Starting phenix.real_space_refine on Fri Feb 16 17:39:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mdt_23779/02_2024/7mdt_23779.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mdt_23779/02_2024/7mdt_23779.map 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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mdt_23779/02_2024/7mdt_23779.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mdt_23779/02_2024/7mdt_23779.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mdt_23779/02_2024/7mdt_23779.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mdt_23779/02_2024/7mdt_23779.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= 0.003 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 111 5.16 5 C 9973 2.51 5 N 2678 2.21 5 O 3194 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 57": "OD1" <-> "OD2" Residue "A PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 468": "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 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 92": "OD1" <-> "OD2" Residue "H ASP 32": "OD1" <-> "OD2" Residue "H TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 15956 Number of models: 1 Model: "" Number of chains: 31 Chain: "A" Number of atoms: 3469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3469 Classifications: {'peptide': 439} Link IDs: {'PTRANS': 22, 'TRANS': 416} Chain breaks: 3 Chain: "B" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 971 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain breaks: 1 Chain: "L" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 796 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 4, 'TRANS': 105} Chain: "H" Number of atoms: 894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 894 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 2, 'TRANS': 114} Chain: "C" Number of atoms: 3393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3393 Classifications: {'peptide': 428} Link IDs: {'PTRANS': 22, 'TRANS': 405} Chain breaks: 4 Chain: "E" Number of atoms: 3428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3428 Classifications: {'peptide': 433} Link IDs: {'PTRANS': 22, 'TRANS': 410} Chain breaks: 4 Chain: "D" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 971 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain breaks: 1 Chain: "F" Number of atoms: 963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 963 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "Q" 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: "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: 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: "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: 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: "V" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "W" 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: "X" 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: "Y" 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: "Z" 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: "a" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "E" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 8.80, per 1000 atoms: 0.55 Number of scatterers: 15956 At special positions: 0 Unit cell: (138.02, 126.69, 144.2, 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 111 16.00 O 3194 8.00 N 2678 7.00 C 9973 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=35, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 73 " distance=2.02 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.05 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.02 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=2.04 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " 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=2.11 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 H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 73 " distance=2.05 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.04 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.02 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.02 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.04 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.02 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS D 605 " distance=2.09 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 73 " distance=2.02 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.05 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.04 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.02 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.02 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.04 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.02 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " 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 ALPHA1-3 " BMA P 3 " - " MAN P 4 " " BMA V 3 " - " MAN V 4 " " BMA a 3 " - " MAN a 4 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " NAG-ASN " NAG A 601 " - " ASN A 392 " " NAG A 602 " - " ASN A 88 " " NAG A 603 " - " ASN A 234 " " NAG A 604 " - " ASN A 276 " " NAG A 605 " - " ASN A 295 " " NAG A 606 " - " ASN A 355 " " NAG A 607 " - " ASN A 462 " " NAG A 608 " - " ASN A 301 " " NAG A 609 " - " ASN A 339 " " NAG A 610 " - " ASN A 363 " " NAG C 601 " - " ASN C 137 " " NAG C 602 " - " ASN C 133 " " NAG C 603 " - " ASN C 363 " " NAG C 604 " - " ASN C 392 " " NAG C 605 " - " ASN C 88 " " NAG C 606 " - " ASN C 234 " " NAG C 607 " - " ASN C 276 " " NAG C 608 " - " ASN C 295 " " NAG C 609 " - " ASN C 355 " " NAG C 610 " - " ASN C 301 " " NAG C 611 " - " ASN C 448 " " NAG C 612 " - " ASN C 339 " " NAG E 601 " - " ASN E 137 " " NAG E 602 " - " ASN E 133 " " NAG E 603 " - " ASN E 363 " " NAG E 604 " - " ASN E 88 " " NAG E 605 " - " ASN E 234 " " NAG E 606 " - " ASN E 276 " " NAG E 607 " - " ASN E 295 " " NAG E 608 " - " ASN E 301 " " NAG E 609 " - " ASN E 160 " " NAG G 1 " - " ASN A 156 " " NAG I 1 " - " ASN A 137 " " NAG J 1 " - " ASN A 133 " " NAG K 1 " - " ASN A 332 " " NAG M 1 " - " ASN A 197 " " NAG N 1 " - " ASN A 386 " " NAG O 1 " - " ASN A 160 " " NAG P 1 " - " ASN A 262 " " NAG Q 1 " - " ASN A 448 " " NAG R 1 " - " ASN C 156 " " NAG S 1 " - " ASN C 332 " " NAG T 1 " - " ASN C 386 " " NAG U 1 " - " ASN C 160 " " NAG V 1 " - " ASN C 262 " " NAG W 1 " - " ASN E 156 " " NAG X 1 " - " ASN E 332 " " NAG Y 1 " - " ASN E 197 " " NAG Z 1 " - " ASN E 386 " " NAG a 1 " - " ASN E 262 " " NAG b 1 " - " ASN E 448 " Time building additional restraints: 7.36 Conformation dependent library (CDL) restraints added in 2.9 seconds 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3522 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 38 sheets defined 25.2% alpha, 53.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.26 Creating SS restraints... Processing helix chain 'A' and resid 67 through 73 Processing helix chain 'A' and resid 96 through 98 No H-bonds generated for 'chain 'A' and resid 96 through 98' Processing helix chain 'A' and resid 99 through 117 Processing helix chain 'A' and resid 139 through 151 removed outlier: 3.732A pdb=" N ARG A 151 " --> pdb=" O ASP A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 350 Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 387 through 391 Processing helix chain 'A' and resid 476 through 484 removed outlier: 3.906A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 528 removed outlier: 4.423A pdb=" N GLY B 527 " --> pdb=" O GLY B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 535 Processing helix chain 'B' and resid 536 through 542 Processing helix chain 'B' and resid 570 through 596 Processing helix chain 'B' and resid 618 through 624 Processing helix chain 'B' and resid 627 through 635 removed outlier: 4.067A pdb=" N LYS B 633 " --> pdb=" O LEU B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 663 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'C' and resid 67 through 74 Processing helix chain 'C' and resid 98 through 117 removed outlier: 3.977A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N ILE C 109 " --> pdb=" O HIS C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 151 Processing helix chain 'C' and resid 335 through 350 removed outlier: 5.163A pdb=" N GLU C 340 " --> pdb=" O ALA C 336 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N GLY C 343 " --> pdb=" O ASN C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 353 No H-bonds generated for 'chain 'C' and resid 351 through 353' Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 476 through 484 removed outlier: 3.949A pdb=" N SER C 481 " --> pdb=" O ASP C 477 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 73 Processing helix chain 'E' and resid 98 through 117 removed outlier: 4.089A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 350 Processing helix chain 'E' and resid 351 through 353 No H-bonds generated for 'chain 'E' and resid 351 through 353' Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 387 through 391 Processing helix chain 'E' and resid 476 through 484 removed outlier: 3.935A pdb=" N SER E 481 " --> pdb=" O ASP E 477 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 528 removed outlier: 4.252A pdb=" N GLY D 527 " --> pdb=" O GLY D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 537 through 542 Processing helix chain 'D' and resid 570 through 596 Processing helix chain 'D' and resid 611 through 615 Processing helix chain 'D' and resid 618 through 624 Processing helix chain 'D' and resid 627 through 635 Processing helix chain 'D' and resid 638 through 662 Processing helix chain 'F' and resid 523 through 528 removed outlier: 4.299A pdb=" N GLY F 527 " --> pdb=" O GLY F 524 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 537 through 542 Processing helix chain 'F' and resid 570 through 596 Processing helix chain 'F' and resid 618 through 622 Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 638 through 661 Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.261A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 76 removed outlier: 4.436A pdb=" N VAL A 75 " --> pdb=" O CYS A 54 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AA6, first strand: chain 'A' and resid 200 through 203 removed outlier: 6.038A pdb=" N ALA A 200 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N TYR A 435 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 261 removed outlier: 3.567A pdb=" N GLY A 451 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 10.505A pdb=" N VAL A 442 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 11.212A pdb=" N CYS A 296 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 10.127A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.516A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.751A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 10.642A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.173A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.173A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N THR A 450 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 271 through 274 removed outlier: 6.772A pdb=" N THR A 450 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 10.173A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.173A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.642A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.751A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.516A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 10.127A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.212A pdb=" N CYS A 296 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 10.505A pdb=" N VAL A 442 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N THR A 467 " --> pdb=" O ASP A 457 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 304 through 312 removed outlier: 6.491A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 19 through 24 Processing sheet with id=AB2, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.574A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLY L 95B" --> pdb=" O ASP L 92 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.574A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.556A pdb=" N LEU H 101 " --> pdb=" O LEU H 96 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N LEU H 96 " --> pdb=" O LEU H 101 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N TRP H 103 " --> pdb=" O ARG H 94 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N ARG H 94 " --> pdb=" O TRP H 103 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N GLN H 105 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N CYS H 92 " --> pdb=" O GLN H 105 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASP H 33 " --> pdb=" O THR H 95 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N MET H 34 " --> pdb=" O SER H 50 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N SER H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 18 through 22 Processing sheet with id=AB6, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.378A pdb=" N VAL D 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N VAL C 38 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N THR D 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N TYR C 40 " --> pdb=" O CYS D 604 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N CYS D 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 45 through 47 removed outlier: 4.890A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AB9, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AC1, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AC2, first strand: chain 'C' and resid 200 through 203 removed outlier: 5.954A pdb=" N ALA C 200 " --> pdb=" O ALA C 433 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N TYR C 435 " --> pdb=" O ALA C 200 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 256 through 257 removed outlier: 3.649A pdb=" N SER C 375 " --> pdb=" O THR C 257 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 315 through 323 removed outlier: 6.461A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N ILE C 323 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ASN C 301 " --> pdb=" O ILE C 323 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER C 375 " --> pdb=" O THR C 257 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 256 through 257 removed outlier: 3.649A pdb=" N SER C 375 " --> pdb=" O THR C 257 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N THR C 450 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 10.132A pdb=" N THR C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 9.170A pdb=" N ASN C 448 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.714A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.780A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 11.559A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 10.156A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.227A pdb=" N CYS C 296 " --> pdb=" O VAL C 442 " (cutoff:3.500A) removed outlier: 10.454A pdb=" N VAL C 442 " --> pdb=" O CYS C 296 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 360 through 361 removed outlier: 6.514A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) removed outlier: 10.454A pdb=" N VAL C 442 " --> pdb=" O CYS C 296 " (cutoff:3.500A) removed outlier: 11.227A pdb=" N CYS C 296 " --> pdb=" O VAL C 442 " (cutoff:3.500A) removed outlier: 10.156A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.559A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 9.780A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 10.714A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.170A pdb=" N ASN C 448 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.132A pdb=" N THR C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N THR C 450 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER C 375 " --> pdb=" O THR C 257 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 259 through 261 removed outlier: 6.556A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 10.454A pdb=" N VAL C 442 " --> pdb=" O CYS C 296 " (cutoff:3.500A) removed outlier: 11.227A pdb=" N CYS C 296 " --> pdb=" O VAL C 442 " (cutoff:3.500A) removed outlier: 10.156A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.559A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 9.780A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 10.714A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.170A pdb=" N ASN C 448 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.132A pdb=" N THR C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N THR C 450 " --> pdb=" O PHE C 288 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 315 through 323 removed outlier: 6.461A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N ILE C 323 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ASN C 301 " --> pdb=" O ILE C 323 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N THR C 450 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 10.132A pdb=" N THR C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 9.170A pdb=" N ASN C 448 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.714A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.780A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 11.559A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 10.156A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.227A pdb=" N CYS C 296 " --> pdb=" O VAL C 442 " (cutoff:3.500A) removed outlier: 10.454A pdb=" N VAL C 442 " --> pdb=" O CYS C 296 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 259 through 261 removed outlier: 6.556A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 271 through 274 removed outlier: 6.871A pdb=" N THR C 450 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 10.132A pdb=" N THR C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 9.170A pdb=" N ASN C 448 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.714A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.780A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 11.559A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 10.156A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.227A pdb=" N CYS C 296 " --> pdb=" O VAL C 442 " (cutoff:3.500A) removed outlier: 10.454A pdb=" N VAL C 442 " --> pdb=" O CYS C 296 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 360 through 361 removed outlier: 6.514A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) removed outlier: 10.454A pdb=" N VAL C 442 " --> pdb=" O CYS C 296 " (cutoff:3.500A) removed outlier: 11.227A pdb=" N CYS C 296 " --> pdb=" O VAL C 442 " (cutoff:3.500A) removed outlier: 10.156A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.559A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 9.780A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 10.714A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.170A pdb=" N ASN C 448 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.132A pdb=" N THR C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N THR C 450 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ASN C 301 " --> pdb=" O ILE C 323 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N ILE C 323 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.311A pdb=" N VAL F 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N VAL E 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N THR F 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N TYR E 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N CYS F 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 45 through 47 Processing sheet with id=AD5, first strand: chain 'E' and resid 75 through 76 removed outlier: 4.452A pdb=" N VAL E 75 " --> pdb=" O CYS E 54 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AD7, first strand: chain 'E' and resid 169 through 177 Processing sheet with id=AD8, first strand: chain 'E' and resid 200 through 203 removed outlier: 5.923A pdb=" N ALA E 200 " --> pdb=" O ALA E 433 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N TYR E 435 " --> pdb=" O ALA E 200 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 256 through 257 removed outlier: 3.539A pdb=" N SER E 375 " --> pdb=" O THR E 257 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 12.123A pdb=" N ILE E 284 " --> pdb=" O ASP E 457 " (cutoff:3.500A) removed outlier: 11.288A pdb=" N ASP E 457 " --> pdb=" O ILE E 284 " (cutoff:3.500A) removed outlier: 10.449A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 10.889A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 12.289A pdb=" N PHE E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 12.034A pdb=" N ILE E 453 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 10.583A pdb=" N THR E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N GLY E 451 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE E 443 " --> pdb=" O ARG E 298 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N ASN E 300 " --> pdb=" O GLY E 441 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N GLY E 441 " --> pdb=" O ASN E 300 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 259 through 261 removed outlier: 6.552A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N GLY E 441 " --> pdb=" O ASN E 300 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N ASN E 300 " --> pdb=" O GLY E 441 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE E 443 " --> pdb=" O ARG E 298 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N GLY E 451 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 10.583A pdb=" N THR E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 12.034A pdb=" N ILE E 453 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 12.289A pdb=" N PHE E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 10.889A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 10.449A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 11.288A pdb=" N ASP E 457 " --> pdb=" O ILE E 284 " (cutoff:3.500A) removed outlier: 12.123A pdb=" N ILE E 284 " --> pdb=" O ASP E 457 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 284 through 302 current: chain 'E' and resid 358 through 361 Processing sheet with id=AE2, first strand: chain 'E' and resid 304 through 312 removed outlier: 6.860A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) 720 hydrogen bonds defined for protein. 1926 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: 6.59 Time building geometry restraints manager: 7.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 3514 1.32 - 1.46: 5065 1.46 - 1.59: 7472 1.59 - 1.73: 60 1.73 - 1.87: 146 Bond restraints: 16257 Sorted by residual: bond pdb=" NE ARG C 503 " pdb=" CZ ARG C 503 " ideal model delta sigma weight residual 1.326 1.415 -0.089 1.10e-02 8.26e+03 6.50e+01 bond pdb=" CA THR E 132 " pdb=" C THR E 132 " ideal model delta sigma weight residual 1.520 1.555 -0.036 4.80e-03 4.34e+04 5.56e+01 bond pdb=" CB LEU F 663 " pdb=" CG LEU F 663 " ideal model delta sigma weight residual 1.530 1.649 -0.119 2.00e-02 2.50e+03 3.55e+01 bond pdb=" CB LEU D 663 " pdb=" CG LEU D 663 " ideal model delta sigma weight residual 1.530 1.648 -0.118 2.00e-02 2.50e+03 3.49e+01 bond pdb=" CB ILE C 396 " pdb=" CG1 ILE C 396 " ideal model delta sigma weight residual 1.530 1.647 -0.117 2.00e-02 2.50e+03 3.42e+01 ... (remaining 16252 not shown) Histogram of bond angle deviations from ideal: 97.62 - 110.68: 5954 110.68 - 123.74: 15189 123.74 - 136.79: 914 136.79 - 149.85: 0 149.85 - 162.91: 4 Bond angle restraints: 22061 Sorted by residual: angle pdb=" C2 NAG C 606 " pdb=" N2 NAG C 606 " pdb=" C7 NAG C 606 " ideal model delta sigma weight residual 124.56 162.91 -38.35 3.00e+00 1.11e-01 1.63e+02 angle pdb=" C2 NAG V 1 " pdb=" N2 NAG V 1 " pdb=" C7 NAG V 1 " ideal model delta sigma weight residual 124.56 161.82 -37.26 3.00e+00 1.11e-01 1.54e+02 angle pdb=" C2 NAG I 2 " pdb=" N2 NAG I 2 " pdb=" C7 NAG I 2 " ideal model delta sigma weight residual 124.56 161.68 -37.12 3.00e+00 1.11e-01 1.53e+02 angle pdb=" C2 NAG P 1 " pdb=" N2 NAG P 1 " pdb=" C7 NAG P 1 " ideal model delta sigma weight residual 124.56 160.64 -36.08 3.00e+00 1.11e-01 1.45e+02 angle pdb=" N GLN L 79 " pdb=" CA GLN L 79 " pdb=" C GLN L 79 " ideal model delta sigma weight residual 110.52 98.94 11.58 1.48e+00 4.57e-01 6.12e+01 ... (remaining 22056 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.72: 10421 21.72 - 43.43: 233 43.43 - 65.15: 82 65.15 - 86.87: 33 86.87 - 108.59: 16 Dihedral angle restraints: 10785 sinusoidal: 5341 harmonic: 5444 Sorted by residual: dihedral pdb=" CB CYS C 126 " pdb=" SG CYS C 126 " pdb=" SG CYS C 196 " pdb=" CB CYS C 196 " ideal model delta sinusoidal sigma weight residual 93.00 156.03 -63.03 1 1.00e+01 1.00e-02 5.25e+01 dihedral pdb=" CB CYS E 126 " pdb=" SG CYS E 126 " pdb=" SG CYS E 196 " pdb=" CB CYS E 196 " ideal model delta sinusoidal sigma weight residual 93.00 154.63 -61.63 1 1.00e+01 1.00e-02 5.04e+01 dihedral pdb=" CB CYS A 126 " pdb=" SG CYS A 126 " pdb=" SG CYS A 196 " pdb=" CB CYS A 196 " ideal model delta sinusoidal sigma weight residual 93.00 150.50 -57.50 1 1.00e+01 1.00e-02 4.44e+01 ... (remaining 10782 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.107: 1785 0.107 - 0.213: 568 0.213 - 0.320: 211 0.320 - 0.427: 102 0.427 - 0.533: 45 Chirality restraints: 2711 Sorted by residual: chirality pdb=" C1 NAG Z 2 " pdb=" O4 NAG Z 1 " pdb=" C2 NAG Z 2 " pdb=" O5 NAG Z 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.67 0.27 2.00e-02 2.50e+03 1.84e+02 chirality pdb=" C1 NAG Y 2 " pdb=" O4 NAG Y 1 " pdb=" C2 NAG Y 2 " pdb=" O5 NAG Y 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.66 0.26 2.00e-02 2.50e+03 1.74e+02 chirality pdb=" C1 NAG M 2 " pdb=" O4 NAG M 1 " pdb=" C2 NAG M 2 " pdb=" O5 NAG M 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-02 2.50e+03 1.48e+02 ... (remaining 2708 not shown) Planarity restraints: 2757 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 339 " 0.077 2.00e-02 2.50e+03 8.02e-02 8.05e+01 pdb=" CG ASN C 339 " -0.033 2.00e-02 2.50e+03 pdb=" OD1 ASN C 339 " -0.017 2.00e-02 2.50e+03 pdb=" ND2 ASN C 339 " -0.124 2.00e-02 2.50e+03 pdb=" C1 NAG C 612 " 0.097 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 234 " 0.072 2.00e-02 2.50e+03 7.42e-02 6.88e+01 pdb=" CG ASN E 234 " -0.032 2.00e-02 2.50e+03 pdb=" OD1 ASN E 234 " -0.018 2.00e-02 2.50e+03 pdb=" ND2 ASN E 234 " -0.113 2.00e-02 2.50e+03 pdb=" C1 NAG E 605 " 0.091 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 88 " -0.068 2.00e-02 2.50e+03 7.18e-02 6.44e+01 pdb=" CG ASN E 88 " 0.028 2.00e-02 2.50e+03 pdb=" OD1 ASN E 88 " 0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN E 88 " 0.112 2.00e-02 2.50e+03 pdb=" C1 NAG E 604 " -0.087 2.00e-02 2.50e+03 ... (remaining 2754 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.88: 5685 2.88 - 3.39: 14100 3.39 - 3.89: 26158 3.89 - 4.40: 30245 4.40 - 4.90: 48013 Nonbonded interactions: 124201 Sorted by model distance: nonbonded pdb=" N GLN L 79 " pdb=" O GLN L 79 " model vdw 2.380 2.496 nonbonded pdb=" NZ LYS A 46 " pdb=" OD2 ASP B 632 " model vdw 2.403 2.520 nonbonded pdb=" N LEU D 544 " pdb=" O LEU D 544 " model vdw 2.415 2.496 nonbonded pdb=" OD1 ASP E 474 " pdb=" N MET E 475 " model vdw 2.429 2.520 nonbonded pdb=" OD1 ASP H 72 " pdb=" NZ LYS H 75 " model vdw 2.434 2.520 ... (remaining 124196 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 34 through 57 or resid 66 through 457 or resid 466 through \ 503 or resid 601 through 609)) selection = (chain 'C' and (resid 34 through 503 or resid 603 through 611)) selection = (chain 'E' and (resid 34 through 57 or resid 66 through 457 or resid 466 through \ 503 or resid 601 through 609)) } ncs_group { reference = (chain 'B' and resid 521 through 663) selection = (chain 'D' and (resid 521 through 546 or resid 569 through 663)) selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'b' } ncs_group { reference = chain 'P' selection = chain 'V' selection = chain 'a' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 10.690 Check model and map are aligned: 0.240 Set scattering table: 0.160 Process input model: 46.350 Find NCS groups from input model: 1.120 Set up NCS constraints: 0.210 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: 0.000 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 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 : 0.023 0.134 16257 Z= 1.464 Angle : 1.808 38.348 22061 Z= 1.140 Chirality : 0.146 0.533 2711 Planarity : 0.008 0.044 2706 Dihedral : 11.861 108.585 7158 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 0.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.12 % Allowed : 0.48 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.19), residues: 1848 helix: 0.22 (0.25), residues: 379 sheet: 0.82 (0.23), residues: 481 loop : 0.49 (0.19), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.010 TRP H 103 HIS 0.009 0.002 HIS C 374 PHE 0.032 0.006 PHE C 383 TYR 0.051 0.007 TYR L 36 ARG 0.013 0.001 ARG C 166 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 1666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 450 time to evaluate : 1.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 ILE cc_start: 0.8911 (mt) cc_final: 0.8487 (mt) REVERT: A 217 TYR cc_start: 0.8997 (m-80) cc_final: 0.8443 (m-80) REVERT: A 279 ASN cc_start: 0.8205 (t0) cc_final: 0.7893 (t0) REVERT: A 315 GLN cc_start: 0.8572 (mm-40) cc_final: 0.8082 (mt0) REVERT: A 485 LYS cc_start: 0.8817 (mttt) cc_final: 0.8557 (mtmt) REVERT: B 599 SER cc_start: 0.8856 (t) cc_final: 0.8570 (p) REVERT: B 652 GLN cc_start: 0.8051 (mt0) cc_final: 0.7510 (mt0) REVERT: L 69 THR cc_start: 0.8660 (p) cc_final: 0.8419 (t) REVERT: H 31 ARG cc_start: 0.8229 (mtp85) cc_final: 0.8012 (mtt-85) REVERT: H 81 GLN cc_start: 0.7872 (tp40) cc_final: 0.7576 (mm110) REVERT: C 207 LYS cc_start: 0.8741 (mmtt) cc_final: 0.8442 (ptmt) REVERT: E 125 LEU cc_start: 0.8821 (mt) cc_final: 0.8564 (mt) REVERT: E 239 CYS cc_start: 0.7422 (t) cc_final: 0.7018 (t) REVERT: E 486 TYR cc_start: 0.9415 (m-80) cc_final: 0.9179 (m-80) REVERT: D 625 ASN cc_start: 0.8402 (t0) cc_final: 0.8194 (t0) REVERT: D 640 GLN cc_start: 0.8158 (mm-40) cc_final: 0.7881 (tp40) REVERT: F 575 GLN cc_start: 0.8245 (mm-40) cc_final: 0.7742 (tt0) REVERT: F 635 ILE cc_start: 0.8721 (pt) cc_final: 0.8370 (pt) outliers start: 2 outliers final: 0 residues processed: 452 average time/residue: 0.3207 time to fit residues: 206.3429 Evaluate side-chains 274 residues out of total 1666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 274 time to evaluate : 1.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 157 optimal weight: 1.9990 chunk 140 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 95 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 145 optimal weight: 0.9980 chunk 56 optimal weight: 6.9990 chunk 88 optimal weight: 0.8980 chunk 108 optimal weight: 3.9990 chunk 168 optimal weight: 0.3980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS A 302 ASN A 428 GLN A 478 ASN B 630 GLN L 51 ASN L 94 ASN H 82AASN ** C 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 374 HIS C 432 GLN E 103 GLN E 374 HIS E 478 ASN D 543 ASN F 618 ASN F 630 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 16257 Z= 0.273 Angle : 0.715 12.477 22061 Z= 0.375 Chirality : 0.051 0.471 2711 Planarity : 0.004 0.040 2706 Dihedral : 9.261 74.155 3633 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.70 % Allowed : 9.42 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.20), residues: 1848 helix: 1.84 (0.28), residues: 382 sheet: 0.85 (0.24), residues: 478 loop : 0.14 (0.20), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP E 69 HIS 0.007 0.001 HIS E 374 PHE 0.028 0.002 PHE C 53 TYR 0.016 0.002 TYR L 50 ARG 0.006 0.001 ARG A 192 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 308 time to evaluate : 1.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 GLN cc_start: 0.7871 (pm20) cc_final: 0.7534 (pm20) REVERT: A 125 LEU cc_start: 0.8905 (tp) cc_final: 0.8490 (tp) REVERT: A 315 GLN cc_start: 0.8547 (mm-40) cc_final: 0.8143 (mt0) REVERT: A 485 LYS cc_start: 0.8779 (mttt) cc_final: 0.8436 (mtmm) REVERT: B 626 MET cc_start: 0.8323 (OUTLIER) cc_final: 0.7936 (ttm) REVERT: H 86 ASP cc_start: 0.8724 (m-30) cc_final: 0.8505 (m-30) REVERT: C 207 LYS cc_start: 0.8693 (mmtt) cc_final: 0.8375 (ptmt) REVERT: D 545 LEU cc_start: 0.9230 (tp) cc_final: 0.8979 (tp) REVERT: D 661 LEU cc_start: 0.9286 (mm) cc_final: 0.9026 (mp) outliers start: 45 outliers final: 19 residues processed: 332 average time/residue: 0.2702 time to fit residues: 133.5616 Evaluate side-chains 269 residues out of total 1666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 249 time to evaluate : 1.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain B residue 543 ASN Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain L residue 80 THR Chi-restraints excluded: chain L residue 103 ARG Chi-restraints excluded: chain C residue 33 ASN Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain E residue 88 ASN Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 368 ASP Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain F residue 632 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 93 optimal weight: 0.0980 chunk 52 optimal weight: 4.9990 chunk 140 optimal weight: 4.9990 chunk 115 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 169 optimal weight: 6.9990 chunk 182 optimal weight: 5.9990 chunk 150 optimal weight: 0.8980 chunk 167 optimal weight: 0.8980 chunk 57 optimal weight: 0.6980 chunk 135 optimal weight: 3.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN A 478 ASN L 51 ASN L 94 ASN C 85 HIS C 99 ASN C 195 ASN E 478 ASN D 625 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.3207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 16257 Z= 0.244 Angle : 0.605 11.605 22061 Z= 0.315 Chirality : 0.047 0.277 2711 Planarity : 0.004 0.038 2706 Dihedral : 7.832 59.493 3633 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.46 % Allowed : 11.88 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.20), residues: 1848 helix: 2.04 (0.28), residues: 380 sheet: 0.80 (0.24), residues: 470 loop : -0.26 (0.19), residues: 998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 427 HIS 0.005 0.001 HIS E 249 PHE 0.027 0.002 PHE C 53 TYR 0.018 0.001 TYR E 484 ARG 0.004 0.000 ARG A 360 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 275 time to evaluate : 1.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 GLN cc_start: 0.8525 (mm-40) cc_final: 0.8123 (mt0) REVERT: L 79 GLN cc_start: 0.8292 (mp10) cc_final: 0.7498 (pt0) REVERT: H 20 LEU cc_start: 0.9222 (mm) cc_final: 0.9011 (mp) REVERT: H 105 GLN cc_start: 0.8114 (mm-40) cc_final: 0.7846 (mp10) REVERT: C 99 ASN cc_start: 0.7991 (t0) cc_final: 0.7678 (t0) REVERT: C 100 MET cc_start: 0.8744 (mtp) cc_final: 0.8385 (mtp) REVERT: C 492 GLU cc_start: 0.8084 (mt-10) cc_final: 0.7852 (mt-10) REVERT: E 486 TYR cc_start: 0.9296 (m-80) cc_final: 0.8926 (m-80) outliers start: 41 outliers final: 24 residues processed: 298 average time/residue: 0.2612 time to fit residues: 117.8030 Evaluate side-chains 268 residues out of total 1666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 244 time to evaluate : 1.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain B residue 540 GLN Chi-restraints excluded: chain B residue 543 ASN Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 651 ASN Chi-restraints excluded: chain H residue 95 THR Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 88 ASN Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 368 ASP Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain F residue 632 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 167 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 18 optimal weight: 3.9990 chunk 80 optimal weight: 7.9990 chunk 113 optimal weight: 4.9990 chunk 169 optimal weight: 10.0000 chunk 179 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 160 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 51 ASN L 94 ASN C 72 HIS E 85 HIS E 478 ASN D 625 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.3728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 16257 Z= 0.387 Angle : 0.666 11.137 22061 Z= 0.341 Chirality : 0.050 0.475 2711 Planarity : 0.004 0.045 2706 Dihedral : 7.483 57.896 3633 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.24 % Allowed : 11.64 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.19), residues: 1848 helix: 2.01 (0.28), residues: 381 sheet: 0.70 (0.24), residues: 450 loop : -0.69 (0.19), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 427 HIS 0.013 0.002 HIS A 105 PHE 0.023 0.002 PHE C 53 TYR 0.020 0.002 TYR H 58 ARG 0.005 0.001 ARG D 542 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 256 time to evaluate : 1.845 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 426 MET cc_start: 0.7558 (mtm) cc_final: 0.7267 (mtm) REVERT: H 105 GLN cc_start: 0.8075 (mm-40) cc_final: 0.7558 (mp10) REVERT: C 492 GLU cc_start: 0.8109 (mt-10) cc_final: 0.7845 (mt-10) REVERT: E 40 TYR cc_start: 0.9181 (t80) cc_final: 0.8891 (t80) REVERT: E 271 MET cc_start: 0.8942 (OUTLIER) cc_final: 0.8677 (mtp) REVERT: E 486 TYR cc_start: 0.9338 (m-80) cc_final: 0.8881 (m-80) REVERT: F 571 TRP cc_start: 0.7792 (m100) cc_final: 0.7545 (m100) outliers start: 54 outliers final: 30 residues processed: 287 average time/residue: 0.2666 time to fit residues: 115.7583 Evaluate side-chains 265 residues out of total 1666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 234 time to evaluate : 1.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain H residue 95 THR Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 178 ARG Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 88 ASN Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 271 MET Chi-restraints excluded: chain E residue 368 ASP Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 464 THR Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 648 GLU Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain F residue 636 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 149 optimal weight: 6.9990 chunk 102 optimal weight: 0.9980 chunk 2 optimal weight: 5.9990 chunk 133 optimal weight: 0.9980 chunk 74 optimal weight: 9.9990 chunk 153 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 161 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 94 ASN E 478 ASN D 625 ASN F 575 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.3982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16257 Z= 0.253 Angle : 0.582 11.175 22061 Z= 0.301 Chirality : 0.048 0.476 2711 Planarity : 0.004 0.038 2706 Dihedral : 7.209 59.975 3633 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.64 % Allowed : 13.63 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.20), residues: 1848 helix: 2.01 (0.28), residues: 394 sheet: 0.55 (0.24), residues: 471 loop : -0.75 (0.19), residues: 983 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 427 HIS 0.007 0.001 HIS A 105 PHE 0.021 0.002 PHE C 53 TYR 0.015 0.001 TYR L 50 ARG 0.004 0.000 ARG B 542 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 242 time to evaluate : 1.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 426 MET cc_start: 0.7775 (mtm) cc_final: 0.7368 (mtt) REVERT: B 542 ARG cc_start: 0.8171 (ttp80) cc_final: 0.7933 (ttp80) REVERT: L 79 GLN cc_start: 0.8439 (mp10) cc_final: 0.7478 (pt0) REVERT: C 100 MET cc_start: 0.8659 (mtp) cc_final: 0.8258 (mtp) REVERT: C 161 MET cc_start: 0.8877 (tpt) cc_final: 0.8670 (tpt) REVERT: E 271 MET cc_start: 0.8923 (OUTLIER) cc_final: 0.8700 (mtp) REVERT: E 486 TYR cc_start: 0.9297 (m-80) cc_final: 0.8840 (m-80) outliers start: 44 outliers final: 31 residues processed: 266 average time/residue: 0.2717 time to fit residues: 109.4764 Evaluate side-chains 268 residues out of total 1666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 236 time to evaluate : 1.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 478 ASN Chi-restraints excluded: chain B residue 540 GLN Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain H residue 73 ASN Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 95 THR Chi-restraints excluded: chain H residue 98 ASP Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 376 PHE Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 88 ASN Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 215 ILE Chi-restraints excluded: chain E residue 271 MET Chi-restraints excluded: chain E residue 368 ASP Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 440 GLN Chi-restraints excluded: chain F residue 616 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 60 optimal weight: 0.0470 chunk 161 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 105 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 179 optimal weight: 0.5980 chunk 149 optimal weight: 7.9990 chunk 83 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 59 optimal weight: 0.0980 chunk 94 optimal weight: 4.9990 overall best weight: 0.7280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 478 ASN D 625 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.4172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16257 Z= 0.176 Angle : 0.531 9.891 22061 Z= 0.276 Chirality : 0.047 0.557 2711 Planarity : 0.004 0.045 2706 Dihedral : 6.815 58.162 3633 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.16 % Allowed : 14.47 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.20), residues: 1848 helix: 2.16 (0.28), residues: 394 sheet: 0.59 (0.24), residues: 468 loop : -0.74 (0.19), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 427 HIS 0.005 0.001 HIS C 374 PHE 0.020 0.001 PHE C 53 TYR 0.021 0.001 TYR E 484 ARG 0.006 0.000 ARG L 54 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 252 time to evaluate : 2.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 542 ARG cc_start: 0.8167 (ttp80) cc_final: 0.7949 (ttp-170) REVERT: L 79 GLN cc_start: 0.8333 (mp10) cc_final: 0.7537 (pt0) REVERT: C 99 ASN cc_start: 0.8068 (t0) cc_final: 0.7828 (t0) REVERT: C 150 MET cc_start: 0.8491 (mmm) cc_final: 0.8291 (tpt) REVERT: E 271 MET cc_start: 0.8929 (OUTLIER) cc_final: 0.8694 (mtp) REVERT: E 486 TYR cc_start: 0.9259 (m-80) cc_final: 0.8679 (m-80) REVERT: F 659 ASP cc_start: 0.8034 (OUTLIER) cc_final: 0.7679 (m-30) outliers start: 36 outliers final: 27 residues processed: 271 average time/residue: 0.2651 time to fit residues: 108.7516 Evaluate side-chains 266 residues out of total 1666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 237 time to evaluate : 1.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 478 ASN Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain B residue 540 GLN Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 95 THR Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 339 ASN Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 88 ASN Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 215 ILE Chi-restraints excluded: chain E residue 271 MET Chi-restraints excluded: chain E residue 368 ASP Chi-restraints excluded: chain D residue 648 GLU Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 659 ASP Chi-restraints excluded: chain F residue 661 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 173 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 131 optimal weight: 4.9990 chunk 101 optimal weight: 4.9990 chunk 151 optimal weight: 4.9990 chunk 100 optimal weight: 0.9980 chunk 179 optimal weight: 0.0770 chunk 112 optimal weight: 0.9980 chunk 109 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 overall best weight: 1.4142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 ASN ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 66 HIS E 478 ASN D 625 ASN F 653 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.4304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 16257 Z= 0.268 Angle : 0.563 8.923 22061 Z= 0.290 Chirality : 0.047 0.495 2711 Planarity : 0.004 0.039 2706 Dihedral : 6.853 57.159 3633 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.58 % Allowed : 15.31 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.20), residues: 1848 helix: 2.12 (0.28), residues: 395 sheet: 0.50 (0.24), residues: 472 loop : -0.85 (0.19), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 427 HIS 0.005 0.001 HIS A 105 PHE 0.021 0.002 PHE C 376 TYR 0.021 0.001 TYR A 191 ARG 0.005 0.000 ARG A 166 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 242 time to evaluate : 1.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 542 ARG cc_start: 0.8182 (ttp80) cc_final: 0.7968 (ttp-170) REVERT: L 79 GLN cc_start: 0.8376 (mp10) cc_final: 0.7491 (pt0) REVERT: C 125 LEU cc_start: 0.9230 (OUTLIER) cc_final: 0.8956 (tt) REVERT: E 271 MET cc_start: 0.8892 (OUTLIER) cc_final: 0.8689 (mtp) REVERT: E 486 TYR cc_start: 0.9251 (m-80) cc_final: 0.8636 (m-80) outliers start: 43 outliers final: 35 residues processed: 266 average time/residue: 0.2498 time to fit residues: 102.2288 Evaluate side-chains 272 residues out of total 1666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 235 time to evaluate : 1.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain A residue 478 ASN Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain B residue 540 GLN Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain H residue 73 ASN Chi-restraints excluded: chain H residue 95 THR Chi-restraints excluded: chain H residue 98 ASP Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 339 ASN Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 88 ASN Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 271 MET Chi-restraints excluded: chain E residue 368 ASP Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 440 GLN Chi-restraints excluded: chain D residue 648 GLU Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain F residue 636 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 110 optimal weight: 0.7980 chunk 71 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 54 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 113 optimal weight: 4.9990 chunk 122 optimal weight: 0.0570 chunk 88 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 140 optimal weight: 2.9990 overall best weight: 1.1702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 478 ASN D 625 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.4409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16257 Z= 0.228 Angle : 0.550 8.202 22061 Z= 0.284 Chirality : 0.046 0.483 2711 Planarity : 0.004 0.037 2706 Dihedral : 6.806 56.760 3633 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.94 % Allowed : 14.95 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.20), residues: 1848 helix: 2.14 (0.28), residues: 395 sheet: 0.49 (0.24), residues: 470 loop : -0.85 (0.19), residues: 983 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 427 HIS 0.005 0.001 HIS C 374 PHE 0.018 0.002 PHE C 376 TYR 0.020 0.001 TYR E 484 ARG 0.007 0.000 ARG A 166 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 245 time to evaluate : 1.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 439 ILE cc_start: 0.9153 (mt) cc_final: 0.8920 (tt) REVERT: B 542 ARG cc_start: 0.8299 (ttp80) cc_final: 0.8098 (ttp-170) REVERT: L 79 GLN cc_start: 0.8422 (mp10) cc_final: 0.7520 (pt0) REVERT: E 271 MET cc_start: 0.8871 (OUTLIER) cc_final: 0.8646 (mtp) REVERT: E 486 TYR cc_start: 0.9262 (m-80) cc_final: 0.8653 (m-80) REVERT: F 659 ASP cc_start: 0.7877 (OUTLIER) cc_final: 0.7530 (m-30) outliers start: 49 outliers final: 39 residues processed: 271 average time/residue: 0.2685 time to fit residues: 110.9261 Evaluate side-chains 279 residues out of total 1666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 238 time to evaluate : 1.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain A residue 478 ASN Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain B residue 540 GLN Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 73 ASN Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 95 THR Chi-restraints excluded: chain H residue 98 ASP Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 88 ASN Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 271 MET Chi-restraints excluded: chain E residue 368 ASP Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 440 GLN Chi-restraints excluded: chain D residue 648 GLU Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 659 ASP Chi-restraints excluded: chain F residue 661 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 163 optimal weight: 5.9990 chunk 171 optimal weight: 3.9990 chunk 156 optimal weight: 4.9990 chunk 167 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 chunk 131 optimal weight: 0.9980 chunk 51 optimal weight: 4.9990 chunk 150 optimal weight: 6.9990 chunk 158 optimal weight: 1.9990 chunk 166 optimal weight: 0.8980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 625 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.4500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16257 Z= 0.221 Angle : 0.549 8.196 22061 Z= 0.284 Chirality : 0.046 0.467 2711 Planarity : 0.004 0.038 2706 Dihedral : 6.747 57.758 3633 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.46 % Allowed : 15.43 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.20), residues: 1848 helix: 2.18 (0.28), residues: 395 sheet: 0.47 (0.24), residues: 471 loop : -0.87 (0.19), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 427 HIS 0.005 0.001 HIS A 249 PHE 0.019 0.002 PHE C 376 TYR 0.016 0.001 TYR H 58 ARG 0.006 0.000 ARG A 166 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 242 time to evaluate : 1.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 542 ARG cc_start: 0.8295 (ttp80) cc_final: 0.8086 (ttp-170) REVERT: L 50 TYR cc_start: 0.7764 (t80) cc_final: 0.7487 (m-80) REVERT: L 79 GLN cc_start: 0.8446 (mp10) cc_final: 0.7518 (pt0) REVERT: C 440 GLN cc_start: 0.8419 (tp40) cc_final: 0.7928 (tt0) REVERT: E 271 MET cc_start: 0.8868 (OUTLIER) cc_final: 0.8657 (mtp) REVERT: E 486 TYR cc_start: 0.9231 (m-80) cc_final: 0.8616 (m-80) outliers start: 41 outliers final: 37 residues processed: 263 average time/residue: 0.2693 time to fit residues: 107.3861 Evaluate side-chains 274 residues out of total 1666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 236 time to evaluate : 1.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain A residue 478 ASN Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain B residue 540 GLN Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 95 THR Chi-restraints excluded: chain H residue 98 ASP Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 339 ASN Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 88 ASN Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 271 MET Chi-restraints excluded: chain E residue 368 ASP Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 440 GLN Chi-restraints excluded: chain D residue 625 ASN Chi-restraints excluded: chain D residue 648 GLU Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain F residue 661 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 109 optimal weight: 2.9990 chunk 176 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 83 optimal weight: 0.6980 chunk 122 optimal weight: 0.9990 chunk 185 optimal weight: 1.9990 chunk 170 optimal weight: 2.9990 chunk 147 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 113 optimal weight: 2.9990 chunk 90 optimal weight: 0.5980 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 195 ASN E 478 ASN D 625 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.4555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 16257 Z= 0.270 Angle : 0.579 13.228 22061 Z= 0.297 Chirality : 0.047 0.466 2711 Planarity : 0.004 0.041 2706 Dihedral : 6.844 57.935 3633 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.52 % Allowed : 15.43 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.20), residues: 1848 helix: 2.11 (0.28), residues: 395 sheet: 0.40 (0.24), residues: 494 loop : -0.90 (0.20), residues: 959 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 112 HIS 0.005 0.001 HIS C 374 PHE 0.020 0.002 PHE C 376 TYR 0.022 0.001 TYR E 484 ARG 0.008 0.000 ARG D 542 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 240 time to evaluate : 1.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 542 ARG cc_start: 0.8314 (ttp80) cc_final: 0.8095 (ttp-170) REVERT: L 50 TYR cc_start: 0.7842 (t80) cc_final: 0.7424 (m-80) REVERT: C 125 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.8965 (tt) REVERT: E 271 MET cc_start: 0.8872 (OUTLIER) cc_final: 0.8669 (mtp) REVERT: E 486 TYR cc_start: 0.9251 (m-80) cc_final: 0.8641 (m-80) outliers start: 42 outliers final: 37 residues processed: 263 average time/residue: 0.2539 time to fit residues: 102.8391 Evaluate side-chains 277 residues out of total 1666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 238 time to evaluate : 1.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain A residue 478 ASN Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain B residue 540 GLN Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 95 THR Chi-restraints excluded: chain H residue 98 ASP Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 88 ASN Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 271 MET Chi-restraints excluded: chain E residue 368 ASP Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain D residue 625 ASN Chi-restraints excluded: chain D residue 648 GLU Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain F residue 661 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 117 optimal weight: 0.8980 chunk 157 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 chunk 136 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 147 optimal weight: 3.9990 chunk 61 optimal weight: 8.9990 chunk 151 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 625 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.114104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.095433 restraints weight = 26157.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.098721 restraints weight = 14062.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.100944 restraints weight = 9355.407| |-----------------------------------------------------------------------------| r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.4605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16257 Z= 0.219 Angle : 0.548 8.296 22061 Z= 0.284 Chirality : 0.046 0.454 2711 Planarity : 0.004 0.040 2706 Dihedral : 6.790 58.671 3633 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.76 % Allowed : 15.61 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.20), residues: 1848 helix: 2.06 (0.28), residues: 401 sheet: 0.41 (0.24), residues: 494 loop : -0.90 (0.20), residues: 953 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 96 HIS 0.005 0.001 HIS C 374 PHE 0.018 0.002 PHE C 376 TYR 0.017 0.001 TYR H 58 ARG 0.007 0.000 ARG D 542 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3275.82 seconds wall clock time: 60 minutes 30.43 seconds (3630.43 seconds total)