Starting phenix.real_space_refine (version: 1.21rc1) on Tue Apr 25 15:00:02 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6um7_20819/04_2023/6um7_20819.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6um7_20819/04_2023/6um7_20819.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6um7_20819/04_2023/6um7_20819.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6um7_20819/04_2023/6um7_20819.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6um7_20819/04_2023/6um7_20819.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6um7_20819/04_2023/6um7_20819.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.009 sd= 0.141 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 135 5.16 5 C 12687 2.51 5 N 3375 2.21 5 O 4137 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 52": "OE1" <-> "OE2" Residue "G PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 20334 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 3613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3613 Classifications: {'peptide': 462} Link IDs: {'CIS': 4, 'PTRANS': 23, 'TRANS': 434} Chain: "H" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'CIS': 3, 'PTRANS': 1, 'TRANS': 127} Chain breaks: 1 Chain: "J" Number of atoms: 991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 991 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "K" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 800 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "D" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'CIS': 3, 'PTRANS': 1, 'TRANS': 127} Chain breaks: 1 Chain: "E" Number of atoms: 3613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3613 Classifications: {'peptide': 462} Link IDs: {'CIS': 4, 'PTRANS': 23, 'TRANS': 434} Chain: "F" Number of atoms: 991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 991 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "G" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 800 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "1" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'CIS': 3, 'PTRANS': 1, 'TRANS': 127} Chain breaks: 1 Chain: "B" Number of atoms: 991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 991 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "C" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 800 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "I" Number of atoms: 3613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3613 Classifications: {'peptide': 462} Link IDs: {'CIS': 4, 'PTRANS': 23, 'TRANS': 434} Chain: "L" 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 chiralities: 3 Chain: "M" 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 chiralities: 3 Chain: "N" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "O" 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 chiralities: 3 Chain: "P" 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 chiralities: 3 Chain: "Q" 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 chiralities: 3 Chain: "R" 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 chiralities: 3 Chain: "S" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "T" 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 chiralities: 3 Chain: "U" 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 chiralities: 3 Chain: "V" 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 chiralities: 3 Chain: "W" 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 chiralities: 3 Chain: "X" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "Y" 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 chiralities: 3 Chain: "Z" 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 chiralities: 3 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "E" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "I" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 10.94, per 1000 atoms: 0.54 Number of scatterers: 20334 At special positions: 0 Unit cell: (160.5, 161.57, 140.17, 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 135 16.00 O 4137 8.00 N 3375 7.00 C 12687 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.27 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.20 Simple disulfide: pdb=" SG CYS A 201 " - pdb=" SG CYS A 433 " distance=2.00 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=1.98 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.08 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.20 Simple disulfide: pdb=" SG CYS H 598 " - pdb=" SG CYS H 604 " distance=2.07 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.09 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 90 " distance=2.02 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.07 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.27 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.20 Simple disulfide: pdb=" SG CYS E 201 " - pdb=" SG CYS E 433 " distance=2.00 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=2.02 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=1.98 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.08 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.19 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.08 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 90 " distance=2.02 Simple disulfide: pdb=" SG CYS 1 598 " - pdb=" SG CYS 1 604 " distance=2.07 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.08 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 90 " distance=2.02 Simple disulfide: pdb=" SG CYS I 54 " - pdb=" SG CYS I 74 " distance=2.27 Simple disulfide: pdb=" SG CYS I 119 " - pdb=" SG CYS I 205 " distance=2.20 Simple disulfide: pdb=" SG CYS I 201 " - pdb=" SG CYS I 433 " distance=2.00 Simple disulfide: pdb=" SG CYS I 218 " - pdb=" SG CYS I 247 " distance=2.03 Simple disulfide: pdb=" SG CYS I 228 " - pdb=" SG CYS I 239 " distance=2.03 Simple disulfide: pdb=" SG CYS I 296 " - pdb=" SG CYS I 331 " distance=1.98 Simple disulfide: pdb=" SG CYS I 378 " - pdb=" SG CYS I 445 " distance=2.08 Simple disulfide: pdb=" SG CYS I 385 " - pdb=" SG CYS I 418 " distance=2.19 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN N 4 " - " MAN N 5 " " MAN S 4 " - " MAN S 5 " " MAN X 4 " - " MAN X 5 " ALPHA1-3 " BMA N 3 " - " MAN N 4 " " BMA S 3 " - " MAN S 4 " " BMA X 3 " - " MAN X 4 " ALPHA1-6 " BMA N 3 " - " MAN N 6 " " BMA S 3 " - " MAN S 6 " " BMA X 3 " - " MAN X 6 " BETA1-4 " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " NAG-ASN " NAG A 619 " - " ASN A 386 " " NAG A 620 " - " ASN A 362 " " NAG A 621 " - " ASN A 197 " " NAG A 622 " - " ASN A 158 " " NAG A 623 " - " ASN A 234 " " NAG A 624 " - " ASN A 88 " " NAG A 625 " - " ASN A 241 " " NAG A 626 " - " ASN A 339 " " NAG E 619 " - " ASN E 386 " " NAG E 620 " - " ASN E 362 " " NAG E 621 " - " ASN E 197 " " NAG E 622 " - " ASN E 158 " " NAG E 623 " - " ASN E 234 " " NAG E 624 " - " ASN E 88 " " NAG E 625 " - " ASN E 241 " " NAG E 626 " - " ASN E 339 " " NAG I 619 " - " ASN I 386 " " NAG I 620 " - " ASN I 362 " " NAG I 621 " - " ASN I 197 " " NAG I 622 " - " ASN I 158 " " NAG I 623 " - " ASN I 234 " " NAG I 624 " - " ASN I 88 " " NAG I 625 " - " ASN I 241 " " NAG I 626 " - " ASN I 339 " " NAG L 1 " - " ASN A 262 " " NAG M 1 " - " ASN A 301 " " NAG N 1 " - " ASN A 332 " " NAG O 1 " - " ASN A 154 " " NAG P 1 " - " ASN A 392 " " NAG Q 1 " - " ASN E 262 " " NAG R 1 " - " ASN E 301 " " NAG S 1 " - " ASN E 332 " " NAG T 1 " - " ASN E 154 " " NAG U 1 " - " ASN E 392 " " NAG V 1 " - " ASN I 262 " " NAG W 1 " - " ASN I 301 " " NAG X 1 " - " ASN I 332 " " NAG Y 1 " - " ASN I 154 " " NAG Z 1 " - " ASN I 392 " Time building additional restraints: 9.35 Conformation dependent library (CDL) restraints added in 3.0 seconds 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4590 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 42 sheets defined 25.5% alpha, 33.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.57 Creating SS restraints... Processing helix chain 'A' and resid 62 through 68 removed outlier: 3.711A pdb=" N HIS A 66 " --> pdb=" O LYS A 63 " (cutoff:3.500A) 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 116 removed outlier: 3.550A pdb=" N GLN A 103 " --> pdb=" O ASP A 99 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU A 116 " --> pdb=" O TRP A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 138 through 151 removed outlier: 3.915A pdb=" N GLU A 151 " --> pdb=" O GLY A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 335 through 350 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 377 through 381 Processing helix chain 'A' and resid 389 through 392 Processing helix chain 'A' and resid 474 through 484 removed outlier: 3.669A pdb=" N ASN A 478 " --> pdb=" O ASP A 474 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'H' and resid 513 through 520 Processing helix chain 'H' and resid 523 through 528 removed outlier: 4.062A pdb=" N GLY H 527 " --> pdb=" O GLY H 524 " (cutoff:3.500A) Processing helix chain 'H' and resid 529 through 536 Processing helix chain 'H' and resid 538 through 543 removed outlier: 3.562A pdb=" N ARG H 542 " --> pdb=" O THR H 538 " (cutoff:3.500A) Processing helix chain 'H' and resid 570 through 597 removed outlier: 3.593A pdb=" N LYS H 574 " --> pdb=" O VAL H 570 " (cutoff:3.500A) Processing helix chain 'H' and resid 611 through 615 Processing helix chain 'H' and resid 618 through 625 Processing helix chain 'H' and resid 627 through 635 removed outlier: 3.545A pdb=" N LYS H 633 " --> pdb=" O LEU H 629 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLU H 634 " --> pdb=" O GLN H 630 " (cutoff:3.500A) Processing helix chain 'H' and resid 638 through 664 Processing helix chain 'J' and resid 28 through 30 No H-bonds generated for 'chain 'J' and resid 28 through 30' Processing helix chain 'J' and resid 74 through 76 No H-bonds generated for 'chain 'J' and resid 74 through 76' Processing helix chain 'J' and resid 87 through 91 Processing helix chain 'K' and resid 25 through 30 Processing helix chain 'K' and resid 81 through 85 Processing helix chain 'D' and resid 513 through 520 Processing helix chain 'D' and resid 523 through 528 removed outlier: 4.061A pdb=" N GLY D 527 " --> pdb=" O GLY D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 536 Processing helix chain 'D' and resid 538 through 543 removed outlier: 3.561A pdb=" N ARG D 542 " --> pdb=" O THR D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 570 through 597 removed outlier: 3.592A pdb=" N LYS D 574 " --> pdb=" O VAL D 570 " (cutoff:3.500A) Processing helix chain 'D' and resid 611 through 615 Processing helix chain 'D' and resid 618 through 625 Processing helix chain 'D' and resid 627 through 635 removed outlier: 3.546A pdb=" N LYS D 633 " --> pdb=" O LEU D 629 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLU D 634 " --> pdb=" O GLN D 630 " (cutoff:3.500A) Processing helix chain 'D' and resid 638 through 664 Processing helix chain 'E' and resid 62 through 68 removed outlier: 3.710A pdb=" N HIS E 66 " --> pdb=" O LYS E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 98 No H-bonds generated for 'chain 'E' and resid 96 through 98' Processing helix chain 'E' and resid 99 through 116 removed outlier: 3.552A pdb=" N GLN E 103 " --> pdb=" O ASP E 99 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU E 116 " --> pdb=" O TRP E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 138 through 151 removed outlier: 3.915A pdb=" N GLU E 151 " --> pdb=" O GLY E 139 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 198 Processing helix chain 'E' and resid 335 through 350 Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 377 through 381 Processing helix chain 'E' and resid 389 through 392 Processing helix chain 'E' and resid 474 through 484 removed outlier: 3.671A pdb=" N ASN E 478 " --> pdb=" O ASP E 474 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 30 No H-bonds generated for 'chain 'F' and resid 28 through 30' Processing helix chain 'F' and resid 74 through 76 No H-bonds generated for 'chain 'F' and resid 74 through 76' Processing helix chain 'F' and resid 87 through 91 Processing helix chain 'G' and resid 25 through 30 Processing helix chain 'G' and resid 81 through 85 Processing helix chain '1' and resid 513 through 520 Processing helix chain '1' and resid 523 through 528 removed outlier: 4.061A pdb=" N GLY 1 527 " --> pdb=" O GLY 1 524 " (cutoff:3.500A) Processing helix chain '1' and resid 529 through 536 Processing helix chain '1' and resid 538 through 543 removed outlier: 3.561A pdb=" N ARG 1 542 " --> pdb=" O THR 1 538 " (cutoff:3.500A) Processing helix chain '1' and resid 570 through 597 removed outlier: 3.591A pdb=" N LYS 1 574 " --> pdb=" O VAL 1 570 " (cutoff:3.500A) Processing helix chain '1' and resid 611 through 615 Processing helix chain '1' and resid 618 through 625 Processing helix chain '1' and resid 627 through 635 removed outlier: 3.547A pdb=" N LYS 1 633 " --> pdb=" O LEU 1 629 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLU 1 634 " --> pdb=" O GLN 1 630 " (cutoff:3.500A) Processing helix chain '1' and resid 638 through 664 Processing helix chain 'B' and resid 28 through 30 No H-bonds generated for 'chain 'B' and resid 28 through 30' Processing helix chain 'B' and resid 74 through 76 No H-bonds generated for 'chain 'B' and resid 74 through 76' Processing helix chain 'B' and resid 87 through 91 Processing helix chain 'C' and resid 25 through 30 Processing helix chain 'C' and resid 81 through 85 Processing helix chain 'I' and resid 62 through 68 removed outlier: 3.710A pdb=" N HIS I 66 " --> pdb=" O LYS I 63 " (cutoff:3.500A) Processing helix chain 'I' and resid 96 through 98 No H-bonds generated for 'chain 'I' and resid 96 through 98' Processing helix chain 'I' and resid 99 through 116 removed outlier: 3.552A pdb=" N GLN I 103 " --> pdb=" O ASP I 99 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU I 116 " --> pdb=" O TRP I 112 " (cutoff:3.500A) Processing helix chain 'I' and resid 122 through 126 Processing helix chain 'I' and resid 138 through 151 removed outlier: 3.914A pdb=" N GLU I 151 " --> pdb=" O GLY I 139 " (cutoff:3.500A) Processing helix chain 'I' and resid 195 through 198 Processing helix chain 'I' and resid 335 through 350 Processing helix chain 'I' and resid 368 through 373 Processing helix chain 'I' and resid 377 through 381 Processing helix chain 'I' and resid 389 through 392 Processing helix chain 'I' and resid 474 through 484 removed outlier: 3.670A pdb=" N ASN I 478 " --> pdb=" O ASP I 474 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N GLU I 482 " --> pdb=" O ASN I 478 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 495 through 498 removed outlier: 5.009A pdb=" N VAL H 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 8.837A pdb=" N VAL A 38 " --> pdb=" O THR H 606 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N THR H 606 " --> pdb=" O VAL A 38 " (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 91 through 94 Processing sheet with id=AA4, first strand: chain 'A' and resid 167 through 175 Processing sheet with id=AA5, first strand: chain 'A' and resid 260 through 261 removed outlier: 8.030A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 11.716A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 12.000A pdb=" N LEU A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 12.023A pdb=" N LEU A 288 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 11.326A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 10.604A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 11.610A pdb=" N ASP A 457 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 12.254A pdb=" N ILE A 284 " --> pdb=" O ASP A 457 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N GLU A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N SER A 334 " --> pdb=" O GLU A 293 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 271 through 273 removed outlier: 12.254A pdb=" N ILE A 284 " --> pdb=" O ASP A 457 " (cutoff:3.500A) removed outlier: 11.610A pdb=" N ASP A 457 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 10.604A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 11.326A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 12.023A pdb=" N LEU A 288 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 12.000A pdb=" N LEU A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 11.716A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N THR A 357 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N PHE A 468 " --> pdb=" O THR A 357 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LYS A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE A 358 " --> pdb=" O TYR A 395 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TYR A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 302 through 308 removed outlier: 7.085A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 423 through 426 removed outlier: 4.866A pdb=" N MET A 426 " --> pdb=" O ARG A 432 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ARG A 432 " --> pdb=" O MET A 426 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'J' and resid 3 through 6 Processing sheet with id=AB1, first strand: chain 'J' and resid 10 through 12 removed outlier: 4.847A pdb=" N TYR J 33 " --> pdb=" O GLY J 99 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ILE J 34 " --> pdb=" O TRP J 50 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N TRP J 50 " --> pdb=" O ILE J 34 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'J' and resid 10 through 12 removed outlier: 4.217A pdb=" N TYR J 116 " --> pdb=" O ARG J 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 9 through 10 removed outlier: 6.364A pdb=" N TRP K 37 " --> pdb=" O MET K 49 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 9 through 10 removed outlier: 6.249A pdb=" N THR K 98 " --> pdb=" O ALA K 94 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'K' and resid 18 through 23 Processing sheet with id=AB6, first strand: chain 'D' and resid 603 through 609 removed outlier: 7.842A pdb=" N THR D 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 8.838A pdb=" N VAL E 38 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N VAL D 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 45 through 47 Processing sheet with id=AB8, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AB9, first strand: chain 'E' and resid 167 through 175 Processing sheet with id=AC1, first strand: chain 'E' and resid 260 through 261 removed outlier: 8.032A pdb=" N GLY E 451 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 11.716A pdb=" N THR E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 12.000A pdb=" N LEU E 453 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 12.021A pdb=" N LEU E 288 " --> pdb=" O LEU E 453 " (cutoff:3.500A) removed outlier: 11.327A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 10.603A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 11.610A pdb=" N ASP E 457 " --> pdb=" O ILE E 284 " (cutoff:3.500A) removed outlier: 12.253A pdb=" N ILE E 284 " --> pdb=" O ASP E 457 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N GLU E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N SER E 334 " --> pdb=" O GLU E 293 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 271 through 273 removed outlier: 12.253A pdb=" N ILE E 284 " --> pdb=" O ASP E 457 " (cutoff:3.500A) removed outlier: 11.610A pdb=" N ASP E 457 " --> pdb=" O ILE E 284 " (cutoff:3.500A) removed outlier: 10.603A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 11.327A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 12.021A pdb=" N LEU E 288 " --> pdb=" O LEU E 453 " (cutoff:3.500A) removed outlier: 12.000A pdb=" N LEU E 453 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 11.716A pdb=" N THR E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N GLY E 451 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N THR E 357 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N PHE E 468 " --> pdb=" O THR E 357 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LYS E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE E 358 " --> pdb=" O TYR E 395 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TYR E 395 " --> pdb=" O ILE E 358 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 302 through 308 removed outlier: 7.085A pdb=" N THR E 303 " --> pdb=" O GLY E 321 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 423 through 426 removed outlier: 4.868A pdb=" N MET E 426 " --> pdb=" O ARG E 432 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ARG E 432 " --> pdb=" O MET E 426 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 3 through 6 Processing sheet with id=AC6, first strand: chain 'F' and resid 10 through 12 removed outlier: 4.847A pdb=" N TYR F 33 " --> pdb=" O GLY F 99 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ILE F 34 " --> pdb=" O TRP F 50 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N TRP F 50 " --> pdb=" O ILE F 34 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 10 through 12 removed outlier: 4.215A pdb=" N TYR F 116 " --> pdb=" O ARG F 98 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 9 through 10 removed outlier: 6.364A pdb=" N TRP G 37 " --> pdb=" O MET G 49 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 9 through 10 removed outlier: 6.251A pdb=" N THR G 98 " --> pdb=" O ALA G 94 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 18 through 23 Processing sheet with id=AD2, first strand: chain '1' and resid 603 through 609 removed outlier: 7.842A pdb=" N THR 1 606 " --> pdb=" O VAL I 38 " (cutoff:3.500A) removed outlier: 8.838A pdb=" N VAL I 38 " --> pdb=" O THR 1 606 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N VAL 1 608 " --> pdb=" O VAL I 36 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 3 through 6 Processing sheet with id=AD4, first strand: chain 'B' and resid 10 through 12 removed outlier: 4.847A pdb=" N TYR B 33 " --> pdb=" O GLY B 99 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ILE B 34 " --> pdb=" O TRP B 50 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N TRP B 50 " --> pdb=" O ILE B 34 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 10 through 12 removed outlier: 4.216A pdb=" N TYR B 116 " --> pdb=" O ARG B 98 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 9 through 10 removed outlier: 6.363A pdb=" N TRP C 37 " --> pdb=" O MET C 49 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 9 through 10 removed outlier: 6.249A pdb=" N THR C 98 " --> pdb=" O ALA C 94 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 18 through 23 Processing sheet with id=AD9, first strand: chain 'I' and resid 45 through 47 Processing sheet with id=AE1, first strand: chain 'I' and resid 91 through 94 Processing sheet with id=AE2, first strand: chain 'I' and resid 167 through 175 Processing sheet with id=AE3, first strand: chain 'I' and resid 260 through 261 removed outlier: 8.031A pdb=" N GLY I 451 " --> pdb=" O THR I 290 " (cutoff:3.500A) removed outlier: 11.717A pdb=" N THR I 290 " --> pdb=" O GLY I 451 " (cutoff:3.500A) removed outlier: 12.002A pdb=" N LEU I 453 " --> pdb=" O LEU I 288 " (cutoff:3.500A) removed outlier: 12.025A pdb=" N LEU I 288 " --> pdb=" O LEU I 453 " (cutoff:3.500A) removed outlier: 11.326A pdb=" N THR I 455 " --> pdb=" O VAL I 286 " (cutoff:3.500A) removed outlier: 10.603A pdb=" N VAL I 286 " --> pdb=" O THR I 455 " (cutoff:3.500A) removed outlier: 11.610A pdb=" N ASP I 457 " --> pdb=" O ILE I 284 " (cutoff:3.500A) removed outlier: 12.254A pdb=" N ILE I 284 " --> pdb=" O ASP I 457 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N GLU I 293 " --> pdb=" O SER I 334 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N SER I 334 " --> pdb=" O GLU I 293 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ALA I 329 " --> pdb=" O CYS I 418 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N PHE I 382 " --> pdb=" O LYS I 421 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'I' and resid 271 through 273 removed outlier: 12.254A pdb=" N ILE I 284 " --> pdb=" O ASP I 457 " (cutoff:3.500A) removed outlier: 11.610A pdb=" N ASP I 457 " --> pdb=" O ILE I 284 " (cutoff:3.500A) removed outlier: 10.603A pdb=" N VAL I 286 " --> pdb=" O THR I 455 " (cutoff:3.500A) removed outlier: 11.326A pdb=" N THR I 455 " --> pdb=" O VAL I 286 " (cutoff:3.500A) removed outlier: 12.025A pdb=" N LEU I 288 " --> pdb=" O LEU I 453 " (cutoff:3.500A) removed outlier: 12.002A pdb=" N LEU I 453 " --> pdb=" O LEU I 288 " (cutoff:3.500A) removed outlier: 11.717A pdb=" N THR I 290 " --> pdb=" O GLY I 451 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N GLY I 451 " --> pdb=" O THR I 290 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N THR I 357 " --> pdb=" O GLU I 466 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N PHE I 468 " --> pdb=" O THR I 357 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LYS I 360 " --> pdb=" O PHE I 468 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE I 358 " --> pdb=" O TYR I 395 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TYR I 395 " --> pdb=" O ILE I 358 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I' and resid 302 through 308 removed outlier: 7.085A pdb=" N THR I 303 " --> pdb=" O GLY I 321 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'I' and resid 423 through 426 removed outlier: 4.867A pdb=" N MET I 426 " --> pdb=" O ARG I 432 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ARG I 432 " --> pdb=" O MET I 426 " (cutoff:3.500A) 810 hydrogen bonds defined for protein. 2025 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: 7.37 Time building geometry restraints manager: 9.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.33: 5203 1.33 - 1.47: 6467 1.47 - 1.62: 8892 1.62 - 1.76: 21 1.76 - 1.90: 165 Bond restraints: 20748 Sorted by residual: bond pdb=" N PRO I 177 " pdb=" CD PRO I 177 " ideal model delta sigma weight residual 1.473 1.689 -0.216 1.40e-02 5.10e+03 2.38e+02 bond pdb=" N PRO A 177 " pdb=" CD PRO A 177 " ideal model delta sigma weight residual 1.473 1.689 -0.216 1.40e-02 5.10e+03 2.38e+02 bond pdb=" N PRO E 177 " pdb=" CD PRO E 177 " ideal model delta sigma weight residual 1.473 1.689 -0.216 1.40e-02 5.10e+03 2.38e+02 bond pdb=" CB HIS A 374 " pdb=" CG HIS A 374 " ideal model delta sigma weight residual 1.497 1.384 0.113 1.40e-02 5.10e+03 6.50e+01 bond pdb=" CB HIS E 374 " pdb=" CG HIS E 374 " ideal model delta sigma weight residual 1.497 1.386 0.111 1.40e-02 5.10e+03 6.29e+01 ... (remaining 20743 not shown) Histogram of bond angle deviations from ideal: 95.53 - 107.45: 1347 107.45 - 119.38: 17071 119.38 - 131.30: 9689 131.30 - 143.22: 84 143.22 - 155.14: 9 Bond angle restraints: 28200 Sorted by residual: angle pdb=" C SER F 84 " pdb=" N ARG F 85 " pdb=" CA ARG F 85 " ideal model delta sigma weight residual 122.68 152.73 -30.05 1.47e+00 4.63e-01 4.18e+02 angle pdb=" C SER B 84 " pdb=" N ARG B 85 " pdb=" CA ARG B 85 " ideal model delta sigma weight residual 122.68 152.62 -29.94 1.47e+00 4.63e-01 4.15e+02 angle pdb=" C SER J 84 " pdb=" N ARG J 85 " pdb=" CA ARG J 85 " ideal model delta sigma weight residual 122.68 152.62 -29.94 1.47e+00 4.63e-01 4.15e+02 angle pdb=" C SER 1 546 " pdb=" N GLY 1 547 " pdb=" CA GLY 1 547 " ideal model delta sigma weight residual 121.70 155.14 -33.44 1.80e+00 3.09e-01 3.45e+02 angle pdb=" C SER D 546 " pdb=" N GLY D 547 " pdb=" CA GLY D 547 " ideal model delta sigma weight residual 121.70 155.07 -33.37 1.80e+00 3.09e-01 3.44e+02 ... (remaining 28195 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.43: 11453 23.43 - 46.85: 238 46.85 - 70.28: 85 70.28 - 93.70: 17 93.70 - 117.13: 3 Dihedral angle restraints: 11796 sinusoidal: 4626 harmonic: 7170 Sorted by residual: dihedral pdb=" CA ARG I 446 " pdb=" C ARG I 446 " pdb=" N SER I 447 " pdb=" CA SER I 447 " ideal model delta harmonic sigma weight residual 180.00 62.87 117.13 0 5.00e+00 4.00e-02 5.49e+02 dihedral pdb=" CA ARG A 446 " pdb=" C ARG A 446 " pdb=" N SER A 447 " pdb=" CA SER A 447 " ideal model delta harmonic sigma weight residual 180.00 62.93 117.07 0 5.00e+00 4.00e-02 5.48e+02 dihedral pdb=" CA ARG E 446 " pdb=" C ARG E 446 " pdb=" N SER E 447 " pdb=" CA SER E 447 " ideal model delta harmonic sigma weight residual 180.00 63.16 116.84 0 5.00e+00 4.00e-02 5.46e+02 ... (remaining 11793 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.940: 3393 0.940 - 1.879: 0 1.879 - 2.819: 0 2.819 - 3.759: 0 3.759 - 4.699: 3 Chirality restraints: 3396 Sorted by residual: chirality pdb=" C1 MAN S 4 " pdb=" O3 BMA S 3 " pdb=" C2 MAN S 4 " pdb=" O5 MAN S 4 " both_signs ideal model delta sigma weight residual False 2.40 1.70 0.70 2.00e-02 2.50e+03 1.22e+03 chirality pdb=" C1 MAN N 4 " pdb=" O3 BMA N 3 " pdb=" C2 MAN N 4 " pdb=" O5 MAN N 4 " both_signs ideal model delta sigma weight residual False 2.40 1.70 0.70 2.00e-02 2.50e+03 1.22e+03 chirality pdb=" C1 MAN X 4 " pdb=" O3 BMA X 3 " pdb=" C2 MAN X 4 " pdb=" O5 MAN X 4 " both_signs ideal model delta sigma weight residual False 2.40 1.71 0.69 2.00e-02 2.50e+03 1.19e+03 ... (remaining 3393 not shown) Planarity restraints: 3528 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG R 2 " -0.344 2.00e-02 2.50e+03 2.97e-01 1.10e+03 pdb=" C7 NAG R 2 " 0.081 2.00e-02 2.50e+03 pdb=" C8 NAG R 2 " -0.057 2.00e-02 2.50e+03 pdb=" N2 NAG R 2 " 0.522 2.00e-02 2.50e+03 pdb=" O7 NAG R 2 " -0.201 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG M 2 " -0.344 2.00e-02 2.50e+03 2.97e-01 1.10e+03 pdb=" C7 NAG M 2 " 0.081 2.00e-02 2.50e+03 pdb=" C8 NAG M 2 " -0.057 2.00e-02 2.50e+03 pdb=" N2 NAG M 2 " 0.521 2.00e-02 2.50e+03 pdb=" O7 NAG M 2 " -0.201 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG W 2 " 0.344 2.00e-02 2.50e+03 2.97e-01 1.10e+03 pdb=" C7 NAG W 2 " -0.081 2.00e-02 2.50e+03 pdb=" C8 NAG W 2 " 0.057 2.00e-02 2.50e+03 pdb=" N2 NAG W 2 " -0.521 2.00e-02 2.50e+03 pdb=" O7 NAG W 2 " 0.201 2.00e-02 2.50e+03 ... (remaining 3525 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 1321 2.69 - 3.24: 20028 3.24 - 3.79: 32047 3.79 - 4.35: 41984 4.35 - 4.90: 66859 Nonbonded interactions: 162239 Sorted by model distance: nonbonded pdb=" OG1 THR E 297 " pdb=" O ILE E 443 " model vdw 2.132 2.440 nonbonded pdb=" OG1 THR I 297 " pdb=" O ILE I 443 " model vdw 2.132 2.440 nonbonded pdb=" OG1 THR A 297 " pdb=" O ILE A 443 " model vdw 2.133 2.440 nonbonded pdb=" OD1 ASN E 339 " pdb=" C1 NAG E 626 " model vdw 2.165 2.776 nonbonded pdb=" OD1 ASN I 339 " pdb=" C1 NAG I 626 " model vdw 2.165 2.776 ... (remaining 162234 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 '1' selection = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'J' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'Y' selection = chain 'Z' } ncs_group { reference = chain 'N' selection = chain 'S' selection = chain 'X' } 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: 2.480 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: 8.650 Check model and map are aligned: 0.330 Set scattering table: 0.190 Process input model: 54.130 Find NCS groups from input model: 1.360 Set up NCS constraints: 0.230 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6512 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 : 0.018 0.216 20748 Z= 1.192 Angle : 2.068 33.444 28200 Z= 1.359 Chirality : 0.177 4.699 3396 Planarity : 0.027 0.297 3489 Dihedral : 11.263 117.128 7107 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.85 % Allowed : 4.96 % Favored : 94.19 % Rotamer Outliers : 0.89 % Cbeta Deviations : 0.52 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.88 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: 0.01 (0.17), residues: 2460 helix: -0.60 (0.23), residues: 399 sheet: 0.62 (0.21), residues: 546 loop : 0.05 (0.17), residues: 1515 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 185 time to evaluate : 2.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 4 residues processed: 203 average time/residue: 0.4006 time to fit residues: 117.3970 Evaluate side-chains 76 residues out of total 2145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 72 time to evaluate : 2.415 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1822 time to fit residues: 4.5228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 207 optimal weight: 5.9990 chunk 186 optimal weight: 5.9990 chunk 103 optimal weight: 8.9990 chunk 63 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 99 optimal weight: 7.9990 chunk 192 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 chunk 117 optimal weight: 7.9990 chunk 143 optimal weight: 7.9990 chunk 223 optimal weight: 2.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 ASN A 287 HIS A 363 GLN A 422 GLN H 575 GLN ** J 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 575 GLN E 203 GLN E 229 ASN E 363 GLN E 422 GLN F 1 GLN F 113 ASN 1 543 ASN ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 203 GLN I 229 ASN I 287 HIS I 363 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7111 moved from start: 0.3551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.049 20748 Z= 0.383 Angle : 0.984 12.705 28200 Z= 0.501 Chirality : 0.054 0.445 3396 Planarity : 0.006 0.077 3489 Dihedral : 6.450 39.879 2676 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.73 % Allowed : 4.23 % Favored : 95.04 % Rotamer Outliers : 1.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.88 % Twisted Proline : 3.03 % Twisted General : 0.17 % 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: -0.33 (0.17), residues: 2460 helix: 0.67 (0.27), residues: 411 sheet: 0.11 (0.18), residues: 720 loop : -0.64 (0.17), residues: 1329 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 2145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 78 time to evaluate : 2.361 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 9 residues processed: 98 average time/residue: 0.3070 time to fit residues: 49.7263 Evaluate side-chains 76 residues out of total 2145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 67 time to evaluate : 2.668 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 9 outliers final: 1 residues processed: 9 average time/residue: 0.1791 time to fit residues: 5.8844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 124 optimal weight: 5.9990 chunk 69 optimal weight: 10.0000 chunk 185 optimal weight: 9.9990 chunk 152 optimal weight: 0.4980 chunk 61 optimal weight: 4.9990 chunk 223 optimal weight: 0.9980 chunk 241 optimal weight: 9.9990 chunk 199 optimal weight: 2.9990 chunk 221 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 179 optimal weight: 3.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 3 GLN G 40 GLN 1 575 GLN B 115 ASN I 422 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.4769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.071 20748 Z= 0.273 Angle : 0.770 13.108 28200 Z= 0.403 Chirality : 0.047 0.300 3396 Planarity : 0.005 0.073 3489 Dihedral : 5.667 32.943 2676 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.61 % Allowed : 4.55 % Favored : 94.84 % Rotamer Outliers : 0.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.88 % Twisted Proline : 3.03 % Twisted General : 0.08 % 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: 0.03 (0.17), residues: 2460 helix: 1.60 (0.28), residues: 399 sheet: 0.12 (0.18), residues: 732 loop : -0.48 (0.18), residues: 1329 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 2145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 76 time to evaluate : 2.671 Fit side-chains outliers start: 12 outliers final: 4 residues processed: 84 average time/residue: 0.3242 time to fit residues: 45.2343 Evaluate side-chains 68 residues out of total 2145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 64 time to evaluate : 2.443 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1996 time to fit residues: 4.5821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 221 optimal weight: 0.9980 chunk 168 optimal weight: 7.9990 chunk 116 optimal weight: 7.9990 chunk 24 optimal weight: 5.9990 chunk 106 optimal weight: 6.9990 chunk 150 optimal weight: 5.9990 chunk 224 optimal weight: 8.9990 chunk 237 optimal weight: 2.9990 chunk 117 optimal weight: 7.9990 chunk 212 optimal weight: 4.9990 chunk 64 optimal weight: 7.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 417 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.7420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.064 20748 Z= 0.394 Angle : 0.885 13.082 28200 Z= 0.450 Chirality : 0.051 0.286 3396 Planarity : 0.006 0.069 3489 Dihedral : 6.135 34.837 2676 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.57 % Allowed : 5.98 % Favored : 93.46 % Rotamer Outliers : 1.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.88 % Twisted Proline : 1.01 % Twisted General : 0.17 % 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: -0.55 (0.17), residues: 2460 helix: 0.98 (0.26), residues: 408 sheet: -0.05 (0.19), residues: 666 loop : -0.93 (0.17), residues: 1386 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 2145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 65 time to evaluate : 2.287 Fit side-chains outliers start: 31 outliers final: 11 residues processed: 87 average time/residue: 0.2881 time to fit residues: 42.8860 Evaluate side-chains 67 residues out of total 2145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 56 time to evaluate : 2.384 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.2450 time to fit residues: 8.3083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 198 optimal weight: 10.0000 chunk 134 optimal weight: 7.9990 chunk 3 optimal weight: 10.0000 chunk 177 optimal weight: 9.9990 chunk 98 optimal weight: 9.9990 chunk 202 optimal weight: 8.9990 chunk 164 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 121 optimal weight: 9.9990 chunk 213 optimal weight: 6.9990 chunk 60 optimal weight: 20.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 350 GLN A 417 GLN A 463 ASN J 113 ASN E 343 GLN E 463 ASN F 39 GLN G 40 GLN ** 1 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 658 GLN B 3 GLN B 115 ASN ** I 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 463 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.9226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.071 20748 Z= 0.521 Angle : 0.961 12.933 28200 Z= 0.488 Chirality : 0.054 0.331 3396 Planarity : 0.006 0.063 3489 Dihedral : 6.498 36.625 2676 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 16.32 Ramachandran Plot: Outliers : 0.61 % Allowed : 7.24 % Favored : 92.15 % Rotamer Outliers : 1.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.88 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.17), residues: 2460 helix: 0.57 (0.25), residues: 408 sheet: -0.43 (0.19), residues: 669 loop : -1.21 (0.17), residues: 1383 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 2145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 60 time to evaluate : 3.020 Fit side-chains outliers start: 34 outliers final: 12 residues processed: 87 average time/residue: 0.2996 time to fit residues: 45.2598 Evaluate side-chains 69 residues out of total 2145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 57 time to evaluate : 2.538 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.2274 time to fit residues: 8.8516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 80 optimal weight: 3.9990 chunk 214 optimal weight: 0.3980 chunk 47 optimal weight: 2.9990 chunk 139 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 238 optimal weight: 0.0170 chunk 197 optimal weight: 7.9990 chunk 110 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 chunk 78 optimal weight: 4.9990 chunk 124 optimal weight: 2.9990 overall best weight: 1.0222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 287 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.9232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.058 20748 Z= 0.188 Angle : 0.730 12.654 28200 Z= 0.370 Chirality : 0.047 0.280 3396 Planarity : 0.004 0.054 3489 Dihedral : 5.648 31.850 2676 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.65 % Allowed : 4.92 % Favored : 94.43 % Rotamer Outliers : 0.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.88 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.61 (0.17), residues: 2460 helix: 1.57 (0.27), residues: 396 sheet: -0.23 (0.19), residues: 672 loop : -1.09 (0.17), residues: 1392 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 2145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 63 time to evaluate : 2.524 Fit side-chains outliers start: 13 outliers final: 4 residues processed: 73 average time/residue: 0.2860 time to fit residues: 37.1281 Evaluate side-chains 63 residues out of total 2145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 59 time to evaluate : 2.588 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1929 time to fit residues: 4.7113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 229 optimal weight: 10.0000 chunk 26 optimal weight: 1.9990 chunk 135 optimal weight: 1.9990 chunk 173 optimal weight: 9.9990 chunk 134 optimal weight: 6.9990 chunk 200 optimal weight: 8.9990 chunk 132 optimal weight: 2.9990 chunk 237 optimal weight: 5.9990 chunk 148 optimal weight: 7.9990 chunk 144 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.9416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 20748 Z= 0.228 Angle : 0.717 12.643 28200 Z= 0.362 Chirality : 0.046 0.307 3396 Planarity : 0.004 0.050 3489 Dihedral : 5.416 32.536 2676 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.61 % Allowed : 5.49 % Favored : 93.90 % Rotamer Outliers : 0.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.88 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.56 (0.17), residues: 2460 helix: 1.69 (0.27), residues: 405 sheet: -0.28 (0.19), residues: 690 loop : -1.07 (0.17), residues: 1365 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 2145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 61 time to evaluate : 2.379 Fit side-chains outliers start: 17 outliers final: 7 residues processed: 70 average time/residue: 0.3187 time to fit residues: 39.7130 Evaluate side-chains 67 residues out of total 2145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 60 time to evaluate : 2.618 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2220 time to fit residues: 5.9809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 146 optimal weight: 3.9990 chunk 94 optimal weight: 9.9990 chunk 141 optimal weight: 0.9990 chunk 71 optimal weight: 30.0000 chunk 46 optimal weight: 9.9990 chunk 45 optimal weight: 0.9980 chunk 150 optimal weight: 8.9990 chunk 161 optimal weight: 0.7980 chunk 117 optimal weight: 9.9990 chunk 22 optimal weight: 8.9990 chunk 186 optimal weight: 8.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 543 ASN C 40 GLN ** I 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.9694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 20748 Z= 0.272 Angle : 0.734 12.532 28200 Z= 0.369 Chirality : 0.047 0.305 3396 Planarity : 0.004 0.049 3489 Dihedral : 5.419 33.326 2676 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.65 % Allowed : 5.77 % Favored : 93.58 % Rotamer Outliers : 0.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.88 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.53 (0.17), residues: 2460 helix: 1.67 (0.27), residues: 405 sheet: -0.28 (0.19), residues: 699 loop : -1.02 (0.17), residues: 1356 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 2145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 59 time to evaluate : 2.700 Fit side-chains outliers start: 9 outliers final: 3 residues processed: 65 average time/residue: 0.2916 time to fit residues: 34.2121 Evaluate side-chains 60 residues out of total 2145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 57 time to evaluate : 2.666 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2065 time to fit residues: 4.3350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 215 optimal weight: 10.0000 chunk 227 optimal weight: 10.0000 chunk 207 optimal weight: 0.9990 chunk 220 optimal weight: 6.9990 chunk 132 optimal weight: 7.9990 chunk 96 optimal weight: 5.9990 chunk 173 optimal weight: 0.7980 chunk 67 optimal weight: 9.9990 chunk 199 optimal weight: 10.0000 chunk 208 optimal weight: 7.9990 chunk 145 optimal weight: 8.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 115 ASN F 115 ASN G 1 GLN 1 658 GLN C 1 GLN ** I 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 1.0112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.049 20748 Z= 0.365 Angle : 0.793 12.422 28200 Z= 0.399 Chirality : 0.048 0.317 3396 Planarity : 0.004 0.049 3489 Dihedral : 5.639 34.757 2676 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.69 % Allowed : 7.20 % Favored : 92.11 % Rotamer Outliers : 0.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.88 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.63 (0.17), residues: 2460 helix: 1.61 (0.27), residues: 387 sheet: -0.30 (0.20), residues: 648 loop : -1.06 (0.17), residues: 1425 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 2145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 57 time to evaluate : 2.487 Fit side-chains outliers start: 13 outliers final: 6 residues processed: 63 average time/residue: 0.2925 time to fit residues: 33.2951 Evaluate side-chains 63 residues out of total 2145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 57 time to evaluate : 2.699 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2559 time to fit residues: 6.5278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 233 optimal weight: 8.9990 chunk 142 optimal weight: 9.9990 chunk 110 optimal weight: 6.9990 chunk 162 optimal weight: 2.9990 chunk 245 optimal weight: 0.8980 chunk 225 optimal weight: 8.9990 chunk 195 optimal weight: 9.9990 chunk 20 optimal weight: 5.9990 chunk 150 optimal weight: 8.9990 chunk 119 optimal weight: 8.9990 chunk 155 optimal weight: 8.9990 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 658 GLN F 115 ASN ** I 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 1.0451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.065 20748 Z= 0.391 Angle : 0.811 12.281 28200 Z= 0.407 Chirality : 0.049 0.317 3396 Planarity : 0.004 0.049 3489 Dihedral : 5.778 35.094 2676 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.73 % Allowed : 7.07 % Favored : 92.20 % Rotamer Outliers : 0.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.88 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -0.81 (0.17), residues: 2460 helix: 1.47 (0.27), residues: 387 sheet: -0.45 (0.20), residues: 654 loop : -1.16 (0.17), residues: 1419 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 2145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 57 time to evaluate : 2.660 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 57 average time/residue: 0.2977 time to fit residues: 31.3292 Evaluate side-chains 58 residues out of total 2145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 56 time to evaluate : 2.444 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1847 time to fit residues: 3.8848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 207 optimal weight: 5.9990 chunk 59 optimal weight: 7.9990 chunk 179 optimal weight: 6.9990 chunk 28 optimal weight: 0.9980 chunk 54 optimal weight: 0.5980 chunk 195 optimal weight: 9.9990 chunk 81 optimal weight: 5.9990 chunk 200 optimal weight: 1.9990 chunk 24 optimal weight: 8.9990 chunk 36 optimal weight: 40.0000 chunk 171 optimal weight: 8.9990 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 115 ASN ** I 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.040138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.033233 restraints weight = 184015.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.034079 restraints weight = 110069.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.034633 restraints weight = 81211.256| |-----------------------------------------------------------------------------| r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 1.0533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 20748 Z= 0.269 Angle : 0.746 12.170 28200 Z= 0.374 Chirality : 0.047 0.316 3396 Planarity : 0.004 0.045 3489 Dihedral : 5.544 33.756 2676 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.73 % Allowed : 6.46 % Favored : 92.80 % Rotamer Outliers : 0.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.88 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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 (0.17), residues: 2460 helix: 1.69 (0.27), residues: 387 sheet: -0.34 (0.20), residues: 648 loop : -1.11 (0.17), residues: 1425 =============================================================================== Job complete usr+sys time: 2744.54 seconds wall clock time: 55 minutes 35.83 seconds (3335.83 seconds total)