Starting phenix.real_space_refine (version: 1.21rc1) on Tue Apr 25 11:57:02 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oro_20176/04_2023/6oro_20176.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oro_20176/04_2023/6oro_20176.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oro_20176/04_2023/6oro_20176.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oro_20176/04_2023/6oro_20176.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oro_20176/04_2023/6oro_20176.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oro_20176/04_2023/6oro_20176.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.213 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 120 5.16 5 C 12543 2.51 5 N 3345 2.21 5 O 4077 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 327": "NH1" <-> "NH2" Residue "B ARG 456": "NH1" <-> "NH2" Residue "B ARG 469": "NH1" <-> "NH2" Residue "D ARG 66": "NH1" <-> "NH2" Residue "E ARG 8": "NH1" <-> "NH2" Residue "E ARG 61": "NH1" <-> "NH2" Residue "E TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 308": "NH1" <-> "NH2" Residue "G ARG 327": "NH1" <-> "NH2" Residue "G ARG 456": "NH1" <-> "NH2" Residue "G ARG 469": "NH1" <-> "NH2" Residue "H ARG 66": "NH1" <-> "NH2" Residue "I PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 327": "NH1" <-> "NH2" Residue "I ARG 456": "NH1" <-> "NH2" Residue "I ARG 469": "NH1" <-> "NH2" Residue "J ARG 66": "NH1" <-> "NH2" Residue "K ARG 8": "NH1" <-> "NH2" Residue "K ARG 61": "NH1" <-> "NH2" Residue "K TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 8": "NH1" <-> "NH2" Residue "L ARG 61": "NH1" <-> "NH2" Residue "L TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 20085 Number of models: 1 Model: "" Number of chains: 45 Chain: "A" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 987 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "B" Number of atoms: 3540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3540 Classifications: {'peptide': 449} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 425} Chain breaks: 3 Chain: "C" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 987 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "D" Number of atoms: 935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 935 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "E" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 806 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 6, 'TRANS': 101} Chain: "F" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 987 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "G" Number of atoms: 3540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3540 Classifications: {'peptide': 449} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 425} Chain breaks: 3 Chain: "H" Number of atoms: 935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 935 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "I" Number of atoms: 3540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3540 Classifications: {'peptide': 449} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 425} Chain breaks: 3 Chain: "J" Number of atoms: 935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 935 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "K" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 806 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 6, 'TRANS': 101} Chain: "L" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 806 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 6, 'TRANS': 101} Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "O" Number of atoms: 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 chiralities: 4 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 chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "W" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "X" 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 chiralities: 4 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "f" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "g" 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 chiralities: 4 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "I" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 10.15, per 1000 atoms: 0.51 Number of scatterers: 20085 At special positions: 0 Unit cell: (143.6, 132.112, 153.652, 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 120 16.00 O 4077 8.00 N 3345 7.00 C 12543 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.02 Simple disulfide: pdb=" SG CYS B 119 " - pdb=" SG CYS B 205 " distance=2.03 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 196 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 157 " distance=2.03 Simple disulfide: pdb=" SG CYS B 218 " - pdb=" SG CYS B 247 " distance=2.03 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 239 " distance=2.04 Simple disulfide: pdb=" SG CYS B 296 " - pdb=" SG CYS B 331 " distance=2.02 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 445 " distance=2.02 Simple disulfide: pdb=" SG CYS B 385 " - pdb=" SG CYS B 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 598 " - pdb=" SG CYS C 604 " distance=2.02 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.04 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.04 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.02 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.03 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.03 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.03 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.03 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.04 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.02 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.02 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS I 119 " - pdb=" SG CYS I 205 " distance=2.03 Simple disulfide: pdb=" SG CYS I 126 " - pdb=" SG CYS I 196 " distance=2.03 Simple disulfide: pdb=" SG CYS I 131 " - pdb=" SG CYS I 157 " distance=2.03 Simple disulfide: pdb=" SG CYS I 218 " - pdb=" SG CYS I 247 " distance=2.03 Simple disulfide: pdb=" SG CYS I 228 " - pdb=" SG CYS I 239 " distance=2.04 Simple disulfide: pdb=" SG CYS I 296 " - pdb=" SG CYS I 331 " distance=2.02 Simple disulfide: pdb=" SG CYS I 378 " - pdb=" SG CYS I 445 " distance=2.02 Simple disulfide: pdb=" SG CYS I 385 " - pdb=" SG CYS I 418 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.04 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 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=3, symmetry=0 Links applied ALPHA1-2 " MAN N 4 " - " MAN N 5 " " MAN N 5 " - " MAN N 6 " " MAN W 4 " - " MAN W 5 " " MAN W 5 " - " MAN W 6 " " MAN f 4 " - " MAN f 5 " " MAN f 5 " - " MAN f 6 " ALPHA1-3 " BMA N 3 " - " MAN N 4 " " BMA W 3 " - " MAN W 4 " " BMA f 3 " - " MAN f 4 " ALPHA1-6 " BMA O 3 " - " MAN O 4 " " BMA X 3 " - " MAN X 4 " " BMA g 3 " - " MAN g 4 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " NAG-ASN " NAG A 701 " - " ASN A 611 " " NAG A 702 " - " ASN A 618 " " NAG A 703 " - " ASN A 637 " " NAG B 620 " - " ASN B 88 " " NAG B 625 " - " ASN B 339 " " NAG B 626 " - " ASN B 355 " " NAG B 629 " - " ASN B 276 " " NAG C 701 " - " ASN C 611 " " NAG C 702 " - " ASN C 618 " " NAG C 703 " - " ASN C 637 " " NAG F 701 " - " ASN F 611 " " NAG F 702 " - " ASN F 637 " " NAG F 703 " - " ASN F 618 " " NAG G 620 " - " ASN G 88 " " NAG G 625 " - " ASN G 339 " " NAG G 626 " - " ASN G 355 " " NAG G 629 " - " ASN G 276 " " NAG I 620 " - " ASN I 88 " " NAG I 625 " - " ASN I 339 " " NAG I 626 " - " ASN I 355 " " NAG I 629 " - " ASN I 276 " " NAG M 1 " - " ASN B 160 " " NAG N 1 " - " ASN B 332 " " NAG O 1 " - " ASN B 262 " " NAG P 1 " - " ASN B 448 " " NAG Q 1 " - " ASN B 295 " " NAG R 1 " - " ASN B 197 " " NAG S 1 " - " ASN B 392 " " NAG T 1 " - " ASN B 386 " " NAG U 1 " - " ASN B 301 " " NAG V 1 " - " ASN G 160 " " NAG W 1 " - " ASN G 332 " " NAG X 1 " - " ASN G 262 " " NAG Y 1 " - " ASN G 448 " " NAG Z 1 " - " ASN G 295 " " NAG a 1 " - " ASN G 197 " " NAG b 1 " - " ASN G 392 " " NAG c 1 " - " ASN G 386 " " NAG d 1 " - " ASN G 301 " " NAG e 1 " - " ASN I 160 " " NAG f 1 " - " ASN I 332 " " NAG g 1 " - " ASN I 262 " " NAG h 1 " - " ASN I 448 " " NAG i 1 " - " ASN I 295 " " NAG j 1 " - " ASN I 197 " " NAG k 1 " - " ASN I 392 " " NAG l 1 " - " ASN I 386 " " NAG m 1 " - " ASN I 301 " Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 9.09 Conformation dependent library (CDL) restraints added in 2.8 seconds 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4440 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 42 sheets defined 15.0% alpha, 18.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.32 Creating SS restraints... Processing helix chain 'A' and resid 529 through 534 removed outlier: 3.724A pdb=" N SER A 534 " --> pdb=" O MET A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 543 removed outlier: 3.774A pdb=" N ASN A 543 " --> pdb=" O VAL A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 595 removed outlier: 3.527A pdb=" N ALA A 578 " --> pdb=" O LYS A 574 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU A 581 " --> pdb=" O GLN A 577 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL A 583 " --> pdb=" O ARG A 579 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N HIS A 585 " --> pdb=" O LEU A 581 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TYR A 586 " --> pdb=" O ALA A 582 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG A 588 " --> pdb=" O GLU A 584 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ASP A 589 " --> pdb=" O HIS A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 624 removed outlier: 3.730A pdb=" N TRP A 623 " --> pdb=" O LEU A 619 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP A 624 " --> pdb=" O SER A 620 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 619 through 624' Processing helix chain 'A' and resid 627 through 635 removed outlier: 4.437A pdb=" N LYS A 633 " --> pdb=" O LEU A 629 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU A 634 " --> pdb=" O GLN A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 649 removed outlier: 4.356A pdb=" N GLU A 647 " --> pdb=" O TYR A 643 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER A 649 " --> pdb=" O LEU A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 659 removed outlier: 3.526A pdb=" N LYS A 655 " --> pdb=" O ASN A 651 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N ASN A 656 " --> pdb=" O GLN A 652 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 113 removed outlier: 3.740A pdb=" N ILE B 109 " --> pdb=" O HIS B 105 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N LEU B 111 " --> pdb=" O ASP B 107 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASP B 113 " --> pdb=" O ILE B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 117 removed outlier: 3.536A pdb=" N LYS B 117 " --> pdb=" O GLN B 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 114 through 117' Processing helix chain 'B' and resid 177 through 179 No H-bonds generated for 'chain 'B' and resid 177 through 179' Processing helix chain 'B' and resid 334 through 349 removed outlier: 3.670A pdb=" N GLU B 340 " --> pdb=" O ALA B 336 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS B 347 " --> pdb=" O GLY B 343 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLN B 348 " --> pdb=" O LYS B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 353 removed outlier: 3.571A pdb=" N PHE B 353 " --> pdb=" O ARG B 350 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 350 through 353' Processing helix chain 'B' and resid 368 through 373 removed outlier: 3.617A pdb=" N THR B 372 " --> pdb=" O ASP B 368 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR B 373 " --> pdb=" O LEU B 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 368 through 373' Processing helix chain 'B' and resid 474 through 480 removed outlier: 3.711A pdb=" N ASP B 477 " --> pdb=" O ASP B 474 " (cutoff:3.500A) Processing helix chain 'C' and resid 529 through 534 removed outlier: 3.725A pdb=" N SER C 534 " --> pdb=" O MET C 530 " (cutoff:3.500A) Processing helix chain 'C' and resid 538 through 543 removed outlier: 3.776A pdb=" N ASN C 543 " --> pdb=" O VAL C 539 " (cutoff:3.500A) Processing helix chain 'C' and resid 572 through 595 removed outlier: 3.528A pdb=" N ALA C 578 " --> pdb=" O LYS C 574 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU C 581 " --> pdb=" O GLN C 577 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL C 583 " --> pdb=" O ARG C 579 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N HIS C 585 " --> pdb=" O LEU C 581 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TYR C 586 " --> pdb=" O ALA C 582 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG C 588 " --> pdb=" O GLU C 584 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ASP C 589 " --> pdb=" O HIS C 585 " (cutoff:3.500A) Processing helix chain 'C' and resid 619 through 624 removed outlier: 3.731A pdb=" N TRP C 623 " --> pdb=" O LEU C 619 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASP C 624 " --> pdb=" O SER C 620 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 619 through 624' Processing helix chain 'C' and resid 627 through 635 removed outlier: 4.437A pdb=" N LYS C 633 " --> pdb=" O LEU C 629 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU C 634 " --> pdb=" O GLN C 630 " (cutoff:3.500A) Processing helix chain 'C' and resid 641 through 649 removed outlier: 4.356A pdb=" N GLU C 647 " --> pdb=" O TYR C 643 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER C 649 " --> pdb=" O LEU C 645 " (cutoff:3.500A) Processing helix chain 'C' and resid 650 through 659 removed outlier: 3.527A pdb=" N LYS C 655 " --> pdb=" O ASN C 651 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N ASN C 656 " --> pdb=" O GLN C 652 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 removed outlier: 3.725A pdb=" N SER F 534 " --> pdb=" O MET F 530 " (cutoff:3.500A) Processing helix chain 'F' and resid 538 through 543 removed outlier: 3.775A pdb=" N ASN F 543 " --> pdb=" O VAL F 539 " (cutoff:3.500A) Processing helix chain 'F' and resid 572 through 595 removed outlier: 3.527A pdb=" N ALA F 578 " --> pdb=" O LYS F 574 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU F 581 " --> pdb=" O GLN F 577 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL F 583 " --> pdb=" O ARG F 579 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N HIS F 585 " --> pdb=" O LEU F 581 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N TYR F 586 " --> pdb=" O ALA F 582 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG F 588 " --> pdb=" O GLU F 584 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ASP F 589 " --> pdb=" O HIS F 585 " (cutoff:3.500A) Processing helix chain 'F' and resid 619 through 624 removed outlier: 3.618A pdb=" N TRP F 623 " --> pdb=" O LEU F 619 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 635 removed outlier: 4.438A pdb=" N LYS F 633 " --> pdb=" O LEU F 629 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU F 634 " --> pdb=" O GLN F 630 " (cutoff:3.500A) Processing helix chain 'F' and resid 641 through 649 removed outlier: 4.356A pdb=" N GLU F 647 " --> pdb=" O TYR F 643 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER F 649 " --> pdb=" O LEU F 645 " (cutoff:3.500A) Processing helix chain 'F' and resid 650 through 659 removed outlier: 3.526A pdb=" N LYS F 655 " --> pdb=" O ASN F 651 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N ASN F 656 " --> pdb=" O GLN F 652 " (cutoff:3.500A) Processing helix chain 'G' and resid 105 through 113 removed outlier: 3.739A pdb=" N ILE G 109 " --> pdb=" O HIS G 105 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N LEU G 111 " --> pdb=" O ASP G 107 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASP G 113 " --> pdb=" O ILE G 109 " (cutoff:3.500A) Processing helix chain 'G' and resid 114 through 117 removed outlier: 3.535A pdb=" N LYS G 117 " --> pdb=" O GLN G 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 114 through 117' Processing helix chain 'G' and resid 139 through 151 removed outlier: 4.134A pdb=" N MET G 150 " --> pdb=" O LEU G 139 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ARG G 151 " --> pdb=" O SER G 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 139 through 151' Processing helix chain 'G' and resid 177 through 179 No H-bonds generated for 'chain 'G' and resid 177 through 179' Processing helix chain 'G' and resid 334 through 349 removed outlier: 3.670A pdb=" N GLU G 340 " --> pdb=" O ALA G 336 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS G 347 " --> pdb=" O GLY G 343 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLN G 348 " --> pdb=" O LYS G 344 " (cutoff:3.500A) Processing helix chain 'G' and resid 350 through 353 removed outlier: 3.570A pdb=" N PHE G 353 " --> pdb=" O ARG G 350 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 350 through 353' Processing helix chain 'G' and resid 368 through 373 removed outlier: 3.617A pdb=" N THR G 372 " --> pdb=" O ASP G 368 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR G 373 " --> pdb=" O LEU G 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 368 through 373' Processing helix chain 'G' and resid 474 through 480 removed outlier: 3.711A pdb=" N ASP G 477 " --> pdb=" O ASP G 474 " (cutoff:3.500A) Processing helix chain 'I' and resid 105 through 113 removed outlier: 3.740A pdb=" N ILE I 109 " --> pdb=" O HIS I 105 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N LEU I 111 " --> pdb=" O ASP I 107 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASP I 113 " --> pdb=" O ILE I 109 " (cutoff:3.500A) Processing helix chain 'I' and resid 114 through 117 removed outlier: 3.536A pdb=" N LYS I 117 " --> pdb=" O GLN I 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 114 through 117' Processing helix chain 'I' and resid 177 through 179 No H-bonds generated for 'chain 'I' and resid 177 through 179' Processing helix chain 'I' and resid 334 through 349 removed outlier: 3.670A pdb=" N GLU I 340 " --> pdb=" O ALA I 336 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS I 347 " --> pdb=" O GLY I 343 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN I 348 " --> pdb=" O LYS I 344 " (cutoff:3.500A) Processing helix chain 'I' and resid 350 through 353 removed outlier: 3.571A pdb=" N PHE I 353 " --> pdb=" O ARG I 350 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 350 through 353' Processing helix chain 'I' and resid 368 through 373 removed outlier: 3.616A pdb=" N THR I 372 " --> pdb=" O ASP I 368 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR I 373 " --> pdb=" O LEU I 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 368 through 373' Processing helix chain 'I' and resid 474 through 480 removed outlier: 3.711A pdb=" N ASP I 477 " --> pdb=" O ASP I 474 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 603 through 609 removed outlier: 3.590A pdb=" N CYS A 604 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL B 38 " --> pdb=" O CYS A 604 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N THR A 606 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N VAL B 36 " --> pdb=" O THR A 606 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY B 495 " --> pdb=" O TYR B 39 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 45 through 47 removed outlier: 3.845A pdb=" N LYS B 487 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AA4, first strand: chain 'B' and resid 91 through 93 removed outlier: 4.124A pdb=" N GLU B 91 " --> pdb=" O CYS B 239 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N CYS B 239 " --> pdb=" O GLU B 91 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 169 through 175 removed outlier: 3.603A pdb=" N PHE B 159 " --> pdb=" O VAL B 172 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 259 through 261 removed outlier: 4.281A pdb=" N GLY B 451 " --> pdb=" O LEU B 260 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL B 292 " --> pdb=" O ILE B 449 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 284 through 286 removed outlier: 6.750A pdb=" N ARG B 360 " --> pdb=" O PHE B 468 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 297 through 298 removed outlier: 3.739A pdb=" N ILE B 443 " --> pdb=" O ARG B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 304 through 308 removed outlier: 3.510A pdb=" N LYS B 305 " --> pdb=" O TYR B 319 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE B 307 " --> pdb=" O PHE B 317 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 329 through 333 removed outlier: 3.882A pdb=" N ALA B 329 " --> pdb=" O CYS B 418 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS B 421 " --> pdb=" O PHE B 382 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N PHE B 382 " --> pdb=" O LYS B 421 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N PHE B 376 " --> pdb=" O PHE B 383 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 603 through 609 removed outlier: 3.573A pdb=" N CYS C 604 " --> pdb=" O VAL G 38 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL G 38 " --> pdb=" O CYS C 604 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N THR C 606 " --> pdb=" O VAL G 36 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N VAL G 36 " --> pdb=" O THR C 606 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY G 495 " --> pdb=" O TYR G 39 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 5 through 7 removed outlier: 3.505A pdb=" N THR D 77 " --> pdb=" O ASP D 72 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLN D 81 " --> pdb=" O THR D 68 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N THR D 68 " --> pdb=" O GLN D 81 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 46 through 48 removed outlier: 3.901A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL D 37 " --> pdb=" O TYR D 91 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 19 through 22 removed outlier: 3.911A pdb=" N SER E 67 " --> pdb=" O THR E 70 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 88 through 91 removed outlier: 3.970A pdb=" N CYS E 88 " --> pdb=" O GLY E 99 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N VAL E 90 " --> pdb=" O LEU E 97 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N LEU E 97 " --> pdb=" O VAL E 90 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 603 through 609 removed outlier: 3.575A pdb=" N CYS F 604 " --> pdb=" O VAL I 38 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL I 38 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N THR F 606 " --> pdb=" O VAL I 36 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N VAL I 36 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY I 495 " --> pdb=" O TYR I 39 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 45 through 47 removed outlier: 3.845A pdb=" N LYS G 487 " --> pdb=" O LEU G 226 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 53 through 54 Processing sheet with id=AC1, first strand: chain 'G' and resid 91 through 93 removed outlier: 4.125A pdb=" N GLU G 91 " --> pdb=" O CYS G 239 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N CYS G 239 " --> pdb=" O GLU G 91 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 169 through 175 removed outlier: 3.603A pdb=" N PHE G 159 " --> pdb=" O VAL G 172 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 259 through 261 removed outlier: 4.280A pdb=" N GLY G 451 " --> pdb=" O LEU G 260 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL G 292 " --> pdb=" O ILE G 449 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 284 through 286 removed outlier: 6.750A pdb=" N ARG G 360 " --> pdb=" O PHE G 468 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 297 through 298 removed outlier: 3.740A pdb=" N ILE G 443 " --> pdb=" O ARG G 298 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 304 through 307 removed outlier: 3.511A pdb=" N LYS G 305 " --> pdb=" O TYR G 319 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE G 307 " --> pdb=" O PHE G 317 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 329 through 333 removed outlier: 3.883A pdb=" N ALA G 329 " --> pdb=" O CYS G 418 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS G 421 " --> pdb=" O PHE G 382 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N PHE G 382 " --> pdb=" O LYS G 421 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N PHE G 376 " --> pdb=" O PHE G 383 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 5 through 7 removed outlier: 3.506A pdb=" N THR H 77 " --> pdb=" O ASP H 72 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLN H 81 " --> pdb=" O THR H 68 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N THR H 68 " --> pdb=" O GLN H 81 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 46 through 48 removed outlier: 3.901A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL H 37 " --> pdb=" O TYR H 91 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 45 through 47 removed outlier: 3.845A pdb=" N LYS I 487 " --> pdb=" O LEU I 226 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 53 through 54 Processing sheet with id=AD3, first strand: chain 'I' and resid 91 through 93 removed outlier: 4.125A pdb=" N GLU I 91 " --> pdb=" O CYS I 239 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N CYS I 239 " --> pdb=" O GLU I 91 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 169 through 175 removed outlier: 3.603A pdb=" N PHE I 159 " --> pdb=" O VAL I 172 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 259 through 261 removed outlier: 4.280A pdb=" N GLY I 451 " --> pdb=" O LEU I 260 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL I 292 " --> pdb=" O ILE I 449 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 284 through 286 removed outlier: 6.750A pdb=" N ARG I 360 " --> pdb=" O PHE I 468 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 297 through 298 removed outlier: 3.739A pdb=" N ILE I 443 " --> pdb=" O ARG I 298 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 304 through 308 removed outlier: 3.511A pdb=" N LYS I 305 " --> pdb=" O TYR I 319 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE I 307 " --> pdb=" O PHE I 317 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 329 through 333 removed outlier: 3.882A pdb=" N ALA I 329 " --> pdb=" O CYS I 418 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS I 421 " --> pdb=" O PHE I 382 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N PHE I 382 " --> pdb=" O LYS I 421 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N PHE I 376 " --> pdb=" O PHE I 383 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 5 through 7 removed outlier: 3.505A pdb=" N THR J 77 " --> pdb=" O ASP J 72 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLN J 81 " --> pdb=" O THR J 68 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N THR J 68 " --> pdb=" O GLN J 81 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 46 through 48 removed outlier: 3.902A pdb=" N TRP J 36 " --> pdb=" O VAL J 48 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL J 37 " --> pdb=" O TYR J 91 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'K' and resid 19 through 22 removed outlier: 3.910A pdb=" N SER K 67 " --> pdb=" O THR K 70 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'K' and resid 88 through 91 removed outlier: 3.969A pdb=" N CYS K 88 " --> pdb=" O GLY K 99 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N VAL K 90 " --> pdb=" O LEU K 97 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N LEU K 97 " --> pdb=" O VAL K 90 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'L' and resid 19 through 22 removed outlier: 3.911A pdb=" N SER L 67 " --> pdb=" O THR L 70 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'L' and resid 88 through 91 removed outlier: 3.968A pdb=" N CYS L 88 " --> pdb=" O GLY L 99 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N VAL L 90 " --> pdb=" O LEU L 97 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N LEU L 97 " --> pdb=" O VAL L 90 " (cutoff:3.500A) 367 hydrogen bonds defined for protein. 936 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.16 Time building geometry restraints manager: 9.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.12 - 1.26: 3214 1.26 - 1.40: 4782 1.40 - 1.54: 12093 1.54 - 1.68: 230 1.68 - 1.82: 162 Bond restraints: 20481 Sorted by residual: bond pdb=" C ASN F 618 " pdb=" O ASN F 618 " ideal model delta sigma weight residual 1.233 1.118 0.115 1.36e-02 5.41e+03 7.13e+01 bond pdb=" C ASN F 618 " pdb=" N LEU F 619 " ideal model delta sigma weight residual 1.332 1.218 0.114 1.40e-02 5.10e+03 6.62e+01 bond pdb=" C ILE B 309 " pdb=" O ILE B 309 " ideal model delta sigma weight residual 1.236 1.159 0.077 1.19e-02 7.06e+03 4.17e+01 bond pdb=" C ILE G 309 " pdb=" O ILE G 309 " ideal model delta sigma weight residual 1.236 1.164 0.072 1.19e-02 7.06e+03 3.64e+01 bond pdb=" C ALA I 316 " pdb=" O ALA I 316 " ideal model delta sigma weight residual 1.233 1.163 0.071 1.28e-02 6.10e+03 3.05e+01 ... (remaining 20476 not shown) Histogram of bond angle deviations from ideal: 96.11 - 104.53: 343 104.53 - 112.95: 11472 112.95 - 121.36: 10295 121.36 - 129.78: 5476 129.78 - 138.19: 212 Bond angle restraints: 27798 Sorted by residual: angle pdb=" CA PRO G 313 " pdb=" N PRO G 313 " pdb=" CD PRO G 313 " ideal model delta sigma weight residual 111.50 96.11 15.39 1.40e+00 5.10e-01 1.21e+02 angle pdb=" CA PRO B 313 " pdb=" N PRO B 313 " pdb=" CD PRO B 313 " ideal model delta sigma weight residual 111.50 99.17 12.33 1.40e+00 5.10e-01 7.76e+01 angle pdb=" CA PRO I 313 " pdb=" N PRO I 313 " pdb=" CD PRO I 313 " ideal model delta sigma weight residual 111.50 99.85 11.65 1.40e+00 5.10e-01 6.92e+01 angle pdb=" N PRO B 136 " pdb=" CA PRO B 136 " pdb=" C PRO B 136 " ideal model delta sigma weight residual 113.47 101.67 11.80 1.43e+00 4.89e-01 6.81e+01 angle pdb=" N PRO I 136 " pdb=" CA PRO I 136 " pdb=" C PRO I 136 " ideal model delta sigma weight residual 113.47 102.44 11.03 1.43e+00 4.89e-01 5.95e+01 ... (remaining 27793 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.63: 10736 16.63 - 33.25: 538 33.25 - 49.88: 144 49.88 - 66.51: 35 66.51 - 83.14: 31 Dihedral angle restraints: 11484 sinusoidal: 4575 harmonic: 6909 Sorted by residual: dihedral pdb=" CA ASN C 637 " pdb=" C ASN C 637 " pdb=" N TYR C 638 " pdb=" CA TYR C 638 " ideal model delta harmonic sigma weight residual 180.00 130.97 49.03 0 5.00e+00 4.00e-02 9.61e+01 dihedral pdb=" CA ASN A 637 " pdb=" C ASN A 637 " pdb=" N TYR A 638 " pdb=" CA TYR A 638 " ideal model delta harmonic sigma weight residual 180.00 130.97 49.03 0 5.00e+00 4.00e-02 9.61e+01 dihedral pdb=" CA ASN F 637 " pdb=" C ASN F 637 " pdb=" N TYR F 638 " pdb=" CA TYR F 638 " ideal model delta harmonic sigma weight residual 180.00 130.99 49.01 0 5.00e+00 4.00e-02 9.61e+01 ... (remaining 11481 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.302: 3355 0.302 - 0.604: 15 0.604 - 0.907: 3 0.907 - 1.209: 0 1.209 - 1.511: 2 Chirality restraints: 3375 Sorted by residual: chirality pdb=" C1 NAG C 702 " pdb=" ND2 ASN C 618 " pdb=" C2 NAG C 702 " pdb=" O5 NAG C 702 " both_signs ideal model delta sigma weight residual False -2.40 -0.89 -1.51 2.00e-01 2.50e+01 5.71e+01 chirality pdb=" C1 NAG A 702 " pdb=" ND2 ASN A 618 " pdb=" C2 NAG A 702 " pdb=" O5 NAG A 702 " both_signs ideal model delta sigma weight residual False -2.40 -0.89 -1.51 2.00e-01 2.50e+01 5.70e+01 chirality pdb=" C1 NAG B 629 " pdb=" ND2 ASN B 276 " pdb=" C2 NAG B 629 " pdb=" O5 NAG B 629 " both_signs ideal model delta sigma weight residual False -2.40 -1.60 -0.80 2.00e-01 2.50e+01 1.59e+01 ... (remaining 3372 not shown) Planarity restraints: 3480 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG F 617 " -0.030 2.00e-02 2.50e+03 6.10e-02 3.73e+01 pdb=" C ARG F 617 " 0.106 2.00e-02 2.50e+03 pdb=" O ARG F 617 " -0.039 2.00e-02 2.50e+03 pdb=" N ASN F 618 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 309 " 0.024 2.00e-02 2.50e+03 4.75e-02 2.25e+01 pdb=" C ILE B 309 " -0.082 2.00e-02 2.50e+03 pdb=" O ILE B 309 " 0.029 2.00e-02 2.50e+03 pdb=" N GLY B 312 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 703 " 0.049 2.00e-02 2.50e+03 4.05e-02 2.05e+01 pdb=" C7 NAG F 703 " 0.000 2.00e-02 2.50e+03 pdb=" C8 NAG F 703 " 0.032 2.00e-02 2.50e+03 pdb=" N2 NAG F 703 " -0.068 2.00e-02 2.50e+03 pdb=" O7 NAG F 703 " -0.012 2.00e-02 2.50e+03 ... (remaining 3477 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 313 2.62 - 3.19: 16485 3.19 - 3.76: 27050 3.76 - 4.33: 35037 4.33 - 4.90: 58333 Nonbonded interactions: 137218 Sorted by model distance: nonbonded pdb=" O4 NAG F 703 " pdb=" O6 NAG F 703 " model vdw 2.048 2.440 nonbonded pdb=" OE2 GLU C 621 " pdb=" C5 NAG C 702 " model vdw 2.220 3.470 nonbonded pdb=" OE2 GLU A 621 " pdb=" C5 NAG A 702 " model vdw 2.220 3.470 nonbonded pdb=" O VAL H 12 " pdb=" OG SER H 112 " model vdw 2.263 2.440 nonbonded pdb=" O VAL J 12 " pdb=" OG SER J 112 " model vdw 2.263 2.440 ... (remaining 137213 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 'C' selection = chain 'F' } ncs_group { reference = chain 'B' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'E' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'V' selection = chain 'e' } ncs_group { reference = chain 'N' selection = chain 'W' selection = chain 'f' } ncs_group { reference = chain 'O' selection = chain 'X' selection = chain 'g' } ncs_group { reference = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' } 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: 1.120 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: 5.800 Check model and map are aligned: 0.320 Set scattering table: 0.170 Process input model: 50.530 Find NCS groups from input model: 1.410 Set up NCS constraints: 0.360 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 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 : 0.009 0.115 20481 Z= 0.575 Angle : 1.319 17.483 27798 Z= 0.706 Chirality : 0.087 1.511 3375 Planarity : 0.008 0.084 3432 Dihedral : 11.964 80.593 6945 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.59 % Allowed : 13.05 % Favored : 86.35 % Rotamer Outliers : 2.93 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.92 % 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: -5.30 (0.13), residues: 2367 helix: -4.63 (0.15), residues: 330 sheet: -3.26 (0.20), residues: 465 loop : -3.56 (0.12), residues: 1572 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 641 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 580 time to evaluate : 2.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 61 outliers final: 18 residues processed: 610 average time/residue: 0.3383 time to fit residues: 307.6345 Evaluate side-chains 403 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 385 time to evaluate : 2.617 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 1 residues processed: 18 average time/residue: 0.2899 time to fit residues: 11.6822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 197 optimal weight: 3.9990 chunk 177 optimal weight: 1.9990 chunk 98 optimal weight: 0.8980 chunk 60 optimal weight: 0.6980 chunk 119 optimal weight: 9.9990 chunk 94 optimal weight: 1.9990 chunk 183 optimal weight: 0.8980 chunk 70 optimal weight: 0.0170 chunk 111 optimal weight: 4.9990 chunk 136 optimal weight: 0.6980 chunk 212 optimal weight: 0.8980 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 640 GLN ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 114 GLN B 300 ASN B 330 HIS B 428 GLN C 543 ASN C 575 GLN C 591 GLN ** C 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 76 ASN D 81 GLN D 99 GLN ** E 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 137 ASN G 300 ASN G 330 HIS G 440 GLN H 81 GLN I 258 GLN I 300 ASN I 330 HIS J 99 GLN ** K 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN ** L 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 20481 Z= 0.196 Angle : 0.839 18.799 27798 Z= 0.404 Chirality : 0.054 0.595 3375 Planarity : 0.005 0.049 3432 Dihedral : 7.320 48.383 2568 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.17 % Allowed : 11.58 % Favored : 88.26 % Rotamer Outliers : 2.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.52 % 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: -4.85 (0.14), residues: 2367 helix: -3.83 (0.18), residues: 372 sheet: -2.78 (0.18), residues: 597 loop : -3.36 (0.14), residues: 1398 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 472 time to evaluate : 2.388 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 outliers start: 51 outliers final: 30 residues processed: 495 average time/residue: 0.2865 time to fit residues: 223.4099 Evaluate side-chains 422 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 392 time to evaluate : 2.203 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.1982 time to fit residues: 13.7674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 118 optimal weight: 8.9990 chunk 65 optimal weight: 0.0770 chunk 176 optimal weight: 5.9990 chunk 144 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 212 optimal weight: 4.9990 chunk 229 optimal weight: 4.9990 chunk 189 optimal weight: 0.9990 chunk 211 optimal weight: 5.9990 chunk 72 optimal weight: 0.0970 chunk 170 optimal weight: 2.9990 overall best weight: 1.4342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 543 ASN ** C 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 137 ASN G 478 ASN I 432 GLN ** K 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 20481 Z= 0.243 Angle : 0.803 17.170 27798 Z= 0.387 Chirality : 0.052 0.437 3375 Planarity : 0.004 0.045 3432 Dihedral : 6.807 46.626 2568 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.17 % Allowed : 12.46 % Favored : 87.37 % Rotamer Outliers : 2.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.52 % 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: -4.41 (0.15), residues: 2367 helix: -3.10 (0.22), residues: 342 sheet: -2.41 (0.20), residues: 579 loop : -3.26 (0.14), residues: 1446 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 397 time to evaluate : 2.315 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 outliers start: 55 outliers final: 44 residues processed: 422 average time/residue: 0.2886 time to fit residues: 191.3121 Evaluate side-chains 419 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 375 time to evaluate : 2.154 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 0 residues processed: 44 average time/residue: 0.2111 time to fit residues: 19.4106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 210 optimal weight: 9.9990 chunk 160 optimal weight: 5.9990 chunk 110 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 101 optimal weight: 3.9990 chunk 142 optimal weight: 0.0370 chunk 213 optimal weight: 0.6980 chunk 226 optimal weight: 0.8980 chunk 111 optimal weight: 0.9980 chunk 202 optimal weight: 9.9990 chunk 60 optimal weight: 1.9990 overall best weight: 0.7260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 640 GLN D 81 GLN ** F 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 20481 Z= 0.169 Angle : 0.744 16.497 27798 Z= 0.355 Chirality : 0.050 0.433 3375 Planarity : 0.004 0.045 3432 Dihedral : 6.459 47.420 2568 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.17 % Allowed : 11.41 % Favored : 88.42 % Rotamer Outliers : 1.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.44 % 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: -4.07 (0.15), residues: 2367 helix: -2.50 (0.26), residues: 324 sheet: -2.30 (0.20), residues: 630 loop : -3.07 (0.14), residues: 1413 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 414 time to evaluate : 2.367 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 outliers start: 41 outliers final: 27 residues processed: 433 average time/residue: 0.2934 time to fit residues: 200.3501 Evaluate side-chains 400 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 373 time to evaluate : 2.368 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 3 residues processed: 27 average time/residue: 0.1831 time to fit residues: 12.5217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 188 optimal weight: 0.9990 chunk 128 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 168 optimal weight: 4.9990 chunk 93 optimal weight: 0.5980 chunk 193 optimal weight: 0.0970 chunk 156 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 115 optimal weight: 4.9990 chunk 203 optimal weight: 20.0000 chunk 57 optimal weight: 7.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 607 ASN ** C 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 137 ASN G 258 GLN I 99 ASN ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.3178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 20481 Z= 0.172 Angle : 0.727 16.373 27798 Z= 0.348 Chirality : 0.049 0.428 3375 Planarity : 0.004 0.041 3432 Dihedral : 6.189 46.111 2568 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.17 % Allowed : 11.79 % Favored : 88.04 % Rotamer Outliers : 2.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.39 % 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: -3.98 (0.15), residues: 2367 helix: -2.37 (0.25), residues: 354 sheet: -2.11 (0.21), residues: 582 loop : -3.08 (0.14), residues: 1431 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 399 time to evaluate : 2.281 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 outliers start: 48 outliers final: 36 residues processed: 424 average time/residue: 0.2804 time to fit residues: 189.5820 Evaluate side-chains 414 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 378 time to evaluate : 2.427 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 3 residues processed: 36 average time/residue: 0.1858 time to fit residues: 15.7236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 76 optimal weight: 7.9990 chunk 203 optimal weight: 30.0000 chunk 44 optimal weight: 5.9990 chunk 132 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 chunk 226 optimal weight: 10.0000 chunk 187 optimal weight: 0.8980 chunk 104 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 74 optimal weight: 6.9990 chunk 118 optimal weight: 0.8980 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 478 ASN D 99 GLN ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 149 ASN H 81 GLN ** H 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 478 ASN ** K 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.3287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.054 20481 Z= 0.400 Angle : 0.833 15.384 27798 Z= 0.405 Chirality : 0.054 0.439 3375 Planarity : 0.004 0.049 3432 Dihedral : 6.575 42.400 2568 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.17 % Allowed : 14.07 % Favored : 85.76 % Rotamer Outliers : 3.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.52 % 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: -3.93 (0.16), residues: 2367 helix: -2.08 (0.28), residues: 336 sheet: -2.17 (0.21), residues: 594 loop : -3.07 (0.14), residues: 1437 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 373 time to evaluate : 2.362 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 outliers start: 69 outliers final: 49 residues processed: 410 average time/residue: 0.2986 time to fit residues: 193.4859 Evaluate side-chains 411 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 362 time to evaluate : 2.286 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 49 outliers final: 3 residues processed: 49 average time/residue: 0.1851 time to fit residues: 20.2673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 218 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 128 optimal weight: 0.5980 chunk 165 optimal weight: 4.9990 chunk 190 optimal weight: 0.9980 chunk 126 optimal weight: 0.0770 chunk 225 optimal weight: 0.0370 chunk 141 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 104 optimal weight: 5.9990 chunk 139 optimal weight: 0.0970 overall best weight: 0.3614 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 650 GLN D 81 GLN D 99 GLN ** G 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.3506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 20481 Z= 0.156 Angle : 0.730 14.883 27798 Z= 0.349 Chirality : 0.050 0.423 3375 Planarity : 0.004 0.060 3432 Dihedral : 6.126 46.539 2568 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.17 % Allowed : 11.28 % Favored : 88.55 % Rotamer Outliers : 1.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.52 % 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: -3.68 (0.16), residues: 2367 helix: -1.90 (0.28), residues: 324 sheet: -1.94 (0.21), residues: 576 loop : -2.94 (0.14), residues: 1467 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 402 time to evaluate : 2.363 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 outliers start: 28 outliers final: 16 residues processed: 415 average time/residue: 0.3018 time to fit residues: 194.9975 Evaluate side-chains 388 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 372 time to evaluate : 2.389 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 3 residues processed: 16 average time/residue: 0.2189 time to fit residues: 9.2930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 90 optimal weight: 7.9990 chunk 134 optimal weight: 7.9990 chunk 67 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 143 optimal weight: 0.0170 chunk 153 optimal weight: 2.9990 chunk 111 optimal weight: 4.9990 chunk 21 optimal weight: 0.0670 chunk 177 optimal weight: 5.9990 chunk 205 optimal weight: 2.9990 overall best weight: 1.4162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.3606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.030 20481 Z= 0.230 Angle : 0.747 14.759 27798 Z= 0.359 Chirality : 0.051 0.427 3375 Planarity : 0.004 0.046 3432 Dihedral : 6.059 43.251 2568 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.17 % Allowed : 13.05 % Favored : 86.78 % Rotamer Outliers : 1.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.48 % 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: -3.53 (0.16), residues: 2367 helix: -1.61 (0.30), residues: 306 sheet: -1.93 (0.21), residues: 576 loop : -2.82 (0.14), residues: 1485 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 376 time to evaluate : 2.485 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 outliers start: 29 outliers final: 22 residues processed: 393 average time/residue: 0.2966 time to fit residues: 183.8072 Evaluate side-chains 389 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 367 time to evaluate : 2.423 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 3 residues processed: 22 average time/residue: 0.1995 time to fit residues: 11.3413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 216 optimal weight: 9.9990 chunk 197 optimal weight: 3.9990 chunk 210 optimal weight: 10.0000 chunk 126 optimal weight: 0.6980 chunk 91 optimal weight: 2.9990 chunk 165 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 189 optimal weight: 5.9990 chunk 198 optimal weight: 4.9990 chunk 209 optimal weight: 2.9990 chunk 138 optimal weight: 5.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 GLN ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 428 GLN ** K 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.3664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.042 20481 Z= 0.359 Angle : 0.829 13.929 27798 Z= 0.403 Chirality : 0.054 0.445 3375 Planarity : 0.004 0.049 3432 Dihedral : 6.410 42.947 2568 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.17 % Allowed : 14.70 % Favored : 85.13 % Rotamer Outliers : 1.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.52 % 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: -3.71 (0.16), residues: 2367 helix: -1.92 (0.29), residues: 336 sheet: -1.85 (0.20), residues: 594 loop : -3.01 (0.14), residues: 1437 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 370 time to evaluate : 2.359 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 outliers start: 28 outliers final: 18 residues processed: 381 average time/residue: 0.3033 time to fit residues: 181.0456 Evaluate side-chains 375 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 357 time to evaluate : 2.291 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 3 residues processed: 18 average time/residue: 0.1870 time to fit residues: 9.4289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 222 optimal weight: 3.9990 chunk 135 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 chunk 154 optimal weight: 9.9990 chunk 233 optimal weight: 0.2980 chunk 214 optimal weight: 0.2980 chunk 185 optimal weight: 0.4980 chunk 19 optimal weight: 0.9990 chunk 143 optimal weight: 1.9990 chunk 113 optimal weight: 0.9980 chunk 147 optimal weight: 50.0000 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 80 ASN C 570 HIS D 81 GLN ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 99 ASN ** G 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 GLN ** I 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 99 GLN ** K 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.3842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 20481 Z= 0.170 Angle : 0.747 13.470 27798 Z= 0.360 Chirality : 0.050 0.420 3375 Planarity : 0.004 0.051 3432 Dihedral : 6.006 45.533 2568 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.21 % Allowed : 11.87 % Favored : 87.92 % Rotamer Outliers : 0.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.48 % 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: -3.46 (0.16), residues: 2367 helix: -1.62 (0.30), residues: 318 sheet: -1.70 (0.21), residues: 558 loop : -2.85 (0.14), residues: 1491 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 397 time to evaluate : 2.343 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 outliers start: 12 outliers final: 9 residues processed: 402 average time/residue: 0.3060 time to fit residues: 193.7345 Evaluate side-chains 378 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 369 time to evaluate : 2.385 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 3 residues processed: 9 average time/residue: 0.1912 time to fit residues: 6.4373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 197 optimal weight: 4.9990 chunk 56 optimal weight: 6.9990 chunk 171 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 185 optimal weight: 0.9980 chunk 77 optimal weight: 4.9990 chunk 190 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 34 optimal weight: 6.9990 chunk 163 optimal weight: 3.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 80 ASN C 575 GLN ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 80 ASN ** G 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 GLN I 302 ASN ** K 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.130699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.102992 restraints weight = 32957.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.106225 restraints weight = 18699.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.108363 restraints weight = 13107.182| |-----------------------------------------------------------------------------| r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.3868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.044 20481 Z= 0.342 Angle : 0.819 14.686 27798 Z= 0.397 Chirality : 0.053 0.432 3375 Planarity : 0.004 0.050 3432 Dihedral : 6.228 41.677 2568 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.17 % Allowed : 14.53 % Favored : 85.30 % Rotamer Outliers : 1.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.48 % 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: -3.65 (0.16), residues: 2367 helix: -1.84 (0.29), residues: 336 sheet: -2.02 (0.20), residues: 642 loop : -2.88 (0.15), residues: 1389 =============================================================================== Job complete usr+sys time: 4187.90 seconds wall clock time: 77 minutes 1.08 seconds (4621.08 seconds total)