Starting phenix.real_space_refine on Mon Mar 18 06:34:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6um6_20818/03_2024/6um6_20818_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6um6_20818/03_2024/6um6_20818.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6um6_20818/03_2024/6um6_20818.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6um6_20818/03_2024/6um6_20818.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6um6_20818/03_2024/6um6_20818_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6um6_20818/03_2024/6um6_20818_neut.pdb" } resolution = 4.3 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= 0.005 sd= 0.083 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 141 5.16 5 C 12579 2.51 5 N 3363 2.21 5 O 4050 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 175": "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 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 175": "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 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 175": "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" Residue "J PHE 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 20133 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 3612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3612 Classifications: {'peptide': 462} Link IDs: {'CIS': 4, 'PTRANS': 23, 'TRANS': 434} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" 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: "C" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 996 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "D" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 790 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "E" Number of atoms: 3612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3612 Classifications: {'peptide': 462} Link IDs: {'CIS': 4, 'PTRANS': 23, 'TRANS': 434} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "F" 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: "G" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 996 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "H" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 790 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "I" Number of atoms: 3612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3612 Classifications: {'peptide': 462} Link IDs: {'CIS': 4, 'PTRANS': 23, 'TRANS': 434} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "J" 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: "K" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 996 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "L" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 790 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "M" 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: "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: 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: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 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: "R" 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: "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: 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: "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: 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: "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: 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: "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: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "E" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "I" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 10.81, per 1000 atoms: 0.54 Number of scatterers: 20133 At special positions: 0 Unit cell: (159.84, 160.92, 140.4, 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 141 16.00 O 4050 8.00 N 3363 7.00 C 12579 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, 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=2.02 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.02 Simple disulfide: pdb=" SG CYS A 201 " - pdb=" SG CYS A 433 " distance=2.01 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.01 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.26 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.11 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.20 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.08 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.14 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=1.98 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 90 " distance=2.20 Simple disulfide: pdb=" SG CYS D 91 " - pdb=" SG CYS D 101 " distance=2.14 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=2.02 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.02 Simple disulfide: pdb=" SG CYS E 201 " - pdb=" SG CYS E 433 " distance=2.01 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.01 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.26 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.11 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.20 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.08 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.14 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=1.98 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 90 " distance=2.20 Simple disulfide: pdb=" SG CYS H 91 " - pdb=" SG CYS H 101 " distance=2.14 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=2.02 Simple disulfide: pdb=" SG CYS I 126 " - pdb=" SG CYS I 196 " distance=2.02 Simple disulfide: pdb=" SG CYS I 201 " - pdb=" SG CYS I 433 " distance=2.01 Simple disulfide: pdb=" SG CYS I 218 " - pdb=" SG CYS I 247 " distance=2.01 Simple disulfide: pdb=" SG CYS I 228 " - pdb=" SG CYS I 239 " distance=2.26 Simple disulfide: pdb=" SG CYS I 296 " - pdb=" SG CYS I 331 " distance=2.11 Simple disulfide: pdb=" SG CYS I 378 " - pdb=" SG CYS I 445 " distance=2.20 Simple disulfide: pdb=" SG CYS I 385 " - pdb=" SG CYS I 418 " distance=2.07 Simple disulfide: pdb=" SG CYS J 598 " - pdb=" SG CYS J 604 " distance=2.14 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=1.98 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " distance=2.20 Simple disulfide: pdb=" SG CYS L 91 " - pdb=" SG CYS L 101 " distance=2.14 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 Q 3 " - " MAN Q 4 " " BMA V 3 " - " MAN V 4 " " BMA a 3 " - " MAN a 4 " ALPHA1-6 " BMA M 3 " - " MAN M 4 " " BMA R 3 " - " MAN R 4 " " BMA W 3 " - " MAN W 4 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " 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 W 2 " - " BMA W 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " BETA1-6 " NAG N 1 " - " NAG N 2 " " NAG S 1 " - " NAG S 2 " " NAG X 1 " - " NAG X 2 " NAG-ASN " NAG A 610 " - " ASN A 154 " " NAG A 613 " - " ASN A 386 " " NAG A 614 " - " ASN A 197 " " NAG A 615 " - " ASN A 355 " " NAG A 620 " - " ASN A 448 " " NAG A 621 " - " ASN A 234 " " NAG E 610 " - " ASN E 154 " " NAG E 613 " - " ASN E 386 " " NAG E 614 " - " ASN E 197 " " NAG E 615 " - " ASN E 355 " " NAG E 620 " - " ASN E 448 " " NAG E 621 " - " ASN E 234 " " NAG I 610 " - " ASN I 154 " " NAG I 613 " - " ASN I 386 " " NAG I 614 " - " ASN I 197 " " NAG I 615 " - " ASN I 355 " " NAG I 620 " - " ASN I 448 " " NAG I 621 " - " ASN I 234 " " NAG M 1 " - " ASN A 332 " " NAG N 1 " - " ASN A 442 " " NAG O 1 " - " ASN A 301 " " NAG P 1 " - " ASN A 362 " " NAG Q 1 " - " ASN A 262 " " NAG R 1 " - " ASN E 332 " " NAG S 1 " - " ASN E 442 " " NAG T 1 " - " ASN E 301 " " NAG U 1 " - " ASN E 362 " " NAG V 1 " - " ASN E 262 " " NAG W 1 " - " ASN I 332 " " NAG X 1 " - " ASN I 442 " " NAG Y 1 " - " ASN I 301 " " NAG Z 1 " - " ASN I 362 " " NAG a 1 " - " ASN I 262 " Time building additional restraints: 9.08 Conformation dependent library (CDL) restraints added in 3.5 seconds 4908 Ramachandran restraints generated. 2454 Oldfield, 0 Emsley, 2454 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4560 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 42 sheets defined 24.2% alpha, 32.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.61 Creating SS restraints... Processing helix chain 'A' and resid 62 through 68 removed outlier: 3.657A 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: 3.668A pdb=" N GLN A 103 " --> pdb=" O ASP A 99 " (cutoff:3.500A) removed outlier: 3.608A 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: 3.855A 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 474 through 484 removed outlier: 3.549A pdb=" N ASN A 478 " --> pdb=" O ASP A 474 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 520 Processing helix chain 'B' and resid 523 through 536 removed outlier: 3.787A pdb=" N GLY B 527 " --> pdb=" O GLY B 524 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N THR B 529 " --> pdb=" O ALA B 526 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N MET B 530 " --> pdb=" O GLY B 527 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N GLY B 531 " --> pdb=" O SER B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 543 removed outlier: 3.634A pdb=" N ARG B 542 " --> pdb=" O THR B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 597 removed outlier: 3.644A pdb=" N LYS B 574 " --> pdb=" O VAL B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 611 through 615 Processing helix chain 'B' and resid 618 through 625 Processing helix chain 'B' and resid 627 through 635 removed outlier: 3.555A pdb=" N LYS B 633 " --> pdb=" O LEU B 629 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N GLU B 634 " --> pdb=" O GLN B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 664 Processing helix chain 'C' and resid 62 through 65 removed outlier: 3.770A pdb=" N GLN C 65 " --> pdb=" O ARG C 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 62 through 65' Processing helix chain 'C' and resid 87 through 91 removed outlier: 4.029A pdb=" N THR C 91 " --> pdb=" O SER C 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 85 removed outlier: 4.016A pdb=" N GLU D 85 " --> pdb=" O ALA D 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 68 removed outlier: 3.658A 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: 3.668A pdb=" N GLN E 103 " --> pdb=" O ASP E 99 " (cutoff:3.500A) removed outlier: 3.608A 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: 3.856A 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 474 through 484 removed outlier: 3.549A pdb=" N ASN E 478 " --> pdb=" O ASP E 474 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 513 through 520 Processing helix chain 'F' and resid 523 through 536 removed outlier: 3.787A pdb=" N GLY F 527 " --> pdb=" O GLY F 524 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N THR F 529 " --> pdb=" O ALA F 526 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N MET F 530 " --> pdb=" O GLY F 527 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N GLY F 531 " --> pdb=" O SER F 528 " (cutoff:3.500A) Processing helix chain 'F' and resid 538 through 543 removed outlier: 3.635A pdb=" N ARG F 542 " --> pdb=" O THR F 538 " (cutoff:3.500A) Processing helix chain 'F' and resid 570 through 597 removed outlier: 3.644A pdb=" N LYS F 574 " --> pdb=" O VAL F 570 " (cutoff:3.500A) Processing helix chain 'F' and resid 611 through 615 Processing helix chain 'F' and resid 618 through 625 Processing helix chain 'F' and resid 627 through 635 removed outlier: 3.556A pdb=" N LYS F 633 " --> pdb=" O LEU F 629 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N GLU F 634 " --> pdb=" O GLN F 630 " (cutoff:3.500A) Processing helix chain 'F' and resid 638 through 664 Processing helix chain 'G' and resid 62 through 65 removed outlier: 3.770A pdb=" N GLN G 65 " --> pdb=" O ARG G 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 62 through 65' Processing helix chain 'G' and resid 87 through 91 removed outlier: 4.028A pdb=" N THR G 91 " --> pdb=" O SER G 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 81 through 85 removed outlier: 4.016A pdb=" N GLU H 85 " --> pdb=" O ALA H 82 " (cutoff:3.500A) Processing helix chain 'I' and resid 62 through 68 removed outlier: 3.656A 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: 3.668A pdb=" N GLN I 103 " --> pdb=" O ASP I 99 " (cutoff:3.500A) removed outlier: 3.608A 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: 3.856A 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 474 through 484 removed outlier: 3.549A pdb=" N ASN I 478 " --> pdb=" O ASP I 474 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N GLU I 482 " --> pdb=" O ASN I 478 " (cutoff:3.500A) Processing helix chain 'J' and resid 513 through 520 Processing helix chain 'J' and resid 523 through 536 removed outlier: 3.786A pdb=" N GLY J 527 " --> pdb=" O GLY J 524 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N THR J 529 " --> pdb=" O ALA J 526 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N MET J 530 " --> pdb=" O GLY J 527 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N GLY J 531 " --> pdb=" O SER J 528 " (cutoff:3.500A) Processing helix chain 'J' and resid 538 through 543 removed outlier: 3.634A pdb=" N ARG J 542 " --> pdb=" O THR J 538 " (cutoff:3.500A) Processing helix chain 'J' and resid 570 through 597 removed outlier: 3.644A pdb=" N LYS J 574 " --> pdb=" O VAL J 570 " (cutoff:3.500A) Processing helix chain 'J' and resid 611 through 615 Processing helix chain 'J' and resid 618 through 625 Processing helix chain 'J' and resid 627 through 635 removed outlier: 3.555A pdb=" N LYS J 633 " --> pdb=" O LEU J 629 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N GLU J 634 " --> pdb=" O GLN J 630 " (cutoff:3.500A) Processing helix chain 'J' and resid 638 through 664 Processing helix chain 'K' and resid 62 through 65 removed outlier: 3.770A pdb=" N GLN K 65 " --> pdb=" O ARG K 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 62 through 65' Processing helix chain 'K' and resid 87 through 91 removed outlier: 4.029A pdb=" N THR K 91 " --> pdb=" O SER K 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 81 through 85 removed outlier: 4.016A pdb=" N GLU L 85 " --> pdb=" O ALA L 82 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 495 through 498 removed outlier: 5.145A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 9.041A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N THR B 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 174 removed outlier: 3.658A pdb=" N PHE A 174 " --> pdb=" O LYS A 153 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 260 through 261 removed outlier: 3.561A pdb=" N ILE A 443 " --> pdb=" O ARG A 298 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 11.543A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 11.742A pdb=" N LEU A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 11.799A pdb=" N LEU A 288 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 11.144A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 10.487A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 11.591A pdb=" N ASP A 457 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 12.319A pdb=" N ILE A 284 " --> pdb=" O ASP A 457 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N GLU A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N SER A 334 " --> pdb=" O GLU A 293 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL A 295 " --> pdb=" O ASN A 332 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 271 through 273 removed outlier: 12.319A pdb=" N ILE A 284 " --> pdb=" O ASP A 457 " (cutoff:3.500A) removed outlier: 11.591A pdb=" N ASP A 457 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 10.487A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 11.144A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 11.799A pdb=" N LEU A 288 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 11.742A pdb=" N LEU A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 11.543A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE A 443 " --> pdb=" O ARG A 298 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N THR A 357 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N PHE A 468 " --> pdb=" O THR A 357 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N LYS A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLY A 393 " --> pdb=" O TYR A 361 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 304 through 308 Processing sheet with id=AA8, first strand: chain 'A' and resid 423 through 426 removed outlier: 4.788A pdb=" N MET A 426 " --> pdb=" O ARG A 432 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ARG A 432 " --> pdb=" O MET A 426 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 3 through 6 removed outlier: 3.515A pdb=" N VAL C 18 " --> pdb=" O LEU C 83 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 10 through 12 removed outlier: 4.292A pdb=" N GLN C 10 " --> pdb=" O LEU C 122 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA C 92 " --> pdb=" O LEU C 123 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N HIS C 35 " --> pdb=" O THR C 97 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ILE C 34 " --> pdb=" O TRP C 50 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N TRP C 50 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N TRP C 36 " --> pdb=" O MET C 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 10 through 12 removed outlier: 4.292A pdb=" N GLN C 10 " --> pdb=" O LEU C 122 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA C 92 " --> pdb=" O LEU C 123 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N THR C 98 " --> pdb=" O HIS C 116 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N HIS C 116 " --> pdb=" O THR C 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 9 through 12 removed outlier: 6.422A pdb=" N VAL D 10 " --> pdb=" O THR D 108 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 9 through 12 removed outlier: 6.422A pdb=" N VAL D 10 " --> pdb=" O THR D 108 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 17 through 23 Processing sheet with id=AB6, first strand: chain 'E' and resid 495 through 498 removed outlier: 5.144A pdb=" N VAL F 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 9.042A pdb=" N VAL E 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N THR F 606 " --> pdb=" O VAL E 38 " (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 174 removed outlier: 3.658A pdb=" N PHE E 174 " --> pdb=" O LYS E 153 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 260 through 261 removed outlier: 3.561A pdb=" N ILE E 443 " --> pdb=" O ARG E 298 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N GLY E 451 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 11.543A pdb=" N THR E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 11.742A pdb=" N LEU E 453 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 11.799A pdb=" N LEU E 288 " --> pdb=" O LEU E 453 " (cutoff:3.500A) removed outlier: 11.144A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 10.487A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 11.591A pdb=" N ASP E 457 " --> pdb=" O ILE E 284 " (cutoff:3.500A) removed outlier: 12.319A pdb=" N ILE E 284 " --> pdb=" O ASP E 457 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N GLU E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N SER E 334 " --> pdb=" O GLU E 293 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL E 295 " --> pdb=" O ASN E 332 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 271 through 273 removed outlier: 12.319A pdb=" N ILE E 284 " --> pdb=" O ASP E 457 " (cutoff:3.500A) removed outlier: 11.591A pdb=" N ASP E 457 " --> pdb=" O ILE E 284 " (cutoff:3.500A) removed outlier: 10.487A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 11.144A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 11.799A pdb=" N LEU E 288 " --> pdb=" O LEU E 453 " (cutoff:3.500A) removed outlier: 11.742A pdb=" N LEU E 453 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 11.543A pdb=" N THR E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N GLY E 451 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE E 443 " --> pdb=" O ARG E 298 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N THR E 357 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N PHE E 468 " --> pdb=" O THR E 357 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N LYS E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLY E 393 " --> pdb=" O TYR E 361 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 304 through 308 Processing sheet with id=AC4, first strand: chain 'E' and resid 423 through 426 removed outlier: 4.787A pdb=" N MET E 426 " --> pdb=" O ARG E 432 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ARG E 432 " --> pdb=" O MET E 426 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 3 through 6 removed outlier: 3.515A pdb=" N VAL G 18 " --> pdb=" O LEU G 83 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 10 through 12 removed outlier: 4.292A pdb=" N GLN G 10 " --> pdb=" O LEU G 122 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA G 92 " --> pdb=" O LEU G 123 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N HIS G 35 " --> pdb=" O THR G 97 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ILE G 34 " --> pdb=" O TRP G 50 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N TRP G 50 " --> pdb=" O ILE G 34 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N TRP G 36 " --> pdb=" O MET G 48 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 10 through 12 removed outlier: 4.292A pdb=" N GLN G 10 " --> pdb=" O LEU G 122 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA G 92 " --> pdb=" O LEU G 123 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N THR G 98 " --> pdb=" O HIS G 116 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N HIS G 116 " --> pdb=" O THR G 98 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 9 through 12 removed outlier: 6.422A pdb=" N VAL H 10 " --> pdb=" O THR H 108 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 9 through 12 removed outlier: 6.422A pdb=" N VAL H 10 " --> pdb=" O THR H 108 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 17 through 23 Processing sheet with id=AD2, first strand: chain 'I' and resid 495 through 498 removed outlier: 5.144A pdb=" N VAL J 608 " --> pdb=" O VAL I 36 " (cutoff:3.500A) removed outlier: 9.042A pdb=" N VAL I 38 " --> pdb=" O THR J 606 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N THR J 606 " --> pdb=" O VAL I 38 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 45 through 47 Processing sheet with id=AD4, first strand: chain 'I' and resid 91 through 94 Processing sheet with id=AD5, first strand: chain 'I' and resid 167 through 174 removed outlier: 3.658A pdb=" N PHE I 174 " --> pdb=" O LYS I 153 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 260 through 261 removed outlier: 3.561A pdb=" N ILE I 443 " --> pdb=" O ARG I 298 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N GLY I 451 " --> pdb=" O THR I 290 " (cutoff:3.500A) removed outlier: 11.543A pdb=" N THR I 290 " --> pdb=" O GLY I 451 " (cutoff:3.500A) removed outlier: 11.742A pdb=" N LEU I 453 " --> pdb=" O LEU I 288 " (cutoff:3.500A) removed outlier: 11.799A pdb=" N LEU I 288 " --> pdb=" O LEU I 453 " (cutoff:3.500A) removed outlier: 11.144A pdb=" N THR I 455 " --> pdb=" O VAL I 286 " (cutoff:3.500A) removed outlier: 10.487A pdb=" N VAL I 286 " --> pdb=" O THR I 455 " (cutoff:3.500A) removed outlier: 11.591A pdb=" N ASP I 457 " --> pdb=" O ILE I 284 " (cutoff:3.500A) removed outlier: 12.319A pdb=" N ILE I 284 " --> pdb=" O ASP I 457 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N GLU I 293 " --> pdb=" O SER I 334 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N SER I 334 " --> pdb=" O GLU I 293 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL I 295 " --> pdb=" O ASN I 332 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ALA I 329 " --> pdb=" O CYS I 418 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 271 through 273 removed outlier: 12.319A pdb=" N ILE I 284 " --> pdb=" O ASP I 457 " (cutoff:3.500A) removed outlier: 11.591A pdb=" N ASP I 457 " --> pdb=" O ILE I 284 " (cutoff:3.500A) removed outlier: 10.487A pdb=" N VAL I 286 " --> pdb=" O THR I 455 " (cutoff:3.500A) removed outlier: 11.144A pdb=" N THR I 455 " --> pdb=" O VAL I 286 " (cutoff:3.500A) removed outlier: 11.799A pdb=" N LEU I 288 " --> pdb=" O LEU I 453 " (cutoff:3.500A) removed outlier: 11.742A pdb=" N LEU I 453 " --> pdb=" O LEU I 288 " (cutoff:3.500A) removed outlier: 11.543A pdb=" N THR I 290 " --> pdb=" O GLY I 451 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N GLY I 451 " --> pdb=" O THR I 290 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE I 443 " --> pdb=" O ARG I 298 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N THR I 357 " --> pdb=" O GLU I 466 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N PHE I 468 " --> pdb=" O THR I 357 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N LYS I 360 " --> pdb=" O PHE I 468 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLY I 393 " --> pdb=" O TYR I 361 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 304 through 308 Processing sheet with id=AD9, first strand: chain 'I' and resid 423 through 426 removed outlier: 4.788A pdb=" N MET I 426 " --> pdb=" O ARG I 432 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ARG I 432 " --> pdb=" O MET I 426 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'K' and resid 3 through 6 removed outlier: 3.514A pdb=" N VAL K 18 " --> pdb=" O LEU K 83 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'K' and resid 10 through 12 removed outlier: 4.292A pdb=" N GLN K 10 " --> pdb=" O LEU K 122 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA K 92 " --> pdb=" O LEU K 123 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N HIS K 35 " --> pdb=" O THR K 97 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ILE K 34 " --> pdb=" O TRP K 50 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N TRP K 50 " --> pdb=" O ILE K 34 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N TRP K 36 " --> pdb=" O MET K 48 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'K' and resid 10 through 12 removed outlier: 4.292A pdb=" N GLN K 10 " --> pdb=" O LEU K 122 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA K 92 " --> pdb=" O LEU K 123 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N THR K 98 " --> pdb=" O HIS K 116 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N HIS K 116 " --> pdb=" O THR K 98 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.422A pdb=" N VAL L 10 " --> pdb=" O THR L 108 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.422A pdb=" N VAL L 10 " --> pdb=" O THR L 108 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'L' and resid 17 through 23 747 hydrogen bonds defined for protein. 1917 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: 7.16 Time building geometry restraints manager: 9.75 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: 4199 1.32 - 1.47: 7507 1.47 - 1.61: 8652 1.61 - 1.76: 9 1.76 - 1.90: 186 Bond restraints: 20553 Sorted by residual: bond pdb=" C ARG A 469 " pdb=" N PRO A 470 " ideal model delta sigma weight residual 1.332 1.522 -0.190 1.30e-02 5.92e+03 2.15e+02 bond pdb=" C ARG E 469 " pdb=" N PRO E 470 " ideal model delta sigma weight residual 1.332 1.522 -0.190 1.30e-02 5.92e+03 2.14e+02 bond pdb=" C ARG I 469 " pdb=" N PRO I 470 " ideal model delta sigma weight residual 1.332 1.522 -0.190 1.30e-02 5.92e+03 2.13e+02 bond pdb=" CB HIS I 374 " pdb=" CG HIS I 374 " ideal model delta sigma weight residual 1.497 1.384 0.113 1.40e-02 5.10e+03 6.46e+01 bond pdb=" CB HIS A 374 " pdb=" CG HIS A 374 " ideal model delta sigma weight residual 1.497 1.385 0.112 1.40e-02 5.10e+03 6.40e+01 ... (remaining 20548 not shown) Histogram of bond angle deviations from ideal: 89.00 - 102.19: 192 102.19 - 115.38: 13358 115.38 - 128.57: 14146 128.57 - 141.76: 243 141.76 - 154.95: 6 Bond angle restraints: 27945 Sorted by residual: angle pdb=" C SER B 546 " pdb=" N GLY B 547 " pdb=" CA GLY B 547 " ideal model delta sigma weight residual 121.70 154.95 -33.25 1.80e+00 3.09e-01 3.41e+02 angle pdb=" C SER J 546 " pdb=" N GLY J 547 " pdb=" CA GLY J 547 " ideal model delta sigma weight residual 121.70 154.94 -33.24 1.80e+00 3.09e-01 3.41e+02 angle pdb=" C SER F 546 " pdb=" N GLY F 547 " pdb=" CA GLY F 547 " ideal model delta sigma weight residual 121.70 154.91 -33.21 1.80e+00 3.09e-01 3.40e+02 angle pdb=" O ALA A 440 " pdb=" C ALA A 440 " pdb=" N GLY A 441 " ideal model delta sigma weight residual 122.82 102.31 20.51 1.30e+00 5.92e-01 2.49e+02 angle pdb=" O ALA E 440 " pdb=" C ALA E 440 " pdb=" N GLY E 441 " ideal model delta sigma weight residual 122.82 102.31 20.51 1.30e+00 5.92e-01 2.49e+02 ... (remaining 27940 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.76: 12523 22.76 - 45.53: 359 45.53 - 68.29: 87 68.29 - 91.06: 63 91.06 - 113.82: 36 Dihedral angle restraints: 13068 sinusoidal: 5934 harmonic: 7134 Sorted by residual: dihedral pdb=" C ASN E 234 " pdb=" N ASN E 234 " pdb=" CA ASN E 234 " pdb=" CB ASN E 234 " ideal model delta harmonic sigma weight residual -122.60 -101.26 -21.34 0 2.50e+00 1.60e-01 7.28e+01 dihedral pdb=" C ASN I 234 " pdb=" N ASN I 234 " pdb=" CA ASN I 234 " pdb=" CB ASN I 234 " ideal model delta harmonic sigma weight residual -122.60 -101.27 -21.33 0 2.50e+00 1.60e-01 7.28e+01 dihedral pdb=" C ASN A 234 " pdb=" N ASN A 234 " pdb=" CA ASN A 234 " pdb=" CB ASN A 234 " ideal model delta harmonic sigma weight residual -122.60 -101.27 -21.33 0 2.50e+00 1.60e-01 7.28e+01 ... (remaining 13065 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.273: 3211 0.273 - 0.546: 86 0.546 - 0.819: 18 0.819 - 1.092: 0 1.092 - 1.365: 3 Chirality restraints: 3318 Sorted by residual: chirality pdb=" C1 NAG P 2 " pdb=" O4 NAG P 1 " pdb=" C2 NAG P 2 " pdb=" O5 NAG P 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.79 -0.61 2.00e-02 2.50e+03 9.39e+02 chirality pdb=" C1 NAG U 2 " pdb=" O4 NAG U 1 " pdb=" C2 NAG U 2 " pdb=" O5 NAG U 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.79 -0.61 2.00e-02 2.50e+03 9.35e+02 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 -1.79 -0.61 2.00e-02 2.50e+03 9.33e+02 ... (remaining 3315 not shown) Planarity restraints: 3519 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG O 2 " 0.350 2.00e-02 2.50e+03 3.01e-01 1.13e+03 pdb=" C7 NAG O 2 " -0.099 2.00e-02 2.50e+03 pdb=" C8 NAG O 2 " 0.071 2.00e-02 2.50e+03 pdb=" N2 NAG O 2 " -0.524 2.00e-02 2.50e+03 pdb=" O7 NAG O 2 " 0.202 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG T 2 " 0.350 2.00e-02 2.50e+03 3.01e-01 1.13e+03 pdb=" C7 NAG T 2 " -0.099 2.00e-02 2.50e+03 pdb=" C8 NAG T 2 " 0.071 2.00e-02 2.50e+03 pdb=" N2 NAG T 2 " -0.524 2.00e-02 2.50e+03 pdb=" O7 NAG T 2 " 0.202 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG Y 2 " -0.350 2.00e-02 2.50e+03 3.01e-01 1.13e+03 pdb=" C7 NAG Y 2 " 0.099 2.00e-02 2.50e+03 pdb=" C8 NAG Y 2 " -0.071 2.00e-02 2.50e+03 pdb=" N2 NAG Y 2 " 0.524 2.00e-02 2.50e+03 pdb=" O7 NAG Y 2 " -0.202 2.00e-02 2.50e+03 ... (remaining 3516 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 270 2.57 - 3.15: 16689 3.15 - 3.73: 30034 3.73 - 4.32: 42322 4.32 - 4.90: 66764 Nonbonded interactions: 156079 Sorted by model distance: nonbonded pdb=" O3 NAG V 2 " pdb=" O7 NAG V 2 " model vdw 1.987 2.440 nonbonded pdb=" O3 NAG Q 2 " pdb=" O7 NAG Q 2 " model vdw 1.987 2.440 nonbonded pdb=" O3 NAG a 2 " pdb=" O7 NAG a 2 " model vdw 1.987 2.440 nonbonded pdb=" OD1 ASN I 442 " pdb=" C1 NAG X 1 " model vdw 2.030 2.776 nonbonded pdb=" OD1 ASN A 442 " pdb=" C1 NAG N 1 " model vdw 2.031 2.776 ... (remaining 156074 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain '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 'D' selection = chain 'H' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'Q' selection = chain 'R' selection = chain 'V' selection = chain 'W' selection = chain 'a' } ncs_group { reference = chain 'N' selection = chain 'P' selection = chain 'S' selection = chain 'U' selection = chain 'X' selection = chain 'Z' } ncs_group { reference = chain 'O' selection = chain 'T' selection = chain 'Y' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.900 Check model and map are aligned: 0.310 Set scattering table: 0.200 Process input model: 55.090 Find NCS groups from input model: 1.270 Set up NCS constraints: 0.250 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6696 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 0.190 20553 Z= 1.199 Angle : 2.202 33.253 27945 Z= 1.336 Chirality : 0.128 1.365 3318 Planarity : 0.026 0.301 3486 Dihedral : 14.448 113.824 8391 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.98 % Allowed : 5.99 % Favored : 93.03 % Rotamer: Outliers : 0.28 % Allowed : 1.54 % Favored : 98.18 % Cbeta Deviations : 0.66 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.89 % 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: -0.99 (0.16), residues: 2454 helix: -0.55 (0.23), residues: 414 sheet: -0.51 (0.20), residues: 600 loop : -0.70 (0.16), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.008 TRP E 69 HIS 0.007 0.002 HIS L 32 PHE 0.047 0.006 PHE K 32 TYR 0.076 0.008 TYR I 400 ARG 0.006 0.001 ARG G 67 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4908 Ramachandran restraints generated. 2454 Oldfield, 0 Emsley, 2454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4908 Ramachandran restraints generated. 2454 Oldfield, 0 Emsley, 2454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 653 residues out of total 2145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 647 time to evaluate : 2.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 534 SER cc_start: 0.7984 (p) cc_final: 0.7167 (t) REVERT: B 580 VAL cc_start: 0.9494 (t) cc_final: 0.9170 (p) REVERT: B 624 ASP cc_start: 0.9236 (m-30) cc_final: 0.8975 (m-30) REVERT: B 651 ASN cc_start: 0.9220 (m-40) cc_final: 0.8904 (t0) REVERT: D 77 ILE cc_start: 0.8196 (mt) cc_final: 0.7831 (mt) REVERT: D 108 THR cc_start: 0.5435 (m) cc_final: 0.4741 (t) REVERT: E 217 TYR cc_start: 0.6717 (m-80) cc_final: 0.6459 (m-80) REVERT: E 491 ILE cc_start: 0.9038 (mp) cc_final: 0.8812 (mm) REVERT: F 534 SER cc_start: 0.8021 (p) cc_final: 0.7172 (t) REVERT: F 580 VAL cc_start: 0.9425 (t) cc_final: 0.9092 (p) REVERT: F 624 ASP cc_start: 0.9200 (m-30) cc_final: 0.8987 (m-30) REVERT: F 651 ASN cc_start: 0.9191 (m-40) cc_final: 0.8352 (m110) REVERT: H 77 ILE cc_start: 0.7993 (mt) cc_final: 0.7642 (mt) REVERT: H 108 THR cc_start: 0.5242 (m) cc_final: 0.4906 (t) REVERT: I 217 TYR cc_start: 0.6718 (m-80) cc_final: 0.6377 (m-80) REVERT: I 300 ASN cc_start: 0.8668 (OUTLIER) cc_final: 0.8310 (p0) REVERT: I 491 ILE cc_start: 0.9042 (mp) cc_final: 0.8831 (mm) REVERT: J 523 LEU cc_start: 0.6870 (mt) cc_final: 0.6629 (mt) REVERT: J 534 SER cc_start: 0.8153 (p) cc_final: 0.7820 (t) REVERT: J 624 ASP cc_start: 0.9219 (m-30) cc_final: 0.8957 (m-30) REVERT: J 651 ASN cc_start: 0.9259 (m-40) cc_final: 0.8702 (t0) REVERT: K 35 HIS cc_start: 0.4324 (m-70) cc_final: 0.4103 (m-70) REVERT: L 77 ILE cc_start: 0.8089 (mt) cc_final: 0.7686 (mt) REVERT: L 108 THR cc_start: 0.5053 (m) cc_final: 0.4798 (t) outliers start: 6 outliers final: 5 residues processed: 653 average time/residue: 0.3030 time to fit residues: 301.6655 Evaluate side-chains 326 residues out of total 2145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 320 time to evaluate : 2.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 205 optimal weight: 0.9990 chunk 184 optimal weight: 5.9990 chunk 102 optimal weight: 8.9990 chunk 62 optimal weight: 0.6980 chunk 124 optimal weight: 3.9990 chunk 98 optimal weight: 0.9980 chunk 190 optimal weight: 3.9990 chunk 73 optimal weight: 9.9990 chunk 115 optimal weight: 0.7980 chunk 141 optimal weight: 0.0010 chunk 220 optimal weight: 1.9990 overall best weight: 0.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 229 ASN A 249 HIS A 328 GLN A 422 GLN B 540 GLN ** B 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 16 GLN E 103 GLN ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 229 ASN E 328 GLN E 422 GLN ** F 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 16 GLN ** I 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 229 ASN I 328 GLN I 422 GLN J 540 GLN ** J 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 65 GLN L 16 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6768 moved from start: 0.3553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 20553 Z= 0.238 Angle : 0.929 12.786 27945 Z= 0.478 Chirality : 0.052 0.242 3318 Planarity : 0.005 0.073 3486 Dihedral : 12.635 73.698 3963 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.49 % Allowed : 4.69 % Favored : 94.82 % Rotamer: Outliers : 0.65 % Allowed : 2.47 % Favored : 96.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.89 % 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: -0.69 (0.17), residues: 2454 helix: 0.76 (0.26), residues: 393 sheet: -0.21 (0.19), residues: 654 loop : -0.92 (0.16), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP J 631 HIS 0.009 0.001 HIS G 35 PHE 0.028 0.002 PHE I 233 TYR 0.021 0.002 TYR G 33 ARG 0.008 0.001 ARG J 585 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4908 Ramachandran restraints generated. 2454 Oldfield, 0 Emsley, 2454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4908 Ramachandran restraints generated. 2454 Oldfield, 0 Emsley, 2454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 2145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 414 time to evaluate : 2.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU I 32 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 376 PHE cc_start: 0.7235 (m-80) cc_final: 0.6886 (m-80) REVERT: B 530 MET cc_start: 0.8211 (mtt) cc_final: 0.7734 (mtt) REVERT: E 217 TYR cc_start: 0.5809 (m-80) cc_final: 0.5578 (m-80) REVERT: E 376 PHE cc_start: 0.7213 (m-80) cc_final: 0.6958 (m-10) REVERT: E 491 ILE cc_start: 0.9083 (mp) cc_final: 0.8793 (mm) REVERT: F 653 GLN cc_start: 0.9315 (tm-30) cc_final: 0.9104 (tm-30) REVERT: G 11 MET cc_start: 0.6224 (tpt) cc_final: 0.5957 (pmm) REVERT: G 83 LEU cc_start: 0.7593 (mm) cc_final: 0.7383 (mm) REVERT: I 376 PHE cc_start: 0.7575 (m-80) cc_final: 0.7188 (m-80) REVERT: I 491 ILE cc_start: 0.9084 (mp) cc_final: 0.8763 (mm) REVERT: J 530 MET cc_start: 0.8195 (mtt) cc_final: 0.7754 (mtt) REVERT: J 624 ASP cc_start: 0.9201 (m-30) cc_final: 0.8992 (m-30) REVERT: J 653 GLN cc_start: 0.9421 (tm-30) cc_final: 0.8443 (tm-30) outliers start: 14 outliers final: 2 residues processed: 423 average time/residue: 0.2862 time to fit residues: 192.6323 Evaluate side-chains 279 residues out of total 2145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 277 time to evaluate : 2.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 122 optimal weight: 0.3980 chunk 68 optimal weight: 9.9990 chunk 183 optimal weight: 8.9990 chunk 150 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 221 optimal weight: 10.0000 chunk 238 optimal weight: 9.9990 chunk 196 optimal weight: 0.9990 chunk 219 optimal weight: 0.8980 chunk 75 optimal weight: 9.9990 chunk 177 optimal weight: 1.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 46 GLN ** I 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 343 GLN ** J 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 651 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6835 moved from start: 0.4444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20553 Z= 0.201 Angle : 0.786 13.063 27945 Z= 0.404 Chirality : 0.048 0.259 3318 Planarity : 0.004 0.048 3486 Dihedral : 9.373 58.866 3963 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.49 % Allowed : 5.38 % Favored : 94.13 % Rotamer: Outliers : 0.19 % Allowed : 2.66 % Favored : 97.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.89 % Twisted Proline : 0.00 % 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: -0.43 (0.16), residues: 2454 helix: 1.11 (0.26), residues: 375 sheet: 0.11 (0.20), residues: 600 loop : -0.82 (0.16), residues: 1479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP I 427 HIS 0.007 0.001 HIS K 35 PHE 0.018 0.002 PHE C 29 TYR 0.021 0.002 TYR H 51 ARG 0.004 0.001 ARG G 84 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4908 Ramachandran restraints generated. 2454 Oldfield, 0 Emsley, 2454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4908 Ramachandran restraints generated. 2454 Oldfield, 0 Emsley, 2454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 356 time to evaluate : 2.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 442 ASN cc_start: 0.9129 (OUTLIER) cc_final: 0.8633 (p0) REVERT: B 530 MET cc_start: 0.7808 (mtt) cc_final: 0.7353 (mtt) REVERT: E 107 ASP cc_start: 0.7339 (p0) cc_final: 0.6899 (p0) REVERT: E 217 TYR cc_start: 0.5669 (m-80) cc_final: 0.5420 (m-80) REVERT: E 491 ILE cc_start: 0.9170 (mp) cc_final: 0.8843 (mm) REVERT: F 530 MET cc_start: 0.7867 (mtt) cc_final: 0.7405 (mtt) REVERT: F 574 LYS cc_start: 0.9227 (mmmm) cc_final: 0.8873 (mmmm) REVERT: I 104 MET cc_start: 0.6984 (mmp) cc_final: 0.6780 (mmp) REVERT: I 107 ASP cc_start: 0.7230 (p0) cc_final: 0.6890 (p0) REVERT: J 530 MET cc_start: 0.7916 (mtt) cc_final: 0.7457 (mtt) REVERT: K 11 MET cc_start: 0.6692 (tpt) cc_final: 0.6408 (tpt) outliers start: 4 outliers final: 2 residues processed: 360 average time/residue: 0.2811 time to fit residues: 159.6800 Evaluate side-chains 253 residues out of total 2145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 250 time to evaluate : 2.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 218 optimal weight: 8.9990 chunk 166 optimal weight: 2.9990 chunk 114 optimal weight: 0.5980 chunk 24 optimal weight: 10.0000 chunk 105 optimal weight: 9.9990 chunk 148 optimal weight: 7.9990 chunk 221 optimal weight: 20.0000 chunk 234 optimal weight: 0.9980 chunk 115 optimal weight: 3.9990 chunk 210 optimal weight: 5.9990 chunk 63 optimal weight: 8.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 72 HIS ** I 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 343 GLN ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6979 moved from start: 0.4874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 20553 Z= 0.280 Angle : 0.794 14.740 27945 Z= 0.407 Chirality : 0.046 0.221 3318 Planarity : 0.004 0.056 3486 Dihedral : 8.511 57.158 3963 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.49 % Allowed : 5.95 % Favored : 93.56 % Rotamer: Outliers : 0.09 % Allowed : 2.99 % Favored : 96.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.89 % Twisted Proline : 0.00 % 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: -0.38 (0.17), residues: 2454 helix: 1.20 (0.26), residues: 375 sheet: 0.05 (0.20), residues: 606 loop : -0.77 (0.16), residues: 1473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP E 427 HIS 0.007 0.001 HIS E 374 PHE 0.018 0.002 PHE E 376 TYR 0.015 0.002 TYR G 111 ARG 0.006 0.001 ARG L 63 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4908 Ramachandran restraints generated. 2454 Oldfield, 0 Emsley, 2454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4908 Ramachandran restraints generated. 2454 Oldfield, 0 Emsley, 2454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 309 time to evaluate : 2.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 434 MET cc_start: 0.7243 (ptt) cc_final: 0.7028 (ptt) REVERT: A 491 ILE cc_start: 0.9175 (mp) cc_final: 0.8769 (mm) REVERT: B 522 PHE cc_start: 0.8511 (m-80) cc_final: 0.8220 (m-80) REVERT: B 530 MET cc_start: 0.8096 (mtt) cc_final: 0.7657 (mtt) REVERT: D 34 LEU cc_start: 0.7927 (mm) cc_final: 0.7500 (mm) REVERT: E 106 GLU cc_start: 0.6891 (pp20) cc_final: 0.6685 (tm-30) REVERT: E 374 HIS cc_start: 0.6472 (t-90) cc_final: 0.6245 (t70) REVERT: E 491 ILE cc_start: 0.9226 (mp) cc_final: 0.8866 (mm) REVERT: F 530 MET cc_start: 0.8077 (mtt) cc_final: 0.7747 (mtt) REVERT: F 535 MET cc_start: 0.8093 (mmm) cc_final: 0.7856 (mmp) REVERT: F 574 LYS cc_start: 0.9307 (mmmm) cc_final: 0.8991 (mmmm) REVERT: F 624 ASP cc_start: 0.9166 (m-30) cc_final: 0.8454 (p0) REVERT: I 434 MET cc_start: 0.7730 (ptm) cc_final: 0.7340 (ptp) REVERT: J 530 MET cc_start: 0.8019 (mtt) cc_final: 0.7498 (mtt) REVERT: K 11 MET cc_start: 0.6550 (tpt) cc_final: 0.6296 (tpt) outliers start: 2 outliers final: 0 residues processed: 311 average time/residue: 0.2999 time to fit residues: 150.9729 Evaluate side-chains 227 residues out of total 2145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 227 time to evaluate : 2.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 195 optimal weight: 2.9990 chunk 133 optimal weight: 0.8980 chunk 3 optimal weight: 7.9990 chunk 174 optimal weight: 9.9990 chunk 96 optimal weight: 5.9990 chunk 200 optimal weight: 0.0030 chunk 162 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 119 optimal weight: 0.7980 chunk 210 optimal weight: 7.9990 chunk 59 optimal weight: 20.0000 overall best weight: 2.1394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 72 HIS ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 575 GLN ** F 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6982 moved from start: 0.5264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 20553 Z= 0.226 Angle : 0.759 12.990 27945 Z= 0.391 Chirality : 0.046 0.235 3318 Planarity : 0.004 0.062 3486 Dihedral : 8.111 58.913 3963 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.49 % Allowed : 5.70 % Favored : 93.81 % Rotamer: Outliers : 0.09 % Allowed : 2.19 % Favored : 97.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.89 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.17), residues: 2454 helix: 1.16 (0.26), residues: 375 sheet: 0.13 (0.20), residues: 585 loop : -0.72 (0.16), residues: 1494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP E 427 HIS 0.007 0.001 HIS E 374 PHE 0.017 0.002 PHE G 29 TYR 0.026 0.002 TYR C 80 ARG 0.004 0.000 ARG L 63 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4908 Ramachandran restraints generated. 2454 Oldfield, 0 Emsley, 2454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4908 Ramachandran restraints generated. 2454 Oldfield, 0 Emsley, 2454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 318 time to evaluate : 2.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 491 ILE cc_start: 0.9167 (mp) cc_final: 0.8792 (mm) REVERT: B 624 ASP cc_start: 0.9237 (m-30) cc_final: 0.8484 (p0) REVERT: E 106 GLU cc_start: 0.6932 (pp20) cc_final: 0.6694 (tm-30) REVERT: E 107 ASP cc_start: 0.7310 (p0) cc_final: 0.7073 (p0) REVERT: E 483 LEU cc_start: 0.8075 (mm) cc_final: 0.7851 (mm) REVERT: E 491 ILE cc_start: 0.9293 (mp) cc_final: 0.8916 (mm) REVERT: F 530 MET cc_start: 0.7994 (mtm) cc_final: 0.7650 (mtt) REVERT: F 574 LYS cc_start: 0.9285 (mmmm) cc_final: 0.8971 (mmmm) REVERT: I 107 ASP cc_start: 0.7455 (p0) cc_final: 0.6743 (p0) REVERT: I 434 MET cc_start: 0.7621 (ptm) cc_final: 0.7370 (ptt) REVERT: I 491 ILE cc_start: 0.9187 (mp) cc_final: 0.8740 (mm) REVERT: J 530 MET cc_start: 0.8065 (mtt) cc_final: 0.7778 (mtt) REVERT: K 37 LEU cc_start: 0.7806 (tt) cc_final: 0.7588 (tt) outliers start: 2 outliers final: 0 residues processed: 320 average time/residue: 0.2843 time to fit residues: 143.9983 Evaluate side-chains 228 residues out of total 2145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 228 time to evaluate : 2.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 79 optimal weight: 3.9990 chunk 211 optimal weight: 7.9990 chunk 46 optimal weight: 0.2980 chunk 137 optimal weight: 0.4980 chunk 57 optimal weight: 7.9990 chunk 235 optimal weight: 9.9990 chunk 195 optimal weight: 0.9980 chunk 108 optimal weight: 7.9990 chunk 19 optimal weight: 5.9990 chunk 77 optimal weight: 20.0000 chunk 123 optimal weight: 5.9990 overall best weight: 2.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 229 ASN B 575 GLN ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 651 ASN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 229 ASN ** I 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7007 moved from start: 0.5563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 20553 Z= 0.247 Angle : 0.759 13.571 27945 Z= 0.392 Chirality : 0.046 0.222 3318 Planarity : 0.004 0.060 3486 Dihedral : 7.954 57.232 3963 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.49 % Allowed : 5.91 % Favored : 93.60 % Rotamer: Outliers : 0.09 % Allowed : 2.05 % Favored : 97.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.89 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.17), residues: 2454 helix: 1.16 (0.27), residues: 375 sheet: 0.01 (0.20), residues: 603 loop : -0.69 (0.17), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP I 479 HIS 0.004 0.001 HIS K 116 PHE 0.019 0.002 PHE A 376 TYR 0.033 0.002 TYR I 217 ARG 0.005 0.000 ARG H 63 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4908 Ramachandran restraints generated. 2454 Oldfield, 0 Emsley, 2454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4908 Ramachandran restraints generated. 2454 Oldfield, 0 Emsley, 2454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 302 time to evaluate : 2.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 491 ILE cc_start: 0.9213 (mp) cc_final: 0.8810 (mm) REVERT: B 589 ASP cc_start: 0.8742 (p0) cc_final: 0.8529 (p0) REVERT: E 483 LEU cc_start: 0.8171 (mm) cc_final: 0.7901 (mm) REVERT: E 491 ILE cc_start: 0.9288 (mp) cc_final: 0.8913 (mm) REVERT: F 530 MET cc_start: 0.8068 (mtm) cc_final: 0.7699 (mtt) REVERT: F 535 MET cc_start: 0.8218 (mmp) cc_final: 0.7930 (mmp) REVERT: F 574 LYS cc_start: 0.9260 (mmmm) cc_final: 0.8954 (mmmm) REVERT: G 73 ASP cc_start: 0.6717 (p0) cc_final: 0.6347 (m-30) REVERT: H 26 LYS cc_start: 0.7468 (pptt) cc_final: 0.7133 (pptt) REVERT: I 104 MET cc_start: 0.6929 (mmp) cc_final: 0.6600 (mmp) REVERT: I 107 ASP cc_start: 0.7131 (p0) cc_final: 0.6897 (p0) REVERT: J 584 GLU cc_start: 0.8292 (pp20) cc_final: 0.8088 (tm-30) REVERT: K 123 LEU cc_start: 0.7381 (pt) cc_final: 0.7115 (pp) outliers start: 2 outliers final: 0 residues processed: 303 average time/residue: 0.2779 time to fit residues: 134.7027 Evaluate side-chains 222 residues out of total 2145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 222 time to evaluate : 2.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 226 optimal weight: 4.9990 chunk 26 optimal weight: 7.9990 chunk 133 optimal weight: 5.9990 chunk 171 optimal weight: 2.9990 chunk 197 optimal weight: 7.9990 chunk 131 optimal weight: 8.9990 chunk 234 optimal weight: 9.9990 chunk 146 optimal weight: 5.9990 chunk 142 optimal weight: 10.0000 chunk 108 optimal weight: 5.9990 chunk 144 optimal weight: 3.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 229 ASN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 moved from start: 0.6150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 20553 Z= 0.420 Angle : 0.866 12.713 27945 Z= 0.448 Chirality : 0.048 0.224 3318 Planarity : 0.005 0.057 3486 Dihedral : 8.415 59.953 3963 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 19.30 Ramachandran Plot: Outliers : 0.49 % Allowed : 7.86 % Favored : 91.65 % Rotamer: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.89 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.17), residues: 2454 helix: 0.39 (0.25), residues: 390 sheet: -0.08 (0.21), residues: 582 loop : -1.09 (0.16), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.003 TRP B 614 HIS 0.010 0.001 HIS E 374 PHE 0.030 0.003 PHE G 114 TYR 0.028 0.002 TYR I 217 ARG 0.007 0.001 ARG H 63 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4908 Ramachandran restraints generated. 2454 Oldfield, 0 Emsley, 2454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4908 Ramachandran restraints generated. 2454 Oldfield, 0 Emsley, 2454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 279 time to evaluate : 1.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 107 ASP cc_start: 0.7407 (p0) cc_final: 0.6956 (p0) REVERT: F 530 MET cc_start: 0.8128 (mtt) cc_final: 0.7668 (mtt) REVERT: F 535 MET cc_start: 0.8346 (mmp) cc_final: 0.8064 (mmp) REVERT: F 574 LYS cc_start: 0.9270 (mmmm) cc_final: 0.8970 (mmmm) REVERT: F 589 ASP cc_start: 0.8748 (p0) cc_final: 0.8413 (p0) REVERT: G 34 ILE cc_start: 0.7601 (mm) cc_final: 0.7399 (mm) REVERT: G 113 ASN cc_start: 0.7660 (p0) cc_final: 0.7265 (p0) REVERT: I 107 ASP cc_start: 0.7195 (p0) cc_final: 0.6935 (p0) outliers start: 0 outliers final: 0 residues processed: 279 average time/residue: 0.2802 time to fit residues: 124.8654 Evaluate side-chains 208 residues out of total 2145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 208 time to evaluate : 2.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 93 optimal weight: 9.9990 chunk 139 optimal weight: 5.9990 chunk 70 optimal weight: 0.7980 chunk 46 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 148 optimal weight: 5.9990 chunk 159 optimal weight: 5.9990 chunk 115 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 184 optimal weight: 4.9990 chunk 213 optimal weight: 5.9990 overall best weight: 2.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 46 GLN ** I 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7088 moved from start: 0.6282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 20553 Z= 0.245 Angle : 0.777 13.850 27945 Z= 0.399 Chirality : 0.046 0.227 3318 Planarity : 0.005 0.093 3486 Dihedral : 8.135 59.948 3963 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 15.46 Ramachandran Plot: Outliers : 0.49 % Allowed : 6.60 % Favored : 92.91 % Rotamer: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.89 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.17), residues: 2454 helix: 0.84 (0.26), residues: 390 sheet: -0.01 (0.21), residues: 585 loop : -1.07 (0.16), residues: 1479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP A 427 HIS 0.006 0.001 HIS I 374 PHE 0.015 0.002 PHE I 376 TYR 0.022 0.002 TYR K 80 ARG 0.004 0.000 ARG K 84 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4908 Ramachandran restraints generated. 2454 Oldfield, 0 Emsley, 2454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4908 Ramachandran restraints generated. 2454 Oldfield, 0 Emsley, 2454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 297 time to evaluate : 2.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 491 ILE cc_start: 0.9250 (mp) cc_final: 0.8846 (mm) REVERT: C 81 MET cc_start: 0.7460 (mmm) cc_final: 0.5841 (mmm) REVERT: E 106 GLU cc_start: 0.6986 (pp20) cc_final: 0.6707 (tm-30) REVERT: E 107 ASP cc_start: 0.7334 (p0) cc_final: 0.6839 (p0) REVERT: F 530 MET cc_start: 0.8107 (mtt) cc_final: 0.7665 (mtt) REVERT: F 535 MET cc_start: 0.8289 (mmp) cc_final: 0.7989 (mmp) REVERT: F 574 LYS cc_start: 0.9200 (mmmm) cc_final: 0.8870 (mmmm) REVERT: F 589 ASP cc_start: 0.8674 (p0) cc_final: 0.8373 (p0) REVERT: I 434 MET cc_start: 0.7654 (ptm) cc_final: 0.7191 (ptt) REVERT: J 534 SER cc_start: 0.8556 (p) cc_final: 0.8264 (t) REVERT: J 581 LEU cc_start: 0.8861 (mt) cc_final: 0.8142 (mm) outliers start: 0 outliers final: 0 residues processed: 297 average time/residue: 0.2756 time to fit residues: 131.6001 Evaluate side-chains 228 residues out of total 2145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 228 time to evaluate : 2.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 224 optimal weight: 5.9990 chunk 204 optimal weight: 7.9990 chunk 218 optimal weight: 6.9990 chunk 131 optimal weight: 0.8980 chunk 95 optimal weight: 9.9990 chunk 171 optimal weight: 3.9990 chunk 66 optimal weight: 8.9990 chunk 197 optimal weight: 10.0000 chunk 206 optimal weight: 9.9990 chunk 217 optimal weight: 2.9990 chunk 143 optimal weight: 2.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 575 GLN ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 377 ASN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 46 GLN G 113 ASN ** I 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 moved from start: 0.6588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 20553 Z= 0.319 Angle : 0.814 13.497 27945 Z= 0.418 Chirality : 0.047 0.227 3318 Planarity : 0.005 0.082 3486 Dihedral : 8.186 59.831 3963 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 17.20 Ramachandran Plot: Outliers : 0.49 % Allowed : 7.91 % Favored : 91.61 % Rotamer: Outliers : 0.09 % Allowed : 0.56 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.89 % 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: -0.90 (0.17), residues: 2454 helix: 0.55 (0.26), residues: 390 sheet: 0.05 (0.21), residues: 573 loop : -1.21 (0.16), residues: 1491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP I 427 HIS 0.008 0.001 HIS A 249 PHE 0.021 0.002 PHE C 114 TYR 0.027 0.002 TYR K 33 ARG 0.004 0.000 ARG H 63 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4908 Ramachandran restraints generated. 2454 Oldfield, 0 Emsley, 2454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4908 Ramachandran restraints generated. 2454 Oldfield, 0 Emsley, 2454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 279 time to evaluate : 2.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 626 MET cc_start: 0.8665 (tpp) cc_final: 0.8230 (tpp) REVERT: C 81 MET cc_start: 0.7626 (mmm) cc_final: 0.7257 (mmm) REVERT: E 107 ASP cc_start: 0.7098 (p0) cc_final: 0.6855 (p0) REVERT: F 530 MET cc_start: 0.8167 (mtt) cc_final: 0.7724 (mtt) REVERT: F 574 LYS cc_start: 0.9203 (mmmm) cc_final: 0.8885 (mmmm) REVERT: F 589 ASP cc_start: 0.8667 (p0) cc_final: 0.8421 (p0) REVERT: I 104 MET cc_start: 0.7075 (mmp) cc_final: 0.6717 (mmp) REVERT: I 107 ASP cc_start: 0.7235 (p0) cc_final: 0.6798 (p0) REVERT: I 434 MET cc_start: 0.7587 (ptm) cc_final: 0.7141 (ptt) REVERT: L 22 CYS cc_start: 0.2644 (t) cc_final: 0.1916 (t) REVERT: L 90 CYS cc_start: 0.1379 (p) cc_final: -0.0592 (p) outliers start: 2 outliers final: 1 residues processed: 279 average time/residue: 0.2851 time to fit residues: 129.1292 Evaluate side-chains 219 residues out of total 2145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 218 time to evaluate : 2.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 230 optimal weight: 6.9990 chunk 140 optimal weight: 20.0000 chunk 109 optimal weight: 5.9990 chunk 160 optimal weight: 5.9990 chunk 242 optimal weight: 4.9990 chunk 222 optimal weight: 0.8980 chunk 192 optimal weight: 7.9990 chunk 20 optimal weight: 8.9990 chunk 148 optimal weight: 10.0000 chunk 118 optimal weight: 0.9990 chunk 153 optimal weight: 8.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 113 ASN ** I 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 35 HIS K 113 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 0.6827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 20553 Z= 0.335 Angle : 0.828 13.425 27945 Z= 0.425 Chirality : 0.048 0.232 3318 Planarity : 0.005 0.079 3486 Dihedral : 8.232 59.411 3963 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 18.37 Ramachandran Plot: Outliers : 0.57 % Allowed : 7.91 % Favored : 91.52 % Rotamer: Outliers : 0.09 % Allowed : 0.19 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.89 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.16), residues: 2454 helix: 0.35 (0.25), residues: 390 sheet: -0.01 (0.21), residues: 555 loop : -1.33 (0.16), residues: 1509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP I 427 HIS 0.006 0.001 HIS I 374 PHE 0.019 0.002 PHE G 114 TYR 0.057 0.002 TYR A 217 ARG 0.005 0.000 ARG D 56 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4908 Ramachandran restraints generated. 2454 Oldfield, 0 Emsley, 2454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4908 Ramachandran restraints generated. 2454 Oldfield, 0 Emsley, 2454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 270 time to evaluate : 2.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 589 ASP cc_start: 0.9030 (p0) cc_final: 0.8722 (p0) REVERT: B 626 MET cc_start: 0.8721 (tpp) cc_final: 0.8316 (tpp) REVERT: E 483 LEU cc_start: 0.8306 (mm) cc_final: 0.8064 (mm) REVERT: F 522 PHE cc_start: 0.8827 (m-80) cc_final: 0.8591 (m-10) REVERT: F 530 MET cc_start: 0.8244 (mtt) cc_final: 0.7441 (mtt) REVERT: F 574 LYS cc_start: 0.9205 (mmmm) cc_final: 0.8886 (mmmm) REVERT: F 589 ASP cc_start: 0.8664 (p0) cc_final: 0.8399 (p0) REVERT: G 34 ILE cc_start: 0.7675 (mm) cc_final: 0.7464 (mm) REVERT: I 104 MET cc_start: 0.7115 (mmp) cc_final: 0.6808 (mmp) REVERT: I 107 ASP cc_start: 0.7496 (p0) cc_final: 0.6965 (p0) REVERT: I 434 MET cc_start: 0.7619 (ptm) cc_final: 0.7181 (ptt) outliers start: 2 outliers final: 0 residues processed: 270 average time/residue: 0.2760 time to fit residues: 120.5486 Evaluate side-chains 212 residues out of total 2145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 212 time to evaluate : 2.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 205 optimal weight: 5.9990 chunk 59 optimal weight: 20.0000 chunk 177 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 53 optimal weight: 0.0010 chunk 193 optimal weight: 8.9990 chunk 80 optimal weight: 5.9990 chunk 198 optimal weight: 6.9990 chunk 24 optimal weight: 10.0000 chunk 35 optimal weight: 7.9990 chunk 169 optimal weight: 0.9990 overall best weight: 2.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 113 ASN D 62 ASN ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 113 ASN I 103 GLN ** I 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.057446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.044076 restraints weight = 111745.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.045711 restraints weight = 66008.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.046871 restraints weight = 46622.107| |-----------------------------------------------------------------------------| r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.6932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 20553 Z= 0.246 Angle : 0.779 13.973 27945 Z= 0.399 Chirality : 0.047 0.235 3318 Planarity : 0.005 0.089 3486 Dihedral : 7.980 59.634 3963 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 15.46 Ramachandran Plot: Outliers : 0.57 % Allowed : 7.54 % Favored : 91.89 % Rotamer: Outliers : 0.14 % Allowed : 0.05 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.89 % 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: -0.94 (0.17), residues: 2454 helix: 0.50 (0.26), residues: 390 sheet: 0.11 (0.21), residues: 555 loop : -1.27 (0.16), residues: 1509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP A 427 HIS 0.005 0.001 HIS E 374 PHE 0.027 0.002 PHE J 522 TYR 0.023 0.002 TYR A 217 ARG 0.004 0.000 ARG C 84 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3890.02 seconds wall clock time: 71 minutes 39.43 seconds (4299.43 seconds total)