weight: 9.9990 chunk 3 optimal weight: 7.9990 chunk 172 optimal weight: 0.9990 chunk 95 optimal weight: 4.9990 chunk 197 optimal weight: 7.9990 chunk 160 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 118 optimal weight: 0.9980 chunk 208 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 ASN A 216 HIS ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 ASN ** D 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 42 GLN ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 80 ASN J 325 ASN J 363 HIS ** J 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.4674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 20637 Z= 0.244 Angle : 0.645 13.100 27996 Z= 0.324 Chirality : 0.046 0.197 3261 Planarity : 0.005 0.047 3519 Dihedral : 8.311 116.224 3651 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.33 % Favored : 95.55 % Rotamer: Outliers : 3.72 % Allowed : 14.90 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.17), residues: 2427 helix: -1.07 (0.23), residues: 435 sheet: 0.83 (0.22), residues: 582 loop : -0.73 (0.16), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP H 36 HIS 0.006 0.001 HIS D 363 PHE 0.016 0.002 PHE A 53 TYR 0.037 0.003 TYR M 91 ARG 0.007 0.000 ARG K 579 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4854 Ramachandran restraints generated. 2427 Oldfield, 0 Emsley, 2427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4854 Ramachandran restraints generated. 2427 Oldfield, 0 Emsley, 2427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 345 time to evaluate : 2.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 ILE cc_start: 0.8253 (mp) cc_final: 0.7933 (mt) REVERT: A 446 SER cc_start: 0.8726 (m) cc_final: 0.8200 (p) REVERT: L 36 TYR cc_start: 0.7189 (m-80) cc_final: 0.6866 (m-80) REVERT: C 94 GLN cc_start: 0.7084 (tp-100) cc_final: 0.6633 (tp40) REVERT: H 39 GLN cc_start: 0.7241 (OUTLIER) cc_final: 0.6673 (tp-100) REVERT: H 62 HIS cc_start: 0.8460 (OUTLIER) cc_final: 0.8098 (p90) REVERT: H 91 PHE cc_start: 0.6499 (OUTLIER) cc_final: 0.5799 (p90) REVERT: D 446 SER cc_start: 0.8695 (m) cc_final: 0.8178 (p) REVERT: E 629 MET cc_start: 0.7367 (mmm) cc_final: 0.7094 (mmm) REVERT: G 54 ARG cc_start: 0.8503 (mtp-110) cc_final: 0.7983 (mtp180) REVERT: I 43 GLN cc_start: 0.8193 (tp-100) cc_final: 0.7892 (tp-100) REVERT: I 91 PHE cc_start: 0.6431 (OUTLIER) cc_final: 0.5439 (p90) REVERT: J 446 SER cc_start: 0.8700 (m) cc_final: 0.8320 (p) REVERT: K 627 THR cc_start: 0.8126 (p) cc_final: 0.7865 (p) REVERT: M 24 ARG cc_start: 0.6537 (ttm110) cc_final: 0.6300 (ttm-80) REVERT: O 62 HIS cc_start: 0.8353 (OUTLIER) cc_final: 0.8071 (p90) REVERT: O 91 PHE cc_start: 0.6464 (OUTLIER) cc_final: 0.6142 (p90) outliers start: 80 outliers final: 57 residues processed: 386 average time/residue: 0.2897 time to fit residues: 179.3657 Evaluate side-chains 373 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 310 time to evaluate : 2.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 80 ASN Chi-restraints excluded: chain A residue 325 ASN Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 485 LYS Chi-restraints excluded: chain B residue 564 HIS Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain H residue 54 LEU Chi-restraints excluded: chain H residue 62 HIS Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 91 PHE Chi-restraints excluded: chain D residue 80 ASN Chi-restraints excluded: chain D residue 325 ASN Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 485 LYS Chi-restraints excluded: chain E residue 564 HIS Chi-restraints excluded: chain E residue 618 THR Chi-restraints excluded: chain E residue 644 THR Chi-restraints excluded: chain F residue 24 ARG Chi-restraints excluded: chain F residue 82 ASP Chi-restraints excluded: chain G residue 53 ASP Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 88 ASP Chi-restraints excluded: chain I residue 10 GLU Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain I residue 91 PHE Chi-restraints excluded: chain I residue 107 THR Chi-restraints excluded: chain I residue 108 LEU Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain J residue 57 ASP Chi-restraints excluded: chain J residue 74 CYS Chi-restraints excluded: chain J residue 80 ASN Chi-restraints excluded: chain J residue 325 ASN Chi-restraints excluded: chain J residue 373 THR Chi-restraints excluded: chain K residue 563 GLN Chi-restraints excluded: chain K residue 564 HIS Chi-restraints excluded: chain K residue 565 MET Chi-restraints excluded: chain K residue 644 THR Chi-restraints excluded: chain K residue 646 LEU Chi-restraints excluded: chain M residue 82 ASP Chi-restraints excluded: chain N residue 60 SER Chi-restraints excluded: chain N residue 88 ASP Chi-restraints excluded: chain O residue 35 THR Chi-restraints excluded: chain O residue 45 LEU Chi-restraints excluded: chain O residue 54 LEU Chi-restraints excluded: chain O residue 62 HIS Chi-restraints excluded: chain O residue 68 THR Chi-restraints excluded: chain O residue 70 THR Chi-restraints excluded: chain O residue 91 PHE Chi-restraints excluded: chain O residue 107 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 78 optimal weight: 8.9990 chunk 208 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 136 optimal weight: 8.9990 chunk 57 optimal weight: 10.0000 chunk 232 optimal weight: 9.9990 chunk 192 optimal weight: 6.9990 chunk 107 optimal weight: 5.9990 chunk 19 optimal weight: 8.9990 chunk 76 optimal weight: 10.0000 chunk 121 optimal weight: 1.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 42 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 417 GLN ** E 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 325 ASN J 363 HIS ** J 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 417 GLN K 590 GLN M 42 GLN M 79 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.5279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.088 20637 Z= 0.558 Angle : 0.854 13.703 27996 Z= 0.438 Chirality : 0.054 0.200 3261 Planarity : 0.007 0.084 3519 Dihedral : 9.084 122.053 3651 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 15.27 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.02 % Favored : 93.86 % Rotamer: Outliers : 4.70 % Allowed : 15.18 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -1.16 (0.16), residues: 2427 helix: -1.43 (0.23), residues: 414 sheet: 0.56 (0.21), residues: 660 loop : -1.26 (0.16), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP H 36 HIS 0.009 0.002 HIS D 363 PHE 0.024 0.003 PHE D 376 TYR 0.024 0.003 TYR M 91 ARG 0.008 0.001 ARG A 469 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4854 Ramachandran restraints generated. 2427 Oldfield, 0 Emsley, 2427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4854 Ramachandran restraints generated. 2427 Oldfield, 0 Emsley, 2427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 332 time to evaluate : 2.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 ILE cc_start: 0.8140 (mp) cc_final: 0.7794 (mt) REVERT: B 657 GLU cc_start: 0.7774 (tp30) cc_final: 0.7514 (tt0) REVERT: L 36 TYR cc_start: 0.7534 (m-80) cc_final: 0.7204 (m-80) REVERT: C 80 ASP cc_start: 0.5871 (m-30) cc_final: 0.5362 (t0) REVERT: C 94 GLN cc_start: 0.7340 (tp-100) cc_final: 0.6922 (tp-100) REVERT: H 39 GLN cc_start: 0.7349 (OUTLIER) cc_final: 0.6734 (tp-100) REVERT: H 91 PHE cc_start: 0.6899 (OUTLIER) cc_final: 0.5993 (p90) REVERT: D 446 SER cc_start: 0.8973 (m) cc_final: 0.8408 (p) REVERT: E 654 GLU cc_start: 0.8652 (tp30) cc_final: 0.8427 (tp30) REVERT: G 80 ASP cc_start: 0.5925 (m-30) cc_final: 0.5438 (t0) REVERT: I 48 MET cc_start: 0.7961 (ttm) cc_final: 0.7614 (ttt) REVERT: I 91 PHE cc_start: 0.6557 (OUTLIER) cc_final: 0.5708 (p90) REVERT: J 270 ILE cc_start: 0.8394 (mp) cc_final: 0.8128 (mt) REVERT: K 627 THR cc_start: 0.8562 (p) cc_final: 0.8315 (p) REVERT: M 24 ARG cc_start: 0.6750 (ttm110) cc_final: 0.6498 (ttm-80) REVERT: O 62 HIS cc_start: 0.8496 (OUTLIER) cc_final: 0.8064 (p90) REVERT: O 91 PHE cc_start: 0.6878 (OUTLIER) cc_final: 0.6450 (p90) outliers start: 101 outliers final: 84 residues processed: 392 average time/residue: 0.2831 time to fit residues: 177.7351 Evaluate side-chains 389 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 300 time to evaluate : 2.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 325 ASN Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 485 LYS Chi-restraints excluded: chain B residue 522 PHE Chi-restraints excluded: chain B residue 564 HIS Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain C residue 54 ARG Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 54 LEU Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 91 PHE Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 74 CYS Chi-restraints excluded: chain D residue 95 MET Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 216 HIS Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain D residue 325 ASN Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 439 ILE Chi-restraints excluded: chain D residue 485 LYS Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain E residue 564 HIS Chi-restraints excluded: chain E residue 615 SER Chi-restraints excluded: chain E residue 618 THR Chi-restraints excluded: chain E residue 644 THR Chi-restraints excluded: chain F residue 24 ARG Chi-restraints excluded: chain F residue 82 ASP Chi-restraints excluded: chain G residue 53 ASP Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 88 ASP Chi-restraints excluded: chain I residue 10 GLU Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 52 ILE Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain I residue 91 PHE Chi-restraints excluded: chain I residue 108 LEU Chi-restraints excluded: chain J residue 49 THR Chi-restraints excluded: chain J residue 57 ASP Chi-restraints excluded: chain J residue 74 CYS Chi-restraints excluded: chain J residue 95 MET Chi-restraints excluded: chain J residue 201 ILE Chi-restraints excluded: chain J residue 208 VAL Chi-restraints excluded: chain J residue 216 HIS Chi-restraints excluded: chain J residue 232 THR Chi-restraints excluded: chain J residue 294 ILE Chi-restraints excluded: chain J residue 325 ASN Chi-restraints excluded: chain J residue 373 THR Chi-restraints excluded: chain J residue 378 CYS Chi-restraints excluded: chain K residue 563 GLN Chi-restraints excluded: chain K residue 564 HIS Chi-restraints excluded: chain K residue 615 SER Chi-restraints excluded: chain K residue 618 THR Chi-restraints excluded: chain K residue 644 THR Chi-restraints excluded: chain K residue 646 LEU Chi-restraints excluded: chain M residue 82 ASP Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain N residue 53 ASP Chi-restraints excluded: chain N residue 54 ARG Chi-restraints excluded: chain N residue 60 SER Chi-restraints excluded: chain N residue 88 ASP Chi-restraints excluded: chain O residue 35 THR Chi-restraints excluded: chain O residue 45 LEU Chi-restraints excluded: chain O residue 54 LEU Chi-restraints excluded: chain O residue 62 HIS Chi-restraints excluded: chain O residue 68 THR Chi-restraints excluded: chain O residue 70 THR Chi-restraints excluded: chain O residue 91 PHE Chi-restraints excluded: chain O residue 107 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 223 optimal weight: 5.9990 chunk 26 optimal weight: 0.9990 chunk 132 optimal weight: 2.9990 chunk 169 optimal weight: 8.9990 chunk 131 optimal weight: 10.0000 chunk 195 optimal weight: 0.7980 chunk 129 optimal weight: 6.9990 chunk 231 optimal weight: 9.9990 chunk 144 optimal weight: 9.9990 chunk 141 optimal weight: 5.9990 chunk 106 optimal weight: 0.7980 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 ASN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 630 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 ASN D 229 ASN ** D 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 417 GLN ** E 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 80 ASN J 216 HIS J 325 ASN J 363 HIS ** J 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 377 ASN J 417 GLN K 554 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.5447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 20637 Z= 0.308 Angle : 0.695 14.289 27996 Z= 0.355 Chirality : 0.047 0.246 3261 Planarity : 0.005 0.059 3519 Dihedral : 8.518 119.038 3651 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.19 % Favored : 94.68 % Rotamer: Outliers : 4.00 % Allowed : 16.99 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.16), residues: 2427 helix: -1.55 (0.22), residues: 438 sheet: 0.64 (0.22), residues: 609 loop : -1.25 (0.16), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP H 36 HIS 0.006 0.001 HIS A 66 PHE 0.017 0.002 PHE A 53 TYR 0.027 0.002 TYR J 435 ARG 0.006 0.000 ARG K 579 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4854 Ramachandran restraints generated. 2427 Oldfield, 0 Emsley, 2427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4854 Ramachandran restraints generated. 2427 Oldfield, 0 Emsley, 2427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 330 time to evaluate : 2.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 446 SER cc_start: 0.8941 (m) cc_final: 0.8422 (p) REVERT: L 1 GLU cc_start: 0.6593 (OUTLIER) cc_final: 0.6177 (tm-30) REVERT: C 80 ASP cc_start: 0.5884 (m-30) cc_final: 0.5309 (t0) REVERT: C 94 GLN cc_start: 0.7349 (tp-100) cc_final: 0.7017 (tp-100) REVERT: H 39 GLN cc_start: 0.7258 (OUTLIER) cc_final: 0.6668 (tp-100) REVERT: H 91 PHE cc_start: 0.6799 (OUTLIER) cc_final: 0.5840 (p90) REVERT: D 446 SER cc_start: 0.8836 (m) cc_final: 0.8368 (p) REVERT: E 629 MET cc_start: 0.7620 (mmm) cc_final: 0.7416 (mmm) REVERT: E 654 GLU cc_start: 0.8543 (tp30) cc_final: 0.8330 (tp30) REVERT: G 80 ASP cc_start: 0.5880 (m-30) cc_final: 0.5500 (t0) REVERT: G 86 VAL cc_start: 0.8453 (p) cc_final: 0.8235 (p) REVERT: G 94 GLN cc_start: 0.6275 (tp40) cc_final: 0.6072 (tp40) REVERT: I 48 MET cc_start: 0.7839 (ttm) cc_final: 0.7523 (ttt) REVERT: I 91 PHE cc_start: 0.6435 (OUTLIER) cc_final: 0.5591 (p90) REVERT: J 270 ILE cc_start: 0.8372 (mp) cc_final: 0.8069 (mt) REVERT: J 377 ASN cc_start: 0.7968 (t0) cc_final: 0.7411 (t0) REVERT: J 446 SER cc_start: 0.8925 (m) cc_final: 0.8411 (p) REVERT: K 627 THR cc_start: 0.8492 (p) cc_final: 0.8251 (p) REVERT: M 24 ARG cc_start: 0.6668 (ttm110) cc_final: 0.6435 (ttm-80) REVERT: O 97 GLU cc_start: 0.8196 (mm-30) cc_final: 0.7898 (mm-30) outliers start: 86 outliers final: 69 residues processed: 378 average time/residue: 0.3054 time to fit residues: 185.1776 Evaluate side-chains 379 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 306 time to evaluate : 2.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 80 ASN Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 216 HIS Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 325 ASN Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 485 LYS Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain B residue 564 HIS Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain L residue 1 GLU Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 54 ARG Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 54 LEU Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 91 PHE Chi-restraints excluded: chain D residue 74 CYS Chi-restraints excluded: chain D residue 80 ASN Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 216 HIS Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 325 ASN Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 439 ILE Chi-restraints excluded: chain D residue 485 LYS Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain E residue 644 THR Chi-restraints excluded: chain F residue 24 ARG Chi-restraints excluded: chain F residue 82 ASP Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 53 ASP Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain G residue 88 ASP Chi-restraints excluded: chain I residue 10 GLU Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain I residue 91 PHE Chi-restraints excluded: chain I residue 108 LEU Chi-restraints excluded: chain J residue 49 THR Chi-restraints excluded: chain J residue 57 ASP Chi-restraints excluded: chain J residue 80 ASN Chi-restraints excluded: chain J residue 201 ILE Chi-restraints excluded: chain J residue 232 THR Chi-restraints excluded: chain J residue 325 ASN Chi-restraints excluded: chain J residue 373 THR Chi-restraints excluded: chain J residue 378 CYS Chi-restraints excluded: chain K residue 540 GLN Chi-restraints excluded: chain K residue 563 GLN Chi-restraints excluded: chain K residue 564 HIS Chi-restraints excluded: chain K residue 618 THR Chi-restraints excluded: chain K residue 644 THR Chi-restraints excluded: chain K residue 646 LEU Chi-restraints excluded: chain M residue 82 ASP Chi-restraints excluded: chain N residue 74 LEU Chi-restraints excluded: chain N residue 88 ASP Chi-restraints excluded: chain O residue 35 THR Chi-restraints excluded: chain O residue 45 LEU Chi-restraints excluded: chain O residue 54 LEU Chi-restraints excluded: chain O residue 70 THR Chi-restraints excluded: chain O residue 91 PHE Chi-restraints excluded: chain O residue 107 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 143 optimal weight: 5.9990 chunk 92 optimal weight: 5.9990 chunk 138 optimal weight: 1.9990 chunk 69 optimal weight: 0.0050 chunk 45 optimal weight: 9.9990 chunk 44 optimal weight: 0.0970 chunk 147 optimal weight: 9.9990 chunk 157 optimal weight: 10.0000 chunk 114 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 181 optimal weight: 0.9980 overall best weight: 1.0196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 ASN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 ASN D 258 GLN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 417 GLN F 42 GLN ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 80 ASN J 325 ASN J 363 HIS ** J 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 417 GLN K 625 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.5542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 20637 Z= 0.210 Angle : 0.644 14.466 27996 Z= 0.326 Chirality : 0.045 0.194 3261 Planarity : 0.005 0.053 3519 Dihedral : 8.049 115.499 3651 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.44 % Favored : 94.44 % Rotamer: Outliers : 3.54 % Allowed : 17.64 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.17), residues: 2427 helix: -1.26 (0.23), residues: 420 sheet: 0.68 (0.22), residues: 597 loop : -1.22 (0.16), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP O 36 HIS 0.007 0.001 HIS J 66 PHE 0.014 0.002 PHE D 53 TYR 0.025 0.002 TYR L 49 ARG 0.005 0.000 ARG K 579 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4854 Ramachandran restraints generated. 2427 Oldfield, 0 Emsley, 2427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4854 Ramachandran restraints generated. 2427 Oldfield, 0 Emsley, 2427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 331 time to evaluate : 2.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 446 SER cc_start: 0.8843 (m) cc_final: 0.8373 (p) REVERT: L 1 GLU cc_start: 0.6537 (OUTLIER) cc_final: 0.6190 (tm-30) REVERT: L 70 GLU cc_start: 0.7000 (mp0) cc_final: 0.6781 (mp0) REVERT: C 80 ASP cc_start: 0.5836 (m-30) cc_final: 0.5273 (t0) REVERT: C 94 GLN cc_start: 0.7221 (tp-100) cc_final: 0.6934 (tp-100) REVERT: H 12 LYS cc_start: 0.7718 (ttmt) cc_final: 0.7225 (ttpt) REVERT: H 39 GLN cc_start: 0.7176 (OUTLIER) cc_final: 0.6669 (tp-100) REVERT: H 91 PHE cc_start: 0.6629 (OUTLIER) cc_final: 0.5762 (p90) REVERT: D 446 SER cc_start: 0.8711 (m) cc_final: 0.8280 (p) REVERT: E 654 GLU cc_start: 0.8463 (tp30) cc_final: 0.8213 (tp30) REVERT: G 80 ASP cc_start: 0.5856 (m-30) cc_final: 0.5492 (t0) REVERT: I 48 MET cc_start: 0.7844 (ttm) cc_final: 0.7605 (ttp) REVERT: I 91 PHE cc_start: 0.6286 (OUTLIER) cc_final: 0.5479 (p90) REVERT: J 82 GLN cc_start: 0.7545 (tp40) cc_final: 0.7210 (tp40) REVERT: J 270 ILE cc_start: 0.8345 (mp) cc_final: 0.8044 (mt) REVERT: J 377 ASN cc_start: 0.8022 (t0) cc_final: 0.7797 (t0) REVERT: J 446 SER cc_start: 0.8814 (m) cc_final: 0.8383 (p) REVERT: K 627 THR cc_start: 0.8063 (p) cc_final: 0.7772 (p) REVERT: M 70 GLU cc_start: 0.6032 (mm-30) cc_final: 0.5810 (mp0) REVERT: O 62 HIS cc_start: 0.8494 (OUTLIER) cc_final: 0.8053 (p90) REVERT: O 97 GLU cc_start: 0.8080 (mm-30) cc_final: 0.7817 (mm-30) outliers start: 76 outliers final: 62 residues processed: 374 average time/residue: 0.2907 time to fit residues: 172.9164 Evaluate side-chains 379 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 312 time to evaluate : 2.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 80 ASN Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 325 ASN Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 485 LYS Chi-restraints excluded: chain B residue 564 HIS Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain B residue 659 GLU Chi-restraints excluded: chain L residue 1 GLU Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain H residue 54 LEU Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 91 PHE Chi-restraints excluded: chain D residue 74 CYS Chi-restraints excluded: chain D residue 80 ASN Chi-restraints excluded: chain D residue 216 HIS Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain D residue 325 ASN Chi-restraints excluded: chain D residue 439 ILE Chi-restraints excluded: chain D residue 485 LYS Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain E residue 618 THR Chi-restraints excluded: chain E residue 644 THR Chi-restraints excluded: chain F residue 24 ARG Chi-restraints excluded: chain F residue 82 ASP Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 53 ASP Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain G residue 88 ASP Chi-restraints excluded: chain I residue 10 GLU Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain I residue 91 PHE Chi-restraints excluded: chain I residue 108 LEU Chi-restraints excluded: chain J residue 49 THR Chi-restraints excluded: chain J residue 57 ASP Chi-restraints excluded: chain J residue 80 ASN Chi-restraints excluded: chain J residue 294 ILE Chi-restraints excluded: chain J residue 325 ASN Chi-restraints excluded: chain J residue 373 THR Chi-restraints excluded: chain J residue 378 CYS Chi-restraints excluded: chain K residue 540 GLN Chi-restraints excluded: chain K residue 563 GLN Chi-restraints excluded: chain K residue 564 HIS Chi-restraints excluded: chain K residue 615 SER Chi-restraints excluded: chain K residue 646 LEU Chi-restraints excluded: chain M residue 37 GLN Chi-restraints excluded: chain N residue 53 ASP Chi-restraints excluded: chain N residue 60 SER Chi-restraints excluded: chain N residue 88 ASP Chi-restraints excluded: chain O residue 35 THR Chi-restraints excluded: chain O residue 45 LEU Chi-restraints excluded: chain O residue 54 LEU Chi-restraints excluded: chain O residue 62 HIS Chi-restraints excluded: chain O residue 70 THR Chi-restraints excluded: chain O residue 91 PHE Chi-restraints excluded: chain O residue 107 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 210 optimal weight: 3.9990 chunk 221 optimal weight: 0.5980 chunk 202 optimal weight: 0.6980 chunk 215 optimal weight: 40.0000 chunk 129 optimal weight: 0.6980 chunk 93 optimal weight: 5.9990 chunk 169 optimal weight: 7.9990 chunk 66 optimal weight: 9.9990 chunk 194 optimal weight: 0.7980 chunk 203 optimal weight: 0.6980 chunk 214 optimal weight: 9.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 ASN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 ASN D 216 HIS D 363 HIS ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 417 GLN F 38 GLN ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 325 ASN J 363 HIS ** J 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 417 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.5624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20637 Z= 0.182 Angle : 0.627 13.739 27996 Z= 0.316 Chirality : 0.044 0.189 3261 Planarity : 0.005 0.052 3519 Dihedral : 7.636 118.043 3651 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.40 % Favored : 94.48 % Rotamer: Outliers : 3.31 % Allowed : 18.25 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -1.02 (0.17), residues: 2427 helix: -1.14 (0.23), residues: 420 sheet: 0.71 (0.22), residues: 597 loop : -1.17 (0.16), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP H 36 HIS 0.005 0.001 HIS J 66 PHE 0.014 0.002 PHE J 53 TYR 0.024 0.002 TYR M 49 ARG 0.009 0.000 ARG M 18 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4854 Ramachandran restraints generated. 2427 Oldfield, 0 Emsley, 2427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4854 Ramachandran restraints generated. 2427 Oldfield, 0 Emsley, 2427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 333 time to evaluate : 2.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 446 SER cc_start: 0.8788 (m) cc_final: 0.8334 (p) REVERT: L 1 GLU cc_start: 0.6428 (OUTLIER) cc_final: 0.6133 (tm-30) REVERT: L 70 GLU cc_start: 0.6884 (mp0) cc_final: 0.6659 (mp0) REVERT: C 80 ASP cc_start: 0.5748 (m-30) cc_final: 0.5202 (t0) REVERT: C 94 GLN cc_start: 0.7186 (tp-100) cc_final: 0.6927 (tp-100) REVERT: H 12 LYS cc_start: 0.7659 (ttmt) cc_final: 0.7133 (ttpt) REVERT: H 39 GLN cc_start: 0.7186 (OUTLIER) cc_final: 0.6670 (tp-100) REVERT: H 91 PHE cc_start: 0.6687 (OUTLIER) cc_final: 0.5798 (p90) REVERT: D 446 SER cc_start: 0.8662 (m) cc_final: 0.8260 (p) REVERT: E 530 MET cc_start: 0.7995 (mtm) cc_final: 0.7778 (mtp) REVERT: G 54 ARG cc_start: 0.8338 (mtp180) cc_final: 0.8103 (mtp180) REVERT: G 80 ASP cc_start: 0.5823 (m-30) cc_final: 0.5474 (t0) REVERT: I 48 MET cc_start: 0.7803 (ttm) cc_final: 0.7570 (ttp) REVERT: I 91 PHE cc_start: 0.6224 (OUTLIER) cc_final: 0.5476 (p90) REVERT: J 377 ASN cc_start: 0.8004 (t0) cc_final: 0.7558 (t0) REVERT: J 446 SER cc_start: 0.8777 (m) cc_final: 0.8377 (p) REVERT: O 62 HIS cc_start: 0.8488 (OUTLIER) cc_final: 0.8025 (p90) REVERT: O 97 GLU cc_start: 0.8020 (mm-30) cc_final: 0.7772 (mm-30) outliers start: 71 outliers final: 60 residues processed: 375 average time/residue: 0.2938 time to fit residues: 175.7464 Evaluate side-chains 378 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 313 time to evaluate : 2.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 80 ASN Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 216 HIS Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 325 ASN Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 485 LYS Chi-restraints excluded: chain B residue 564 HIS Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain B residue 659 GLU Chi-restraints excluded: chain L residue 1 GLU Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain H residue 54 LEU Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 91 PHE Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 74 CYS Chi-restraints excluded: chain D residue 80 ASN Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain D residue 325 ASN Chi-restraints excluded: chain D residue 439 ILE Chi-restraints excluded: chain D residue 485 LYS Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain F residue 24 ARG Chi-restraints excluded: chain F residue 82 ASP Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 53 ASP Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain G residue 88 ASP Chi-restraints excluded: chain I residue 10 GLU Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain I residue 91 PHE Chi-restraints excluded: chain I residue 108 LEU Chi-restraints excluded: chain J residue 57 ASP Chi-restraints excluded: chain J residue 294 ILE Chi-restraints excluded: chain J residue 325 ASN Chi-restraints excluded: chain J residue 373 THR Chi-restraints excluded: chain J residue 496 ILE Chi-restraints excluded: chain K residue 540 GLN Chi-restraints excluded: chain K residue 563 GLN Chi-restraints excluded: chain K residue 564 HIS Chi-restraints excluded: chain K residue 615 SER Chi-restraints excluded: chain K residue 644 THR Chi-restraints excluded: chain K residue 646 LEU Chi-restraints excluded: chain M residue 37 GLN Chi-restraints excluded: chain N residue 53 ASP Chi-restraints excluded: chain N residue 88 ASP Chi-restraints excluded: chain O residue 45 LEU Chi-restraints excluded: chain O residue 54 LEU Chi-restraints excluded: chain O residue 62 HIS Chi-restraints excluded: chain O residue 70 THR Chi-restraints excluded: chain O residue 91 PHE Chi-restraints excluded: chain O residue 107 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 141 optimal weight: 10.0000 chunk 227 optimal weight: 4.9990 chunk 139 optimal weight: 0.6980 chunk 108 optimal weight: 0.9990 chunk 158 optimal weight: 4.9990 chunk 239 optimal weight: 0.7980 chunk 220 optimal weight: 5.9990 chunk 190 optimal weight: 7.9990 chunk 19 optimal weight: 8.9990 chunk 147 optimal weight: 10.0000 chunk 116 optimal weight: 7.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 80 ASN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 ASN D 88 ASN D 363 HIS ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 417 GLN F 79 GLN ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 325 ASN J 363 HIS ** J 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 417 GLN ** M 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.5796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 20637 Z= 0.329 Angle : 0.704 13.852 27996 Z= 0.358 Chirality : 0.047 0.206 3261 Planarity : 0.005 0.053 3519 Dihedral : 7.799 109.412 3651 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.52 % Favored : 94.36 % Rotamer: Outliers : 3.35 % Allowed : 18.39 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.17), residues: 2427 helix: -1.18 (0.24), residues: 411 sheet: 0.63 (0.23), residues: 573 loop : -1.31 (0.16), residues: 1443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP O 36 HIS 0.007 0.001 HIS D 216 PHE 0.016 0.002 PHE G 43 TYR 0.044 0.002 TYR F 91 ARG 0.008 0.000 ARG M 18 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4854 Ramachandran restraints generated. 2427 Oldfield, 0 Emsley, 2427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4854 Ramachandran restraints generated. 2427 Oldfield, 0 Emsley, 2427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 318 time to evaluate : 2.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 446 SER cc_start: 0.8897 (m) cc_final: 0.8418 (p) REVERT: L 1 GLU cc_start: 0.6527 (OUTLIER) cc_final: 0.6230 (tm-30) REVERT: C 80 ASP cc_start: 0.5476 (m-30) cc_final: 0.5062 (t0) REVERT: C 94 GLN cc_start: 0.7239 (tp-100) cc_final: 0.7038 (tp-100) REVERT: H 12 LYS cc_start: 0.7733 (ttmt) cc_final: 0.7121 (ttmt) REVERT: H 39 GLN cc_start: 0.7257 (OUTLIER) cc_final: 0.6700 (tp-100) REVERT: H 91 PHE cc_start: 0.6748 (OUTLIER) cc_final: 0.5881 (p90) REVERT: D 446 SER cc_start: 0.8819 (m) cc_final: 0.8378 (p) REVERT: E 530 MET cc_start: 0.8151 (mtm) cc_final: 0.7911 (mtp) REVERT: F 70 GLU cc_start: 0.6966 (mp0) cc_final: 0.6511 (mp0) REVERT: I 91 PHE cc_start: 0.6493 (OUTLIER) cc_final: 0.5597 (p90) REVERT: J 270 ILE cc_start: 0.8382 (mp) cc_final: 0.8082 (mt) REVERT: J 446 SER cc_start: 0.8793 (m) cc_final: 0.8342 (p) REVERT: O 62 HIS cc_start: 0.8479 (OUTLIER) cc_final: 0.8025 (p90) REVERT: O 97 GLU cc_start: 0.8160 (mm-30) cc_final: 0.7883 (mm-30) outliers start: 72 outliers final: 65 residues processed: 360 average time/residue: 0.3146 time to fit residues: 180.6193 Evaluate side-chains 377 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 307 time to evaluate : 2.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 80 ASN Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 216 HIS Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 325 ASN Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 485 LYS Chi-restraints excluded: chain B residue 564 HIS Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain B residue 659 GLU Chi-restraints excluded: chain L residue 1 GLU Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain H residue 54 LEU Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 91 PHE Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 74 CYS Chi-restraints excluded: chain D residue 80 ASN Chi-restraints excluded: chain D residue 88 ASN Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain D residue 325 ASN Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 439 ILE Chi-restraints excluded: chain D residue 485 LYS Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain E residue 564 HIS Chi-restraints excluded: chain E residue 618 THR Chi-restraints excluded: chain F residue 24 ARG Chi-restraints excluded: chain F residue 79 GLN Chi-restraints excluded: chain F residue 82 ASP Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 53 ASP Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain G residue 88 ASP Chi-restraints excluded: chain I residue 10 GLU Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 52 ILE Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain I residue 91 PHE Chi-restraints excluded: chain I residue 108 LEU Chi-restraints excluded: chain J residue 49 THR Chi-restraints excluded: chain J residue 57 ASP Chi-restraints excluded: chain J residue 294 ILE Chi-restraints excluded: chain J residue 325 ASN Chi-restraints excluded: chain J residue 373 THR Chi-restraints excluded: chain J residue 496 ILE Chi-restraints excluded: chain K residue 540 GLN Chi-restraints excluded: chain K residue 563 GLN Chi-restraints excluded: chain K residue 564 HIS Chi-restraints excluded: chain K residue 615 SER Chi-restraints excluded: chain K residue 644 THR Chi-restraints excluded: chain K residue 646 LEU Chi-restraints excluded: chain N residue 53 ASP Chi-restraints excluded: chain N residue 60 SER Chi-restraints excluded: chain N residue 88 ASP Chi-restraints excluded: chain O residue 45 LEU Chi-restraints excluded: chain O residue 54 LEU Chi-restraints excluded: chain O residue 62 HIS Chi-restraints excluded: chain O residue 70 THR Chi-restraints excluded: chain O residue 91 PHE Chi-restraints excluded: chain O residue 107 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 151 optimal weight: 0.8980 chunk 202 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 175 optimal weight: 0.8980 chunk 28 optimal weight: 0.4980 chunk 52 optimal weight: 5.9990 chunk 190 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 195 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 88 ASN D 363 HIS ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 417 GLN ** F 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 363 HIS ** J 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 417 GLN ** M 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4511 r_free = 0.4511 target = 0.158859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.133237 restraints weight = 34424.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.136179 restraints weight = 19255.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.137468 restraints weight = 11896.845| |-----------------------------------------------------------------------------| r_work (final): 0.4229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.5818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.342 20637 Z= 0.412 Angle : 0.964 59.185 27996 Z= 0.559 Chirality : 0.051 1.024 3261 Planarity : 0.007 0.188 3519 Dihedral : 7.803 109.312 3651 Min Nonbonded Distance : 1.762 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.64 % Favored : 94.23 % Rotamer: Outliers : 3.45 % Allowed : 18.34 % Favored : 78.21 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 2.86 % 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: -1.22 (0.17), residues: 2427 helix: -1.19 (0.24), residues: 411 sheet: 0.53 (0.22), residues: 591 loop : -1.30 (0.16), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP O 36 HIS 0.005 0.001 HIS D 216 PHE 0.015 0.002 PHE G 43 TYR 0.035 0.002 TYR F 91 ARG 0.006 0.000 ARG M 18 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4372.87 seconds wall clock time: 80 minutes 51.55 seconds (4851.55 seconds total)