Starting phenix.real_space_refine on Mon Mar 18 06:36:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6orq_20178/03_2024/6orq_20178.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6orq_20178/03_2024/6orq_20178.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6orq_20178/03_2024/6orq_20178.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6orq_20178/03_2024/6orq_20178.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6orq_20178/03_2024/6orq_20178.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6orq_20178/03_2024/6orq_20178.pdb" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.144 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 132 5.16 5 C 12626 2.51 5 N 3364 2.21 5 O 4054 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 38": "NH1" <-> "NH2" Residue "D ARG 66": "NH1" <-> "NH2" Residue "D TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 94": "NH1" <-> "NH2" Residue "E ARG 18": "NH1" <-> "NH2" Residue "E ARG 61": "NH1" <-> "NH2" Residue "E PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 327": "NH1" <-> "NH2" Residue "G ARG 456": "NH1" <-> "NH2" Residue "G ARG 469": "NH1" <-> "NH2" Residue "H ARG 38": "NH1" <-> "NH2" Residue "H ARG 66": "NH1" <-> "NH2" Residue "H TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 94": "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 38": "NH1" <-> "NH2" Residue "J ARG 66": "NH1" <-> "NH2" Residue "J TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 94": "NH1" <-> "NH2" Residue "K ARG 18": "NH1" <-> "NH2" Residue "K ARG 61": "NH1" <-> "NH2" Residue "K PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 18": "NH1" <-> "NH2" Residue "L ARG 61": "NH1" <-> "NH2" Residue "L PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 20176 Number of models: 1 Model: "" Number of chains: 40 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: 3573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3573 Classifications: {'peptide': 453} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 429} Chain breaks: 2 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: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 941 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "E" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 847 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 7, 'TRANS': 103} 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: 3573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3573 Classifications: {'peptide': 453} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 429} Chain breaks: 2 Chain: "H" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 941 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "I" Number of atoms: 3573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3573 Classifications: {'peptide': 453} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 429} Chain breaks: 2 Chain: "J" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 941 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "K" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 847 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 7, 'TRANS': 103} Chain: "L" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 847 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 7, 'TRANS': 103} Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "P" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 6 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "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 dihedrals: 9 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "I" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 11.26, per 1000 atoms: 0.56 Number of scatterers: 20176 At special positions: 0 Unit cell: (146.472, 145.036, 162.268, 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 132 16.00 O 4054 8.00 N 3364 7.00 C 12626 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=27, symmetry=0 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.03 Simple disulfide: pdb=" SG CYS B 119 " - pdb=" SG CYS B 205 " distance=2.04 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 196 " distance=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 157 " distance=2.05 Simple disulfide: pdb=" SG CYS B 218 " - pdb=" SG CYS B 247 " distance=2.07 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=2.03 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 445 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.04 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=2.05 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.06 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=2.03 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.03 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.03 Simple disulfide: pdb=" SG CYS I 119 " - pdb=" SG CYS I 205 " distance=2.04 Simple disulfide: pdb=" SG CYS I 126 " - pdb=" SG CYS I 196 " distance=2.04 Simple disulfide: pdb=" SG CYS I 131 " - pdb=" SG CYS I 157 " distance=2.05 Simple disulfide: pdb=" SG CYS I 218 " - pdb=" SG CYS I 247 " distance=2.06 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=2.03 Simple disulfide: pdb=" SG CYS I 378 " - pdb=" SG CYS I 445 " distance=2.03 Simple disulfide: pdb=" SG CYS I 385 " - pdb=" SG CYS I 418 " distance=2.03 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=1, symmetry=0 Links applied ALPHA1-3 " BMA O 3 " - " MAN O 4 " " BMA d 3 " - " MAN d 4 " ALPHA1-6 " BMA O 3 " - " MAN O 5 " " BMA d 3 " - " MAN d 5 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " 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 d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " NAG-ASN " NAG A 701 " - " ASN A 611 " " NAG A 702 " - " ASN A 618 " " NAG A 703 " - " ASN A 637 " " NAG B 601 " - " ASN B 88 " " NAG B 602 " - " ASN B 160 " " NAG B 615 " - " ASN B 295 " " NAG B 616 " - " ASN B 301 " " NAG B 619 " - " ASN B 339 " " NAG B 620 " - " ASN B 355 " " NAG B 623 " - " ASN B 392 " " NAG B 624 " - " ASN B 448 " " 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 618 " " NAG F 703 " - " ASN F 637 " " NAG G 601 " - " ASN G 88 " " NAG G 611 " - " ASN G 295 " " NAG G 617 " - " ASN G 339 " " NAG G 618 " - " ASN G 355 " " NAG G 621 " - " ASN G 392 " " NAG I 601 " - " ASN I 88 " " NAG I 602 " - " ASN I 160 " " NAG I 614 " - " ASN I 295 " " NAG I 615 " - " ASN I 301 " " NAG I 619 " - " ASN I 339 " " NAG I 620 " - " ASN I 355 " " NAG I 623 " - " ASN I 392 " " NAG M 1 " - " ASN B 197 " " NAG N 1 " - " ASN B 234 " " NAG O 1 " - " ASN B 262 " " NAG P 1 " - " ASN B 279 " " NAG Q 1 " - " ASN B 332 " " NAG R 1 " - " ASN B 386 " " NAG S 1 " - " ASN G 160 " " NAG T 1 " - " ASN G 234 " " NAG U 1 " - " ASN G 262 " " NAG V 1 " - " ASN G 279 " " NAG W 1 " - " ASN G 301 " " NAG X 1 " - " ASN G 332 " " NAG Y 1 " - " ASN G 386 " " NAG Z 1 " - " ASN G 448 " " NAG a 1 " - " ASN G 197 " " NAG b 1 " - " ASN I 197 " " NAG c 1 " - " ASN I 234 " " NAG d 1 " - " ASN I 262 " " NAG e 1 " - " ASN I 279 " " NAG f 1 " - " ASN I 332 " " NAG g 1 " - " ASN I 386 " " NAG h 1 " - " ASN I 448 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 8.70 Conformation dependent library (CDL) restraints added in 3.2 seconds 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4512 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 51 sheets defined 20.0% alpha, 15.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.19 Creating SS restraints... Processing helix chain 'A' and resid 529 through 535 removed outlier: 3.743A pdb=" N MET A 535 " --> pdb=" O GLY A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 543 Processing helix chain 'A' and resid 572 through 595 removed outlier: 3.965A pdb=" N ASP A 589 " --> pdb=" O HIS A 585 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLN A 590 " --> pdb=" O TYR A 586 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLN A 591 " --> pdb=" O LEU A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 624 Processing helix chain 'A' and resid 627 through 635 removed outlier: 3.998A pdb=" N LYS A 633 " --> pdb=" O LEU A 629 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLU A 634 " --> pdb=" O GLN A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 652 removed outlier: 3.737A pdb=" N GLY A 644 " --> pdb=" O GLN A 640 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU A 648 " --> pdb=" O GLY A 644 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER A 649 " --> pdb=" O LEU A 645 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN A 650 " --> pdb=" O LEU A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 657 Processing helix chain 'A' and resid 657 through 662 Processing helix chain 'B' and resid 59 through 64 removed outlier: 3.757A pdb=" N THR B 63 " --> pdb=" O LYS B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 67 No H-bonds generated for 'chain 'B' and resid 65 through 67' Processing helix chain 'B' and resid 99 through 117 removed outlier: 3.876A pdb=" N ILE B 108 " --> pdb=" O MET B 104 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE B 109 " --> pdb=" O HIS B 105 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLN B 114 " --> pdb=" O SER B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 139 removed outlier: 3.536A pdb=" N ASN B 137 " --> pdb=" O TYR B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 181 Processing helix chain 'B' and resid 334 through 351 removed outlier: 3.513A pdb=" N LYS B 347 " --> pdb=" O GLY B 343 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N LYS B 351 " --> pdb=" O LYS B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 354 No H-bonds generated for 'chain 'B' and resid 352 through 354' Processing helix chain 'B' and resid 368 through 372 removed outlier: 3.997A pdb=" N VAL B 371 " --> pdb=" O ASP B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 429 removed outlier: 3.668A pdb=" N GLN B 428 " --> pdb=" O ASN B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 483 removed outlier: 3.771A pdb=" N TRP B 479 " --> pdb=" O MET B 475 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU B 482 " --> pdb=" O ASN B 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 529 through 535 removed outlier: 3.743A pdb=" N MET C 535 " --> pdb=" O GLY C 531 " (cutoff:3.500A) Processing helix chain 'C' and resid 538 through 543 Processing helix chain 'C' and resid 572 through 595 removed outlier: 3.966A pdb=" N ASP C 589 " --> pdb=" O HIS C 585 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN C 590 " --> pdb=" O TYR C 586 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLN C 591 " --> pdb=" O LEU C 587 " (cutoff:3.500A) Processing helix chain 'C' and resid 620 through 624 Processing helix chain 'C' and resid 627 through 635 removed outlier: 3.998A pdb=" N LYS C 633 " --> pdb=" O LEU C 629 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLU C 634 " --> pdb=" O GLN C 630 " (cutoff:3.500A) Processing helix chain 'C' and resid 638 through 652 removed outlier: 3.737A pdb=" N GLY C 644 " --> pdb=" O GLN C 640 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU C 648 " --> pdb=" O GLY C 644 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER C 649 " --> pdb=" O LEU C 645 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN C 650 " --> pdb=" O LEU C 646 " (cutoff:3.500A) Processing helix chain 'C' and resid 652 through 657 Processing helix chain 'C' and resid 657 through 662 Processing helix chain 'E' and resid 79 through 83 removed outlier: 3.816A pdb=" N ALA E 83 " --> pdb=" O GLU E 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 535 removed outlier: 3.742A pdb=" N MET F 535 " --> pdb=" O GLY F 531 " (cutoff:3.500A) Processing helix chain 'F' and resid 538 through 543 Processing helix chain 'F' and resid 572 through 595 removed outlier: 3.966A pdb=" N ASP F 589 " --> pdb=" O HIS F 585 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN F 590 " --> pdb=" O TYR F 586 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLN F 591 " --> pdb=" O LEU F 587 " (cutoff:3.500A) Processing helix chain 'F' and resid 620 through 624 Processing helix chain 'F' and resid 627 through 635 removed outlier: 3.998A pdb=" N LYS F 633 " --> pdb=" O LEU F 629 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLU F 634 " --> pdb=" O GLN F 630 " (cutoff:3.500A) Processing helix chain 'F' and resid 638 through 652 removed outlier: 3.737A pdb=" N GLY F 644 " --> pdb=" O GLN F 640 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU F 648 " --> pdb=" O GLY F 644 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER F 649 " --> pdb=" O LEU F 645 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLN F 650 " --> pdb=" O LEU F 646 " (cutoff:3.500A) Processing helix chain 'F' and resid 652 through 657 Processing helix chain 'F' and resid 657 through 662 Processing helix chain 'G' and resid 59 through 64 removed outlier: 3.908A pdb=" N THR G 63 " --> pdb=" O LYS G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 65 through 67 No H-bonds generated for 'chain 'G' and resid 65 through 67' Processing helix chain 'G' and resid 99 through 117 removed outlier: 3.616A pdb=" N ILE G 108 " --> pdb=" O MET G 104 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE G 109 " --> pdb=" O HIS G 105 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLN G 114 " --> pdb=" O SER G 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 134 through 139 removed outlier: 3.554A pdb=" N ASN G 137 " --> pdb=" O TYR G 134 " (cutoff:3.500A) 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 350 removed outlier: 3.522A pdb=" N LYS G 347 " --> pdb=" O GLY G 343 " (cutoff:3.500A) Processing helix chain 'G' and resid 351 through 354 removed outlier: 4.280A pdb=" N GLY G 354 " --> pdb=" O LYS G 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 351 through 354' Processing helix chain 'G' and resid 368 through 373 removed outlier: 4.087A pdb=" N THR G 372 " --> pdb=" O ASP G 368 " (cutoff:3.500A) Processing helix chain 'G' and resid 425 through 429 removed outlier: 3.570A pdb=" N GLN G 428 " --> pdb=" O ASN G 425 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ARG G 429 " --> pdb=" O MET G 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 425 through 429' Processing helix chain 'G' and resid 475 through 483 removed outlier: 3.940A pdb=" N TRP G 479 " --> pdb=" O MET G 475 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU G 482 " --> pdb=" O ASN G 478 " (cutoff:3.500A) Processing helix chain 'I' and resid 59 through 64 removed outlier: 3.796A pdb=" N THR I 63 " --> pdb=" O LYS I 59 " (cutoff:3.500A) Processing helix chain 'I' and resid 65 through 67 No H-bonds generated for 'chain 'I' and resid 65 through 67' Processing helix chain 'I' and resid 99 through 117 removed outlier: 3.777A pdb=" N ILE I 108 " --> pdb=" O MET I 104 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE I 109 " --> pdb=" O HIS I 105 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLN I 114 " --> pdb=" O SER I 110 " (cutoff:3.500A) Processing helix chain 'I' and resid 134 through 139 removed outlier: 3.552A pdb=" N ASN I 137 " --> pdb=" O TYR I 134 " (cutoff:3.500A) 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 350 removed outlier: 3.503A pdb=" N LYS I 347 " --> pdb=" O GLY I 343 " (cutoff:3.500A) Processing helix chain 'I' and resid 351 through 354 removed outlier: 4.259A pdb=" N GLY I 354 " --> pdb=" O LYS I 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 351 through 354' Processing helix chain 'I' and resid 368 through 372 removed outlier: 4.028A pdb=" N VAL I 371 " --> pdb=" O ASP I 368 " (cutoff:3.500A) Processing helix chain 'I' and resid 387 through 390 Processing helix chain 'I' and resid 425 through 429 removed outlier: 3.726A pdb=" N GLN I 428 " --> pdb=" O ASN I 425 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ARG I 429 " --> pdb=" O MET I 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 425 through 429' Processing helix chain 'I' and resid 475 through 481 removed outlier: 3.974A pdb=" N TRP I 479 " --> pdb=" O MET I 475 " (cutoff:3.500A) Processing helix chain 'K' and resid 79 through 83 removed outlier: 3.816A pdb=" N ALA K 83 " --> pdb=" O GLU K 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.817A pdb=" N ALA L 83 " --> pdb=" O GLU L 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 603 through 609 removed outlier: 3.877A pdb=" N CYS A 604 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL B 38 " --> pdb=" O CYS A 604 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N THR A 606 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N VAL B 36 " --> pdb=" O THR A 606 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N TRP B 35 " --> pdb=" O THR B 499 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 45 through 46 removed outlier: 3.818A pdb=" N LYS B 490 " --> pdb=" O LYS B 46 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS B 487 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE B 225 " --> pdb=" O VAL B 245 " (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 92 through 93 Processing sheet with id=AA5, first strand: chain 'B' and resid 130 through 131 removed outlier: 4.046A pdb=" N GLN B 130 " --> pdb=" O SER B 158 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N SER B 158 " --> pdb=" O GLN B 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 160 through 162 Processing sheet with id=AA7, first strand: chain 'B' and resid 182 through 183 Processing sheet with id=AA8, first strand: chain 'B' and resid 202 through 203 removed outlier: 6.582A pdb=" N THR B 202 " --> pdb=" O TYR B 435 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 259 through 261 removed outlier: 4.097A pdb=" N GLY B 451 " --> pdb=" O LEU B 260 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU B 452 " --> pdb=" O VAL B 286 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL B 286 " --> pdb=" O LEU B 452 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 259 through 261 removed outlier: 4.097A pdb=" N GLY B 451 " --> pdb=" O LEU B 260 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL B 292 " --> pdb=" O ILE B 449 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN B 295 " --> pdb=" O ASN B 332 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR B 297 " --> pdb=" O HIS B 330 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N HIS B 330 " --> pdb=" O THR B 297 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N PHE B 376 " --> pdb=" O PHE B 383 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 305 through 308 removed outlier: 3.533A pdb=" N LYS B 305 " --> pdb=" O TYR B 319 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 394 through 395 removed outlier: 3.601A pdb=" N ILE B 359 " --> pdb=" O TRP B 395 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ARG B 360 " --> pdb=" O PHE B 468 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 603 through 609 removed outlier: 3.949A pdb=" N CYS C 604 " --> pdb=" O VAL G 38 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL G 38 " --> pdb=" O CYS C 604 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N THR C 606 " --> pdb=" O VAL G 36 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N VAL G 36 " --> pdb=" O THR C 606 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 19 through 21 Processing sheet with id=AB6, first strand: chain 'D' and resid 48 through 49 removed outlier: 3.621A pdb=" N ALA D 93 " --> pdb=" O SER D 35 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL D 37 " --> pdb=" O TYR D 91 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 45 through 46 Processing sheet with id=AB8, first strand: chain 'E' and resid 48 through 49 Processing sheet with id=AB9, first strand: chain 'E' and resid 63 through 64 removed outlier: 3.973A pdb=" N SER E 63 " --> pdb=" O ASN E 74 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASN E 74 " --> pdb=" O SER E 63 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'F' and resid 603 through 609 removed outlier: 3.908A pdb=" N CYS F 604 " --> pdb=" O VAL I 38 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL I 38 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N THR F 606 " --> pdb=" O VAL I 36 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N VAL I 36 " --> pdb=" O THR F 606 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 45 through 46 removed outlier: 3.524A pdb=" N LYS G 46 " --> pdb=" O LYS G 490 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LYS G 490 " --> pdb=" O LYS G 46 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS G 487 " --> pdb=" O LEU G 226 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE G 225 " --> pdb=" O VAL G 245 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 53 through 54 Processing sheet with id=AC4, first strand: chain 'G' and resid 92 through 93 Processing sheet with id=AC5, first strand: chain 'G' and resid 130 through 132 removed outlier: 4.057A pdb=" N GLN G 130 " --> pdb=" O SER G 158 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N SER G 158 " --> pdb=" O GLN G 130 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N THR G 132 " --> pdb=" O GLN G 156 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 160 through 162 Processing sheet with id=AC7, first strand: chain 'G' and resid 181 through 183 Processing sheet with id=AC8, first strand: chain 'G' and resid 202 through 203 removed outlier: 6.706A pdb=" N THR G 202 " --> pdb=" O TYR G 435 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 271 through 274 Processing sheet with id=AD1, first strand: chain 'G' and resid 374 through 378 removed outlier: 3.731A pdb=" N PHE G 376 " --> pdb=" O PHE G 383 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N HIS G 330 " --> pdb=" O THR G 297 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR G 297 " --> pdb=" O HIS G 330 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASN G 295 " --> pdb=" O ASN G 332 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL G 292 " --> pdb=" O ILE G 449 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 304 through 308 removed outlier: 3.678A pdb=" N LYS G 305 " --> pdb=" O TYR G 319 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 394 through 395 removed outlier: 3.597A pdb=" N ILE G 359 " --> pdb=" O TRP G 395 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ARG G 360 " --> pdb=" O PHE G 468 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 19 through 21 Processing sheet with id=AD5, first strand: chain 'H' and resid 48 through 49 removed outlier: 3.621A pdb=" N ALA H 93 " --> pdb=" O SER H 35 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL H 37 " --> pdb=" O TYR H 91 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 45 through 46 removed outlier: 3.737A pdb=" N LYS I 490 " --> pdb=" O LYS I 46 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE I 225 " --> pdb=" O VAL I 245 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 53 through 55 removed outlier: 3.790A pdb=" N HIS I 216 " --> pdb=" O ALA I 55 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 91 through 93 removed outlier: 4.087A pdb=" N GLU I 91 " --> pdb=" O CYS I 239 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 121 through 122 removed outlier: 3.947A pdb=" N LEU I 122 " --> pdb=" O ILE I 201 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N ILE I 201 " --> pdb=" O LEU I 122 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N THR I 202 " --> pdb=" O TYR I 435 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 130 through 132 removed outlier: 4.110A pdb=" N GLN I 130 " --> pdb=" O SER I 158 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N SER I 158 " --> pdb=" O GLN I 130 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 160 through 162 Processing sheet with id=AE3, first strand: chain 'I' and resid 181 through 183 Processing sheet with id=AE4, first strand: chain 'I' and resid 271 through 274 removed outlier: 3.574A pdb=" N GLN I 287 " --> pdb=" O ILE I 271 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I' and resid 374 through 378 removed outlier: 3.741A pdb=" N PHE I 376 " --> pdb=" O PHE I 383 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N HIS I 330 " --> pdb=" O THR I 297 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR I 297 " --> pdb=" O HIS I 330 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASN I 295 " --> pdb=" O ASN I 332 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N VAL I 292 " --> pdb=" O ILE I 449 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'I' and resid 304 through 308 removed outlier: 3.553A pdb=" N LYS I 305 " --> pdb=" O TYR I 319 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 394 through 395 removed outlier: 3.623A pdb=" N ILE I 359 " --> pdb=" O TRP I 395 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ARG I 360 " --> pdb=" O PHE I 468 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 19 through 21 Processing sheet with id=AE9, first strand: chain 'J' and resid 48 through 49 removed outlier: 3.621A pdb=" N ALA J 93 " --> pdb=" O SER J 35 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL J 37 " --> pdb=" O TYR J 91 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'K' and resid 45 through 46 Processing sheet with id=AF2, first strand: chain 'K' and resid 48 through 49 Processing sheet with id=AF3, first strand: chain 'K' and resid 63 through 64 removed outlier: 3.974A pdb=" N SER K 63 " --> pdb=" O ASN K 74 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASN K 74 " --> pdb=" O SER K 63 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'L' and resid 45 through 46 Processing sheet with id=AF5, first strand: chain 'L' and resid 48 through 49 Processing sheet with id=AF6, first strand: chain 'L' and resid 63 through 64 removed outlier: 3.974A pdb=" N SER L 63 " --> pdb=" O ASN L 74 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASN L 74 " --> pdb=" O SER L 63 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF6 415 hydrogen bonds defined for protein. 1026 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: 6.12 Time building geometry restraints manager: 9.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3261 1.31 - 1.45: 5847 1.45 - 1.58: 11293 1.58 - 1.72: 0 1.72 - 1.85: 186 Bond restraints: 20587 Sorted by residual: bond pdb=" C3 NAG a 1 " pdb=" C4 NAG a 1 " ideal model delta sigma weight residual 1.524 1.449 0.075 2.00e-02 2.50e+03 1.39e+01 bond pdb=" C3 BMA d 3 " pdb=" O3 BMA d 3 " ideal model delta sigma weight residual 1.406 1.476 -0.070 2.00e-02 2.50e+03 1.22e+01 bond pdb=" C4 NAG a 1 " pdb=" C5 NAG a 1 " ideal model delta sigma weight residual 1.532 1.463 0.069 2.00e-02 2.50e+03 1.18e+01 bond pdb=" C3 NAG a 2 " pdb=" C4 NAG a 2 " ideal model delta sigma weight residual 1.524 1.455 0.069 2.00e-02 2.50e+03 1.18e+01 bond pdb=" C7 NAG a 1 " pdb=" C8 NAG a 1 " ideal model delta sigma weight residual 1.509 1.443 0.066 2.00e-02 2.50e+03 1.07e+01 ... (remaining 20582 not shown) Histogram of bond angle deviations from ideal: 92.83 - 101.56: 54 101.56 - 110.28: 5409 110.28 - 119.01: 11754 119.01 - 127.73: 10469 127.73 - 136.46: 248 Bond angle restraints: 27934 Sorted by residual: angle pdb=" N LEU J 45 " pdb=" CA LEU J 45 " pdb=" C LEU J 45 " ideal model delta sigma weight residual 110.80 125.23 -14.43 2.13e+00 2.20e-01 4.59e+01 angle pdb=" N LEU H 45 " pdb=" CA LEU H 45 " pdb=" C LEU H 45 " ideal model delta sigma weight residual 110.80 125.22 -14.42 2.13e+00 2.20e-01 4.58e+01 angle pdb=" N LEU D 45 " pdb=" CA LEU D 45 " pdb=" C LEU D 45 " ideal model delta sigma weight residual 110.80 125.19 -14.39 2.13e+00 2.20e-01 4.57e+01 angle pdb=" C3 NAG a 1 " pdb=" C2 NAG a 1 " pdb=" N2 NAG a 1 " ideal model delta sigma weight residual 110.74 92.83 17.91 3.00e+00 1.11e-01 3.56e+01 angle pdb=" N VAL B 371 " pdb=" CA VAL B 371 " pdb=" C VAL B 371 " ideal model delta sigma weight residual 113.42 106.98 6.44 1.17e+00 7.31e-01 3.03e+01 ... (remaining 27929 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.12: 12478 22.12 - 44.23: 703 44.23 - 66.35: 116 66.35 - 88.47: 74 88.47 - 110.59: 31 Dihedral angle restraints: 13402 sinusoidal: 6382 harmonic: 7020 Sorted by residual: dihedral pdb=" CA LYS J 13 " pdb=" C LYS J 13 " pdb=" N PRO J 14 " pdb=" CA PRO J 14 " ideal model delta harmonic sigma weight residual 180.00 -123.10 -56.90 0 5.00e+00 4.00e-02 1.30e+02 dihedral pdb=" CA LYS H 13 " pdb=" C LYS H 13 " pdb=" N PRO H 14 " pdb=" CA PRO H 14 " ideal model delta harmonic sigma weight residual 180.00 -123.14 -56.86 0 5.00e+00 4.00e-02 1.29e+02 dihedral pdb=" CA LYS D 13 " pdb=" C LYS D 13 " pdb=" N PRO D 14 " pdb=" CA PRO D 14 " ideal model delta harmonic sigma weight residual -180.00 -123.15 -56.85 0 5.00e+00 4.00e-02 1.29e+02 ... (remaining 13399 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.166: 3213 0.166 - 0.333: 109 0.333 - 0.499: 11 0.499 - 0.666: 0 0.666 - 0.832: 4 Chirality restraints: 3337 Sorted by residual: chirality pdb=" C1 NAG a 2 " pdb=" O4 NAG a 1 " pdb=" C2 NAG a 2 " pdb=" O5 NAG a 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-02 2.50e+03 1.65e+02 chirality pdb=" C5 NAG a 1 " pdb=" C4 NAG a 1 " pdb=" C6 NAG a 1 " pdb=" O5 NAG a 1 " both_signs ideal model delta sigma weight residual False -2.41 -1.58 -0.83 2.00e-01 2.50e+01 1.73e+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 -1.61 -0.79 2.00e-01 2.50e+01 1.54e+01 ... (remaining 3334 not shown) Planarity restraints: 3514 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG a 2 " -0.404 2.00e-02 2.50e+03 3.32e-01 1.38e+03 pdb=" C7 NAG a 2 " 0.166 2.00e-02 2.50e+03 pdb=" C8 NAG a 2 " -0.243 2.00e-02 2.50e+03 pdb=" N2 NAG a 2 " 0.545 2.00e-02 2.50e+03 pdb=" O7 NAG a 2 " -0.064 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG a 1 " 0.366 2.00e-02 2.50e+03 3.15e-01 1.24e+03 pdb=" C7 NAG a 1 " -0.127 2.00e-02 2.50e+03 pdb=" C8 NAG a 1 " 0.181 2.00e-02 2.50e+03 pdb=" N2 NAG a 1 " -0.545 2.00e-02 2.50e+03 pdb=" O7 NAG a 1 " 0.124 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS D 13 " 0.064 5.00e-02 4.00e+02 9.67e-02 1.50e+01 pdb=" N PRO D 14 " -0.167 5.00e-02 4.00e+02 pdb=" CA PRO D 14 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO D 14 " 0.053 5.00e-02 4.00e+02 ... (remaining 3511 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 297 2.61 - 3.18: 17193 3.18 - 3.76: 30218 3.76 - 4.33: 37608 4.33 - 4.90: 59246 Nonbonded interactions: 144562 Sorted by model distance: nonbonded pdb=" O4 NAG a 2 " pdb=" O6 NAG a 2 " model vdw 2.039 2.440 nonbonded pdb=" O4 NAG a 1 " pdb=" O6 NAG a 1 " model vdw 2.136 2.440 nonbonded pdb=" OG1 THR J 68 " pdb=" O GLN J 81 " model vdw 2.241 2.440 nonbonded pdb=" OG1 THR H 68 " pdb=" O GLN H 81 " model vdw 2.242 2.440 nonbonded pdb=" OG1 THR D 68 " pdb=" O GLN D 81 " model vdw 2.243 2.440 ... (remaining 144557 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' and (resid 31 through 505 or resid 601 through 619)) selection = chain 'G' selection = (chain 'I' and (resid 31 through 505 or resid 601 through 619)) } 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 'N' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'V' selection = chain 'W' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'e' selection = chain 'g' selection = chain 'h' } ncs_group { reference = chain 'O' selection = chain 'd' } ncs_group { reference = chain 'P' selection = chain 'U' selection = chain 'X' selection = chain 'f' } 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: 0.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.820 Check model and map are aligned: 0.320 Set scattering table: 0.210 Process input model: 52.970 Find NCS groups from input model: 1.460 Set up NCS constraints: 0.320 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 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 : 0.008 0.075 20587 Z= 0.519 Angle : 1.309 17.910 27934 Z= 0.668 Chirality : 0.077 0.832 3337 Planarity : 0.011 0.332 3463 Dihedral : 15.528 110.585 8809 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.34 % Allowed : 16.29 % Favored : 83.38 % Rotamer: Outliers : 1.04 % Allowed : 7.81 % Favored : 91.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 5.88 % Twisted General : 0.61 % 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: -4.97 (0.13), residues: 2388 helix: -4.26 (0.15), residues: 288 sheet: -2.27 (0.23), residues: 459 loop : -3.69 (0.12), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP I 35 HIS 0.013 0.003 HIS E 76 PHE 0.023 0.003 PHE L 98 TYR 0.037 0.004 TYR I 134 ARG 0.015 0.001 ARG K 61 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 640 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 618 time to evaluate : 2.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 540 GLN cc_start: 0.8982 (mp-120) cc_final: 0.8722 (mp10) REVERT: A 574 LYS cc_start: 0.8977 (OUTLIER) cc_final: 0.8333 (mttm) REVERT: A 584 GLU cc_start: 0.8709 (tm-30) cc_final: 0.8317 (tm-30) REVERT: A 588 ARG cc_start: 0.9131 (ttt180) cc_final: 0.8893 (ttt90) REVERT: A 621 GLU cc_start: 0.8832 (tm-30) cc_final: 0.8494 (tm-30) REVERT: A 647 GLU cc_start: 0.9051 (pp20) cc_final: 0.8847 (pp20) REVERT: A 648 GLU cc_start: 0.9036 (pp20) cc_final: 0.8704 (pp20) REVERT: A 654 GLU cc_start: 0.9115 (mm-30) cc_final: 0.8771 (tp30) REVERT: B 80 ASN cc_start: 0.8902 (t0) cc_final: 0.8443 (p0) REVERT: B 104 MET cc_start: 0.8942 (ttm) cc_final: 0.8596 (ttm) REVERT: B 114 GLN cc_start: 0.9278 (tm-30) cc_final: 0.9049 (tm-30) REVERT: B 161 MET cc_start: 0.9228 (tpp) cc_final: 0.8837 (tpp) REVERT: B 256 SER cc_start: 0.9266 (m) cc_final: 0.9012 (m) REVERT: B 340 GLU cc_start: 0.9317 (tp30) cc_final: 0.9109 (tp30) REVERT: C 535 MET cc_start: 0.8927 (mtt) cc_final: 0.8591 (mmm) REVERT: C 542 ARG cc_start: 0.9260 (mtp-110) cc_final: 0.9004 (ttp80) REVERT: C 543 ASN cc_start: 0.8918 (t0) cc_final: 0.8642 (t0) REVERT: C 574 LYS cc_start: 0.9075 (OUTLIER) cc_final: 0.8785 (ttmm) REVERT: C 584 GLU cc_start: 0.8716 (tm-30) cc_final: 0.8345 (tm-30) REVERT: C 621 GLU cc_start: 0.8658 (tm-30) cc_final: 0.8299 (tm-30) REVERT: C 648 GLU cc_start: 0.9151 (pp20) cc_final: 0.8713 (pm20) REVERT: D 34 MET cc_start: 0.9026 (mpt) cc_final: 0.8790 (mmm) REVERT: D 36 TRP cc_start: 0.8331 (m100) cc_final: 0.8021 (m-10) REVERT: D 82 LEU cc_start: 0.9165 (mt) cc_final: 0.8760 (mt) REVERT: D 85 GLU cc_start: 0.8895 (mm-30) cc_final: 0.8472 (pp20) REVERT: E 37 GLN cc_start: 0.7675 (pp30) cc_final: 0.7095 (pp30) REVERT: E 38 GLN cc_start: 0.8843 (pt0) cc_final: 0.8463 (pt0) REVERT: E 47 LEU cc_start: 0.8909 (mm) cc_final: 0.8702 (mm) REVERT: E 72 THR cc_start: 0.7080 (t) cc_final: 0.6755 (t) REVERT: F 574 LYS cc_start: 0.8887 (OUTLIER) cc_final: 0.8665 (ttmm) REVERT: F 584 GLU cc_start: 0.8875 (tm-30) cc_final: 0.8485 (tm-30) REVERT: F 621 GLU cc_start: 0.8845 (tm-30) cc_final: 0.7486 (tm-30) REVERT: F 622 ILE cc_start: 0.9196 (pp) cc_final: 0.7980 (pp) REVERT: F 624 ASP cc_start: 0.8804 (m-30) cc_final: 0.8535 (m-30) REVERT: F 648 GLU cc_start: 0.9104 (pp20) cc_final: 0.8833 (pp20) REVERT: F 654 GLU cc_start: 0.8991 (mm-30) cc_final: 0.8724 (tp30) REVERT: F 655 LYS cc_start: 0.8833 (pptt) cc_final: 0.8614 (pptt) REVERT: G 114 GLN cc_start: 0.9394 (tm-30) cc_final: 0.9115 (tm-30) REVERT: G 150 MET cc_start: 0.8892 (tmt) cc_final: 0.8540 (tmm) REVERT: G 161 MET cc_start: 0.9127 (tpp) cc_final: 0.8759 (tpp) REVERT: G 252 LYS cc_start: 0.9251 (mtmm) cc_final: 0.8993 (mtpp) REVERT: G 302 ASN cc_start: 0.8304 (t0) cc_final: 0.7879 (t0) REVERT: G 321 ASP cc_start: 0.8678 (t70) cc_final: 0.8301 (t70) REVERT: H 1 GLU cc_start: 0.8802 (tm-30) cc_final: 0.8388 (pm20) REVERT: H 29 PHE cc_start: 0.8894 (t80) cc_final: 0.8578 (t80) REVERT: H 51 ILE cc_start: 0.8556 (pt) cc_final: 0.8301 (pt) REVERT: H 67 PHE cc_start: 0.8728 (p90) cc_final: 0.8352 (p90) REVERT: I 80 ASN cc_start: 0.9034 (t0) cc_final: 0.8608 (p0) REVERT: I 114 GLN cc_start: 0.9351 (tm-30) cc_final: 0.9090 (tm-30) REVERT: I 125 LEU cc_start: 0.8971 (tt) cc_final: 0.8673 (tt) REVERT: I 211 GLU cc_start: 0.9021 (tm-30) cc_final: 0.8747 (tm-30) REVERT: I 217 TYR cc_start: 0.8111 (m-10) cc_final: 0.7025 (m-10) REVERT: I 230 ASP cc_start: 0.8785 (t0) cc_final: 0.8570 (t0) REVERT: I 252 LYS cc_start: 0.9348 (mtmm) cc_final: 0.8941 (mtpp) REVERT: I 340 GLU cc_start: 0.9287 (tp30) cc_final: 0.9015 (tm-30) REVERT: I 425 ASN cc_start: 0.9354 (p0) cc_final: 0.9113 (p0) REVERT: I 452 LEU cc_start: 0.9181 (mm) cc_final: 0.8443 (tt) REVERT: I 477 ASP cc_start: 0.9278 (p0) cc_final: 0.9070 (p0) REVERT: I 479 TRP cc_start: 0.8841 (m-10) cc_final: 0.8452 (m-10) REVERT: I 482 GLU cc_start: 0.8905 (mm-30) cc_final: 0.8633 (mm-30) REVERT: J 1 GLU cc_start: 0.8793 (tm-30) cc_final: 0.8244 (pm20) REVERT: J 27 PHE cc_start: 0.8394 (m-10) cc_final: 0.8031 (m-10) REVERT: J 29 PHE cc_start: 0.8710 (t80) cc_final: 0.8480 (t80) REVERT: J 34 MET cc_start: 0.9346 (mpt) cc_final: 0.9105 (mmm) REVERT: J 36 TRP cc_start: 0.8285 (m100) cc_final: 0.7883 (m100) REVERT: J 71 ARG cc_start: 0.8473 (tmt90) cc_final: 0.8155 (ttt-90) REVERT: J 82 LEU cc_start: 0.8863 (mt) cc_final: 0.8015 (mt) REVERT: J 85 GLU cc_start: 0.8818 (mm-30) cc_final: 0.8314 (pp20) REVERT: J 91 TYR cc_start: 0.8743 (m-80) cc_final: 0.8533 (m-80) REVERT: K 37 GLN cc_start: 0.8014 (pp30) cc_final: 0.7190 (pp30) REVERT: K 38 GLN cc_start: 0.8597 (pt0) cc_final: 0.8307 (pp30) REVERT: K 45 LYS cc_start: 0.8632 (tptm) cc_final: 0.8255 (ttpt) REVERT: K 81 GLU cc_start: 0.9277 (pp20) cc_final: 0.8967 (pp20) REVERT: L 37 GLN cc_start: 0.8466 (pp30) cc_final: 0.7784 (pp30) REVERT: L 38 GLN cc_start: 0.8651 (pt0) cc_final: 0.8305 (pp30) REVERT: L 45 LYS cc_start: 0.8997 (tptm) cc_final: 0.8638 (ttpt) outliers start: 22 outliers final: 10 residues processed: 629 average time/residue: 0.3267 time to fit residues: 306.4434 Evaluate side-chains 433 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 420 time to evaluate : 2.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 202 optimal weight: 0.1980 chunk 181 optimal weight: 7.9990 chunk 100 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 122 optimal weight: 0.4980 chunk 97 optimal weight: 5.9990 chunk 188 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 114 optimal weight: 0.8980 chunk 140 optimal weight: 6.9990 chunk 217 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 570 HIS A 590 GLN ** A 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS B 203 GLN B 258 GLN C 570 HIS C 590 GLN C 616 ASN ** C 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 570 HIS F 590 GLN F 616 ASN ** F 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 66 HIS G 293 GLN G 300 ASN G 440 GLN ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 258 GLN ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 20587 Z= 0.220 Angle : 0.878 17.669 27934 Z= 0.423 Chirality : 0.054 0.535 3337 Planarity : 0.006 0.102 3463 Dihedral : 13.095 97.664 4330 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.21 % Allowed : 14.28 % Favored : 85.51 % Rotamer: Outliers : 0.43 % Allowed : 4.88 % Favored : 94.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 5.88 % Twisted General : 0.35 % 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: -4.46 (0.14), residues: 2388 helix: -2.63 (0.20), residues: 372 sheet: -1.62 (0.26), residues: 405 loop : -3.68 (0.12), residues: 1611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 631 HIS 0.010 0.001 HIS K 76 PHE 0.021 0.002 PHE B 376 TYR 0.023 0.002 TYR G 134 ARG 0.005 0.001 ARG I 178 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 583 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 574 time to evaluate : 2.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 535 MET cc_start: 0.8613 (mmt) cc_final: 0.8366 (mmm) REVERT: A 584 GLU cc_start: 0.8967 (tm-30) cc_final: 0.8530 (tm-30) REVERT: A 648 GLU cc_start: 0.9193 (pp20) cc_final: 0.8938 (pp20) REVERT: B 80 ASN cc_start: 0.8883 (t0) cc_final: 0.8359 (p0) REVERT: B 98 ASN cc_start: 0.8474 (t0) cc_final: 0.6879 (t0) REVERT: B 99 ASN cc_start: 0.9270 (m-40) cc_final: 0.8621 (m-40) REVERT: B 102 GLU cc_start: 0.9272 (mp0) cc_final: 0.8804 (mp0) REVERT: B 114 GLN cc_start: 0.9312 (tm-30) cc_final: 0.9069 (tm-30) REVERT: B 161 MET cc_start: 0.9211 (tpp) cc_final: 0.8975 (tpp) REVERT: B 321 ASP cc_start: 0.8989 (t70) cc_final: 0.8494 (t0) REVERT: B 452 LEU cc_start: 0.9434 (pt) cc_final: 0.9144 (pp) REVERT: B 504 ARG cc_start: 0.8802 (tpm170) cc_final: 0.8593 (mmm160) REVERT: C 535 MET cc_start: 0.8906 (mtt) cc_final: 0.8678 (mmm) REVERT: C 584 GLU cc_start: 0.8906 (tm-30) cc_final: 0.8519 (tm-30) REVERT: C 621 GLU cc_start: 0.8718 (tm-30) cc_final: 0.8429 (tm-30) REVERT: C 622 ILE cc_start: 0.9206 (pt) cc_final: 0.8974 (mp) REVERT: C 648 GLU cc_start: 0.9184 (pp20) cc_final: 0.8718 (pm20) REVERT: D 82 MET cc_start: 0.8550 (mmm) cc_final: 0.8270 (mmm) REVERT: D 82 LEU cc_start: 0.8796 (mt) cc_final: 0.8538 (tp) REVERT: D 102 TYR cc_start: 0.9400 (m-80) cc_final: 0.8924 (m-80) REVERT: E 37 GLN cc_start: 0.7931 (pp30) cc_final: 0.7396 (pp30) REVERT: E 45 LYS cc_start: 0.8810 (tptp) cc_final: 0.8390 (ttpp) REVERT: E 72 THR cc_start: 0.6868 (t) cc_final: 0.6273 (t) REVERT: F 577 GLN cc_start: 0.9123 (mt0) cc_final: 0.8818 (mt0) REVERT: F 624 ASP cc_start: 0.8919 (m-30) cc_final: 0.8664 (m-30) REVERT: F 648 GLU cc_start: 0.9152 (pp20) cc_final: 0.8666 (pm20) REVERT: G 98 ASN cc_start: 0.8807 (t0) cc_final: 0.7782 (t0) REVERT: G 102 GLU cc_start: 0.9294 (mp0) cc_final: 0.8914 (mp0) REVERT: G 114 GLN cc_start: 0.9434 (tm-30) cc_final: 0.9157 (tm-30) REVERT: G 302 ASN cc_start: 0.8412 (t0) cc_final: 0.7922 (t0) REVERT: G 321 ASP cc_start: 0.8722 (t70) cc_final: 0.8316 (t70) REVERT: G 426 MET cc_start: 0.8798 (ptm) cc_final: 0.8284 (ptm) REVERT: G 434 MET cc_start: 0.7994 (tmm) cc_final: 0.7572 (tmm) REVERT: H 1 GLU cc_start: 0.8805 (tm-30) cc_final: 0.8343 (pm20) REVERT: H 58 TYR cc_start: 0.6072 (p90) cc_final: 0.5353 (p90) REVERT: H 67 PHE cc_start: 0.8805 (p90) cc_final: 0.8362 (p90) REVERT: I 59 LYS cc_start: 0.8309 (tptp) cc_final: 0.8059 (tptp) REVERT: I 80 ASN cc_start: 0.9056 (t0) cc_final: 0.8626 (p0) REVERT: I 98 ASN cc_start: 0.8621 (t0) cc_final: 0.7836 (t0) REVERT: I 102 GLU cc_start: 0.9263 (mp0) cc_final: 0.8856 (mp0) REVERT: I 114 GLN cc_start: 0.9431 (tm-30) cc_final: 0.9120 (tm-30) REVERT: I 252 LYS cc_start: 0.9328 (mtmm) cc_final: 0.8927 (mtpp) REVERT: I 425 ASN cc_start: 0.9373 (p0) cc_final: 0.9097 (p0) REVERT: I 482 GLU cc_start: 0.8824 (mm-30) cc_final: 0.8605 (mm-30) REVERT: J 1 GLU cc_start: 0.8796 (tm-30) cc_final: 0.8334 (pm20) REVERT: J 29 PHE cc_start: 0.8621 (t80) cc_final: 0.8290 (t80) REVERT: J 36 TRP cc_start: 0.8409 (m100) cc_final: 0.8045 (m100) REVERT: J 85 GLU cc_start: 0.8770 (mm-30) cc_final: 0.8078 (tm-30) REVERT: J 91 TYR cc_start: 0.8717 (m-80) cc_final: 0.8225 (m-80) REVERT: J 102 TYR cc_start: 0.9289 (m-80) cc_final: 0.8604 (m-80) REVERT: K 37 GLN cc_start: 0.8061 (pp30) cc_final: 0.7145 (pp30) REVERT: K 38 GLN cc_start: 0.8643 (pt0) cc_final: 0.7648 (tt0) REVERT: K 45 LYS cc_start: 0.9001 (tptm) cc_final: 0.8762 (ttpt) REVERT: L 37 GLN cc_start: 0.8045 (pp30) cc_final: 0.7398 (pp30) REVERT: L 38 GLN cc_start: 0.8766 (pt0) cc_final: 0.7847 (tt0) REVERT: L 72 THR cc_start: 0.7015 (t) cc_final: 0.6435 (t) REVERT: L 97 THR cc_start: 0.9077 (m) cc_final: 0.8837 (p) outliers start: 9 outliers final: 5 residues processed: 580 average time/residue: 0.3168 time to fit residues: 285.2290 Evaluate side-chains 432 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 427 time to evaluate : 2.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 121 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 181 optimal weight: 9.9990 chunk 148 optimal weight: 10.0000 chunk 60 optimal weight: 2.9990 chunk 218 optimal weight: 30.0000 chunk 235 optimal weight: 10.0000 chunk 194 optimal weight: 9.9990 chunk 216 optimal weight: 10.0000 chunk 74 optimal weight: 6.9990 chunk 175 optimal weight: 8.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS ** B 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 258 GLN B 276 ASN B 330 HIS ** C 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 89 GLN ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 66 HIS G 422 GLN G 440 GLN ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 66 HIS I 440 GLN ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 89 GLN ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 20587 Z= 0.456 Angle : 0.986 16.192 27934 Z= 0.477 Chirality : 0.056 0.506 3337 Planarity : 0.006 0.087 3463 Dihedral : 12.217 99.585 4330 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 21.69 Ramachandran Plot: Outliers : 0.21 % Allowed : 18.38 % Favored : 81.41 % Rotamer: Outliers : 0.24 % Allowed : 7.77 % Favored : 92.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 3.92 % Twisted General : 0.35 % 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: -4.15 (0.15), residues: 2388 helix: -1.36 (0.26), residues: 351 sheet: -1.42 (0.27), residues: 372 loop : -3.70 (0.12), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP C 631 HIS 0.010 0.002 HIS E 76 PHE 0.015 0.002 PHE I 93 TYR 0.024 0.003 TYR A 586 ARG 0.012 0.001 ARG L 61 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 478 time to evaluate : 2.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 535 MET cc_start: 0.8857 (mmt) cc_final: 0.8649 (mmt) REVERT: A 584 GLU cc_start: 0.8876 (tm-30) cc_final: 0.8613 (tm-30) REVERT: A 621 GLU cc_start: 0.8675 (tm-30) cc_final: 0.8412 (tm-30) REVERT: A 648 GLU cc_start: 0.9303 (pp20) cc_final: 0.8709 (pm20) REVERT: B 114 GLN cc_start: 0.9424 (tm-30) cc_final: 0.9216 (tm-30) REVERT: B 452 LEU cc_start: 0.9503 (pt) cc_final: 0.9161 (pp) REVERT: C 530 MET cc_start: 0.9036 (mmp) cc_final: 0.8665 (mmp) REVERT: C 535 MET cc_start: 0.9021 (mtt) cc_final: 0.8766 (mmm) REVERT: C 584 GLU cc_start: 0.8925 (tm-30) cc_final: 0.8637 (tm-30) REVERT: C 621 GLU cc_start: 0.8807 (tm-30) cc_final: 0.8529 (tm-30) REVERT: C 648 GLU cc_start: 0.9319 (pp20) cc_final: 0.8791 (pm20) REVERT: D 39 GLN cc_start: 0.8684 (mm-40) cc_final: 0.8031 (mm-40) REVERT: D 44 ARG cc_start: 0.6584 (mmt180) cc_final: 0.6041 (mmt-90) REVERT: D 82 MET cc_start: 0.8612 (mmm) cc_final: 0.8412 (mmm) REVERT: D 91 TYR cc_start: 0.8009 (m-80) cc_final: 0.7234 (m-10) REVERT: D 102 TYR cc_start: 0.9423 (m-80) cc_final: 0.9098 (m-80) REVERT: E 37 GLN cc_start: 0.7767 (pp30) cc_final: 0.7525 (pp30) REVERT: E 45 LYS cc_start: 0.9034 (tptp) cc_final: 0.8499 (ttpp) REVERT: E 72 THR cc_start: 0.7569 (t) cc_final: 0.6924 (t) REVERT: E 96 TYR cc_start: 0.8628 (m-10) cc_final: 0.8401 (m-10) REVERT: F 621 GLU cc_start: 0.8900 (tm-30) cc_final: 0.7508 (tm-30) REVERT: F 626 MET cc_start: 0.7860 (mtt) cc_final: 0.7350 (mpp) REVERT: F 648 GLU cc_start: 0.9284 (pp20) cc_final: 0.8817 (pm20) REVERT: G 107 ASP cc_start: 0.8549 (p0) cc_final: 0.8314 (p0) REVERT: G 114 GLN cc_start: 0.9489 (tm-30) cc_final: 0.9228 (tm-30) REVERT: G 252 LYS cc_start: 0.9418 (mmtp) cc_final: 0.9137 (mmmm) REVERT: G 321 ASP cc_start: 0.8952 (t70) cc_final: 0.8625 (t70) REVERT: G 434 MET cc_start: 0.8328 (tmm) cc_final: 0.7929 (tmm) REVERT: H 1 GLU cc_start: 0.9111 (tm-30) cc_final: 0.8620 (tm-30) REVERT: H 78 LEU cc_start: 0.8539 (pp) cc_final: 0.8305 (pp) REVERT: I 59 LYS cc_start: 0.8261 (tptp) cc_final: 0.8033 (tptp) REVERT: I 104 MET cc_start: 0.9512 (mmt) cc_final: 0.8619 (tpp) REVERT: I 114 GLN cc_start: 0.9491 (tm-30) cc_final: 0.9240 (tm-30) REVERT: I 252 LYS cc_start: 0.9394 (mtmm) cc_final: 0.9114 (mmmm) REVERT: I 321 ASP cc_start: 0.8672 (t0) cc_final: 0.8419 (t0) REVERT: I 425 ASN cc_start: 0.9397 (p0) cc_final: 0.9194 (p0) REVERT: I 477 ASP cc_start: 0.9471 (p0) cc_final: 0.9234 (p0) REVERT: J 18 LEU cc_start: 0.8136 (mt) cc_final: 0.7838 (mp) REVERT: J 85 GLU cc_start: 0.8849 (mm-30) cc_final: 0.8161 (tm-30) REVERT: J 91 TYR cc_start: 0.8795 (m-80) cc_final: 0.8569 (m-80) REVERT: J 102 TYR cc_start: 0.9202 (m-80) cc_final: 0.8701 (m-80) REVERT: K 24 LYS cc_start: 0.8897 (pptt) cc_final: 0.8679 (pptt) REVERT: K 27 TYR cc_start: 0.7841 (p90) cc_final: 0.7499 (p90) REVERT: K 37 GLN cc_start: 0.7995 (pp30) cc_final: 0.7664 (pp30) REVERT: K 45 LYS cc_start: 0.9113 (tptm) cc_final: 0.8807 (ttpp) REVERT: K 96 TYR cc_start: 0.8051 (m-10) cc_final: 0.7829 (m-10) REVERT: L 37 GLN cc_start: 0.7812 (pp30) cc_final: 0.7255 (pp30) REVERT: L 38 GLN cc_start: 0.8695 (pt0) cc_final: 0.8361 (pt0) REVERT: L 82 ASP cc_start: 0.8882 (m-30) cc_final: 0.8631 (m-30) outliers start: 5 outliers final: 3 residues processed: 482 average time/residue: 0.3147 time to fit residues: 229.9213 Evaluate side-chains 369 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 366 time to evaluate : 2.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 215 optimal weight: 0.9990 chunk 164 optimal weight: 9.9990 chunk 113 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 146 optimal weight: 0.8980 chunk 219 optimal weight: 6.9990 chunk 231 optimal weight: 8.9990 chunk 114 optimal weight: 0.9990 chunk 207 optimal weight: 7.9990 chunk 62 optimal weight: 4.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS B 258 GLN ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 616 ASN ** F 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 66 HIS G 440 GLN ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20587 Z= 0.203 Angle : 0.833 14.521 27934 Z= 0.403 Chirality : 0.053 0.382 3337 Planarity : 0.005 0.089 3463 Dihedral : 10.957 93.331 4330 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 15.78 Ramachandran Plot: Outliers : 0.13 % Allowed : 14.61 % Favored : 85.26 % Rotamer: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 4.90 % Twisted General : 0.30 % 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: -3.90 (0.15), residues: 2388 helix: -1.14 (0.27), residues: 354 sheet: -1.32 (0.26), residues: 396 loop : -3.54 (0.13), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP L 35 HIS 0.014 0.002 HIS E 76 PHE 0.019 0.001 PHE E 98 TYR 0.019 0.002 TYR I 134 ARG 0.006 0.000 ARG E 61 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 525 time to evaluate : 2.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 584 GLU cc_start: 0.8850 (tm-30) cc_final: 0.8609 (tm-30) REVERT: A 617 ARG cc_start: 0.8500 (mtt180) cc_final: 0.7941 (mtm-85) REVERT: A 621 GLU cc_start: 0.8570 (tm-30) cc_final: 0.8285 (tm-30) REVERT: A 648 GLU cc_start: 0.9250 (pp20) cc_final: 0.8664 (pm20) REVERT: A 654 GLU cc_start: 0.9134 (tp30) cc_final: 0.8925 (tp30) REVERT: B 98 ASN cc_start: 0.7855 (t0) cc_final: 0.7432 (t0) REVERT: B 114 GLN cc_start: 0.9372 (tm-30) cc_final: 0.9150 (tm-30) REVERT: B 452 LEU cc_start: 0.9390 (pt) cc_final: 0.9069 (pp) REVERT: C 530 MET cc_start: 0.8792 (mmp) cc_final: 0.8485 (mmp) REVERT: C 584 GLU cc_start: 0.8892 (tm-30) cc_final: 0.8432 (tm-30) REVERT: C 621 GLU cc_start: 0.8629 (tm-30) cc_final: 0.8330 (tm-30) REVERT: C 648 GLU cc_start: 0.9279 (pp20) cc_final: 0.8715 (pm20) REVERT: D 91 TYR cc_start: 0.8024 (m-80) cc_final: 0.7417 (m-10) REVERT: D 102 TYR cc_start: 0.9347 (m-80) cc_final: 0.9066 (m-80) REVERT: E 37 GLN cc_start: 0.7743 (pp30) cc_final: 0.6861 (pp30) REVERT: E 45 LYS cc_start: 0.8999 (tptp) cc_final: 0.8629 (ttpp) REVERT: E 72 THR cc_start: 0.7232 (t) cc_final: 0.6644 (t) REVERT: E 78 VAL cc_start: 0.8283 (m) cc_final: 0.8038 (p) REVERT: E 82 ASP cc_start: 0.8871 (m-30) cc_final: 0.8480 (m-30) REVERT: F 530 MET cc_start: 0.8948 (mmp) cc_final: 0.8655 (mmp) REVERT: F 621 GLU cc_start: 0.8868 (tm-30) cc_final: 0.8614 (tm-30) REVERT: F 648 GLU cc_start: 0.9216 (pp20) cc_final: 0.8706 (pm20) REVERT: G 98 ASN cc_start: 0.8524 (t0) cc_final: 0.7503 (t0) REVERT: G 102 GLU cc_start: 0.9262 (mp0) cc_final: 0.8760 (mp0) REVERT: G 104 MET cc_start: 0.9282 (ttp) cc_final: 0.8945 (mtp) REVERT: G 114 GLN cc_start: 0.9448 (tm-30) cc_final: 0.9221 (tm-30) REVERT: G 150 MET cc_start: 0.9068 (tmm) cc_final: 0.8762 (tmm) REVERT: G 161 MET cc_start: 0.9241 (tpp) cc_final: 0.9040 (tpp) REVERT: G 252 LYS cc_start: 0.9418 (mmtp) cc_final: 0.9108 (mmmm) REVERT: G 321 ASP cc_start: 0.8861 (t70) cc_final: 0.8641 (t70) REVERT: G 325 ASP cc_start: 0.8860 (p0) cc_final: 0.8427 (p0) REVERT: G 426 MET cc_start: 0.8454 (ptp) cc_final: 0.8251 (ptm) REVERT: G 427 TRP cc_start: 0.8658 (m-90) cc_final: 0.8353 (m-90) REVERT: G 434 MET cc_start: 0.8181 (tmm) cc_final: 0.7817 (tmm) REVERT: H 13 LYS cc_start: 0.9131 (tppt) cc_final: 0.8839 (tppt) REVERT: H 39 GLN cc_start: 0.8284 (tp40) cc_final: 0.7740 (tm-30) REVERT: H 67 PHE cc_start: 0.8571 (p90) cc_final: 0.8285 (p90) REVERT: H 87 THR cc_start: 0.8111 (p) cc_final: 0.7573 (p) REVERT: I 59 LYS cc_start: 0.8167 (tptp) cc_final: 0.7900 (tptp) REVERT: I 98 ASN cc_start: 0.8395 (t0) cc_final: 0.7758 (t0) REVERT: I 102 GLU cc_start: 0.9260 (mp0) cc_final: 0.8863 (mp0) REVERT: I 114 GLN cc_start: 0.9449 (tm-30) cc_final: 0.9167 (tm-30) REVERT: I 425 ASN cc_start: 0.9361 (p0) cc_final: 0.9040 (p0) REVERT: I 434 MET cc_start: 0.9252 (tpp) cc_final: 0.8870 (tpp) REVERT: J 36 TRP cc_start: 0.8586 (m100) cc_final: 0.7697 (m-10) REVERT: J 47 TRP cc_start: 0.5953 (m-90) cc_final: 0.5710 (m-90) REVERT: J 89 MET cc_start: 0.8429 (mmp) cc_final: 0.7406 (tpt) REVERT: J 91 TYR cc_start: 0.8647 (m-80) cc_final: 0.8273 (m-80) REVERT: K 37 GLN cc_start: 0.7760 (pp30) cc_final: 0.7019 (pp30) REVERT: K 45 LYS cc_start: 0.9161 (tptm) cc_final: 0.8851 (ttpp) REVERT: K 103 LYS cc_start: 0.8507 (mmmm) cc_final: 0.8235 (tppp) REVERT: L 37 GLN cc_start: 0.7825 (pp30) cc_final: 0.7272 (pp30) REVERT: L 72 THR cc_start: 0.7065 (t) cc_final: 0.6481 (t) outliers start: 0 outliers final: 0 residues processed: 525 average time/residue: 0.3297 time to fit residues: 265.0987 Evaluate side-chains 393 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 393 time to evaluate : 2.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 193 optimal weight: 9.9990 chunk 131 optimal weight: 6.9990 chunk 3 optimal weight: 5.9990 chunk 172 optimal weight: 5.9990 chunk 95 optimal weight: 0.8980 chunk 197 optimal weight: 8.9990 chunk 160 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 118 optimal weight: 10.0000 chunk 208 optimal weight: 10.0000 chunk 58 optimal weight: 7.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 203 GLN B 352 HIS ** B 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 330 HIS G 440 GLN ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 66 HIS ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 89 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.3419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 20587 Z= 0.461 Angle : 0.972 14.144 27934 Z= 0.471 Chirality : 0.056 0.473 3337 Planarity : 0.006 0.083 3463 Dihedral : 11.228 96.820 4330 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 23.35 Ramachandran Plot: Outliers : 0.21 % Allowed : 19.18 % Favored : 80.61 % Rotamer: Outliers : 0.14 % Allowed : 4.88 % Favored : 94.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 4.90 % Twisted General : 0.35 % 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: -4.03 (0.15), residues: 2388 helix: -1.01 (0.27), residues: 354 sheet: -1.34 (0.28), residues: 357 loop : -3.67 (0.12), residues: 1677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.003 TRP L 35 HIS 0.010 0.002 HIS I 66 PHE 0.015 0.002 PHE J 27 TYR 0.028 0.003 TYR I 217 ARG 0.006 0.001 ARG J 44 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 433 time to evaluate : 2.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 584 GLU cc_start: 0.8903 (tm-30) cc_final: 0.8673 (tm-30) REVERT: A 621 GLU cc_start: 0.8752 (tm-30) cc_final: 0.8336 (tm-30) REVERT: A 626 MET cc_start: 0.7647 (mtm) cc_final: 0.6923 (mtm) REVERT: A 648 GLU cc_start: 0.9326 (pp20) cc_final: 0.8815 (pm20) REVERT: A 654 GLU cc_start: 0.9274 (mm-30) cc_final: 0.9068 (tp30) REVERT: B 102 GLU cc_start: 0.9297 (mp0) cc_final: 0.9092 (mp0) REVERT: B 203 GLN cc_start: 0.9103 (OUTLIER) cc_final: 0.8711 (pp30) REVERT: B 452 LEU cc_start: 0.9459 (pt) cc_final: 0.9113 (pp) REVERT: C 530 MET cc_start: 0.9178 (mmp) cc_final: 0.8765 (mmp) REVERT: C 584 GLU cc_start: 0.9000 (tm-30) cc_final: 0.8668 (tm-30) REVERT: C 622 ILE cc_start: 0.9371 (pt) cc_final: 0.9128 (pt) REVERT: C 634 GLU cc_start: 0.9163 (tm-30) cc_final: 0.8736 (tm-30) REVERT: C 648 GLU cc_start: 0.9359 (pp20) cc_final: 0.8795 (pm20) REVERT: D 39 GLN cc_start: 0.8717 (mm-40) cc_final: 0.8302 (mm110) REVERT: D 102 TYR cc_start: 0.9389 (m-80) cc_final: 0.9182 (m-80) REVERT: E 24 LYS cc_start: 0.8893 (pptt) cc_final: 0.8634 (pptt) REVERT: E 45 LYS cc_start: 0.8948 (tptp) cc_final: 0.8500 (ttpp) REVERT: E 72 THR cc_start: 0.7693 (t) cc_final: 0.7246 (t) REVERT: E 82 ASP cc_start: 0.8929 (m-30) cc_final: 0.8676 (m-30) REVERT: E 96 TYR cc_start: 0.8622 (m-10) cc_final: 0.8315 (m-10) REVERT: E 97 THR cc_start: 0.9093 (p) cc_final: 0.8878 (t) REVERT: F 621 GLU cc_start: 0.8989 (tm-30) cc_final: 0.8728 (tm-30) REVERT: F 624 ASP cc_start: 0.8812 (m-30) cc_final: 0.8586 (m-30) REVERT: F 648 GLU cc_start: 0.9328 (pp20) cc_final: 0.8819 (pm20) REVERT: G 93 PHE cc_start: 0.8365 (m-10) cc_final: 0.7966 (m-10) REVERT: G 104 MET cc_start: 0.9218 (ttp) cc_final: 0.8885 (mtp) REVERT: G 114 GLN cc_start: 0.9512 (tm-30) cc_final: 0.9235 (tm-30) REVERT: G 150 MET cc_start: 0.9177 (tmm) cc_final: 0.8883 (tmm) REVERT: G 434 MET cc_start: 0.8224 (tmm) cc_final: 0.7927 (tmm) REVERT: H 39 GLN cc_start: 0.8173 (tp40) cc_final: 0.7647 (tm-30) REVERT: H 67 PHE cc_start: 0.8640 (p90) cc_final: 0.8243 (p90) REVERT: H 78 LEU cc_start: 0.8459 (pp) cc_final: 0.8249 (pp) REVERT: H 87 THR cc_start: 0.8027 (p) cc_final: 0.7495 (p) REVERT: I 59 LYS cc_start: 0.8303 (tptp) cc_final: 0.8018 (tptp) REVERT: I 95 MET cc_start: 0.9158 (ptm) cc_final: 0.8908 (ptm) REVERT: I 114 GLN cc_start: 0.9517 (tm-30) cc_final: 0.9162 (tm-30) REVERT: I 150 MET cc_start: 0.9143 (tmm) cc_final: 0.8602 (tmm) REVERT: I 321 ASP cc_start: 0.8793 (t0) cc_final: 0.8563 (t0) REVERT: I 434 MET cc_start: 0.9196 (tpp) cc_final: 0.8935 (tpp) REVERT: J 91 TYR cc_start: 0.8761 (m-80) cc_final: 0.8197 (m-80) REVERT: J 102 TYR cc_start: 0.9202 (m-80) cc_final: 0.8876 (m-80) REVERT: K 35 TRP cc_start: 0.8652 (m-10) cc_final: 0.8388 (m-10) REVERT: K 37 GLN cc_start: 0.7985 (pp30) cc_final: 0.7682 (pp30) REVERT: K 45 LYS cc_start: 0.9137 (tptm) cc_final: 0.8880 (ttpp) REVERT: K 81 GLU cc_start: 0.9394 (pp20) cc_final: 0.9132 (pp20) REVERT: L 37 GLN cc_start: 0.7890 (pp30) cc_final: 0.7375 (pp30) REVERT: L 38 GLN cc_start: 0.8761 (pt0) cc_final: 0.8465 (pt0) REVERT: L 72 THR cc_start: 0.7046 (t) cc_final: 0.6550 (t) REVERT: L 80 GLU cc_start: 0.7865 (tt0) cc_final: 0.7630 (tm-30) REVERT: L 82 ASP cc_start: 0.8897 (m-30) cc_final: 0.8636 (m-30) outliers start: 3 outliers final: 0 residues processed: 435 average time/residue: 0.3171 time to fit residues: 212.0336 Evaluate side-chains 357 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 356 time to evaluate : 2.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 78 optimal weight: 9.9990 chunk 208 optimal weight: 7.9990 chunk 45 optimal weight: 4.9990 chunk 136 optimal weight: 6.9990 chunk 57 optimal weight: 7.9990 chunk 232 optimal weight: 0.5980 chunk 192 optimal weight: 4.9990 chunk 107 optimal weight: 20.0000 chunk 19 optimal weight: 0.8980 chunk 76 optimal weight: 0.8980 chunk 121 optimal weight: 8.9990 overall best weight: 2.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 585 HIS ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS ** C 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 585 HIS F 616 ASN ** F 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 66 HIS ** G 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 440 GLN ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.3526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 20587 Z= 0.273 Angle : 0.855 12.572 27934 Z= 0.416 Chirality : 0.053 0.390 3337 Planarity : 0.005 0.074 3463 Dihedral : 10.519 90.494 4330 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 18.72 Ramachandran Plot: Outliers : 0.13 % Allowed : 16.67 % Favored : 83.21 % Rotamer: Outliers : 0.05 % Allowed : 2.94 % Favored : 97.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 5.88 % Twisted General : 0.30 % 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: -3.92 (0.15), residues: 2388 helix: -0.93 (0.27), residues: 354 sheet: -1.43 (0.27), residues: 366 loop : -3.56 (0.13), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP L 35 HIS 0.015 0.002 HIS E 76 PHE 0.017 0.001 PHE D 27 TYR 0.024 0.002 TYR J 58 ARG 0.005 0.001 ARG H 44 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 468 time to evaluate : 2.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 584 GLU cc_start: 0.8830 (tm-30) cc_final: 0.8629 (tm-30) REVERT: A 621 GLU cc_start: 0.8696 (tm-30) cc_final: 0.8250 (tm-30) REVERT: A 626 MET cc_start: 0.7759 (mtm) cc_final: 0.6978 (mtm) REVERT: A 648 GLU cc_start: 0.9298 (pp20) cc_final: 0.8679 (pm20) REVERT: B 98 ASN cc_start: 0.7759 (t0) cc_final: 0.7095 (t0) REVERT: B 102 GLU cc_start: 0.9300 (mp0) cc_final: 0.9075 (mp0) REVERT: B 427 TRP cc_start: 0.8901 (m100) cc_final: 0.8610 (m100) REVERT: B 452 LEU cc_start: 0.9379 (pt) cc_final: 0.9053 (pp) REVERT: C 584 GLU cc_start: 0.8979 (tm-30) cc_final: 0.8612 (tm-30) REVERT: C 634 GLU cc_start: 0.9136 (tm-30) cc_final: 0.8848 (tm-30) REVERT: C 635 ILE cc_start: 0.9326 (mp) cc_final: 0.8424 (mp) REVERT: C 648 GLU cc_start: 0.9295 (pp20) cc_final: 0.8760 (pm20) REVERT: E 24 LYS cc_start: 0.8835 (pptt) cc_final: 0.8616 (pptt) REVERT: E 37 GLN cc_start: 0.6965 (pp30) cc_final: 0.6753 (pp30) REVERT: E 45 LYS cc_start: 0.8966 (tptp) cc_final: 0.8682 (ttpp) REVERT: E 72 THR cc_start: 0.7638 (t) cc_final: 0.7143 (t) REVERT: E 82 ASP cc_start: 0.8938 (m-30) cc_final: 0.8723 (m-30) REVERT: E 87 TYR cc_start: 0.8399 (m-80) cc_final: 0.8157 (m-80) REVERT: F 621 GLU cc_start: 0.8901 (tm-30) cc_final: 0.8609 (tm-30) REVERT: F 648 GLU cc_start: 0.9315 (pp20) cc_final: 0.8783 (pm20) REVERT: G 104 MET cc_start: 0.9207 (ttp) cc_final: 0.8975 (mtp) REVERT: G 114 GLN cc_start: 0.9497 (tm-30) cc_final: 0.9241 (tm-30) REVERT: G 150 MET cc_start: 0.9155 (tmm) cc_final: 0.8870 (tmm) REVERT: G 426 MET cc_start: 0.8738 (ptp) cc_final: 0.8153 (ptm) REVERT: G 427 TRP cc_start: 0.8764 (m-90) cc_final: 0.8534 (m-90) REVERT: G 434 MET cc_start: 0.8187 (tmm) cc_final: 0.7953 (tmm) REVERT: G 492 GLU cc_start: 0.8244 (tm-30) cc_final: 0.7847 (tm-30) REVERT: H 67 PHE cc_start: 0.8851 (p90) cc_final: 0.8279 (p90) REVERT: I 59 LYS cc_start: 0.8260 (tptp) cc_final: 0.7961 (tptp) REVERT: I 98 ASN cc_start: 0.8530 (t0) cc_final: 0.7883 (t0) REVERT: I 102 GLU cc_start: 0.9324 (mp0) cc_final: 0.8886 (mp0) REVERT: I 104 MET cc_start: 0.9421 (mmm) cc_final: 0.8673 (mmt) REVERT: I 114 GLN cc_start: 0.9472 (tm-30) cc_final: 0.9211 (tm-30) REVERT: I 425 ASN cc_start: 0.9279 (p0) cc_final: 0.8959 (p0) REVERT: I 434 MET cc_start: 0.9155 (tpp) cc_final: 0.8708 (tpp) REVERT: I 475 MET cc_start: 0.7389 (tmm) cc_final: 0.7136 (tmm) REVERT: J 36 TRP cc_start: 0.8670 (m100) cc_final: 0.7821 (m-10) REVERT: J 71 ARG cc_start: 0.8292 (ttt-90) cc_final: 0.8029 (tmt-80) REVERT: J 89 MET cc_start: 0.8331 (mmp) cc_final: 0.7271 (tpt) REVERT: J 91 TYR cc_start: 0.8786 (m-80) cc_final: 0.8268 (m-80) REVERT: J 102 TYR cc_start: 0.9086 (m-80) cc_final: 0.8821 (m-80) REVERT: K 24 LYS cc_start: 0.8718 (pptt) cc_final: 0.8512 (pptt) REVERT: K 37 GLN cc_start: 0.7706 (pp30) cc_final: 0.7166 (pp30) REVERT: K 45 LYS cc_start: 0.9220 (tptm) cc_final: 0.8977 (ttpp) REVERT: K 81 GLU cc_start: 0.9364 (pp20) cc_final: 0.9127 (pp20) REVERT: K 82 ASP cc_start: 0.9145 (m-30) cc_final: 0.8943 (m-30) REVERT: L 37 GLN cc_start: 0.7880 (pp30) cc_final: 0.7301 (pp30) REVERT: L 38 GLN cc_start: 0.8816 (pt0) cc_final: 0.8514 (pt0) REVERT: L 72 THR cc_start: 0.6579 (t) cc_final: 0.6040 (t) REVERT: L 79 GLU cc_start: 0.9023 (tm-30) cc_final: 0.8577 (mp0) REVERT: L 80 GLU cc_start: 0.7099 (tt0) cc_final: 0.6641 (tt0) REVERT: L 82 ASP cc_start: 0.8924 (m-30) cc_final: 0.8038 (m-30) outliers start: 1 outliers final: 0 residues processed: 468 average time/residue: 0.3047 time to fit residues: 219.4179 Evaluate side-chains 381 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 381 time to evaluate : 2.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 223 optimal weight: 7.9990 chunk 26 optimal weight: 0.8980 chunk 132 optimal weight: 5.9990 chunk 169 optimal weight: 3.9990 chunk 131 optimal weight: 1.9990 chunk 195 optimal weight: 7.9990 chunk 129 optimal weight: 5.9990 chunk 231 optimal weight: 3.9990 chunk 144 optimal weight: 6.9990 chunk 141 optimal weight: 5.9990 chunk 106 optimal weight: 6.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 585 HIS ** A 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 66 HIS J 76 ASN ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.3694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 20587 Z= 0.340 Angle : 0.876 12.704 27934 Z= 0.428 Chirality : 0.053 0.414 3337 Planarity : 0.005 0.068 3463 Dihedral : 10.514 90.034 4330 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 20.61 Ramachandran Plot: Outliers : 0.13 % Allowed : 18.59 % Favored : 81.28 % Rotamer: Outliers : 0.05 % Allowed : 2.89 % Favored : 97.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 4.90 % Twisted General : 0.30 % 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 (0.15), residues: 2388 helix: -0.87 (0.27), residues: 354 sheet: -1.54 (0.26), residues: 387 loop : -3.57 (0.13), residues: 1647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP I 479 HIS 0.013 0.002 HIS E 76 PHE 0.013 0.002 PHE B 93 TYR 0.028 0.002 TYR H 58 ARG 0.006 0.001 ARG E 61 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 449 time to evaluate : 2.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 584 GLU cc_start: 0.8930 (tm-30) cc_final: 0.8632 (tm-30) REVERT: A 621 GLU cc_start: 0.8697 (tm-30) cc_final: 0.8399 (tm-30) REVERT: A 626 MET cc_start: 0.7774 (mtm) cc_final: 0.7127 (mtm) REVERT: A 648 GLU cc_start: 0.9295 (pp20) cc_final: 0.8798 (pm20) REVERT: B 93 PHE cc_start: 0.8412 (m-10) cc_final: 0.8202 (m-10) REVERT: B 102 GLU cc_start: 0.9277 (mp0) cc_final: 0.9060 (mp0) REVERT: B 150 MET cc_start: 0.8956 (tmm) cc_final: 0.8563 (tmm) REVERT: B 217 TYR cc_start: 0.7606 (m-80) cc_final: 0.7374 (m-80) REVERT: B 427 TRP cc_start: 0.8992 (m100) cc_final: 0.8720 (m100) REVERT: C 530 MET cc_start: 0.8958 (mmp) cc_final: 0.8453 (mmp) REVERT: C 584 GLU cc_start: 0.9012 (tm-30) cc_final: 0.8651 (tm-30) REVERT: C 634 GLU cc_start: 0.9122 (tm-30) cc_final: 0.8684 (tm-30) REVERT: C 648 GLU cc_start: 0.9329 (pp20) cc_final: 0.8780 (pm20) REVERT: D 71 ARG cc_start: 0.8523 (ttt-90) cc_final: 0.8229 (tmt-80) REVERT: D 100 MET cc_start: 0.9306 (mpp) cc_final: 0.8808 (mpp) REVERT: E 24 LYS cc_start: 0.8939 (pptt) cc_final: 0.8460 (pptt) REVERT: E 37 GLN cc_start: 0.6929 (pp30) cc_final: 0.6667 (pp30) REVERT: E 45 LYS cc_start: 0.8947 (tptp) cc_final: 0.8683 (ttpp) REVERT: E 78 VAL cc_start: 0.8135 (m) cc_final: 0.7888 (p) REVERT: E 82 ASP cc_start: 0.8886 (m-30) cc_final: 0.8471 (m-30) REVERT: F 621 GLU cc_start: 0.8913 (tm-30) cc_final: 0.8566 (tm-30) REVERT: F 624 ASP cc_start: 0.8867 (m-30) cc_final: 0.8610 (m-30) REVERT: F 634 GLU cc_start: 0.9178 (tm-30) cc_final: 0.8920 (tm-30) REVERT: F 648 GLU cc_start: 0.9285 (pp20) cc_final: 0.8811 (pm20) REVERT: G 98 ASN cc_start: 0.8735 (t0) cc_final: 0.8450 (t0) REVERT: G 114 GLN cc_start: 0.9504 (tm-30) cc_final: 0.9204 (tm-30) REVERT: G 150 MET cc_start: 0.9187 (tmm) cc_final: 0.8596 (tmm) REVERT: G 426 MET cc_start: 0.8782 (ptp) cc_final: 0.8078 (ptm) REVERT: G 434 MET cc_start: 0.8207 (tmm) cc_final: 0.7981 (tmm) REVERT: H 39 GLN cc_start: 0.8157 (mm-40) cc_final: 0.7618 (mm110) REVERT: H 67 PHE cc_start: 0.8861 (p90) cc_final: 0.8280 (p90) REVERT: H 85 GLU cc_start: 0.8894 (pp20) cc_final: 0.8546 (pp20) REVERT: I 59 LYS cc_start: 0.8284 (tptp) cc_final: 0.7945 (tptp) REVERT: I 98 ASN cc_start: 0.8210 (t0) cc_final: 0.7391 (t0) REVERT: I 102 GLU cc_start: 0.9374 (mp0) cc_final: 0.8704 (mp0) REVERT: I 114 GLN cc_start: 0.9439 (tm-30) cc_final: 0.9120 (tm-30) REVERT: I 252 LYS cc_start: 0.9414 (mtmm) cc_final: 0.9166 (mmmm) REVERT: I 425 ASN cc_start: 0.9289 (p0) cc_final: 0.8967 (p0) REVERT: I 434 MET cc_start: 0.9096 (tpp) cc_final: 0.8666 (tpp) REVERT: I 475 MET cc_start: 0.7241 (tmm) cc_final: 0.6955 (tmm) REVERT: J 57 THR cc_start: 0.7885 (m) cc_final: 0.7197 (m) REVERT: J 67 PHE cc_start: 0.8824 (p90) cc_final: 0.8427 (p90) REVERT: J 78 LEU cc_start: 0.8956 (pt) cc_final: 0.8621 (pt) REVERT: J 91 TYR cc_start: 0.8757 (m-80) cc_final: 0.8225 (m-80) REVERT: J 102 TYR cc_start: 0.9130 (m-80) cc_final: 0.8913 (m-80) REVERT: K 24 LYS cc_start: 0.9039 (pptt) cc_final: 0.8698 (pptt) REVERT: K 35 TRP cc_start: 0.8581 (m-10) cc_final: 0.8309 (m-10) REVERT: K 45 LYS cc_start: 0.9271 (tptm) cc_final: 0.8951 (ttpp) REVERT: K 81 GLU cc_start: 0.9360 (pp20) cc_final: 0.9070 (pp20) REVERT: L 37 GLN cc_start: 0.7886 (pp30) cc_final: 0.7314 (pp30) REVERT: L 38 GLN cc_start: 0.8795 (pt0) cc_final: 0.8503 (pt0) REVERT: L 72 THR cc_start: 0.6674 (t) cc_final: 0.5971 (t) REVERT: L 82 ASP cc_start: 0.9093 (m-30) cc_final: 0.8860 (m-30) outliers start: 1 outliers final: 0 residues processed: 449 average time/residue: 0.3021 time to fit residues: 209.1637 Evaluate side-chains 362 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 362 time to evaluate : 2.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 143 optimal weight: 10.0000 chunk 92 optimal weight: 8.9990 chunk 138 optimal weight: 3.9990 chunk 69 optimal weight: 0.0040 chunk 45 optimal weight: 2.9990 chunk 44 optimal weight: 8.9990 chunk 147 optimal weight: 0.8980 chunk 157 optimal weight: 5.9990 chunk 114 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 181 optimal weight: 4.9990 overall best weight: 1.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 585 HIS ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS B 276 ASN ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 585 HIS ** F 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 652 GLN G 67 ASN ** G 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 440 GLN ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.3810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20587 Z= 0.216 Angle : 0.832 12.530 27934 Z= 0.403 Chirality : 0.052 0.370 3337 Planarity : 0.005 0.064 3463 Dihedral : 10.045 85.424 4330 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 16.71 Ramachandran Plot: Outliers : 0.13 % Allowed : 15.54 % Favored : 84.34 % Rotamer: Outliers : 0.05 % Allowed : 1.66 % Favored : 98.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 4.90 % Twisted General : 0.35 % 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: -3.76 (0.15), residues: 2388 helix: -0.76 (0.27), residues: 354 sheet: -1.45 (0.26), residues: 393 loop : -3.44 (0.13), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP G 427 HIS 0.012 0.002 HIS E 76 PHE 0.015 0.001 PHE K 98 TYR 0.030 0.002 TYR J 58 ARG 0.005 0.000 ARG J 44 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 488 time to evaluate : 2.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 584 GLU cc_start: 0.8864 (tm-30) cc_final: 0.8617 (tm-30) REVERT: A 634 GLU cc_start: 0.9059 (tm-30) cc_final: 0.8854 (tm-30) REVERT: A 648 GLU cc_start: 0.9233 (pp20) cc_final: 0.8627 (pm20) REVERT: B 98 ASN cc_start: 0.7843 (t0) cc_final: 0.7073 (t0) REVERT: B 102 GLU cc_start: 0.9300 (mp0) cc_final: 0.9061 (mp0) REVERT: B 150 MET cc_start: 0.8922 (tmm) cc_final: 0.8628 (tmm) REVERT: B 321 ASP cc_start: 0.9153 (t70) cc_final: 0.8948 (t70) REVERT: B 427 TRP cc_start: 0.8908 (m100) cc_final: 0.8643 (m100) REVERT: C 584 GLU cc_start: 0.8929 (tm-30) cc_final: 0.8441 (tm-30) REVERT: C 634 GLU cc_start: 0.9126 (tm-30) cc_final: 0.8907 (tm-30) REVERT: C 635 ILE cc_start: 0.9373 (mp) cc_final: 0.8396 (mp) REVERT: C 645 LEU cc_start: 0.9411 (tp) cc_final: 0.8965 (tp) REVERT: C 648 GLU cc_start: 0.9288 (pp20) cc_final: 0.8740 (pm20) REVERT: D 44 ARG cc_start: 0.6167 (mmt-90) cc_final: 0.5619 (mmt-90) REVERT: D 67 PHE cc_start: 0.8725 (p90) cc_final: 0.8127 (p90) REVERT: E 24 LYS cc_start: 0.8855 (pptt) cc_final: 0.8549 (pptt) REVERT: E 37 GLN cc_start: 0.7038 (pp30) cc_final: 0.6756 (pp30) REVERT: E 45 LYS cc_start: 0.8933 (tptp) cc_final: 0.8652 (ttpp) REVERT: E 78 VAL cc_start: 0.8015 (m) cc_final: 0.7713 (p) REVERT: E 82 ASP cc_start: 0.8836 (m-30) cc_final: 0.8421 (m-30) REVERT: F 621 GLU cc_start: 0.8800 (tm-30) cc_final: 0.8462 (tm-30) REVERT: F 624 ASP cc_start: 0.8848 (m-30) cc_final: 0.8632 (m-30) REVERT: F 645 LEU cc_start: 0.9264 (tp) cc_final: 0.8781 (tp) REVERT: F 648 GLU cc_start: 0.9228 (pp20) cc_final: 0.8740 (pm20) REVERT: G 98 ASN cc_start: 0.8910 (t0) cc_final: 0.7714 (t0) REVERT: G 102 GLU cc_start: 0.9263 (mp0) cc_final: 0.8843 (mp0) REVERT: G 114 GLN cc_start: 0.9432 (tm-30) cc_final: 0.9196 (tm-30) REVERT: G 150 MET cc_start: 0.9199 (tmm) cc_final: 0.8662 (tmm) REVERT: G 239 CYS cc_start: 0.5207 (p) cc_final: 0.4969 (p) REVERT: G 321 ASP cc_start: 0.9069 (t70) cc_final: 0.8820 (t70) REVERT: G 434 MET cc_start: 0.8221 (tmm) cc_final: 0.7989 (tmm) REVERT: H 67 PHE cc_start: 0.8711 (p90) cc_final: 0.7982 (p90) REVERT: I 59 LYS cc_start: 0.8263 (tptp) cc_final: 0.7924 (tptp) REVERT: I 98 ASN cc_start: 0.8342 (t0) cc_final: 0.7992 (t0) REVERT: I 102 GLU cc_start: 0.9295 (mp0) cc_final: 0.8923 (mp0) REVERT: I 114 GLN cc_start: 0.9443 (tm-30) cc_final: 0.9198 (tm-30) REVERT: I 252 LYS cc_start: 0.9373 (mtmm) cc_final: 0.9115 (mmmm) REVERT: I 425 ASN cc_start: 0.9311 (p0) cc_final: 0.8948 (p0) REVERT: I 434 MET cc_start: 0.9111 (tpp) cc_final: 0.8907 (tpt) REVERT: J 57 THR cc_start: 0.7891 (m) cc_final: 0.7137 (t) REVERT: J 67 PHE cc_start: 0.8930 (p90) cc_final: 0.8368 (p90) REVERT: J 71 ARG cc_start: 0.8275 (ttt-90) cc_final: 0.7972 (tmt-80) REVERT: J 78 LEU cc_start: 0.8931 (pt) cc_final: 0.8716 (pt) REVERT: J 89 MET cc_start: 0.8333 (mmp) cc_final: 0.7236 (tpt) REVERT: J 91 TYR cc_start: 0.8782 (m-80) cc_final: 0.8287 (m-80) REVERT: J 102 TYR cc_start: 0.9073 (m-80) cc_final: 0.8868 (m-80) REVERT: K 24 LYS cc_start: 0.9033 (pptt) cc_final: 0.8638 (pptt) REVERT: K 45 LYS cc_start: 0.9137 (tptm) cc_final: 0.8812 (ttpp) REVERT: L 37 GLN cc_start: 0.7950 (pp30) cc_final: 0.7314 (pp30) REVERT: L 38 GLN cc_start: 0.8769 (pt0) cc_final: 0.8409 (pt0) REVERT: L 72 THR cc_start: 0.6310 (t) cc_final: 0.5805 (t) REVERT: L 82 ASP cc_start: 0.9102 (m-30) cc_final: 0.8888 (m-30) outliers start: 1 outliers final: 0 residues processed: 488 average time/residue: 0.3010 time to fit residues: 228.3042 Evaluate side-chains 393 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 393 time to evaluate : 2.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 210 optimal weight: 8.9990 chunk 221 optimal weight: 9.9990 chunk 202 optimal weight: 10.0000 chunk 215 optimal weight: 5.9990 chunk 129 optimal weight: 1.9990 chunk 93 optimal weight: 7.9990 chunk 169 optimal weight: 0.9990 chunk 66 optimal weight: 4.9990 chunk 194 optimal weight: 0.9980 chunk 203 optimal weight: 0.8980 chunk 214 optimal weight: 3.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 585 HIS ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS B 276 ASN ** C 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 GLN ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 53 ASN ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 585 HIS F 616 ASN ** F 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 652 GLN G 67 ASN ** G 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 66 HIS J 76 ASN ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 53 ASN ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.3965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 20587 Z= 0.230 Angle : 0.832 12.856 27934 Z= 0.404 Chirality : 0.052 0.375 3337 Planarity : 0.005 0.064 3463 Dihedral : 9.914 82.945 4330 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 17.87 Ramachandran Plot: Outliers : 0.04 % Allowed : 16.79 % Favored : 83.17 % Rotamer: Outliers : 0.24 % Allowed : 0.99 % Favored : 98.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 3.92 % Twisted General : 0.26 % 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: -3.67 (0.16), residues: 2388 helix: -0.62 (0.28), residues: 354 sheet: -1.47 (0.25), residues: 408 loop : -3.39 (0.13), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP L 35 HIS 0.012 0.002 HIS E 76 PHE 0.015 0.001 PHE K 98 TYR 0.032 0.002 TYR J 58 ARG 0.005 0.000 ARG A 617 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 476 time to evaluate : 2.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 584 GLU cc_start: 0.8883 (tm-30) cc_final: 0.8548 (tm-30) REVERT: A 634 GLU cc_start: 0.9067 (tm-30) cc_final: 0.8852 (tm-30) REVERT: A 648 GLU cc_start: 0.9211 (pp20) cc_final: 0.8638 (pm20) REVERT: B 98 ASN cc_start: 0.8391 (t0) cc_final: 0.7106 (t0) REVERT: B 102 GLU cc_start: 0.9300 (mp0) cc_final: 0.9077 (mp0) REVERT: B 427 TRP cc_start: 0.8965 (m100) cc_final: 0.8737 (m100) REVERT: C 584 GLU cc_start: 0.8933 (tm-30) cc_final: 0.8558 (tm-30) REVERT: C 629 LEU cc_start: 0.9190 (mt) cc_final: 0.8843 (tp) REVERT: C 634 GLU cc_start: 0.9175 (tm-30) cc_final: 0.8944 (tm-30) REVERT: C 635 ILE cc_start: 0.9372 (mp) cc_final: 0.8402 (mp) REVERT: C 645 LEU cc_start: 0.9438 (tp) cc_final: 0.8987 (tp) REVERT: C 648 GLU cc_start: 0.9273 (pp20) cc_final: 0.8755 (pm20) REVERT: C 655 LYS cc_start: 0.9047 (mmtt) cc_final: 0.8771 (mppt) REVERT: D 44 ARG cc_start: 0.5884 (mmt-90) cc_final: 0.5399 (mmt-90) REVERT: D 67 PHE cc_start: 0.8592 (p90) cc_final: 0.8061 (p90) REVERT: D 71 ARG cc_start: 0.8443 (ttt-90) cc_final: 0.8176 (tmt-80) REVERT: E 24 LYS cc_start: 0.8857 (pptt) cc_final: 0.8551 (pptt) REVERT: E 37 GLN cc_start: 0.7064 (pp30) cc_final: 0.6835 (pp30) REVERT: E 45 LYS cc_start: 0.8903 (tptp) cc_final: 0.8657 (ttpp) REVERT: E 78 VAL cc_start: 0.7978 (m) cc_final: 0.7701 (p) REVERT: E 82 ASP cc_start: 0.8919 (m-30) cc_final: 0.8449 (m-30) REVERT: F 535 MET cc_start: 0.9101 (mmt) cc_final: 0.8892 (mmt) REVERT: F 621 GLU cc_start: 0.8821 (tm-30) cc_final: 0.8467 (tm-30) REVERT: F 624 ASP cc_start: 0.8856 (m-30) cc_final: 0.8613 (m-30) REVERT: F 645 LEU cc_start: 0.9273 (tp) cc_final: 0.8792 (tp) REVERT: F 648 GLU cc_start: 0.9238 (pp20) cc_final: 0.8741 (pm20) REVERT: G 98 ASN cc_start: 0.8820 (t0) cc_final: 0.7615 (t0) REVERT: G 102 GLU cc_start: 0.9242 (mp0) cc_final: 0.8815 (mp0) REVERT: G 104 MET cc_start: 0.9115 (ttp) cc_final: 0.8484 (ttp) REVERT: G 114 GLN cc_start: 0.9438 (tm-30) cc_final: 0.9194 (tm-30) REVERT: G 150 MET cc_start: 0.9249 (tmm) cc_final: 0.8765 (tmm) REVERT: G 194 ILE cc_start: 0.9185 (tp) cc_final: 0.8976 (tp) REVERT: G 321 ASP cc_start: 0.9077 (t70) cc_final: 0.8825 (t70) REVERT: G 434 MET cc_start: 0.8274 (tmm) cc_final: 0.8040 (tmm) REVERT: G 475 MET cc_start: 0.7644 (tmm) cc_final: 0.6836 (tmm) REVERT: H 13 LYS cc_start: 0.9024 (tppt) cc_final: 0.8739 (tppt) REVERT: H 27 PHE cc_start: 0.8261 (m-80) cc_final: 0.8053 (m-80) REVERT: H 39 GLN cc_start: 0.8189 (mm-40) cc_final: 0.7834 (mm-40) REVERT: H 67 PHE cc_start: 0.8744 (p90) cc_final: 0.8079 (p90) REVERT: I 59 LYS cc_start: 0.8264 (tptp) cc_final: 0.7956 (tptp) REVERT: I 98 ASN cc_start: 0.8336 (t0) cc_final: 0.8050 (t0) REVERT: I 102 GLU cc_start: 0.9268 (mp0) cc_final: 0.8995 (mp0) REVERT: I 114 GLN cc_start: 0.9443 (tm-30) cc_final: 0.9169 (tm-30) REVERT: I 252 LYS cc_start: 0.9367 (mtmm) cc_final: 0.9107 (mmmm) REVERT: I 425 ASN cc_start: 0.9288 (p0) cc_final: 0.9027 (p0) REVERT: J 44 ARG cc_start: 0.5480 (mmt180) cc_final: 0.4798 (mmt-90) REVERT: J 57 THR cc_start: 0.7844 (m) cc_final: 0.7090 (t) REVERT: J 67 PHE cc_start: 0.8713 (p90) cc_final: 0.8183 (p90) REVERT: J 78 LEU cc_start: 0.8916 (pt) cc_final: 0.8663 (pt) REVERT: J 89 MET cc_start: 0.8360 (mmp) cc_final: 0.7220 (tpt) REVERT: K 24 LYS cc_start: 0.9048 (pptt) cc_final: 0.8621 (pptt) REVERT: K 37 GLN cc_start: 0.7491 (pp30) cc_final: 0.7076 (pp30) REVERT: K 45 LYS cc_start: 0.9124 (tptm) cc_final: 0.8838 (ttpp) REVERT: K 103 LYS cc_start: 0.8774 (mmmm) cc_final: 0.8528 (tppp) REVERT: L 37 GLN cc_start: 0.7929 (pp30) cc_final: 0.7340 (pp30) REVERT: L 38 GLN cc_start: 0.8638 (pt0) cc_final: 0.8275 (pt0) REVERT: L 72 THR cc_start: 0.6612 (t) cc_final: 0.6159 (t) REVERT: L 80 GLU cc_start: 0.7248 (tt0) cc_final: 0.7033 (tt0) outliers start: 5 outliers final: 0 residues processed: 476 average time/residue: 0.2953 time to fit residues: 217.8693 Evaluate side-chains 391 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 391 time to evaluate : 2.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 141 optimal weight: 2.9990 chunk 227 optimal weight: 7.9990 chunk 139 optimal weight: 4.9990 chunk 108 optimal weight: 4.9990 chunk 158 optimal weight: 8.9990 chunk 239 optimal weight: 9.9990 chunk 220 optimal weight: 6.9990 chunk 190 optimal weight: 5.9990 chunk 19 optimal weight: 0.9990 chunk 147 optimal weight: 0.7980 chunk 116 optimal weight: 9.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 585 HIS ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS B 302 ASN ** C 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 53 ASN ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 585 HIS ** F 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 67 ASN ** G 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 53 ASN ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 53 ASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.4070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 20587 Z= 0.305 Angle : 0.865 12.609 27934 Z= 0.422 Chirality : 0.053 0.395 3337 Planarity : 0.005 0.059 3463 Dihedral : 10.063 83.576 4330 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 19.96 Ramachandran Plot: Outliers : 0.04 % Allowed : 17.84 % Favored : 82.12 % Rotamer: Outliers : 0.24 % Allowed : 0.57 % Favored : 99.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 1.96 % Twisted General : 0.30 % 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: -3.70 (0.15), residues: 2388 helix: -0.70 (0.27), residues: 369 sheet: -1.52 (0.26), residues: 393 loop : -3.40 (0.13), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP L 35 HIS 0.013 0.002 HIS E 76 PHE 0.015 0.002 PHE K 98 TYR 0.033 0.002 TYR J 58 ARG 0.008 0.001 ARG A 617 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 460 time to evaluate : 2.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 574 LYS cc_start: 0.8404 (mttp) cc_final: 0.8087 (mtpp) REVERT: A 584 GLU cc_start: 0.8906 (tm-30) cc_final: 0.8607 (tm-30) REVERT: A 648 GLU cc_start: 0.9199 (pp20) cc_final: 0.8733 (pm20) REVERT: B 98 ASN cc_start: 0.8384 (t0) cc_final: 0.6987 (t0) REVERT: B 102 GLU cc_start: 0.9343 (mp0) cc_final: 0.8608 (pm20) REVERT: B 104 MET cc_start: 0.8973 (ttp) cc_final: 0.8447 (ttp) REVERT: C 573 ILE cc_start: 0.9212 (pt) cc_final: 0.8936 (pt) REVERT: C 577 GLN cc_start: 0.9120 (mt0) cc_final: 0.8878 (mt0) REVERT: C 584 GLU cc_start: 0.8960 (tm-30) cc_final: 0.8588 (tm-30) REVERT: C 629 LEU cc_start: 0.9341 (mt) cc_final: 0.9102 (tp) REVERT: C 645 LEU cc_start: 0.9417 (tp) cc_final: 0.8986 (tp) REVERT: C 648 GLU cc_start: 0.9306 (pp20) cc_final: 0.8787 (pm20) REVERT: C 657 GLU cc_start: 0.9163 (mp0) cc_final: 0.8387 (mp0) REVERT: C 658 GLN cc_start: 0.9299 (tp40) cc_final: 0.9024 (tm-30) REVERT: D 39 GLN cc_start: 0.8377 (mm110) cc_final: 0.8129 (mm110) REVERT: D 44 ARG cc_start: 0.5735 (mmt-90) cc_final: 0.5237 (mmt-90) REVERT: D 71 ARG cc_start: 0.8490 (ttt-90) cc_final: 0.8217 (tmt-80) REVERT: D 85 GLU cc_start: 0.8506 (pp20) cc_final: 0.8127 (pp20) REVERT: E 24 LYS cc_start: 0.8937 (pptt) cc_final: 0.8574 (pptt) REVERT: E 37 GLN cc_start: 0.7059 (pp30) cc_final: 0.6824 (pp30) REVERT: E 45 LYS cc_start: 0.8980 (tptp) cc_final: 0.8692 (ttpp) REVERT: E 78 VAL cc_start: 0.7991 (m) cc_final: 0.7737 (p) REVERT: E 82 ASP cc_start: 0.8850 (m-30) cc_final: 0.8401 (m-30) REVERT: F 535 MET cc_start: 0.9108 (mmt) cc_final: 0.8888 (mmt) REVERT: F 605 CYS cc_start: 0.8717 (m) cc_final: 0.8198 (t) REVERT: F 621 GLU cc_start: 0.8823 (tm-30) cc_final: 0.8498 (tm-30) REVERT: F 624 ASP cc_start: 0.8809 (m-30) cc_final: 0.8551 (m-30) REVERT: F 648 GLU cc_start: 0.9243 (pp20) cc_final: 0.8783 (pm20) REVERT: G 98 ASN cc_start: 0.8569 (t0) cc_final: 0.8045 (t0) REVERT: G 104 MET cc_start: 0.9048 (ttp) cc_final: 0.8388 (ttp) REVERT: G 114 GLN cc_start: 0.9439 (tm-30) cc_final: 0.9155 (tm-30) REVERT: G 150 MET cc_start: 0.9262 (tmm) cc_final: 0.8780 (tmm) REVERT: G 434 MET cc_start: 0.8221 (tmm) cc_final: 0.7971 (tmm) REVERT: H 13 LYS cc_start: 0.9016 (tppt) cc_final: 0.8771 (tppt) REVERT: H 27 PHE cc_start: 0.8427 (m-80) cc_final: 0.8185 (m-80) REVERT: H 39 GLN cc_start: 0.8291 (mm-40) cc_final: 0.8014 (mm-40) REVERT: H 67 PHE cc_start: 0.8754 (p90) cc_final: 0.8059 (p90) REVERT: H 78 LEU cc_start: 0.8850 (pt) cc_final: 0.8644 (pt) REVERT: H 89 MET cc_start: 0.8428 (mmp) cc_final: 0.7181 (tpt) REVERT: I 59 LYS cc_start: 0.8233 (tptp) cc_final: 0.7997 (tptp) REVERT: I 98 ASN cc_start: 0.8381 (t0) cc_final: 0.8020 (t0) REVERT: I 102 GLU cc_start: 0.9300 (mp0) cc_final: 0.8997 (mp0) REVERT: I 114 GLN cc_start: 0.9476 (tm-30) cc_final: 0.9173 (tm-30) REVERT: I 252 LYS cc_start: 0.9391 (mtmm) cc_final: 0.9151 (mmmm) REVERT: I 425 ASN cc_start: 0.9319 (p0) cc_final: 0.9073 (p0) REVERT: I 434 MET cc_start: 0.9277 (tpp) cc_final: 0.9009 (tpp) REVERT: I 475 MET cc_start: 0.8245 (tpt) cc_final: 0.7557 (tpp) REVERT: J 57 THR cc_start: 0.7644 (m) cc_final: 0.6996 (t) REVERT: J 67 PHE cc_start: 0.8681 (p90) cc_final: 0.8106 (p90) REVERT: K 24 LYS cc_start: 0.9087 (pptt) cc_final: 0.8650 (pptt) REVERT: K 37 GLN cc_start: 0.7515 (pp30) cc_final: 0.7035 (pp30) REVERT: K 45 LYS cc_start: 0.9133 (tptm) cc_final: 0.8807 (ttpp) REVERT: L 37 GLN cc_start: 0.7995 (pp30) cc_final: 0.7363 (pp30) REVERT: L 38 GLN cc_start: 0.8662 (pt0) cc_final: 0.8184 (pt0) REVERT: L 72 THR cc_start: 0.6492 (t) cc_final: 0.5983 (t) outliers start: 5 outliers final: 1 residues processed: 461 average time/residue: 0.2997 time to fit residues: 213.8778 Evaluate side-chains 380 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 379 time to evaluate : 2.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 151 optimal weight: 4.9990 chunk 202 optimal weight: 0.9990 chunk 58 optimal weight: 5.9990 chunk 175 optimal weight: 8.9990 chunk 28 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 190 optimal weight: 5.9990 chunk 79 optimal weight: 7.9990 chunk 195 optimal weight: 0.9990 chunk 24 optimal weight: 8.9990 chunk 35 optimal weight: 4.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 585 HIS ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS C 540 GLN ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 585 HIS ** F 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 66 HIS G 67 ASN ** G 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 66 HIS J 76 ASN ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 6 GLN ** K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 53 ASN ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 53 ASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.085050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.067221 restraints weight = 70112.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.069303 restraints weight = 38964.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.070745 restraints weight = 26317.377| |-----------------------------------------------------------------------------| r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.4182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 20587 Z= 0.277 Angle : 0.856 12.344 27934 Z= 0.418 Chirality : 0.053 0.416 3337 Planarity : 0.005 0.058 3463 Dihedral : 9.967 82.042 4330 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 19.60 Ramachandran Plot: Outliers : 0.08 % Allowed : 17.84 % Favored : 82.08 % Rotamer: Outliers : 0.28 % Allowed : 0.62 % Favored : 99.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 3.92 % Twisted General : 0.30 % 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: 2388 helix: -0.62 (0.27), residues: 369 sheet: -1.51 (0.26), residues: 393 loop : -3.36 (0.13), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.003 TRP K 35 HIS 0.013 0.002 HIS E 76 PHE 0.018 0.001 PHE D 67 TYR 0.040 0.002 TYR K 96 ARG 0.007 0.001 ARG J 44 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4647.13 seconds wall clock time: 84 minutes 52.37 seconds (5092.37 seconds total)