Starting phenix.real_space_refine on Mon Mar 18 17:09:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k39_22653/03_2024/7k39_22653.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k39_22653/03_2024/7k39_22653.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k39_22653/03_2024/7k39_22653.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k39_22653/03_2024/7k39_22653.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k39_22653/03_2024/7k39_22653.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k39_22653/03_2024/7k39_22653.pdb" } resolution = 3.0 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= 0.009 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 99 5.16 5 C 13452 2.51 5 N 3639 2.21 5 O 4371 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 119": "OE1" <-> "OE2" Residue "A TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 280": "OE1" <-> "OE2" Residue "B GLU 15": "OE1" <-> "OE2" Residue "B ARG 54": "NH1" <-> "NH2" Residue "B GLU 67": "OE1" <-> "OE2" Residue "B GLU 69": "OE1" <-> "OE2" Residue "B ARG 124": "NH1" <-> "NH2" Residue "B TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 165": "OE1" <-> "OE2" Residue "C TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 119": "OE1" <-> "OE2" Residue "C TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 280": "OE1" <-> "OE2" Residue "D GLU 15": "OE1" <-> "OE2" Residue "D ARG 54": "NH1" <-> "NH2" Residue "D GLU 67": "OE1" <-> "OE2" Residue "D GLU 69": "OE1" <-> "OE2" Residue "D ARG 124": "NH1" <-> "NH2" Residue "D TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 165": "OE1" <-> "OE2" Residue "E TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 119": "OE1" <-> "OE2" Residue "E TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 280": "OE1" <-> "OE2" Residue "F GLU 15": "OE1" <-> "OE2" Residue "F ARG 54": "NH1" <-> "NH2" Residue "F GLU 67": "OE1" <-> "OE2" Residue "F GLU 69": "OE1" <-> "OE2" Residue "F ARG 124": "NH1" <-> "NH2" Residue "F TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 165": "OE1" <-> "OE2" Residue "G ARG 17": "NH1" <-> "NH2" Residue "G TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 46": "OE1" <-> "OE2" Residue "H TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 98": "NH1" <-> "NH2" Residue "H TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 17": "NH1" <-> "NH2" Residue "I PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 46": "OE1" <-> "OE2" Residue "J TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 98": "NH1" <-> "NH2" Residue "J TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 113": "NH1" <-> "NH2" Residue "K PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 166": "OE1" <-> "OE2" Residue "K PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 46": "OE1" <-> "OE2" Residue "L TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 98": "NH1" <-> "NH2" Residue "L TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 21561 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 2454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2454 Classifications: {'peptide': 318} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 298} Chain: "B" Number of atoms: 1398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1398 Classifications: {'peptide': 172} Link IDs: {'TRANS': 171} Chain: "C" Number of atoms: 2454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2454 Classifications: {'peptide': 318} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 298} Chain: "D" Number of atoms: 1398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1398 Classifications: {'peptide': 172} Link IDs: {'TRANS': 171} Chain: "E" Number of atoms: 2454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2454 Classifications: {'peptide': 318} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 298} Chain: "F" Number of atoms: 1398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1398 Classifications: {'peptide': 172} Link IDs: {'TRANS': 171} Chain: "G" Number of atoms: 1502 Number of conformers: 2 Conformer: "B" Number of residues, atoms: 202, 1501 Classifications: {'peptide': 202} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 189} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 1 Conformer: "A" Number of residues, atoms: 202, 1500 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 189} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 1528 Chain: "H" Number of atoms: 1608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1608 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 11, 'TRANS': 200} Chain breaks: 1 Chain: "I" Number of atoms: 1502 Number of conformers: 2 Conformer: "B" Number of residues, atoms: 202, 1501 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 12, 'TRANS': 189} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 1 Conformer: "A" Number of residues, atoms: 202, 1500 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 189} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 1528 Chain: "J" Number of atoms: 1608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1608 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 11, 'TRANS': 200} Chain breaks: 1 Chain: "K" Number of atoms: 1502 Number of conformers: 2 Conformer: "B" Number of residues, atoms: 202, 1501 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 12, 'TRANS': 189} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 1 Conformer: "A" Number of residues, atoms: 202, 1500 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 189} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 1528 Chain: "L" Number of atoms: 1608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1608 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 11, 'TRANS': 200} Chain breaks: 1 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: 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: "O" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} 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: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 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: "R" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} 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: "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: 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: "U" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} 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: "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: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 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: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 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: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 13.90, per 1000 atoms: 0.64 Number of scatterers: 21561 At special positions: 0 Unit cell: (184.87, 184.87, 146.3, 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 99 16.00 O 4371 8.00 N 3639 7.00 C 13452 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=30, symmetry=0 Simple disulfide: pdb=" SG CYS A 14 " - pdb=" SG CYS B 137 " distance=2.09 Simple disulfide: pdb=" SG CYS A 52 " - pdb=" SG CYS A 277 " distance=2.02 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 76 " distance=2.03 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 139 " distance=2.03 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 305 " distance=2.02 Simple disulfide: pdb=" SG CYS B 144 " - pdb=" SG CYS B 148 " distance=2.03 Simple disulfide: pdb=" SG CYS C 14 " - pdb=" SG CYS D 137 " distance=2.16 Simple disulfide: pdb=" SG CYS C 52 " - pdb=" SG CYS C 277 " distance=2.02 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 76 " distance=2.03 Simple disulfide: pdb=" SG CYS C 97 " - pdb=" SG CYS C 139 " distance=2.03 Simple disulfide: pdb=" SG CYS C 281 " - pdb=" SG CYS C 305 " distance=2.02 Simple disulfide: pdb=" SG CYS D 144 " - pdb=" SG CYS D 148 " distance=2.03 Simple disulfide: pdb=" SG CYS E 14 " - pdb=" SG CYS F 137 " distance=1.90 Simple disulfide: pdb=" SG CYS E 52 " - pdb=" SG CYS E 277 " distance=2.02 Simple disulfide: pdb=" SG CYS E 64 " - pdb=" SG CYS E 76 " distance=2.03 Simple disulfide: pdb=" SG CYS E 97 " - pdb=" SG CYS E 139 " distance=2.03 Simple disulfide: pdb=" SG CYS E 281 " - pdb=" SG CYS E 305 " distance=2.02 Simple disulfide: pdb=" SG CYS F 144 " - pdb=" SG CYS F 148 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 90 " distance=2.04 Simple disulfide: pdb=" SG CYS G 139 " - pdb=" SG CYS G 199 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 150 " - pdb=" SG CYS H 206 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 90 " distance=2.04 Simple disulfide: pdb=" SG CYS I 139 " - pdb=" SG CYS I 199 " distance=2.04 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 150 " - pdb=" SG CYS J 206 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 90 " distance=2.04 Simple disulfide: pdb=" SG CYS K 139 " - pdb=" SG CYS K 199 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 150 " - pdb=" SG CYS L 206 " 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=0, symmetry=0 Links applied ALPHA1-2 " MAN O 5 " - " MAN O 6 " " MAN R 5 " - " MAN R 6 " " MAN U 5 " - " MAN U 6 " ALPHA1-3 " BMA N 3 " - " MAN N 4 " " BMA O 3 " - " MAN O 8 " " MAN O 4 " - " MAN O 7 " " BMA Q 3 " - " MAN Q 4 " " BMA R 3 " - " MAN R 8 " " MAN R 4 " - " MAN R 7 " " BMA T 3 " - " MAN T 4 " " BMA U 3 " - " MAN U 8 " " MAN U 4 " - " MAN U 7 " ALPHA1-6 " BMA N 3 " - " MAN N 5 " " BMA O 3 " - " MAN O 4 " " MAN O 4 " - " MAN O 5 " " BMA Q 3 " - " MAN Q 5 " " BMA R 3 " - " MAN R 4 " " MAN R 4 " - " MAN R 5 " " BMA T 3 " - " MAN T 5 " " BMA U 3 " - " MAN U 4 " " MAN U 4 " - " MAN U 5 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " NAG-ASN " NAG A 401 " - " ASN A 22 " " NAG A 402 " - " ASN A 81 " " NAG B 301 " - " ASN B 154 " " NAG C 401 " - " ASN C 22 " " NAG C 402 " - " ASN C 81 " " NAG D 301 " - " ASN D 154 " " NAG E 401 " - " ASN E 22 " " NAG E 402 " - " ASN E 81 " " NAG F 301 " - " ASN F 154 " " NAG M 1 " - " ASN A 38 " " NAG N 1 " - " ASN A 165 " " NAG O 1 " - " ASN A 285 " " NAG P 1 " - " ASN C 38 " " NAG Q 1 " - " ASN C 165 " " NAG R 1 " - " ASN C 285 " " NAG S 1 " - " ASN E 38 " " NAG T 1 " - " ASN E 165 " " NAG U 1 " - " ASN E 285 " Time building additional restraints: 8.86 Conformation dependent library (CDL) restraints added in 3.6 seconds 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4962 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 63 sheets defined 19.0% alpha, 31.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.61 Creating SS restraints... Processing helix chain 'A' and resid 65 through 72 Processing helix chain 'A' and resid 73 through 80 removed outlier: 5.312A pdb=" N VAL A 78 " --> pdb=" O HIS A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 116 Processing helix chain 'A' and resid 187 through 195 Processing helix chain 'B' and resid 38 through 50 removed outlier: 4.422A pdb=" N GLY B 50 " --> pdb=" O ASP B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 126 Processing helix chain 'B' and resid 145 through 155 Processing helix chain 'B' and resid 159 through 161 No H-bonds generated for 'chain 'B' and resid 159 through 161' Processing helix chain 'B' and resid 162 through 172 Processing helix chain 'C' and resid 65 through 72 Processing helix chain 'C' and resid 73 through 80 removed outlier: 5.312A pdb=" N VAL C 78 " --> pdb=" O HIS C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 116 Processing helix chain 'C' and resid 187 through 195 Processing helix chain 'D' and resid 38 through 50 removed outlier: 4.423A pdb=" N GLY D 50 " --> pdb=" O ASP D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 126 Processing helix chain 'D' and resid 145 through 155 Processing helix chain 'D' and resid 159 through 161 No H-bonds generated for 'chain 'D' and resid 159 through 161' Processing helix chain 'D' and resid 162 through 172 Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 73 through 80 removed outlier: 5.312A pdb=" N VAL E 78 " --> pdb=" O HIS E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 116 Processing helix chain 'E' and resid 187 through 195 Processing helix chain 'F' and resid 38 through 50 removed outlier: 4.423A pdb=" N GLY F 50 " --> pdb=" O ASP F 46 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 126 Processing helix chain 'F' and resid 145 through 155 Processing helix chain 'F' and resid 159 through 161 No H-bonds generated for 'chain 'F' and resid 159 through 161' Processing helix chain 'F' and resid 162 through 172 Processing helix chain 'G' and resid 81 through 85 Processing helix chain 'G' and resid 126 through 133 Processing helix chain 'G' and resid 187 through 192 removed outlier: 3.670A pdb=" N GLU G 192 " --> pdb=" O LYS G 188 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 106 through 110 Processing helix chain 'H' and resid 197 through 202 removed outlier: 3.660A pdb=" N THR H 201 " --> pdb=" O SER H 197 " (cutoff:3.500A) Processing helix chain 'I' and resid 81 through 85 Processing helix chain 'I' and resid 126 through 132 Processing helix chain 'I' and resid 188 through 192 removed outlier: 3.592A pdb=" N GLU I 192 " --> pdb=" O LYS I 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 188 through 192' Processing helix chain 'J' and resid 28 through 32 Processing helix chain 'J' and resid 62 through 65 Processing helix chain 'J' and resid 87 through 91 Processing helix chain 'J' and resid 106 through 110 Processing helix chain 'J' and resid 197 through 202 removed outlier: 3.661A pdb=" N THR J 201 " --> pdb=" O SER J 197 " (cutoff:3.500A) Processing helix chain 'K' and resid 81 through 85 Processing helix chain 'K' and resid 126 through 132 removed outlier: 3.728A pdb=" N LEU K 130 " --> pdb=" O SER K 126 " (cutoff:3.500A) Processing helix chain 'K' and resid 187 through 194 Processing helix chain 'L' and resid 28 through 32 Processing helix chain 'L' and resid 62 through 65 Processing helix chain 'L' and resid 87 through 91 Processing helix chain 'L' and resid 106 through 110 Processing helix chain 'L' and resid 197 through 202 removed outlier: 3.660A pdb=" N THR L 201 " --> pdb=" O SER L 197 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 33 through 37 removed outlier: 4.766A pdb=" N TYR B 22 " --> pdb=" O ASP B 37 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 24 through 26 Processing sheet with id=AA3, first strand: chain 'A' and resid 39 through 41 Processing sheet with id=AA4, first strand: chain 'A' and resid 43 through 44 Processing sheet with id=AA5, first strand: chain 'A' and resid 51 through 54 removed outlier: 5.983A pdb=" N ILE A 51 " --> pdb=" O ASP A 275 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N CYS A 277 " --> pdb=" O ILE A 51 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASN A 53 " --> pdb=" O CYS A 277 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 58 through 61 Processing sheet with id=AA7, first strand: chain 'A' and resid 100 through 101 removed outlier: 6.883A pdb=" N ASP A 101 " --> pdb=" O ILE A 232 " (cutoff:3.500A) removed outlier: 8.953A pdb=" N TRP A 234 " --> pdb=" O ASP A 101 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N ILE A 179 " --> pdb=" O GLY A 256 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N GLY A 256 " --> pdb=" O ILE A 179 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 100 through 101 removed outlier: 6.883A pdb=" N ASP A 101 " --> pdb=" O ILE A 232 " (cutoff:3.500A) removed outlier: 8.953A pdb=" N TRP A 234 " --> pdb=" O ASP A 101 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N ILE A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 130 through 131 Processing sheet with id=AB1, first strand: chain 'A' and resid 136 through 141 removed outlier: 7.531A pdb=" N ALA A 138 " --> pdb=" O GLY A 144 " (cutoff:3.500A) removed outlier: 10.546A pdb=" N GLY A 144 " --> pdb=" O ALA A 138 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 164 through 169 Processing sheet with id=AB3, first strand: chain 'A' and resid 286 through 288 removed outlier: 4.217A pdb=" N CYS A 281 " --> pdb=" O ILE A 288 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 33 through 37 removed outlier: 4.766A pdb=" N TYR D 22 " --> pdb=" O ASP D 37 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 24 through 26 Processing sheet with id=AB6, first strand: chain 'C' and resid 39 through 41 Processing sheet with id=AB7, first strand: chain 'C' and resid 43 through 44 Processing sheet with id=AB8, first strand: chain 'C' and resid 51 through 54 removed outlier: 5.983A pdb=" N ILE C 51 " --> pdb=" O ASP C 275 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N CYS C 277 " --> pdb=" O ILE C 51 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASN C 53 " --> pdb=" O CYS C 277 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'C' and resid 58 through 61 Processing sheet with id=AC1, first strand: chain 'C' and resid 100 through 101 removed outlier: 6.883A pdb=" N ASP C 101 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 8.953A pdb=" N TRP C 234 " --> pdb=" O ASP C 101 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N ILE C 179 " --> pdb=" O GLY C 256 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N GLY C 256 " --> pdb=" O ILE C 179 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 100 through 101 removed outlier: 6.883A pdb=" N ASP C 101 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 8.953A pdb=" N TRP C 234 " --> pdb=" O ASP C 101 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N ILE C 179 " --> pdb=" O PRO C 254 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 130 through 131 Processing sheet with id=AC4, first strand: chain 'C' and resid 136 through 141 removed outlier: 7.531A pdb=" N ALA C 138 " --> pdb=" O GLY C 144 " (cutoff:3.500A) removed outlier: 10.547A pdb=" N GLY C 144 " --> pdb=" O ALA C 138 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 164 through 169 Processing sheet with id=AC6, first strand: chain 'C' and resid 286 through 288 removed outlier: 4.217A pdb=" N CYS C 281 " --> pdb=" O ILE C 288 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 33 through 37 removed outlier: 4.766A pdb=" N TYR F 22 " --> pdb=" O ASP F 37 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 24 through 26 Processing sheet with id=AC9, first strand: chain 'E' and resid 39 through 41 Processing sheet with id=AD1, first strand: chain 'E' and resid 43 through 44 Processing sheet with id=AD2, first strand: chain 'E' and resid 51 through 54 removed outlier: 5.983A pdb=" N ILE E 51 " --> pdb=" O ASP E 275 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N CYS E 277 " --> pdb=" O ILE E 51 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASN E 53 " --> pdb=" O CYS E 277 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'E' and resid 58 through 61 Processing sheet with id=AD4, first strand: chain 'E' and resid 100 through 101 removed outlier: 6.884A pdb=" N ASP E 101 " --> pdb=" O ILE E 232 " (cutoff:3.500A) removed outlier: 8.953A pdb=" N TRP E 234 " --> pdb=" O ASP E 101 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N ILE E 179 " --> pdb=" O GLY E 256 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N GLY E 256 " --> pdb=" O ILE E 179 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 100 through 101 removed outlier: 6.884A pdb=" N ASP E 101 " --> pdb=" O ILE E 232 " (cutoff:3.500A) removed outlier: 8.953A pdb=" N TRP E 234 " --> pdb=" O ASP E 101 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N ILE E 179 " --> pdb=" O PRO E 254 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 130 through 131 Processing sheet with id=AD7, first strand: chain 'E' and resid 136 through 141 removed outlier: 7.531A pdb=" N ALA E 138 " --> pdb=" O GLY E 144 " (cutoff:3.500A) removed outlier: 10.546A pdb=" N GLY E 144 " --> pdb=" O ALA E 138 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 164 through 169 Processing sheet with id=AD9, first strand: chain 'E' and resid 286 through 288 removed outlier: 4.218A pdb=" N CYS E 281 " --> pdb=" O ILE E 288 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 10 through 11 removed outlier: 3.521A pdb=" N THR G 109 " --> pdb=" O VAL G 10 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N TRP G 37 " --> pdb=" O LEU G 49 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 17 through 22 Processing sheet with id=AE3, first strand: chain 'G' and resid 119 through 123 removed outlier: 4.016A pdb=" N VAL G 138 " --> pdb=" O PHE G 123 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N TYR G 178 " --> pdb=" O ASN G 143 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N SER G 179 " --> pdb=" O THR G 169 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 149 through 155 removed outlier: 4.175A pdb=" N LYS G 150 " --> pdb=" O THR G 202 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TYR G 197 " --> pdb=" O PHE G 214 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AE6, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.697A pdb=" N GLU H 10 " --> pdb=" O THR H 123 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.697A pdb=" N GLU H 10 " --> pdb=" O THR H 123 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N VAL H 115 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 130 through 134 removed outlier: 6.033A pdb=" N TYR H 186 " --> pdb=" O ASP H 154 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N SER H 189 " --> pdb=" O PRO H 177 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N VAL H 191 " --> pdb=" O THR H 175 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N THR H 175 " --> pdb=" O VAL H 191 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N THR H 193 " --> pdb=" O VAL H 173 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N VAL H 173 " --> pdb=" O THR H 193 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 160 through 164 Processing sheet with id=AF1, first strand: chain 'I' and resid 4 through 5 removed outlier: 3.865A pdb=" N THR I 5 " --> pdb=" O THR I 23 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'I' and resid 9 through 12 removed outlier: 6.443A pdb=" N TRP I 37 " --> pdb=" O LEU I 49 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'I' and resid 119 through 123 removed outlier: 3.713A pdb=" N VAL I 138 " --> pdb=" O PHE I 123 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N TYR I 178 " --> pdb=" O ASN I 143 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'I' and resid 150 through 154 Processing sheet with id=AF5, first strand: chain 'J' and resid 3 through 6 Processing sheet with id=AF6, first strand: chain 'J' and resid 10 through 11 removed outlier: 6.697A pdb=" N GLU J 10 " --> pdb=" O THR J 123 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'J' and resid 10 through 11 removed outlier: 6.697A pdb=" N GLU J 10 " --> pdb=" O THR J 123 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N VAL J 115 " --> pdb=" O ARG J 98 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'J' and resid 130 through 134 removed outlier: 6.033A pdb=" N TYR J 186 " --> pdb=" O ASP J 154 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N SER J 189 " --> pdb=" O PRO J 177 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N VAL J 191 " --> pdb=" O THR J 175 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N THR J 175 " --> pdb=" O VAL J 191 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N THR J 193 " --> pdb=" O VAL J 173 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N VAL J 173 " --> pdb=" O THR J 193 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'J' and resid 160 through 164 Processing sheet with id=AG1, first strand: chain 'K' and resid 10 through 12 removed outlier: 3.678A pdb=" N THR K 109 " --> pdb=" O VAL K 10 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLY K 12 " --> pdb=" O THR K 109 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N TRP K 37 " --> pdb=" O LEU K 49 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'K' and resid 17 through 22 Processing sheet with id=AG3, first strand: chain 'K' and resid 119 through 123 removed outlier: 3.650A pdb=" N PHE K 123 " --> pdb=" O VAL K 138 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N VAL K 138 " --> pdb=" O PHE K 123 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N TYR K 178 " --> pdb=" O ASN K 143 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'K' and resid 158 through 159 removed outlier: 3.519A pdb=" N LYS K 150 " --> pdb=" O THR K 202 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'L' and resid 3 through 6 Processing sheet with id=AG6, first strand: chain 'L' and resid 10 through 11 removed outlier: 6.698A pdb=" N GLU L 10 " --> pdb=" O THR L 123 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N ARG L 38 " --> pdb=" O TRP L 47 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N TRP L 47 " --> pdb=" O ARG L 38 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'L' and resid 10 through 11 removed outlier: 6.698A pdb=" N GLU L 10 " --> pdb=" O THR L 123 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N VAL L 115 " --> pdb=" O ARG L 98 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'L' and resid 130 through 134 removed outlier: 6.033A pdb=" N TYR L 186 " --> pdb=" O ASP L 154 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N SER L 189 " --> pdb=" O PRO L 177 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N VAL L 191 " --> pdb=" O THR L 175 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N THR L 175 " --> pdb=" O VAL L 191 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N THR L 193 " --> pdb=" O VAL L 173 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N VAL L 173 " --> pdb=" O THR L 193 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'L' and resid 160 through 164 914 hydrogen bonds defined for protein. 2319 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.51 Time building geometry restraints manager: 9.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6927 1.34 - 1.46: 5129 1.46 - 1.58: 9814 1.58 - 1.70: 0 1.70 - 1.82: 138 Bond restraints: 22008 Sorted by residual: bond pdb=" C3 MAN R 4 " pdb=" O3 MAN R 4 " ideal model delta sigma weight residual 1.408 1.446 -0.038 2.00e-02 2.50e+03 3.66e+00 bond pdb=" C3 MAN U 4 " pdb=" O3 MAN U 4 " ideal model delta sigma weight residual 1.408 1.446 -0.038 2.00e-02 2.50e+03 3.52e+00 bond pdb=" C3 MAN O 4 " pdb=" O3 MAN O 4 " ideal model delta sigma weight residual 1.408 1.445 -0.037 2.00e-02 2.50e+03 3.40e+00 bond pdb=" C1 NAG M 2 " pdb=" O5 NAG M 2 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.78e+00 bond pdb=" C1 NAG P 2 " pdb=" O5 NAG P 2 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.73e+00 ... (remaining 22003 not shown) Histogram of bond angle deviations from ideal: 98.71 - 105.77: 491 105.77 - 112.82: 12335 112.82 - 119.88: 6667 119.88 - 126.93: 10087 126.93 - 133.99: 306 Bond angle restraints: 29886 Sorted by residual: angle pdb=" N GLN G 6 " pdb=" CA GLN G 6 " pdb=" C GLN G 6 " ideal model delta sigma weight residual 108.22 112.26 -4.04 9.00e-01 1.23e+00 2.02e+01 angle pdb=" N LYS G 195 " pdb=" CA LYS G 195 " pdb=" CB LYS G 195 " ideal model delta sigma weight residual 114.17 110.11 4.06 1.14e+00 7.69e-01 1.27e+01 angle pdb=" N TYR L 54 " pdb=" CA TYR L 54 " pdb=" CB TYR L 54 " ideal model delta sigma weight residual 114.17 110.13 4.04 1.14e+00 7.69e-01 1.26e+01 angle pdb=" N LEU D 52 " pdb=" CA LEU D 52 " pdb=" C LEU D 52 " ideal model delta sigma weight residual 114.56 110.08 4.48 1.27e+00 6.20e-01 1.24e+01 angle pdb=" N TYR H 54 " pdb=" CA TYR H 54 " pdb=" CB TYR H 54 " ideal model delta sigma weight residual 114.17 110.16 4.01 1.14e+00 7.69e-01 1.24e+01 ... (remaining 29881 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.89: 12943 21.89 - 43.79: 722 43.79 - 65.68: 105 65.68 - 87.58: 51 87.58 - 109.47: 24 Dihedral angle restraints: 13845 sinusoidal: 6087 harmonic: 7758 Sorted by residual: dihedral pdb=" CB CYS I 139 " pdb=" SG CYS I 139 " pdb=" SG CYS I 199 " pdb=" CB CYS I 199 " ideal model delta sinusoidal sigma weight residual 93.00 32.50 60.50 1 1.00e+01 1.00e-02 4.87e+01 dihedral pdb=" CB CYS G 139 " pdb=" SG CYS G 139 " pdb=" SG CYS G 199 " pdb=" CB CYS G 199 " ideal model delta sinusoidal sigma weight residual 93.00 38.48 54.52 1 1.00e+01 1.00e-02 4.03e+01 dihedral pdb=" CA CYS E 14 " pdb=" CB CYS E 14 " pdb=" SG CYS E 14 " pdb=" SG CYS F 137 " ideal model delta sinusoidal sigma weight residual 79.00 3.02 75.98 1 2.00e+01 2.50e-03 1.82e+01 ... (remaining 13842 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 2921 0.069 - 0.137: 525 0.137 - 0.206: 46 0.206 - 0.275: 6 0.275 - 0.343: 9 Chirality restraints: 3507 Sorted by residual: chirality pdb=" C3 MAN O 4 " pdb=" C2 MAN O 4 " pdb=" C4 MAN O 4 " pdb=" O3 MAN O 4 " both_signs ideal model delta sigma weight residual False 2.47 2.13 0.34 2.00e-01 2.50e+01 2.95e+00 chirality pdb=" C3 MAN U 4 " pdb=" C2 MAN U 4 " pdb=" C4 MAN U 4 " pdb=" O3 MAN U 4 " both_signs ideal model delta sigma weight residual False 2.47 2.13 0.34 2.00e-01 2.50e+01 2.91e+00 chirality pdb=" C3 MAN R 4 " pdb=" C2 MAN R 4 " pdb=" C4 MAN R 4 " pdb=" O3 MAN R 4 " both_signs ideal model delta sigma weight residual False 2.47 2.13 0.34 2.00e-01 2.50e+01 2.87e+00 ... (remaining 3504 not shown) Planarity restraints: 3795 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE F 3 " -0.007 2.00e-02 2.50e+03 1.14e-02 2.28e+00 pdb=" CG PHE F 3 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 PHE F 3 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE F 3 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE F 3 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE F 3 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE F 3 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 3 " -0.007 2.00e-02 2.50e+03 1.14e-02 2.26e+00 pdb=" CG PHE D 3 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 PHE D 3 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE D 3 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE D 3 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE D 3 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE D 3 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA I 13 " -0.025 5.00e-02 4.00e+02 3.73e-02 2.23e+00 pdb=" N PRO I 14 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO I 14 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO I 14 " -0.021 5.00e-02 4.00e+02 ... (remaining 3792 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 382 2.66 - 3.22: 19898 3.22 - 3.78: 33617 3.78 - 4.34: 47755 4.34 - 4.90: 79170 Nonbonded interactions: 180822 Sorted by model distance: nonbonded pdb=" OE1 GLU B 74 " pdb=" NE2 GLN B 78 " model vdw 2.099 2.520 nonbonded pdb=" OE1 GLU D 74 " pdb=" NE2 GLN D 78 " model vdw 2.099 2.520 nonbonded pdb=" OE1 GLU F 74 " pdb=" NE2 GLN F 78 " model vdw 2.100 2.520 nonbonded pdb=" OE1 GLN G 129 " pdb=" OG SER G 136 " model vdw 2.103 2.440 nonbonded pdb=" O SER G 92 " pdb=" OG SER G 100 " model vdw 2.105 2.440 ... (remaining 180817 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 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = (chain 'G' and (resid 2 through 113 or resid 115 through 169 or resid 171 throug \ h 217)) selection = (chain 'I' and (resid 2 through 113 or resid 115 through 169 or resid 171 throug \ h 217)) selection = (chain 'K' and (resid 2 through 113 or resid 115 through 169 or resid 171 throug \ h 217)) } ncs_group { reference = chain 'H' selection = chain 'J' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'P' selection = chain 'S' } ncs_group { reference = chain 'N' selection = chain 'Q' selection = chain 'T' } ncs_group { reference = chain 'O' selection = chain 'R' selection = chain 'U' } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.640 Check model and map are aligned: 0.330 Set scattering table: 0.200 Process input model: 59.520 Find NCS groups from input model: 1.350 Set up NCS constraints: 0.230 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 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 : 0.007 0.053 22008 Z= 0.492 Angle : 0.784 9.137 29886 Z= 0.404 Chirality : 0.054 0.343 3507 Planarity : 0.004 0.037 3777 Dihedral : 14.867 109.474 8793 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.16), residues: 2670 helix: 2.05 (0.25), residues: 363 sheet: -0.31 (0.17), residues: 834 loop : -1.10 (0.16), residues: 1473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 50 HIS 0.004 0.001 HIS C 18 PHE 0.024 0.002 PHE F 3 TYR 0.018 0.002 TYR I 178 ARG 0.006 0.000 ARG G 17 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 412 time to evaluate : 2.386 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: A 31 ASP cc_start: 0.7923 (m-30) cc_final: 0.7606 (m-30) REVERT: A 45 SER cc_start: 0.9230 (p) cc_final: 0.8876 (t) REVERT: A 189 GLN cc_start: 0.8670 (tm-30) cc_final: 0.8365 (tm-30) REVERT: A 190 GLU cc_start: 0.8549 (tt0) cc_final: 0.8349 (tt0) REVERT: A 268 MET cc_start: 0.9011 (ttm) cc_final: 0.8750 (ttm) REVERT: A 280 GLU cc_start: 0.8108 (mm-30) cc_final: 0.7848 (tp30) REVERT: B 17 MET cc_start: 0.8411 (tpp) cc_final: 0.8133 (ttm) REVERT: B 76 ARG cc_start: 0.8565 (mtp180) cc_final: 0.8089 (mtt180) REVERT: C 35 GLU cc_start: 0.8078 (tt0) cc_final: 0.7596 (tt0) REVERT: C 77 ASP cc_start: 0.7971 (m-30) cc_final: 0.7628 (m-30) REVERT: C 173 ASN cc_start: 0.8175 (p0) cc_final: 0.7690 (t0) REVERT: C 307 LYS cc_start: 0.8435 (mttp) cc_final: 0.8223 (mmtt) REVERT: D 17 MET cc_start: 0.8310 (tpp) cc_final: 0.7631 (ttm) REVERT: D 32 THR cc_start: 0.8561 (m) cc_final: 0.8319 (p) REVERT: D 47 GLN cc_start: 0.9047 (mt0) cc_final: 0.8697 (mt0) REVERT: D 62 LYS cc_start: 0.8833 (mmtm) cc_final: 0.8562 (mptm) REVERT: D 133 MET cc_start: 0.9006 (mtm) cc_final: 0.8747 (mtp) REVERT: D 150 GLU cc_start: 0.7269 (pp20) cc_final: 0.6417 (tm-30) REVERT: E 31 ASP cc_start: 0.7725 (m-30) cc_final: 0.7355 (m-30) REVERT: E 77 ASP cc_start: 0.8061 (m-30) cc_final: 0.7857 (m-30) REVERT: E 189 GLN cc_start: 0.8675 (tm-30) cc_final: 0.8469 (tm130) REVERT: F 40 SER cc_start: 0.8687 (m) cc_final: 0.8222 (p) REVERT: F 47 GLN cc_start: 0.8804 (mt0) cc_final: 0.8408 (mt0) REVERT: F 82 LYS cc_start: 0.9038 (mttt) cc_final: 0.8716 (mttt) REVERT: F 105 GLN cc_start: 0.8643 (tp40) cc_final: 0.8368 (tp-100) REVERT: F 115 MET cc_start: 0.8892 (tpt) cc_final: 0.8496 (tpt) REVERT: F 133 MET cc_start: 0.8947 (mtm) cc_final: 0.8563 (mtm) REVERT: F 139 LYS cc_start: 0.8694 (tttp) cc_final: 0.8440 (ttmm) REVERT: F 150 GLU cc_start: 0.7307 (pp20) cc_final: 0.6715 (tp30) REVERT: G 81 GLN cc_start: 0.7257 (pm20) cc_final: 0.7029 (pm20) REVERT: G 201 VAL cc_start: 0.5634 (p) cc_final: 0.5413 (p) REVERT: H 13 LYS cc_start: 0.9127 (ttpt) cc_final: 0.8820 (mmtp) REVERT: H 81 MET cc_start: 0.8996 (ttp) cc_final: 0.8576 (ttt) REVERT: H 87 ARG cc_start: 0.8092 (mtm-85) cc_final: 0.7816 (mtp85) REVERT: H 159 PRO cc_start: 0.6635 (Cg_exo) cc_final: 0.6429 (Cg_endo) REVERT: H 181 GLN cc_start: 0.7483 (tt0) cc_final: 0.6912 (mt0) REVERT: I 55 ASN cc_start: 0.7727 (t0) cc_final: 0.7270 (t0) REVERT: I 167 SER cc_start: 0.8256 (t) cc_final: 0.7766 (m) REVERT: J 59 LYS cc_start: 0.8898 (tptp) cc_final: 0.8460 (tppp) REVERT: J 106 MET cc_start: 0.8452 (mtm) cc_final: 0.8235 (mtm) REVERT: J 181 GLN cc_start: 0.7721 (tt0) cc_final: 0.6863 (mt0) REVERT: J 185 LEU cc_start: 0.8571 (mp) cc_final: 0.8075 (mt) REVERT: K 18 VAL cc_start: 0.7938 (t) cc_final: 0.7569 (p) REVERT: L 13 LYS cc_start: 0.9018 (ttpt) cc_final: 0.8662 (mptm) REVERT: L 54 TYR cc_start: 0.8131 (t80) cc_final: 0.7896 (t80) REVERT: L 59 LYS cc_start: 0.8687 (tptp) cc_final: 0.8354 (tptm) REVERT: L 62 LYS cc_start: 0.8614 (tppt) cc_final: 0.8369 (tttp) REVERT: L 87 ARG cc_start: 0.7646 (mtm-85) cc_final: 0.7424 (mtp85) REVERT: L 181 GLN cc_start: 0.7635 (tt0) cc_final: 0.6522 (mt0) outliers start: 0 outliers final: 1 residues processed: 412 average time/residue: 1.4592 time to fit residues: 673.3749 Evaluate side-chains 275 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 274 time to evaluate : 2.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 18 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 225 optimal weight: 7.9990 chunk 202 optimal weight: 4.9990 chunk 112 optimal weight: 0.7980 chunk 69 optimal weight: 0.2980 chunk 136 optimal weight: 0.5980 chunk 108 optimal weight: 1.9990 chunk 209 optimal weight: 0.0170 chunk 80 optimal weight: 0.9980 chunk 127 optimal weight: 1.9990 chunk 155 optimal weight: 0.9980 chunk 242 optimal weight: 8.9990 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 GLN B 12 ASN B 125 GLN C 191 GLN D 125 GLN E 191 GLN F 125 GLN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 6 GLN I 36 HIS I 91 GLN ** I 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 36 HIS ** K 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.1280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 22008 Z= 0.202 Angle : 0.621 9.450 29886 Z= 0.305 Chirality : 0.048 0.379 3507 Planarity : 0.004 0.040 3777 Dihedral : 10.534 76.474 3983 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 2.52 % Allowed : 8.47 % Favored : 89.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.16), residues: 2670 helix: 2.60 (0.26), residues: 363 sheet: -0.06 (0.18), residues: 807 loop : -1.02 (0.15), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 47 HIS 0.004 0.001 HIS D 106 PHE 0.013 0.001 PHE B 9 TYR 0.018 0.002 TYR A 100 ARG 0.005 0.000 ARG B 123 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 287 time to evaluate : 2.690 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: A 15 LEU cc_start: 0.8957 (mp) cc_final: 0.8674 (mt) REVERT: A 31 ASP cc_start: 0.7948 (m-30) cc_final: 0.7668 (m-30) REVERT: A 189 GLN cc_start: 0.8577 (tm-30) cc_final: 0.8297 (tm-30) REVERT: A 280 GLU cc_start: 0.8065 (mm-30) cc_final: 0.7799 (tp30) REVERT: B 121 LYS cc_start: 0.8635 (ttpt) cc_final: 0.8161 (ttpt) REVERT: C 35 GLU cc_start: 0.8060 (tt0) cc_final: 0.7569 (tt0) REVERT: C 77 ASP cc_start: 0.7874 (m-30) cc_final: 0.7552 (m-30) REVERT: C 173 ASN cc_start: 0.8173 (p0) cc_final: 0.7787 (t0) REVERT: C 307 LYS cc_start: 0.8482 (mttp) cc_final: 0.8157 (mmtt) REVERT: D 17 MET cc_start: 0.8295 (tpp) cc_final: 0.7725 (ttm) REVERT: D 47 GLN cc_start: 0.8962 (mt0) cc_final: 0.8621 (mt0) REVERT: D 65 GLN cc_start: 0.8908 (mt0) cc_final: 0.8583 (mt0) REVERT: D 137 CYS cc_start: 0.7071 (OUTLIER) cc_final: 0.6748 (p) REVERT: D 150 GLU cc_start: 0.7141 (pp20) cc_final: 0.6268 (tm-30) REVERT: E 31 ASP cc_start: 0.7740 (m-30) cc_final: 0.7360 (m-30) REVERT: E 189 GLN cc_start: 0.8626 (tm-30) cc_final: 0.8318 (tp40) REVERT: F 47 GLN cc_start: 0.8768 (mt0) cc_final: 0.8364 (mt0) REVERT: F 105 GLN cc_start: 0.8656 (tp40) cc_final: 0.8431 (tp-100) REVERT: F 110 LEU cc_start: 0.8715 (tt) cc_final: 0.8504 (tp) REVERT: F 115 MET cc_start: 0.8795 (tpt) cc_final: 0.8441 (tpt) REVERT: F 133 MET cc_start: 0.8919 (mtm) cc_final: 0.8649 (mtp) REVERT: F 150 GLU cc_start: 0.7259 (pp20) cc_final: 0.6604 (tp30) REVERT: G 16 GLN cc_start: 0.6867 (pm20) cc_final: 0.6547 (pm20) REVERT: H 81 MET cc_start: 0.9064 (ttp) cc_final: 0.8722 (ttt) REVERT: H 181 GLN cc_start: 0.7534 (tt0) cc_final: 0.6918 (mt0) REVERT: I 55 ASN cc_start: 0.7571 (t0) cc_final: 0.7210 (t0) REVERT: I 91 GLN cc_start: 0.8550 (OUTLIER) cc_final: 0.8184 (tm-30) REVERT: I 167 SER cc_start: 0.8333 (t) cc_final: 0.7866 (m) REVERT: J 181 GLN cc_start: 0.7720 (tt0) cc_final: 0.6894 (mt0) REVERT: J 185 LEU cc_start: 0.8564 (mp) cc_final: 0.8048 (mt) REVERT: J 219 LYS cc_start: 0.6512 (OUTLIER) cc_final: 0.6098 (tppt) REVERT: K 81 GLN cc_start: 0.6565 (mt0) cc_final: 0.5694 (pt0) REVERT: L 10 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.7775 (mp0) REVERT: L 62 LYS cc_start: 0.8538 (tppt) cc_final: 0.8333 (mttp) REVERT: L 181 GLN cc_start: 0.7692 (tt0) cc_final: 0.6515 (mt0) outliers start: 59 outliers final: 33 residues processed: 312 average time/residue: 1.4587 time to fit residues: 511.1893 Evaluate side-chains 288 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 251 time to evaluate : 2.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 19 ASP Chi-restraints excluded: chain B residue 34 GLN Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain D residue 18 ILE Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 137 CYS Chi-restraints excluded: chain E residue 208 ARG Chi-restraints excluded: chain E residue 321 ARG Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain F residue 19 ASP Chi-restraints excluded: chain F residue 42 GLN Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain G residue 137 VAL Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 82 GLU Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain I residue 36 HIS Chi-restraints excluded: chain I residue 91 GLN Chi-restraints excluded: chain I residue 107 LYS Chi-restraints excluded: chain J residue 219 LYS Chi-restraints excluded: chain K residue 36 HIS Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain L residue 3 GLN Chi-restraints excluded: chain L residue 10 GLU Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain L residue 82 GLU Chi-restraints excluded: chain L residue 190 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 134 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 201 optimal weight: 10.0000 chunk 165 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 242 optimal weight: 5.9990 chunk 262 optimal weight: 8.9990 chunk 216 optimal weight: 0.9990 chunk 240 optimal weight: 4.9990 chunk 82 optimal weight: 7.9990 chunk 194 optimal weight: 9.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 12 ASN ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 197 GLN ** D 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 6 GLN ** I 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 GLN ** K 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 43 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 22008 Z= 0.488 Angle : 0.704 10.664 29886 Z= 0.348 Chirality : 0.051 0.372 3507 Planarity : 0.005 0.047 3777 Dihedral : 10.560 76.179 3983 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 3.21 % Allowed : 11.34 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.16), residues: 2670 helix: 2.00 (0.26), residues: 378 sheet: -0.05 (0.18), residues: 843 loop : -1.11 (0.16), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 92 HIS 0.012 0.002 HIS I 36 PHE 0.018 0.002 PHE B 24 TYR 0.059 0.002 TYR K 145 ARG 0.006 0.001 ARG L 38 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 262 time to evaluate : 2.058 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: A 31 ASP cc_start: 0.7994 (m-30) cc_final: 0.7730 (m-30) REVERT: A 189 GLN cc_start: 0.8660 (tm-30) cc_final: 0.8400 (tm-30) REVERT: B 17 MET cc_start: 0.8471 (ttm) cc_final: 0.7671 (ttm) REVERT: B 110 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8495 (tp) REVERT: C 35 GLU cc_start: 0.8092 (tt0) cc_final: 0.7631 (tt0) REVERT: C 173 ASN cc_start: 0.8227 (p0) cc_final: 0.7644 (t0) REVERT: D 17 MET cc_start: 0.8420 (tpp) cc_final: 0.7712 (ttm) REVERT: D 47 GLN cc_start: 0.9039 (mt0) cc_final: 0.8741 (mt0) REVERT: D 150 GLU cc_start: 0.7268 (pp20) cc_final: 0.6430 (tm-30) REVERT: E 31 ASP cc_start: 0.7816 (m-30) cc_final: 0.7418 (m-30) REVERT: E 32 ASP cc_start: 0.7768 (m-30) cc_final: 0.7517 (m-30) REVERT: E 189 GLN cc_start: 0.8630 (tm-30) cc_final: 0.8106 (tm-30) REVERT: E 190 GLU cc_start: 0.8511 (tt0) cc_final: 0.8305 (tt0) REVERT: E 210 GLN cc_start: 0.9018 (OUTLIER) cc_final: 0.8651 (pt0) REVERT: E 315 LYS cc_start: 0.8790 (mmtt) cc_final: 0.8583 (mmtp) REVERT: F 17 MET cc_start: 0.8367 (ttm) cc_final: 0.8160 (ttm) REVERT: F 62 LYS cc_start: 0.9028 (OUTLIER) cc_final: 0.8434 (mttp) REVERT: F 115 MET cc_start: 0.8755 (tpt) cc_final: 0.8536 (tpt) REVERT: F 121 LYS cc_start: 0.8675 (ttpt) cc_final: 0.8157 (tttm) REVERT: F 133 MET cc_start: 0.9004 (mtm) cc_final: 0.8631 (mtp) REVERT: F 150 GLU cc_start: 0.7296 (pp20) cc_final: 0.6620 (tp30) REVERT: H 38 ARG cc_start: 0.8804 (OUTLIER) cc_final: 0.7933 (ptp90) REVERT: H 81 MET cc_start: 0.9120 (ttp) cc_final: 0.8786 (ttt) REVERT: H 87 ARG cc_start: 0.7629 (mtp85) cc_final: 0.7329 (mtp85) REVERT: H 181 GLN cc_start: 0.7552 (tt0) cc_final: 0.6895 (mt0) REVERT: I 55 ASN cc_start: 0.7635 (t0) cc_final: 0.7245 (t0) REVERT: I 167 SER cc_start: 0.8379 (t) cc_final: 0.7950 (m) REVERT: J 181 GLN cc_start: 0.7721 (tt0) cc_final: 0.6899 (mt0) REVERT: J 185 LEU cc_start: 0.8559 (mp) cc_final: 0.8096 (mt) REVERT: J 219 LYS cc_start: 0.6523 (OUTLIER) cc_final: 0.6118 (tppt) REVERT: K 22 CYS cc_start: 0.6679 (t) cc_final: 0.6395 (t) REVERT: K 107 LYS cc_start: 0.8499 (mtpm) cc_final: 0.8041 (mtpt) REVERT: L 10 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.7626 (mp0) REVERT: L 114 ASP cc_start: 0.8829 (OUTLIER) cc_final: 0.8503 (p0) REVERT: L 181 GLN cc_start: 0.7684 (tt0) cc_final: 0.6526 (mt0) outliers start: 75 outliers final: 44 residues processed: 303 average time/residue: 1.4220 time to fit residues: 485.1382 Evaluate side-chains 298 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 247 time to evaluate : 2.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 173 ASN Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 34 GLN Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain D residue 18 ILE Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 173 ASN Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 208 ARG Chi-restraints excluded: chain E residue 210 GLN Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain F residue 19 ASP Chi-restraints excluded: chain F residue 34 GLN Chi-restraints excluded: chain F residue 46 ASP Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 62 LYS Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain G residue 36 HIS Chi-restraints excluded: chain G residue 137 VAL Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 62 LYS Chi-restraints excluded: chain H residue 82 GLU Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain I residue 77 ILE Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 114 ASP Chi-restraints excluded: chain J residue 152 VAL Chi-restraints excluded: chain J residue 219 LYS Chi-restraints excluded: chain L residue 3 GLN Chi-restraints excluded: chain L residue 10 GLU Chi-restraints excluded: chain L residue 82 GLU Chi-restraints excluded: chain L residue 114 ASP Chi-restraints excluded: chain L residue 123 THR Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain L residue 190 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 239 optimal weight: 5.9990 chunk 182 optimal weight: 20.0000 chunk 126 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 115 optimal weight: 0.7980 chunk 163 optimal weight: 30.0000 chunk 243 optimal weight: 10.0000 chunk 258 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 231 optimal weight: 0.8980 chunk 69 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 12 ASN B 125 GLN ** D 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 6 GLN ** I 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 36 HIS K 39 GLN K 171 GLN ** K 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 22008 Z= 0.263 Angle : 0.615 10.649 29886 Z= 0.302 Chirality : 0.048 0.329 3507 Planarity : 0.004 0.040 3777 Dihedral : 9.620 67.225 3983 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.70 % Allowed : 13.52 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.16), residues: 2670 helix: 2.22 (0.27), residues: 381 sheet: -0.16 (0.18), residues: 837 loop : -0.99 (0.16), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 50 HIS 0.004 0.001 HIS D 106 PHE 0.015 0.002 PHE D 9 TYR 0.017 0.002 TYR F 162 ARG 0.008 0.000 ARG I 17 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 255 time to evaluate : 2.298 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: A 31 ASP cc_start: 0.8019 (m-30) cc_final: 0.7763 (m-30) REVERT: A 104 ASP cc_start: 0.7453 (OUTLIER) cc_final: 0.7188 (t0) REVERT: A 189 GLN cc_start: 0.8652 (tm-30) cc_final: 0.8400 (tm-30) REVERT: B 17 MET cc_start: 0.8673 (ttm) cc_final: 0.8182 (ttm) REVERT: B 150 GLU cc_start: 0.7148 (pp20) cc_final: 0.6555 (tp30) REVERT: C 35 GLU cc_start: 0.7992 (tt0) cc_final: 0.7533 (tt0) REVERT: C 173 ASN cc_start: 0.8190 (p0) cc_final: 0.7746 (t0) REVERT: C 260 MET cc_start: 0.8775 (mtp) cc_final: 0.8493 (mtp) REVERT: D 17 MET cc_start: 0.8195 (tpp) cc_final: 0.7909 (ttm) REVERT: D 47 GLN cc_start: 0.9010 (mt0) cc_final: 0.8687 (mt0) REVERT: D 150 GLU cc_start: 0.7154 (pp20) cc_final: 0.6407 (tm-30) REVERT: E 31 ASP cc_start: 0.7753 (m-30) cc_final: 0.7403 (m-30) REVERT: E 32 ASP cc_start: 0.7953 (m-30) cc_final: 0.7704 (m-30) REVERT: F 17 MET cc_start: 0.8511 (ttm) cc_final: 0.8297 (ttm) REVERT: F 74 GLU cc_start: 0.7776 (mp0) cc_final: 0.7525 (mp0) REVERT: F 121 LYS cc_start: 0.8603 (ttpt) cc_final: 0.8067 (tttm) REVERT: F 133 MET cc_start: 0.8974 (mtm) cc_final: 0.8598 (mtp) REVERT: H 38 ARG cc_start: 0.8738 (OUTLIER) cc_final: 0.8068 (ptp90) REVERT: H 81 MET cc_start: 0.9090 (ttp) cc_final: 0.8781 (ttt) REVERT: H 155 TYR cc_start: 0.6297 (p90) cc_final: 0.5374 (p90) REVERT: I 89 TYR cc_start: 0.9071 (m-80) cc_final: 0.8868 (m-80) REVERT: I 167 SER cc_start: 0.8372 (t) cc_final: 0.7965 (m) REVERT: J 38 ARG cc_start: 0.8582 (OUTLIER) cc_final: 0.7109 (ptp-170) REVERT: J 83 MET cc_start: 0.7875 (tpp) cc_final: 0.7436 (ttm) REVERT: J 180 LEU cc_start: 0.7569 (OUTLIER) cc_final: 0.7078 (mm) REVERT: J 181 GLN cc_start: 0.7667 (tt0) cc_final: 0.6783 (mt0) REVERT: J 185 LEU cc_start: 0.8554 (mp) cc_final: 0.8037 (mt) REVERT: L 10 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.7587 (mp0) REVERT: L 181 GLN cc_start: 0.7751 (tt0) cc_final: 0.6631 (mt0) outliers start: 63 outliers final: 41 residues processed: 293 average time/residue: 1.3967 time to fit residues: 461.9664 Evaluate side-chains 299 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 253 time to evaluate : 2.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 173 ASN Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 19 ASP Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain D residue 18 ILE Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain E residue 173 ASN Chi-restraints excluded: chain E residue 208 ARG Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain F residue 19 ASP Chi-restraints excluded: chain F residue 34 GLN Chi-restraints excluded: chain F residue 42 GLN Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain G residue 36 HIS Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 62 LYS Chi-restraints excluded: chain H residue 82 GLU Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain J residue 10 GLU Chi-restraints excluded: chain J residue 38 ARG Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 152 VAL Chi-restraints excluded: chain J residue 180 LEU Chi-restraints excluded: chain J residue 190 SER Chi-restraints excluded: chain K residue 36 HIS Chi-restraints excluded: chain L residue 10 GLU Chi-restraints excluded: chain L residue 54 TYR Chi-restraints excluded: chain L residue 82 GLU Chi-restraints excluded: chain L residue 123 THR Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain L residue 190 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 214 optimal weight: 2.9990 chunk 146 optimal weight: 5.9990 chunk 3 optimal weight: 0.1980 chunk 192 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 220 optimal weight: 4.9990 chunk 178 optimal weight: 8.9990 chunk 0 optimal weight: 3.9990 chunk 131 optimal weight: 0.7980 chunk 231 optimal weight: 0.0050 chunk 65 optimal weight: 2.9990 overall best weight: 1.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 12 ASN B 125 GLN ** D 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 174 HIS K 36 HIS K 39 GLN ** K 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 43 GLN ** L 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 22008 Z= 0.318 Angle : 0.629 9.581 29886 Z= 0.309 Chirality : 0.048 0.359 3507 Planarity : 0.004 0.040 3777 Dihedral : 9.371 64.512 3983 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 3.17 % Allowed : 14.55 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.16), residues: 2670 helix: 2.19 (0.27), residues: 381 sheet: -0.13 (0.18), residues: 837 loop : -0.99 (0.16), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 92 HIS 0.005 0.001 HIS E 184 PHE 0.016 0.002 PHE D 9 TYR 0.044 0.002 TYR K 145 ARG 0.006 0.001 ARG E 321 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 258 time to evaluate : 2.654 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: A 31 ASP cc_start: 0.7962 (m-30) cc_final: 0.7732 (m-30) REVERT: A 104 ASP cc_start: 0.7476 (OUTLIER) cc_final: 0.7147 (t0) REVERT: A 189 GLN cc_start: 0.8691 (tm-30) cc_final: 0.8477 (tm-30) REVERT: B 17 MET cc_start: 0.8654 (ttm) cc_final: 0.8144 (ttm) REVERT: B 150 GLU cc_start: 0.7212 (pp20) cc_final: 0.6683 (tp30) REVERT: C 35 GLU cc_start: 0.8019 (tt0) cc_final: 0.7525 (tt0) REVERT: C 173 ASN cc_start: 0.8182 (p0) cc_final: 0.7707 (t0) REVERT: C 260 MET cc_start: 0.8797 (mtp) cc_final: 0.8515 (mtp) REVERT: D 17 MET cc_start: 0.8183 (tpp) cc_final: 0.7894 (ttm) REVERT: D 47 GLN cc_start: 0.9026 (mt0) cc_final: 0.8676 (mt0) REVERT: D 150 GLU cc_start: 0.7184 (pp20) cc_final: 0.6450 (tm-30) REVERT: E 31 ASP cc_start: 0.7929 (m-30) cc_final: 0.7575 (m-30) REVERT: E 32 ASP cc_start: 0.7956 (m-30) cc_final: 0.7710 (m-30) REVERT: F 17 MET cc_start: 0.8536 (ttm) cc_final: 0.8324 (ttm) REVERT: F 74 GLU cc_start: 0.7816 (mt-10) cc_final: 0.7575 (mp0) REVERT: F 112 ASP cc_start: 0.8514 (t70) cc_final: 0.8245 (t0) REVERT: F 121 LYS cc_start: 0.8611 (ttpt) cc_final: 0.8080 (tttm) REVERT: F 133 MET cc_start: 0.8999 (mtm) cc_final: 0.8617 (mtp) REVERT: H 38 ARG cc_start: 0.8774 (OUTLIER) cc_final: 0.7976 (ptp90) REVERT: H 81 MET cc_start: 0.9102 (ttp) cc_final: 0.8795 (ttt) REVERT: H 155 TYR cc_start: 0.6268 (p90) cc_final: 0.5434 (p90) REVERT: I 22 CYS cc_start: 0.6550 (t) cc_final: 0.6174 (t) REVERT: I 167 SER cc_start: 0.8376 (t) cc_final: 0.7973 (p) REVERT: J 38 ARG cc_start: 0.8706 (OUTLIER) cc_final: 0.7315 (ptp-170) REVERT: J 83 MET cc_start: 0.7844 (tpp) cc_final: 0.7486 (ttm) REVERT: J 180 LEU cc_start: 0.7586 (OUTLIER) cc_final: 0.7111 (mm) REVERT: J 181 GLN cc_start: 0.7677 (tt0) cc_final: 0.6812 (mt0) REVERT: J 185 LEU cc_start: 0.8553 (mp) cc_final: 0.8078 (mt) REVERT: L 10 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.7575 (mp0) REVERT: L 114 ASP cc_start: 0.8857 (OUTLIER) cc_final: 0.8606 (p0) REVERT: L 181 GLN cc_start: 0.7791 (tt0) cc_final: 0.6688 (mt0) outliers start: 74 outliers final: 49 residues processed: 299 average time/residue: 1.4066 time to fit residues: 475.0395 Evaluate side-chains 306 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 251 time to evaluate : 2.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 173 ASN Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 19 ASP Chi-restraints excluded: chain B residue 34 GLN Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain D residue 11 GLU Chi-restraints excluded: chain D residue 18 ILE Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 173 ASN Chi-restraints excluded: chain E residue 208 ARG Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain F residue 34 GLN Chi-restraints excluded: chain F residue 42 GLN Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain G residue 36 HIS Chi-restraints excluded: chain G residue 137 VAL Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 54 TYR Chi-restraints excluded: chain H residue 62 LYS Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain I residue 36 HIS Chi-restraints excluded: chain J residue 38 ARG Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 114 ASP Chi-restraints excluded: chain J residue 152 VAL Chi-restraints excluded: chain J residue 180 LEU Chi-restraints excluded: chain J residue 190 SER Chi-restraints excluded: chain K residue 36 HIS Chi-restraints excluded: chain L residue 3 GLN Chi-restraints excluded: chain L residue 10 GLU Chi-restraints excluded: chain L residue 54 TYR Chi-restraints excluded: chain L residue 82 GLU Chi-restraints excluded: chain L residue 114 ASP Chi-restraints excluded: chain L residue 123 THR Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain L residue 190 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 86 optimal weight: 0.1980 chunk 232 optimal weight: 9.9990 chunk 51 optimal weight: 0.0970 chunk 151 optimal weight: 0.1980 chunk 63 optimal weight: 0.8980 chunk 258 optimal weight: 3.9990 chunk 214 optimal weight: 0.5980 chunk 119 optimal weight: 0.0870 chunk 21 optimal weight: 1.9990 chunk 85 optimal weight: 0.5980 chunk 135 optimal weight: 1.9990 overall best weight: 0.2356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 165 ASN ** I 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 GLN ** K 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 43 GLN L 165 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 22008 Z= 0.144 Angle : 0.575 9.951 29886 Z= 0.281 Chirality : 0.046 0.378 3507 Planarity : 0.004 0.040 3777 Dihedral : 8.399 55.738 3983 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.23 % Allowed : 16.17 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.16), residues: 2670 helix: 2.87 (0.26), residues: 363 sheet: -0.04 (0.18), residues: 861 loop : -0.84 (0.16), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP K 37 HIS 0.005 0.001 HIS K 36 PHE 0.016 0.001 PHE B 3 TYR 0.018 0.001 TYR F 162 ARG 0.008 0.000 ARG I 17 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 281 time to evaluate : 2.550 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: A 31 ASP cc_start: 0.7965 (m-30) cc_final: 0.7743 (m-30) REVERT: A 104 ASP cc_start: 0.7328 (OUTLIER) cc_final: 0.7041 (t0) REVERT: A 189 GLN cc_start: 0.8585 (tm-30) cc_final: 0.8356 (tm-30) REVERT: B 17 MET cc_start: 0.8635 (ttm) cc_final: 0.7780 (ttm) REVERT: B 150 GLU cc_start: 0.7135 (pp20) cc_final: 0.6555 (tp30) REVERT: C 14 CYS cc_start: 0.6411 (m) cc_final: 0.6020 (m) REVERT: C 35 GLU cc_start: 0.7967 (tt0) cc_final: 0.7527 (tt0) REVERT: C 82 GLU cc_start: 0.8858 (mm-30) cc_final: 0.8555 (mm-30) REVERT: C 173 ASN cc_start: 0.8114 (p0) cc_final: 0.7756 (t0) REVERT: D 65 GLN cc_start: 0.8847 (mt0) cc_final: 0.8590 (mt0) REVERT: D 150 GLU cc_start: 0.7163 (pp20) cc_final: 0.6811 (tp30) REVERT: E 31 ASP cc_start: 0.7917 (m-30) cc_final: 0.7704 (m-30) REVERT: E 32 ASP cc_start: 0.7924 (m-30) cc_final: 0.7697 (m-30) REVERT: E 173 ASN cc_start: 0.8093 (p0) cc_final: 0.7408 (t0) REVERT: E 238 LYS cc_start: 0.8612 (mttt) cc_final: 0.8339 (mmtt) REVERT: F 47 GLN cc_start: 0.8801 (mt0) cc_final: 0.8563 (mt0) REVERT: F 133 MET cc_start: 0.8924 (mtm) cc_final: 0.8566 (mtp) REVERT: G 55 ASN cc_start: 0.7621 (t0) cc_final: 0.7185 (t0) REVERT: G 68 LYS cc_start: 0.8123 (tttt) cc_final: 0.6303 (tptp) REVERT: H 59 LYS cc_start: 0.8862 (OUTLIER) cc_final: 0.8660 (tptm) REVERT: H 65 GLN cc_start: 0.8350 (mm-40) cc_final: 0.8060 (mm-40) REVERT: H 81 MET cc_start: 0.9067 (ttp) cc_final: 0.8794 (ttt) REVERT: H 155 TYR cc_start: 0.6265 (p90) cc_final: 0.5610 (p90) REVERT: H 171 SER cc_start: 0.7443 (t) cc_final: 0.7189 (p) REVERT: I 167 SER cc_start: 0.8305 (t) cc_final: 0.7981 (p) REVERT: J 38 ARG cc_start: 0.8504 (OUTLIER) cc_final: 0.7211 (ptp-170) REVERT: J 83 MET cc_start: 0.7657 (tpp) cc_final: 0.7432 (ttm) REVERT: J 181 GLN cc_start: 0.7697 (tt0) cc_final: 0.6810 (mt0) REVERT: J 185 LEU cc_start: 0.8578 (mp) cc_final: 0.8129 (mt) REVERT: K 81 GLN cc_start: 0.6798 (mt0) cc_final: 0.5889 (pt0) REVERT: K 107 LYS cc_start: 0.8244 (mtpm) cc_final: 0.7789 (mtpt) REVERT: L 13 LYS cc_start: 0.9047 (ttpt) cc_final: 0.8695 (mptm) REVERT: L 127 LYS cc_start: 0.8102 (tppt) cc_final: 0.7803 (mmmm) REVERT: L 181 GLN cc_start: 0.7672 (tt0) cc_final: 0.6626 (mt0) outliers start: 52 outliers final: 26 residues processed: 307 average time/residue: 1.3994 time to fit residues: 484.5600 Evaluate side-chains 291 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 262 time to evaluate : 2.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain B residue 19 ASP Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain D residue 11 GLU Chi-restraints excluded: chain D residue 18 ILE Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain F residue 34 GLN Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain G residue 137 VAL Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 54 TYR Chi-restraints excluded: chain H residue 59 LYS Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 38 ARG Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 152 VAL Chi-restraints excluded: chain J residue 190 SER Chi-restraints excluded: chain K residue 36 HIS Chi-restraints excluded: chain L residue 54 TYR Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain L residue 123 THR Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain L residue 190 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 249 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 147 optimal weight: 1.9990 chunk 188 optimal weight: 1.9990 chunk 146 optimal weight: 5.9990 chunk 217 optimal weight: 0.4980 chunk 144 optimal weight: 0.6980 chunk 257 optimal weight: 2.9990 chunk 161 optimal weight: 0.0980 chunk 156 optimal weight: 4.9990 chunk 118 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 23 GLN ** I 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 81 GLN ** I 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 GLN ** K 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 22008 Z= 0.240 Angle : 0.596 9.639 29886 Z= 0.291 Chirality : 0.047 0.341 3507 Planarity : 0.004 0.041 3777 Dihedral : 8.257 57.025 3983 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.14 % Allowed : 16.86 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.16), residues: 2670 helix: 2.86 (0.26), residues: 363 sheet: -0.04 (0.17), residues: 897 loop : -0.84 (0.16), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 92 HIS 0.007 0.001 HIS K 36 PHE 0.016 0.001 PHE D 9 TYR 0.030 0.001 TYR K 145 ARG 0.010 0.000 ARG D 123 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 266 time to evaluate : 2.064 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 31 ASP cc_start: 0.7944 (m-30) cc_final: 0.7699 (m-30) REVERT: A 173 ASN cc_start: 0.7838 (OUTLIER) cc_final: 0.7588 (p0) REVERT: A 189 GLN cc_start: 0.8612 (tm-30) cc_final: 0.8377 (tm-30) REVERT: B 17 MET cc_start: 0.8576 (ttm) cc_final: 0.7890 (ttm) REVERT: B 150 GLU cc_start: 0.7167 (pp20) cc_final: 0.6550 (tp30) REVERT: C 14 CYS cc_start: 0.6365 (m) cc_final: 0.5959 (m) REVERT: C 35 GLU cc_start: 0.7950 (tt0) cc_final: 0.7511 (tt0) REVERT: C 82 GLU cc_start: 0.8906 (mm-30) cc_final: 0.8608 (mm-30) REVERT: C 126 THR cc_start: 0.8716 (m) cc_final: 0.8465 (p) REVERT: C 173 ASN cc_start: 0.8138 (p0) cc_final: 0.7760 (t0) REVERT: C 260 MET cc_start: 0.8789 (mtp) cc_final: 0.8494 (mtp) REVERT: D 65 GLN cc_start: 0.8885 (mt0) cc_final: 0.8622 (mt0) REVERT: D 150 GLU cc_start: 0.7192 (pp20) cc_final: 0.6317 (tp30) REVERT: E 31 ASP cc_start: 0.7915 (m-30) cc_final: 0.7585 (m-30) REVERT: E 32 ASP cc_start: 0.7934 (m-30) cc_final: 0.7704 (m-30) REVERT: E 173 ASN cc_start: 0.8073 (OUTLIER) cc_final: 0.7405 (t0) REVERT: F 133 MET cc_start: 0.8970 (mtm) cc_final: 0.8608 (mtp) REVERT: G 55 ASN cc_start: 0.7655 (t0) cc_final: 0.7178 (t0) REVERT: H 65 GLN cc_start: 0.8346 (mm-40) cc_final: 0.7980 (mm-40) REVERT: H 81 MET cc_start: 0.9090 (ttp) cc_final: 0.8781 (ttt) REVERT: H 87 ARG cc_start: 0.7786 (OUTLIER) cc_final: 0.7152 (mtp85) REVERT: H 171 SER cc_start: 0.7435 (t) cc_final: 0.7177 (p) REVERT: I 167 SER cc_start: 0.8305 (t) cc_final: 0.7983 (m) REVERT: J 38 ARG cc_start: 0.8609 (OUTLIER) cc_final: 0.7283 (ptp-170) REVERT: J 83 MET cc_start: 0.7706 (tpp) cc_final: 0.7421 (ttm) REVERT: J 180 LEU cc_start: 0.7622 (OUTLIER) cc_final: 0.7230 (mm) REVERT: J 181 GLN cc_start: 0.7625 (tt0) cc_final: 0.6819 (mt0) REVERT: J 185 LEU cc_start: 0.8556 (mp) cc_final: 0.8062 (mt) REVERT: K 107 LYS cc_start: 0.8286 (mtpm) cc_final: 0.7814 (mtpt) REVERT: L 10 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.7773 (mp0) REVERT: L 114 ASP cc_start: 0.8779 (OUTLIER) cc_final: 0.8403 (p0) REVERT: L 181 GLN cc_start: 0.7674 (tt0) cc_final: 0.6679 (mt0) outliers start: 50 outliers final: 33 residues processed: 296 average time/residue: 1.3829 time to fit residues: 461.7921 Evaluate side-chains 304 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 264 time to evaluate : 2.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 173 ASN Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 19 ASP Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain D residue 11 GLU Chi-restraints excluded: chain D residue 18 ILE Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 173 ASN Chi-restraints excluded: chain F residue 19 ASP Chi-restraints excluded: chain F residue 34 GLN Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain G residue 137 VAL Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 54 TYR Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain I residue 36 HIS Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 38 ARG Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 152 VAL Chi-restraints excluded: chain J residue 180 LEU Chi-restraints excluded: chain J residue 190 SER Chi-restraints excluded: chain L residue 10 GLU Chi-restraints excluded: chain L residue 54 TYR Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain L residue 114 ASP Chi-restraints excluded: chain L residue 123 THR Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain L residue 190 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 159 optimal weight: 5.9990 chunk 102 optimal weight: 0.6980 chunk 153 optimal weight: 7.9990 chunk 77 optimal weight: 0.7980 chunk 50 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 163 optimal weight: 9.9990 chunk 175 optimal weight: 0.9980 chunk 127 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 202 optimal weight: 0.3980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 GLN ** D 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 23 GLN ** I 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 81 GLN ** I 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 GLN ** K 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 22008 Z= 0.217 Angle : 0.587 9.802 29886 Z= 0.287 Chirality : 0.047 0.331 3507 Planarity : 0.004 0.041 3777 Dihedral : 7.876 56.354 3983 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.31 % Allowed : 16.65 % Favored : 81.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.16), residues: 2670 helix: 2.88 (0.26), residues: 363 sheet: -0.01 (0.17), residues: 897 loop : -0.80 (0.16), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 153 HIS 0.004 0.001 HIS D 106 PHE 0.015 0.001 PHE D 9 TYR 0.030 0.001 TYR K 145 ARG 0.009 0.000 ARG D 123 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 261 time to evaluate : 2.553 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: A 31 ASP cc_start: 0.7910 (m-30) cc_final: 0.7584 (m-30) REVERT: A 173 ASN cc_start: 0.7853 (OUTLIER) cc_final: 0.7612 (p0) REVERT: A 189 GLN cc_start: 0.8608 (tm-30) cc_final: 0.8379 (tm-30) REVERT: B 17 MET cc_start: 0.8564 (ttm) cc_final: 0.7891 (ttm) REVERT: B 150 GLU cc_start: 0.7217 (pp20) cc_final: 0.6651 (tp30) REVERT: C 14 CYS cc_start: 0.6251 (m) cc_final: 0.5841 (m) REVERT: C 35 GLU cc_start: 0.7998 (tt0) cc_final: 0.7512 (tt0) REVERT: C 82 GLU cc_start: 0.8899 (mm-30) cc_final: 0.8599 (mm-30) REVERT: C 126 THR cc_start: 0.8728 (m) cc_final: 0.8483 (p) REVERT: C 173 ASN cc_start: 0.8126 (p0) cc_final: 0.7635 (t0) REVERT: C 212 THR cc_start: 0.8943 (t) cc_final: 0.8700 (m) REVERT: C 260 MET cc_start: 0.8773 (mtp) cc_final: 0.8501 (mtp) REVERT: D 65 GLN cc_start: 0.8873 (mt0) cc_final: 0.8611 (mt0) REVERT: D 150 GLU cc_start: 0.7182 (pp20) cc_final: 0.6352 (tp30) REVERT: E 31 ASP cc_start: 0.7965 (m-30) cc_final: 0.7756 (m-30) REVERT: E 32 ASP cc_start: 0.7923 (m-30) cc_final: 0.7701 (m-30) REVERT: E 173 ASN cc_start: 0.8053 (OUTLIER) cc_final: 0.7428 (t0) REVERT: F 12 ASN cc_start: 0.7604 (t0) cc_final: 0.6901 (t0) REVERT: F 112 ASP cc_start: 0.8553 (t70) cc_final: 0.8340 (t0) REVERT: F 133 MET cc_start: 0.8968 (mtm) cc_final: 0.8609 (mtp) REVERT: F 150 GLU cc_start: 0.7354 (pp20) cc_final: 0.6640 (tp30) REVERT: G 55 ASN cc_start: 0.7649 (t0) cc_final: 0.7173 (t0) REVERT: H 65 GLN cc_start: 0.8356 (mm-40) cc_final: 0.8076 (mm-40) REVERT: H 81 MET cc_start: 0.9092 (ttp) cc_final: 0.8760 (ttt) REVERT: H 87 ARG cc_start: 0.7781 (OUTLIER) cc_final: 0.7180 (mtp85) REVERT: H 171 SER cc_start: 0.7408 (t) cc_final: 0.7151 (p) REVERT: J 38 ARG cc_start: 0.8615 (OUTLIER) cc_final: 0.7310 (ptp-170) REVERT: J 181 GLN cc_start: 0.7615 (tt0) cc_final: 0.6787 (mt0) REVERT: J 185 LEU cc_start: 0.8575 (mp) cc_final: 0.8071 (mt) REVERT: K 107 LYS cc_start: 0.8265 (mtpm) cc_final: 0.7826 (mtpt) REVERT: L 114 ASP cc_start: 0.8748 (OUTLIER) cc_final: 0.8448 (p0) REVERT: L 181 GLN cc_start: 0.7733 (tt0) cc_final: 0.6801 (mt0) outliers start: 54 outliers final: 36 residues processed: 291 average time/residue: 1.3984 time to fit residues: 459.3357 Evaluate side-chains 300 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 259 time to evaluate : 2.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 173 ASN Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 19 ASP Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain D residue 11 GLU Chi-restraints excluded: chain D residue 18 ILE Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 173 ASN Chi-restraints excluded: chain F residue 19 ASP Chi-restraints excluded: chain F residue 34 GLN Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain G residue 137 VAL Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 54 TYR Chi-restraints excluded: chain H residue 62 LYS Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain I residue 36 HIS Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 38 ARG Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 152 VAL Chi-restraints excluded: chain J residue 190 SER Chi-restraints excluded: chain L residue 54 TYR Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain L residue 114 ASP Chi-restraints excluded: chain L residue 123 THR Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain L residue 190 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 234 optimal weight: 0.7980 chunk 246 optimal weight: 0.8980 chunk 224 optimal weight: 2.9990 chunk 239 optimal weight: 0.5980 chunk 144 optimal weight: 0.6980 chunk 104 optimal weight: 0.9990 chunk 188 optimal weight: 1.9990 chunk 73 optimal weight: 0.5980 chunk 216 optimal weight: 2.9990 chunk 226 optimal weight: 0.7980 chunk 238 optimal weight: 9.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 23 GLN ** I 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 81 GLN ** I 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 GLN ** K 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 43 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22008 Z= 0.211 Angle : 0.584 9.969 29886 Z= 0.285 Chirality : 0.047 0.335 3507 Planarity : 0.004 0.043 3777 Dihedral : 7.555 57.978 3983 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 2.27 % Allowed : 17.07 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.16), residues: 2670 helix: 2.90 (0.26), residues: 363 sheet: 0.03 (0.18), residues: 897 loop : -0.78 (0.16), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 153 HIS 0.004 0.001 HIS D 106 PHE 0.014 0.001 PHE B 3 TYR 0.020 0.001 TYR F 162 ARG 0.009 0.000 ARG D 123 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 267 time to evaluate : 2.525 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: A 31 ASP cc_start: 0.8027 (m-30) cc_final: 0.7724 (m-30) REVERT: A 173 ASN cc_start: 0.7826 (OUTLIER) cc_final: 0.7147 (t160) REVERT: A 189 GLN cc_start: 0.8611 (tm-30) cc_final: 0.8396 (tm-30) REVERT: B 17 MET cc_start: 0.8555 (ttm) cc_final: 0.7893 (ttm) REVERT: B 150 GLU cc_start: 0.7166 (pp20) cc_final: 0.6577 (tp30) REVERT: C 14 CYS cc_start: 0.6224 (m) cc_final: 0.5805 (m) REVERT: C 35 GLU cc_start: 0.8024 (tt0) cc_final: 0.7558 (tt0) REVERT: C 82 GLU cc_start: 0.8892 (mm-30) cc_final: 0.8595 (mm-30) REVERT: C 126 THR cc_start: 0.8710 (m) cc_final: 0.8474 (p) REVERT: C 173 ASN cc_start: 0.8117 (p0) cc_final: 0.7611 (t0) REVERT: C 212 THR cc_start: 0.8954 (t) cc_final: 0.8717 (m) REVERT: C 260 MET cc_start: 0.8765 (mtp) cc_final: 0.8494 (mtp) REVERT: D 65 GLN cc_start: 0.8879 (mt0) cc_final: 0.8625 (mt0) REVERT: D 150 GLU cc_start: 0.7176 (pp20) cc_final: 0.6350 (tp30) REVERT: E 31 ASP cc_start: 0.7965 (m-30) cc_final: 0.7669 (m-30) REVERT: E 32 ASP cc_start: 0.7919 (m-30) cc_final: 0.7698 (m-30) REVERT: E 173 ASN cc_start: 0.8039 (OUTLIER) cc_final: 0.7505 (t0) REVERT: F 12 ASN cc_start: 0.7632 (t0) cc_final: 0.7183 (t0) REVERT: F 112 ASP cc_start: 0.8551 (t70) cc_final: 0.8335 (t0) REVERT: F 133 MET cc_start: 0.8962 (mtm) cc_final: 0.8602 (mtp) REVERT: F 150 GLU cc_start: 0.7355 (pp20) cc_final: 0.6638 (tp30) REVERT: G 55 ASN cc_start: 0.7650 (t0) cc_final: 0.7170 (t0) REVERT: G 68 LYS cc_start: 0.8062 (tttt) cc_final: 0.6236 (tptt) REVERT: H 65 GLN cc_start: 0.8344 (mm-40) cc_final: 0.8031 (mm-40) REVERT: H 81 MET cc_start: 0.9105 (ttp) cc_final: 0.8743 (ttt) REVERT: H 87 ARG cc_start: 0.7772 (OUTLIER) cc_final: 0.6966 (mtp85) REVERT: I 63 ARG cc_start: 0.7708 (mtm-85) cc_final: 0.7467 (mtm-85) REVERT: J 38 ARG cc_start: 0.8620 (OUTLIER) cc_final: 0.7351 (ptp-170) REVERT: J 181 GLN cc_start: 0.7576 (tt0) cc_final: 0.7207 (mp10) REVERT: J 185 LEU cc_start: 0.8575 (mp) cc_final: 0.8369 (mt) REVERT: K 81 GLN cc_start: 0.6749 (mt0) cc_final: 0.6078 (pt0) REVERT: K 107 LYS cc_start: 0.8250 (mtpm) cc_final: 0.7804 (mtpt) REVERT: L 114 ASP cc_start: 0.8737 (OUTLIER) cc_final: 0.8427 (p0) REVERT: L 181 GLN cc_start: 0.7734 (tt0) cc_final: 0.6839 (mt0) outliers start: 53 outliers final: 41 residues processed: 296 average time/residue: 1.3856 time to fit residues: 464.5443 Evaluate side-chains 304 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 258 time to evaluate : 2.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 173 ASN Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 19 ASP Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain D residue 11 GLU Chi-restraints excluded: chain D residue 18 ILE Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 173 ASN Chi-restraints excluded: chain F residue 19 ASP Chi-restraints excluded: chain F residue 34 GLN Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 53 ASN Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain G residue 36 HIS Chi-restraints excluded: chain G residue 137 VAL Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 54 TYR Chi-restraints excluded: chain H residue 62 LYS Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain I residue 36 HIS Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 38 ARG Chi-restraints excluded: chain J residue 54 TYR Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 152 VAL Chi-restraints excluded: chain J residue 190 SER Chi-restraints excluded: chain L residue 54 TYR Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain L residue 114 ASP Chi-restraints excluded: chain L residue 123 THR Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain L residue 190 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 157 optimal weight: 2.9990 chunk 253 optimal weight: 4.9990 chunk 154 optimal weight: 20.0000 chunk 120 optimal weight: 2.9990 chunk 176 optimal weight: 0.2980 chunk 266 optimal weight: 2.9990 chunk 244 optimal weight: 9.9990 chunk 211 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 163 optimal weight: 7.9990 chunk 129 optimal weight: 3.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 36 HIS H 23 GLN I 36 HIS K 36 HIS K 39 GLN K 81 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 22008 Z= 0.450 Angle : 0.684 13.513 29886 Z= 0.337 Chirality : 0.051 0.414 3507 Planarity : 0.005 0.047 3777 Dihedral : 8.116 58.550 3983 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 2.23 % Allowed : 17.37 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.16), residues: 2670 helix: 1.99 (0.27), residues: 387 sheet: -0.04 (0.18), residues: 855 loop : -0.81 (0.16), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 92 HIS 0.006 0.001 HIS E 184 PHE 0.018 0.002 PHE F 9 TYR 0.033 0.002 TYR K 145 ARG 0.008 0.001 ARG D 123 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 259 time to evaluate : 2.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 ASP cc_start: 0.7990 (m-30) cc_final: 0.7685 (m-30) REVERT: A 189 GLN cc_start: 0.8718 (tm-30) cc_final: 0.8459 (tm-30) REVERT: B 17 MET cc_start: 0.8552 (ttm) cc_final: 0.7955 (ttm) REVERT: B 148 CYS cc_start: 0.5923 (t) cc_final: 0.5227 (t) REVERT: B 150 GLU cc_start: 0.7274 (pp20) cc_final: 0.6672 (tp30) REVERT: C 14 CYS cc_start: 0.6423 (m) cc_final: 0.6015 (m) REVERT: C 35 GLU cc_start: 0.8029 (tt0) cc_final: 0.7595 (tt0) REVERT: C 173 ASN cc_start: 0.8176 (p0) cc_final: 0.7593 (t0) REVERT: D 12 ASN cc_start: 0.7655 (t0) cc_final: 0.7222 (t0) REVERT: D 53 ASN cc_start: 0.7670 (OUTLIER) cc_final: 0.7381 (m110) REVERT: D 150 GLU cc_start: 0.7217 (pp20) cc_final: 0.6355 (tp30) REVERT: E 31 ASP cc_start: 0.7990 (m-30) cc_final: 0.7680 (m-30) REVERT: E 32 ASP cc_start: 0.7930 (m-30) cc_final: 0.7693 (m-30) REVERT: E 173 ASN cc_start: 0.8081 (OUTLIER) cc_final: 0.7497 (t0) REVERT: F 12 ASN cc_start: 0.7685 (t0) cc_final: 0.6994 (t0) REVERT: F 121 LYS cc_start: 0.8584 (ttpt) cc_final: 0.8083 (tttm) REVERT: F 133 MET cc_start: 0.9011 (mtm) cc_final: 0.8608 (mtp) REVERT: F 150 GLU cc_start: 0.7383 (pp20) cc_final: 0.6557 (tp30) REVERT: G 55 ASN cc_start: 0.7739 (t0) cc_final: 0.7203 (t0) REVERT: G 56 ARG cc_start: 0.8144 (mtm110) cc_final: 0.7824 (mtm110) REVERT: H 65 GLN cc_start: 0.8384 (mm-40) cc_final: 0.8009 (mm-40) REVERT: H 81 MET cc_start: 0.9161 (ttp) cc_final: 0.8793 (ttt) REVERT: H 87 ARG cc_start: 0.7835 (OUTLIER) cc_final: 0.6949 (mtp85) REVERT: J 38 ARG cc_start: 0.8754 (OUTLIER) cc_final: 0.7355 (ptp-170) REVERT: J 181 GLN cc_start: 0.7588 (tt0) cc_final: 0.7194 (mp-120) REVERT: J 185 LEU cc_start: 0.8541 (mp) cc_final: 0.8312 (mt) REVERT: K 107 LYS cc_start: 0.8443 (mtpm) cc_final: 0.8006 (mtpt) REVERT: K 141 LEU cc_start: 0.6999 (mp) cc_final: 0.6242 (tt) REVERT: L 83 MET cc_start: 0.8492 (mmt) cc_final: 0.8046 (mmt) REVERT: L 114 ASP cc_start: 0.8837 (OUTLIER) cc_final: 0.8505 (p0) REVERT: L 181 GLN cc_start: 0.7641 (tt0) cc_final: 0.6743 (mt0) outliers start: 52 outliers final: 41 residues processed: 289 average time/residue: 1.4087 time to fit residues: 459.4803 Evaluate side-chains 294 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 248 time to evaluate : 2.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 173 ASN Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 19 ASP Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain D residue 11 GLU Chi-restraints excluded: chain D residue 18 ILE Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 53 ASN Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 173 ASN Chi-restraints excluded: chain F residue 19 ASP Chi-restraints excluded: chain F residue 34 GLN Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 53 ASN Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain G residue 36 HIS Chi-restraints excluded: chain G residue 137 VAL Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 54 TYR Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain I residue 36 HIS Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 38 ARG Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 152 VAL Chi-restraints excluded: chain J residue 190 SER Chi-restraints excluded: chain K residue 36 HIS Chi-restraints excluded: chain L residue 54 TYR Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain L residue 114 ASP Chi-restraints excluded: chain L residue 123 THR Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain L residue 190 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 168 optimal weight: 0.0870 chunk 225 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 195 optimal weight: 8.9990 chunk 31 optimal weight: 0.7980 chunk 58 optimal weight: 0.6980 chunk 212 optimal weight: 0.9990 chunk 88 optimal weight: 0.7980 chunk 217 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 23 GLN ** I 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 GLN K 81 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.144331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.100161 restraints weight = 29901.687| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 3.67 r_work: 0.2791 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2643 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2559 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2559 r_free = 0.2559 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2559 r_free = 0.2559 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2559 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.211 22008 Z= 0.374 Angle : 0.995 57.299 29886 Z= 0.617 Chirality : 0.050 0.564 3507 Planarity : 0.005 0.145 3777 Dihedral : 8.114 58.421 3983 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 2.35 % Allowed : 17.37 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.16), residues: 2670 helix: 1.99 (0.27), residues: 387 sheet: -0.07 (0.18), residues: 855 loop : -0.82 (0.16), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 37 HIS 0.184 0.005 HIS I 36 PHE 0.017 0.002 PHE F 9 TYR 0.032 0.002 TYR K 145 ARG 0.007 0.001 ARG D 123 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8460.95 seconds wall clock time: 151 minutes 3.12 seconds (9063.12 seconds total)