Starting phenix.real_space_refine on Thu Feb 15 03:49:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eji_28183/02_2024/8eji_28183.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eji_28183/02_2024/8eji_28183.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eji_28183/02_2024/8eji_28183.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eji_28183/02_2024/8eji_28183.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eji_28183/02_2024/8eji_28183.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eji_28183/02_2024/8eji_28183.pdb" } resolution = 3.81 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= 0.003 sd= 0.032 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 97 5.16 5 C 6886 2.51 5 N 1742 2.21 5 O 2298 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 228": "OE1" <-> "OE2" Residue "A TYR 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 229": "OD1" <-> "OD2" Residue "B TYR 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 1": "OE1" <-> "OE2" Residue "H PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 68": "OE1" <-> "OE2" Residue "L PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 229": "OD1" <-> "OD2" Residue "C TYR 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 11023 Number of models: 1 Model: "" Number of chains: 32 Chain: "A" Number of atoms: 1516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1516 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 4, 'TRANS': 186} Chain breaks: 1 Chain: "a" Number of atoms: 1286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1286 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 4, 'TRANS': 154} Chain: "B" Number of atoms: 1504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1504 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 4, 'TRANS': 185} Chain breaks: 1 Chain: "b" Number of atoms: 1223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1223 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 3, 'TRANS': 146} Chain breaks: 1 Chain: "H" Number of atoms: 923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 923 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "L" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 821 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 101} Chain: "C" Number of atoms: 1504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1504 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 4, 'TRANS': 185} Chain breaks: 1 Chain: "c" Number of atoms: 1232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1232 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 3, 'TRANS': 147} Chain breaks: 1 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" 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: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 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: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" 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: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" 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: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 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 Time building chain proxies: 6.25, per 1000 atoms: 0.57 Number of scatterers: 11023 At special positions: 0 Unit cell: (125.4, 96.14, 107.635, 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 97 16.00 O 2298 8.00 N 1742 7.00 C 6886 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=23, symmetry=0 Simple disulfide: pdb=" SG CYS A 86 " - pdb=" SG CYS A 231 " distance=2.03 Simple disulfide: pdb=" SG CYS A 118 " - pdb=" SG CYS A 155 " distance=2.03 Simple disulfide: pdb=" SG CYS A 180 " - pdb=" SG CYS A 212 " distance=2.03 Simple disulfide: pdb=" SG CYS A 207 " - pdb=" SG CYS a 360 " distance=2.04 Simple disulfide: pdb=" SG CYS a 279 " - pdb=" SG CYS a 292 " distance=2.04 Simple disulfide: pdb=" SG CYS a 301 " - pdb=" SG CYS a 310 " distance=2.03 Simple disulfide: pdb=" SG CYS a 364 " - pdb=" SG CYS a 385 " distance=2.01 Simple disulfide: pdb=" SG CYS B 86 " - pdb=" SG CYS B 231 " distance=2.02 Simple disulfide: pdb=" SG CYS B 118 " - pdb=" SG CYS B 155 " distance=2.04 Simple disulfide: pdb=" SG CYS B 180 " - pdb=" SG CYS B 212 " distance=2.03 Simple disulfide: pdb=" SG CYS B 207 " - pdb=" SG CYS b 360 " distance=2.08 Simple disulfide: pdb=" SG CYS b 279 " - pdb=" SG CYS b 292 " distance=2.03 Simple disulfide: pdb=" SG CYS b 301 " - pdb=" SG CYS b 310 " distance=2.03 Simple disulfide: pdb=" SG CYS b 364 " - pdb=" SG CYS b 385 " distance=2.02 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 105 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 104 " distance=2.04 Simple disulfide: pdb=" SG CYS C 86 " - pdb=" SG CYS C 231 " distance=2.02 Simple disulfide: pdb=" SG CYS C 118 " - pdb=" SG CYS C 155 " distance=2.04 Simple disulfide: pdb=" SG CYS C 180 " - pdb=" SG CYS C 212 " distance=2.04 Simple disulfide: pdb=" SG CYS C 207 " - pdb=" SG CYS c 360 " distance=2.08 Simple disulfide: pdb=" SG CYS c 279 " - pdb=" SG CYS c 292 " distance=2.03 Simple disulfide: pdb=" SG CYS c 301 " - pdb=" SG CYS c 310 " distance=2.03 Simple disulfide: pdb=" SG CYS c 364 " - pdb=" SG CYS c 385 " distance=2.02 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 R 4 " - " MAN R 5 " " MAN W 4 " - " MAN W 5 " ALPHA1-3 " BMA E 3 " - " MAN E 4 " " BMA G 3 " - " MAN G 4 " " BMA J 3 " - " MAN J 4 " " MAN J 4 " - " MAN J 5 " " BMA M 3 " - " MAN M 4 " " BMA R 3 " - " MAN R 4 " " BMA W 3 " - " MAN W 4 " ALPHA1-6 " MAN E 4 " - " MAN E 5 " " BMA G 3 " - " MAN G 5 " " BMA M 3 " - " MAN M 5 " " BMA R 3 " - " MAN R 6 " " BMA W 3 " - " MAN W 6 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " 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 V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " NAG-ASN " NAG B 301 " - " ASN B 89 " " NAG B 302 " - " ASN B 99 " " NAG B 303 " - " ASN B 109 " " NAG B 304 " - " ASN B 119 " " NAG C 301 " - " ASN C 89 " " NAG C 302 " - " ASN C 99 " " NAG C 303 " - " ASN C 109 " " NAG C 304 " - " ASN C 119 " " NAG D 1 " - " ASN A 79 " " NAG E 1 " - " ASN A 89 " " NAG F 1 " - " ASN A 99 " " NAG G 1 " - " ASN A 109 " " NAG I 1 " - " ASN A 119 " " NAG J 1 " - " ASN A 167 " " NAG K 1 " - " ASN A 224 " " NAG M 1 " - " ASN a 365 " " NAG N 1 " - " ASN a 373 " " NAG O 1 " - " ASN B 79 " " NAG P 1 " - " ASN B 167 " " NAG Q 1 " - " ASN B 224 " " NAG R 1 " - " ASN b 365 " " NAG S 1 " - " ASN b 373 " " NAG T 1 " - " ASN C 79 " " NAG U 1 " - " ASN C 167 " " NAG V 1 " - " ASN C 224 " " NAG W 1 " - " ASN c 365 " " NAG X 1 " - " ASN c 373 " " NAG a 701 " - " ASN a 390 " " NAG a 702 " - " ASN a 395 " " NAG b 701 " - " ASN b 390 " " NAG b 702 " - " ASN b 395 " " NAG c 701 " - " ASN c 390 " " NAG c 702 " - " ASN c 395 " Time building additional restraints: 6.06 Conformation dependent library (CDL) restraints added in 1.9 seconds 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2362 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 18 sheets defined 37.9% alpha, 20.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.27 Creating SS restraints... Processing helix chain 'A' and resid 74 through 79 Processing helix chain 'A' and resid 119 through 127 Processing helix chain 'A' and resid 130 through 143 Processing helix chain 'A' and resid 149 through 151 No H-bonds generated for 'chain 'A' and resid 149 through 151' Processing helix chain 'A' and resid 182 through 195 Processing helix chain 'A' and resid 198 through 204 Processing helix chain 'A' and resid 209 through 213 removed outlier: 3.946A pdb=" N ILE A 213 " --> pdb=" O TRP A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 245 removed outlier: 3.603A pdb=" N LEU A 245 " --> pdb=" O TYR A 241 " (cutoff:3.500A) Processing helix chain 'a' and resid 294 through 304 Processing helix chain 'a' and resid 307 through 326 Processing helix chain 'a' and resid 329 through 333 removed outlier: 3.541A pdb=" N SER a 333 " --> pdb=" O ALA a 330 " (cutoff:3.500A) Processing helix chain 'a' and resid 336 through 339 Processing helix chain 'a' and resid 340 through 345 Processing helix chain 'a' and resid 346 through 359 removed outlier: 3.587A pdb=" N ILE a 350 " --> pdb=" O ASN a 346 " (cutoff:3.500A) Processing helix chain 'a' and resid 395 through 418 removed outlier: 5.603A pdb=" N ASP a 401 " --> pdb=" O THR a 397 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N ASP a 402 " --> pdb=" O HIS a 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 65 No H-bonds generated for 'chain 'B' and resid 63 through 65' Processing helix chain 'B' and resid 74 through 79 removed outlier: 3.544A pdb=" N THR B 77 " --> pdb=" O ASN B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 127 Processing helix chain 'B' and resid 130 through 143 Processing helix chain 'B' and resid 149 through 151 No H-bonds generated for 'chain 'B' and resid 149 through 151' Processing helix chain 'B' and resid 169 through 171 No H-bonds generated for 'chain 'B' and resid 169 through 171' Processing helix chain 'B' and resid 182 through 195 Processing helix chain 'B' and resid 195 through 203 removed outlier: 4.384A pdb=" N TYR B 200 " --> pdb=" O TRP B 196 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ILE B 201 " --> pdb=" O GLY B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 247 removed outlier: 3.819A pdb=" N SER B 246 " --> pdb=" O LEU B 242 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N GLN B 247 " --> pdb=" O GLY B 243 " (cutoff:3.500A) Processing helix chain 'b' and resid 281 through 285 Processing helix chain 'b' and resid 294 through 302 removed outlier: 3.559A pdb=" N ASN b 302 " --> pdb=" O VAL b 298 " (cutoff:3.500A) Processing helix chain 'b' and resid 307 through 326 Processing helix chain 'b' and resid 333 through 345 removed outlier: 3.894A pdb=" N LYS b 339 " --> pdb=" O GLN b 335 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N ASN b 342 " --> pdb=" O ASN b 338 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ALA b 343 " --> pdb=" O LYS b 339 " (cutoff:3.500A) Processing helix chain 'b' and resid 346 through 359 removed outlier: 3.603A pdb=" N ILE b 350 " --> pdb=" O ASN b 346 " (cutoff:3.500A) Processing helix chain 'b' and resid 395 through 398 Processing helix chain 'b' and resid 399 through 417 Processing helix chain 'H' and resid 29 through 37 Processing helix chain 'H' and resid 96 through 100 Processing helix chain 'L' and resid 95 through 99 removed outlier: 4.017A pdb=" N PHE L 99 " --> pdb=" O PRO L 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 65 No H-bonds generated for 'chain 'C' and resid 63 through 65' Processing helix chain 'C' and resid 74 through 79 removed outlier: 3.543A pdb=" N THR C 77 " --> pdb=" O ASN C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 127 Processing helix chain 'C' and resid 130 through 143 Processing helix chain 'C' and resid 149 through 151 No H-bonds generated for 'chain 'C' and resid 149 through 151' Processing helix chain 'C' and resid 169 through 171 No H-bonds generated for 'chain 'C' and resid 169 through 171' Processing helix chain 'C' and resid 182 through 195 Processing helix chain 'C' and resid 195 through 203 removed outlier: 4.385A pdb=" N TYR C 200 " --> pdb=" O TRP C 196 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ILE C 201 " --> pdb=" O GLY C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 247 removed outlier: 3.818A pdb=" N SER C 246 " --> pdb=" O LEU C 242 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N GLN C 247 " --> pdb=" O GLY C 243 " (cutoff:3.500A) Processing helix chain 'c' and resid 281 through 285 Processing helix chain 'c' and resid 294 through 302 removed outlier: 3.559A pdb=" N ASN c 302 " --> pdb=" O VAL c 298 " (cutoff:3.500A) Processing helix chain 'c' and resid 307 through 326 Processing helix chain 'c' and resid 333 through 345 removed outlier: 3.895A pdb=" N LYS c 339 " --> pdb=" O GLN c 335 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N ASN c 342 " --> pdb=" O ASN c 338 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ALA c 343 " --> pdb=" O LYS c 339 " (cutoff:3.500A) Processing helix chain 'c' and resid 346 through 359 removed outlier: 3.604A pdb=" N ILE c 350 " --> pdb=" O ASN c 346 " (cutoff:3.500A) Processing helix chain 'c' and resid 395 through 398 Processing helix chain 'c' and resid 399 through 418 Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 62 Processing sheet with id=AA2, first strand: chain 'A' and resid 84 through 88 removed outlier: 3.628A pdb=" N GLY A 102 " --> pdb=" O THR A 225 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'a' and resid 279 through 281 Processing sheet with id=AA4, first strand: chain 'a' and resid 388 through 389 Processing sheet with id=AA5, first strand: chain 'B' and resid 61 through 62 Processing sheet with id=AA6, first strand: chain 'B' and resid 71 through 72 removed outlier: 9.249A pdb=" N TYR b 366 " --> pdb=" O VAL b 388 " (cutoff:3.500A) removed outlier: 10.373A pdb=" N VAL b 388 " --> pdb=" O TYR b 366 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N LYS b 368 " --> pdb=" O TRP b 386 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 84 through 87 Processing sheet with id=AA8, first strand: chain 'b' and resid 278 through 280 removed outlier: 3.635A pdb=" N LYS b 291 " --> pdb=" O LEU b 280 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'H' and resid 11 through 13 removed outlier: 6.923A pdb=" N MET H 39 " --> pdb=" O TYR H 55 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N TYR H 55 " --> pdb=" O MET H 39 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N TRP H 41 " --> pdb=" O VAL H 53 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 11 through 13 Processing sheet with id=AB3, first strand: chain 'L' and resid 5 through 7 Processing sheet with id=AB4, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.563A pdb=" N LEU L 11 " --> pdb=" O ASP L 125 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N LEU L 39 " --> pdb=" O ASN L 55 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ASN L 55 " --> pdb=" O LEU L 39 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N TRP L 41 " --> pdb=" O LEU L 53 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.563A pdb=" N LEU L 11 " --> pdb=" O ASP L 125 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 61 through 62 Processing sheet with id=AB7, first strand: chain 'C' and resid 71 through 72 removed outlier: 9.249A pdb=" N TYR c 366 " --> pdb=" O VAL c 388 " (cutoff:3.500A) removed outlier: 10.372A pdb=" N VAL c 388 " --> pdb=" O TYR c 366 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N LYS c 368 " --> pdb=" O TRP c 386 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 84 through 87 Processing sheet with id=AB9, first strand: chain 'c' and resid 278 through 280 removed outlier: 3.635A pdb=" N LYS c 291 " --> pdb=" O LEU c 280 " (cutoff:3.500A) 456 hydrogen bonds defined for protein. 1185 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: 3.44 Time building geometry restraints manager: 6.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 2105 1.32 - 1.45: 3702 1.45 - 1.59: 5255 1.59 - 1.72: 36 1.72 - 1.86: 146 Bond restraints: 11244 Sorted by residual: bond pdb=" CB HIS A 170 " pdb=" CG HIS A 170 " ideal model delta sigma weight residual 1.497 1.407 0.090 1.40e-02 5.10e+03 4.16e+01 bond pdb=" CB HIS A 93 " pdb=" CG HIS A 93 " ideal model delta sigma weight residual 1.497 1.412 0.085 1.40e-02 5.10e+03 3.71e+01 bond pdb=" CB HIS a 354 " pdb=" CG HIS a 354 " ideal model delta sigma weight residual 1.497 1.414 0.083 1.40e-02 5.10e+03 3.55e+01 bond pdb=" CB LEU a 372 " pdb=" CG LEU a 372 " ideal model delta sigma weight residual 1.530 1.422 0.108 2.00e-02 2.50e+03 2.89e+01 bond pdb=" CB HIS H 40 " pdb=" CG HIS H 40 " ideal model delta sigma weight residual 1.497 1.423 0.074 1.40e-02 5.10e+03 2.76e+01 ... (remaining 11239 not shown) Histogram of bond angle deviations from ideal: 98.03 - 105.26: 231 105.26 - 112.49: 5772 112.49 - 119.72: 4397 119.72 - 126.95: 4672 126.95 - 134.18: 154 Bond angle restraints: 15226 Sorted by residual: angle pdb=" N LEU a 382 " pdb=" CA LEU a 382 " pdb=" C LEU a 382 " ideal model delta sigma weight residual 109.83 99.24 10.59 1.27e+00 6.20e-01 6.96e+01 angle pdb=" C SER a 267 " pdb=" CA SER a 267 " pdb=" CB SER a 267 " ideal model delta sigma weight residual 117.23 107.05 10.18 1.36e+00 5.41e-01 5.61e+01 angle pdb=" C TRP c 370 " pdb=" CA TRP c 370 " pdb=" CB TRP c 370 " ideal model delta sigma weight residual 110.85 98.41 12.44 1.70e+00 3.46e-01 5.36e+01 angle pdb=" C TRP b 370 " pdb=" CA TRP b 370 " pdb=" CB TRP b 370 " ideal model delta sigma weight residual 110.85 98.45 12.40 1.70e+00 3.46e-01 5.32e+01 angle pdb=" N LEU c 382 " pdb=" CA LEU c 382 " pdb=" C LEU c 382 " ideal model delta sigma weight residual 109.50 99.00 10.50 1.47e+00 4.63e-01 5.10e+01 ... (remaining 15221 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.72: 7300 21.72 - 43.44: 225 43.44 - 65.16: 43 65.16 - 86.88: 75 86.88 - 108.60: 54 Dihedral angle restraints: 7697 sinusoidal: 4029 harmonic: 3668 Sorted by residual: dihedral pdb=" CB CYS H 23 " pdb=" SG CYS H 23 " pdb=" SG CYS H 105 " pdb=" CB CYS H 105 " ideal model delta sinusoidal sigma weight residual 93.00 166.90 -73.90 1 1.00e+01 1.00e-02 6.94e+01 dihedral pdb=" CB CYS C 86 " pdb=" SG CYS C 86 " pdb=" SG CYS C 231 " pdb=" CB CYS C 231 " ideal model delta sinusoidal sigma weight residual -86.00 -158.57 72.57 1 1.00e+01 1.00e-02 6.72e+01 dihedral pdb=" CB CYS B 86 " pdb=" SG CYS B 86 " pdb=" SG CYS B 231 " pdb=" CB CYS B 231 " ideal model delta sinusoidal sigma weight residual -86.00 -158.53 72.53 1 1.00e+01 1.00e-02 6.72e+01 ... (remaining 7694 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.119: 1292 0.119 - 0.239: 409 0.239 - 0.358: 146 0.358 - 0.478: 62 0.478 - 0.597: 9 Chirality restraints: 1918 Sorted by residual: chirality pdb=" C1 BMA R 3 " pdb=" O4 NAG R 2 " pdb=" C2 BMA R 3 " pdb=" O5 BMA R 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.90 -0.50 2.00e-02 2.50e+03 6.36e+02 chirality pdb=" C1 BMA W 3 " pdb=" O4 NAG W 2 " pdb=" C2 BMA W 3 " pdb=" O5 BMA W 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-02 2.50e+03 4.47e+02 chirality pdb=" C1 MAN W 5 " pdb=" O2 MAN W 4 " pdb=" C2 MAN W 5 " pdb=" O5 MAN W 5 " both_signs ideal model delta sigma weight residual False 2.40 2.75 -0.35 2.00e-02 2.50e+03 3.00e+02 ... (remaining 1915 not shown) Planarity restraints: 1836 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG S 2 " -0.355 2.00e-02 2.50e+03 3.06e-01 1.17e+03 pdb=" C7 NAG S 2 " 0.086 2.00e-02 2.50e+03 pdb=" C8 NAG S 2 " -0.131 2.00e-02 2.50e+03 pdb=" N2 NAG S 2 " 0.544 2.00e-02 2.50e+03 pdb=" O7 NAG S 2 " -0.143 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG X 2 " 0.355 2.00e-02 2.50e+03 3.05e-01 1.17e+03 pdb=" C7 NAG X 2 " -0.086 2.00e-02 2.50e+03 pdb=" C8 NAG X 2 " 0.131 2.00e-02 2.50e+03 pdb=" N2 NAG X 2 " -0.543 2.00e-02 2.50e+03 pdb=" O7 NAG X 2 " 0.143 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG R 1 " -0.349 2.00e-02 2.50e+03 3.02e-01 1.14e+03 pdb=" C7 NAG R 1 " 0.080 2.00e-02 2.50e+03 pdb=" C8 NAG R 1 " -0.089 2.00e-02 2.50e+03 pdb=" N2 NAG R 1 " 0.537 2.00e-02 2.50e+03 pdb=" O7 NAG R 1 " -0.179 2.00e-02 2.50e+03 ... (remaining 1833 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 3323 2.83 - 3.35: 10668 3.35 - 3.86: 18681 3.86 - 4.38: 22634 4.38 - 4.90: 35563 Nonbonded interactions: 90869 Sorted by model distance: nonbonded pdb=" O4 MAN J 4 " pdb=" O6 MAN J 4 " model vdw 2.309 2.440 nonbonded pdb=" NZ LYS a 339 " pdb=" OD2 ASP B 251 " model vdw 2.409 2.520 nonbonded pdb=" OD2 ASP H 82 " pdb=" NZ LYS H 85 " model vdw 2.410 2.520 nonbonded pdb=" OG SER L 26 " pdb=" OE1 GLN L 27 " model vdw 2.419 2.440 nonbonded pdb=" N ASP c 306 " pdb=" OD1 ASP c 306 " model vdw 2.419 2.520 ... (remaining 90864 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' and (resid 59 through 171 or resid 179 through 255)) selection = (chain 'B' and resid 59 through 255) selection = (chain 'C' and resid 59 through 255) } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'K' selection = chain 'N' selection = chain 'O' selection = chain 'T' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'J' selection = chain 'M' } ncs_group { reference = chain 'I' selection = chain 'P' selection = chain 'Q' selection = chain 'S' selection = chain 'U' selection = chain 'V' selection = chain 'X' } ncs_group { reference = chain 'R' selection = chain 'W' } ncs_group { reference = (chain 'a' and (resid 260 through 268 or resid 277 through 417 or resid 701 thro \ ugh 702)) selection = chain 'b' selection = (chain 'c' and (resid 260 through 417 or resid 701 through 702)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.280 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: 6.140 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 34.320 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 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 : 0.022 0.134 11244 Z= 1.378 Angle : 1.848 13.663 15226 Z= 1.168 Chirality : 0.148 0.597 1918 Planarity : 0.018 0.306 1803 Dihedral : 16.973 108.601 5266 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 3.33 % 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 (0.23), residues: 1231 helix: -0.12 (0.25), residues: 358 sheet: 0.71 (0.33), residues: 232 loop : 0.27 (0.25), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.009 TRP A 196 HIS 0.015 0.003 HIS c 374 PHE 0.034 0.006 PHE L 118 TYR 0.056 0.009 TYR a 363 ARG 0.005 0.001 ARG C 248 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 331 time to evaluate : 1.126 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 82 MET cc_start: 0.9141 (ptp) cc_final: 0.8918 (ptp) REVERT: A 134 MET cc_start: 0.9087 (tpp) cc_final: 0.8266 (tpp) REVERT: a 284 MET cc_start: 0.9002 (mtp) cc_final: 0.8580 (mtt) REVERT: a 347 ASP cc_start: 0.8227 (p0) cc_final: 0.7863 (p0) REVERT: a 405 GLN cc_start: 0.8905 (tp40) cc_final: 0.8532 (tp-100) REVERT: a 408 ASP cc_start: 0.8508 (m-30) cc_final: 0.8101 (t70) REVERT: b 289 GLU cc_start: 0.7726 (mm-30) cc_final: 0.7130 (pm20) REVERT: b 312 MET cc_start: 0.8916 (mmm) cc_final: 0.8691 (mmm) REVERT: H 39 MET cc_start: 0.8371 (mmm) cc_final: 0.8029 (mmt) REVERT: H 126 VAL cc_start: 0.9228 (t) cc_final: 0.9008 (p) REVERT: L 98 ASP cc_start: 0.8550 (m-30) cc_final: 0.8193 (m-30) outliers start: 0 outliers final: 0 residues processed: 331 average time/residue: 0.2584 time to fit residues: 116.0509 Evaluate side-chains 146 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 9.9990 chunk 93 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 62 optimal weight: 5.9990 chunk 49 optimal weight: 0.8980 chunk 96 optimal weight: 0.4980 chunk 37 optimal weight: 0.8980 chunk 58 optimal weight: 0.1980 chunk 71 optimal weight: 0.9980 chunk 111 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 170 HIS A 179 HIS A 247 GLN a 305 HIS ** B 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 149 GLN C 146 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.3348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 11244 Z= 0.251 Angle : 0.858 16.399 15226 Z= 0.425 Chirality : 0.052 0.335 1918 Planarity : 0.004 0.038 1803 Dihedral : 14.289 86.664 2929 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.98 % Favored : 95.94 % Rotamer: Outliers : 2.58 % Allowed : 9.69 % Favored : 87.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.13 (0.23), residues: 1231 helix: 0.55 (0.26), residues: 369 sheet: 0.96 (0.35), residues: 207 loop : -0.42 (0.23), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP c 370 HIS 0.007 0.001 HIS A 93 PHE 0.024 0.002 PHE C 117 TYR 0.017 0.002 TYR A 66 ARG 0.006 0.001 ARG H 81 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 193 time to evaluate : 1.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 PHE cc_start: 0.8014 (m-80) cc_final: 0.7530 (m-10) REVERT: A 134 MET cc_start: 0.9086 (tpp) cc_final: 0.7761 (tpp) REVERT: a 278 TYR cc_start: 0.7173 (t80) cc_final: 0.6958 (t80) REVERT: a 284 MET cc_start: 0.8904 (mtp) cc_final: 0.8652 (mtt) REVERT: a 311 ASP cc_start: 0.9108 (m-30) cc_final: 0.8720 (t0) REVERT: a 332 MET cc_start: 0.8898 (tmm) cc_final: 0.8080 (tmm) REVERT: a 347 ASP cc_start: 0.8115 (p0) cc_final: 0.7405 (p0) REVERT: a 405 GLN cc_start: 0.8887 (tp40) cc_final: 0.8632 (tp40) REVERT: a 408 ASP cc_start: 0.8421 (m-30) cc_final: 0.8040 (t70) REVERT: B 140 PHE cc_start: 0.8807 (t80) cc_final: 0.8468 (t80) REVERT: B 189 GLN cc_start: 0.8973 (mt0) cc_final: 0.8712 (tt0) REVERT: B 192 MET cc_start: 0.8697 (tpt) cc_final: 0.8446 (tpp) REVERT: B 214 MET cc_start: 0.7438 (OUTLIER) cc_final: 0.7098 (pmm) REVERT: b 312 MET cc_start: 0.9003 (mmm) cc_final: 0.8787 (mmm) REVERT: b 347 ASP cc_start: 0.7500 (p0) cc_final: 0.7026 (p0) REVERT: L 106 GLN cc_start: 0.7927 (pp30) cc_final: 0.7626 (pp30) REVERT: c 312 MET cc_start: 0.8970 (mmm) cc_final: 0.8214 (mmm) REVERT: c 370 TRP cc_start: 0.7771 (m-10) cc_final: 0.7227 (m-10) outliers start: 29 outliers final: 13 residues processed: 208 average time/residue: 0.2200 time to fit residues: 65.7531 Evaluate side-chains 162 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 148 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 179 HIS Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 214 MET Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain b residue 295 ASN Chi-restraints excluded: chain b residue 355 LEU Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain c residue 286 ILE Chi-restraints excluded: chain c residue 345 ILE Chi-restraints excluded: chain c residue 380 THR Chi-restraints excluded: chain c residue 411 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 62 optimal weight: 0.9990 chunk 34 optimal weight: 10.0000 chunk 92 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 111 optimal weight: 0.0270 chunk 120 optimal weight: 0.9990 chunk 99 optimal weight: 5.9990 chunk 110 optimal weight: 0.5980 chunk 38 optimal weight: 5.9990 chunk 89 optimal weight: 8.9990 overall best weight: 1.3244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 179 HIS ** a 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 HIS ** b 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 43 GLN C 93 HIS C 127 ASN ** C 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.4025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11244 Z= 0.240 Angle : 0.766 11.301 15226 Z= 0.373 Chirality : 0.048 0.329 1918 Planarity : 0.004 0.038 1803 Dihedral : 11.238 78.894 2929 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 2.49 % Allowed : 13.16 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.01 (0.23), residues: 1231 helix: 0.80 (0.27), residues: 371 sheet: 0.81 (0.33), residues: 224 loop : -0.75 (0.23), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 210 HIS 0.009 0.001 HIS A 115 PHE 0.022 0.002 PHE c 399 TYR 0.021 0.002 TYR A 62 ARG 0.006 0.001 ARG b 314 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 161 time to evaluate : 1.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 MET cc_start: 0.9180 (tpp) cc_final: 0.7863 (tpp) REVERT: a 284 MET cc_start: 0.8875 (mtp) cc_final: 0.8332 (mtt) REVERT: a 311 ASP cc_start: 0.9108 (m-30) cc_final: 0.8847 (t0) REVERT: a 332 MET cc_start: 0.9219 (tmm) cc_final: 0.7870 (tmm) REVERT: a 347 ASP cc_start: 0.8157 (p0) cc_final: 0.7455 (p0) REVERT: a 382 LEU cc_start: 0.9301 (tt) cc_final: 0.9094 (tt) REVERT: a 408 ASP cc_start: 0.8431 (m-30) cc_final: 0.7996 (t70) REVERT: B 192 MET cc_start: 0.8774 (tpt) cc_final: 0.8442 (tpp) REVERT: b 347 ASP cc_start: 0.7578 (p0) cc_final: 0.7336 (p0) REVERT: L 87 PHE cc_start: 0.8245 (m-80) cc_final: 0.7897 (m-10) REVERT: L 97 ASP cc_start: 0.8661 (t0) cc_final: 0.8321 (t0) REVERT: c 361 ILE cc_start: 0.8849 (OUTLIER) cc_final: 0.8629 (tt) REVERT: c 370 TRP cc_start: 0.7660 (m-10) cc_final: 0.7448 (m-10) outliers start: 28 outliers final: 20 residues processed: 179 average time/residue: 0.2374 time to fit residues: 59.8968 Evaluate side-chains 157 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 136 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 CYS Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain a residue 414 MET Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain b residue 295 ASN Chi-restraints excluded: chain b residue 311 ASP Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 39 LEU Chi-restraints excluded: chain C residue 76 GLU Chi-restraints excluded: chain C residue 90 ASN Chi-restraints excluded: chain C residue 118 CYS Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain c residue 286 ILE Chi-restraints excluded: chain c residue 345 ILE Chi-restraints excluded: chain c residue 361 ILE Chi-restraints excluded: chain c residue 380 THR Chi-restraints excluded: chain c residue 417 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 110 optimal weight: 2.9990 chunk 84 optimal weight: 8.9990 chunk 58 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 53 optimal weight: 9.9990 chunk 75 optimal weight: 1.9990 chunk 112 optimal weight: 0.8980 chunk 118 optimal weight: 2.9990 chunk 106 optimal weight: 0.8980 chunk 32 optimal weight: 7.9990 chunk 99 optimal weight: 6.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 247 GLN ** a 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 354 HIS ** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 319 ASN b 335 GLN H 120 GLN L 120 GLN C 146 ASN ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.4561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11244 Z= 0.284 Angle : 0.748 9.454 15226 Z= 0.365 Chirality : 0.048 0.336 1918 Planarity : 0.004 0.043 1803 Dihedral : 9.679 68.447 2929 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 3.47 % Allowed : 12.71 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.11 (0.23), residues: 1231 helix: 0.79 (0.27), residues: 380 sheet: 0.86 (0.34), residues: 224 loop : -0.97 (0.23), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP b 283 HIS 0.011 0.001 HIS A 115 PHE 0.018 0.002 PHE C 117 TYR 0.018 0.002 TYR A 62 ARG 0.004 0.000 ARG H 81 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 154 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.7977 (OUTLIER) cc_final: 0.7642 (mtt) REVERT: a 284 MET cc_start: 0.8939 (mtp) cc_final: 0.8573 (mtt) REVERT: a 311 ASP cc_start: 0.9111 (m-30) cc_final: 0.8902 (t0) REVERT: a 347 ASP cc_start: 0.8340 (p0) cc_final: 0.7711 (p0) REVERT: a 408 ASP cc_start: 0.8386 (m-30) cc_final: 0.8031 (t70) REVERT: B 67 GLU cc_start: 0.7420 (tm-30) cc_final: 0.7169 (tm-30) REVERT: B 192 MET cc_start: 0.8893 (tpt) cc_final: 0.8537 (tpp) REVERT: b 289 GLU cc_start: 0.7851 (mm-30) cc_final: 0.7551 (mm-30) REVERT: b 347 ASP cc_start: 0.7762 (p0) cc_final: 0.7536 (p0) REVERT: b 384 LYS cc_start: 0.9012 (OUTLIER) cc_final: 0.8695 (mptt) REVERT: L 87 PHE cc_start: 0.8275 (m-80) cc_final: 0.7809 (m-10) REVERT: L 97 ASP cc_start: 0.8797 (t0) cc_final: 0.8416 (t0) REVERT: L 106 GLN cc_start: 0.8032 (pp30) cc_final: 0.7824 (pp30) REVERT: c 361 ILE cc_start: 0.8834 (OUTLIER) cc_final: 0.8494 (tp) REVERT: c 370 TRP cc_start: 0.7786 (m-10) cc_final: 0.7501 (m-10) REVERT: c 414 MET cc_start: 0.9569 (ppp) cc_final: 0.9222 (ppp) outliers start: 39 outliers final: 25 residues processed: 177 average time/residue: 0.1931 time to fit residues: 48.8502 Evaluate side-chains 165 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 137 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain b residue 295 ASN Chi-restraints excluded: chain b residue 384 LYS Chi-restraints excluded: chain H residue 81 ARG Chi-restraints excluded: chain H residue 120 GLN Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 39 LEU Chi-restraints excluded: chain C residue 76 GLU Chi-restraints excluded: chain C residue 90 ASN Chi-restraints excluded: chain C residue 114 ASN Chi-restraints excluded: chain C residue 118 CYS Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain c residue 286 ILE Chi-restraints excluded: chain c residue 361 ILE Chi-restraints excluded: chain c residue 380 THR Chi-restraints excluded: chain c residue 411 ILE Chi-restraints excluded: chain c residue 417 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 67 optimal weight: 8.9990 chunk 1 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 chunk 49 optimal weight: 6.9990 chunk 101 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 60 optimal weight: 0.9980 chunk 106 optimal weight: 0.6980 chunk 30 optimal weight: 0.8980 chunk 40 optimal weight: 7.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.4817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11244 Z= 0.206 Angle : 0.697 8.708 15226 Z= 0.337 Chirality : 0.046 0.321 1918 Planarity : 0.003 0.043 1803 Dihedral : 8.982 59.368 2929 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 3.47 % Allowed : 13.78 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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 (0.23), residues: 1231 helix: 0.95 (0.27), residues: 373 sheet: 0.90 (0.34), residues: 224 loop : -0.92 (0.23), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP b 283 HIS 0.012 0.001 HIS A 115 PHE 0.014 0.001 PHE L 87 TYR 0.019 0.002 TYR B 219 ARG 0.003 0.000 ARG b 356 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 147 time to evaluate : 1.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 MET cc_start: 0.8460 (OUTLIER) cc_final: 0.8242 (mtm) REVERT: A 96 MET cc_start: 0.7840 (OUTLIER) cc_final: 0.7560 (mtt) REVERT: A 134 MET cc_start: 0.9223 (tpp) cc_final: 0.7687 (tpp) REVERT: a 262 PHE cc_start: 0.7189 (p90) cc_final: 0.6754 (p90) REVERT: a 284 MET cc_start: 0.8963 (mtp) cc_final: 0.8567 (mtt) REVERT: a 347 ASP cc_start: 0.8288 (p0) cc_final: 0.7658 (p0) REVERT: a 408 ASP cc_start: 0.8324 (m-30) cc_final: 0.8019 (t70) REVERT: B 67 GLU cc_start: 0.7615 (tm-30) cc_final: 0.7410 (tm-30) REVERT: B 134 MET cc_start: 0.8507 (OUTLIER) cc_final: 0.8153 (ttm) REVERT: B 192 MET cc_start: 0.8888 (tpt) cc_final: 0.8508 (tpp) REVERT: b 384 LYS cc_start: 0.9020 (OUTLIER) cc_final: 0.8792 (mptt) REVERT: L 87 PHE cc_start: 0.8178 (m-80) cc_final: 0.7910 (m-10) REVERT: L 97 ASP cc_start: 0.8691 (t0) cc_final: 0.8217 (t0) REVERT: C 96 MET cc_start: 0.7817 (mmm) cc_final: 0.7598 (mmm) REVERT: C 228 GLU cc_start: 0.7877 (pp20) cc_final: 0.7640 (tp30) REVERT: c 361 ILE cc_start: 0.8817 (OUTLIER) cc_final: 0.8586 (tt) REVERT: c 370 TRP cc_start: 0.7651 (m-10) cc_final: 0.7351 (m-10) REVERT: c 414 MET cc_start: 0.9531 (ppp) cc_final: 0.9249 (ppp) outliers start: 39 outliers final: 21 residues processed: 173 average time/residue: 0.2255 time to fit residues: 56.0682 Evaluate side-chains 158 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 132 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 MET Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 114 ASN Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain b residue 295 ASN Chi-restraints excluded: chain b residue 384 LYS Chi-restraints excluded: chain b residue 408 ASP Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 39 LEU Chi-restraints excluded: chain C residue 90 ASN Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 114 ASN Chi-restraints excluded: chain C residue 118 CYS Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain c residue 286 ILE Chi-restraints excluded: chain c residue 306 ASP Chi-restraints excluded: chain c residue 361 ILE Chi-restraints excluded: chain c residue 417 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 107 optimal weight: 8.9990 chunk 23 optimal weight: 5.9990 chunk 69 optimal weight: 9.9990 chunk 29 optimal weight: 0.9990 chunk 119 optimal weight: 4.9990 chunk 98 optimal weight: 10.0000 chunk 55 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 114 optimal weight: 0.9980 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 405 GLN a 409 ASN ** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 95 GLN C 127 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.5084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11244 Z= 0.184 Angle : 0.664 9.087 15226 Z= 0.320 Chirality : 0.045 0.318 1918 Planarity : 0.003 0.043 1803 Dihedral : 7.928 50.608 2929 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 3.20 % Allowed : 14.04 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.09 (0.24), residues: 1231 helix: 0.94 (0.27), residues: 375 sheet: 1.00 (0.34), residues: 225 loop : -0.84 (0.24), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 227 HIS 0.013 0.001 HIS A 115 PHE 0.013 0.001 PHE C 117 TYR 0.017 0.001 TYR B 219 ARG 0.004 0.000 ARG c 314 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 157 time to evaluate : 1.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.7788 (OUTLIER) cc_final: 0.7507 (mtt) REVERT: A 134 MET cc_start: 0.9233 (tpp) cc_final: 0.7614 (tpp) REVERT: a 262 PHE cc_start: 0.7336 (p90) cc_final: 0.6931 (p90) REVERT: a 284 MET cc_start: 0.8906 (mtp) cc_final: 0.8464 (mtp) REVERT: a 347 ASP cc_start: 0.8309 (p0) cc_final: 0.7608 (p0) REVERT: a 408 ASP cc_start: 0.8295 (m-30) cc_final: 0.7963 (t70) REVERT: B 134 MET cc_start: 0.8501 (OUTLIER) cc_final: 0.8162 (ttm) REVERT: B 192 MET cc_start: 0.8868 (tpt) cc_final: 0.8513 (tpp) REVERT: B 219 TYR cc_start: 0.8710 (m-80) cc_final: 0.8420 (m-80) REVERT: b 289 GLU cc_start: 0.7791 (mm-30) cc_final: 0.7463 (mm-30) REVERT: b 347 ASP cc_start: 0.7630 (p0) cc_final: 0.7400 (p0) REVERT: L 87 PHE cc_start: 0.8220 (m-80) cc_final: 0.7896 (m-10) REVERT: L 97 ASP cc_start: 0.8738 (t0) cc_final: 0.8274 (t0) REVERT: C 185 ASN cc_start: 0.8672 (m-40) cc_final: 0.8059 (m-40) REVERT: C 228 GLU cc_start: 0.7822 (pp20) cc_final: 0.7601 (tp30) REVERT: c 370 TRP cc_start: 0.7690 (m-10) cc_final: 0.7394 (m-10) outliers start: 36 outliers final: 20 residues processed: 180 average time/residue: 0.2181 time to fit residues: 57.0037 Evaluate side-chains 152 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 130 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain a residue 270 GLU Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 114 ASN Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 39 LEU Chi-restraints excluded: chain C residue 76 GLU Chi-restraints excluded: chain C residue 90 ASN Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 114 ASN Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 155 CYS Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain c residue 306 ASP Chi-restraints excluded: chain c residue 417 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 13 optimal weight: 6.9990 chunk 67 optimal weight: 7.9990 chunk 86 optimal weight: 5.9990 chunk 100 optimal weight: 7.9990 chunk 66 optimal weight: 5.9990 chunk 118 optimal weight: 3.9990 chunk 74 optimal weight: 0.0870 chunk 72 optimal weight: 0.9980 chunk 54 optimal weight: 0.0370 chunk 73 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 overall best weight: 1.0238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 247 GLN ** a 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.5259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 11244 Z= 0.204 Angle : 0.676 10.059 15226 Z= 0.328 Chirality : 0.045 0.317 1918 Planarity : 0.003 0.047 1803 Dihedral : 7.639 48.321 2929 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 3.29 % Allowed : 14.67 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.11 (0.24), residues: 1231 helix: 1.00 (0.27), residues: 375 sheet: 1.08 (0.35), residues: 223 loop : -0.88 (0.24), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 196 HIS 0.013 0.001 HIS A 115 PHE 0.014 0.001 PHE b 316 TYR 0.015 0.001 TYR B 219 ARG 0.005 0.000 ARG c 314 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 143 time to evaluate : 1.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.7890 (OUTLIER) cc_final: 0.7614 (mtt) REVERT: A 134 MET cc_start: 0.9221 (tpp) cc_final: 0.7618 (tpp) REVERT: a 284 MET cc_start: 0.8899 (mtp) cc_final: 0.8390 (mtp) REVERT: a 347 ASP cc_start: 0.8432 (p0) cc_final: 0.7789 (p0) REVERT: a 408 ASP cc_start: 0.8319 (m-30) cc_final: 0.7969 (t70) REVERT: B 134 MET cc_start: 0.8497 (OUTLIER) cc_final: 0.8178 (ttm) REVERT: B 192 MET cc_start: 0.8881 (tpt) cc_final: 0.8542 (tpp) REVERT: b 289 GLU cc_start: 0.7794 (mm-30) cc_final: 0.7452 (mm-30) REVERT: L 87 PHE cc_start: 0.8277 (m-80) cc_final: 0.8057 (m-10) REVERT: L 89 LEU cc_start: 0.8297 (tp) cc_final: 0.8048 (tp) REVERT: L 97 ASP cc_start: 0.8764 (t0) cc_final: 0.8331 (t0) REVERT: C 185 ASN cc_start: 0.8673 (m-40) cc_final: 0.8076 (m-40) REVERT: C 228 GLU cc_start: 0.7735 (pp20) cc_final: 0.7514 (tp30) REVERT: c 348 GLN cc_start: 0.8675 (mm-40) cc_final: 0.8397 (mm-40) REVERT: c 370 TRP cc_start: 0.7729 (m-10) cc_final: 0.7427 (m-10) outliers start: 37 outliers final: 28 residues processed: 170 average time/residue: 0.2171 time to fit residues: 53.9065 Evaluate side-chains 164 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 134 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain a residue 270 GLU Chi-restraints excluded: chain a residue 301 CYS Chi-restraints excluded: chain a residue 345 ILE Chi-restraints excluded: chain a residue 414 MET Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 114 ASN Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain b residue 295 ASN Chi-restraints excluded: chain b residue 408 ASP Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 39 LEU Chi-restraints excluded: chain C residue 76 GLU Chi-restraints excluded: chain C residue 90 ASN Chi-restraints excluded: chain C residue 114 ASN Chi-restraints excluded: chain C residue 118 CYS Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 155 CYS Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain c residue 306 ASP Chi-restraints excluded: chain c residue 313 LEU Chi-restraints excluded: chain c residue 417 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 70 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 80 optimal weight: 0.1980 chunk 58 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 93 optimal weight: 5.9990 chunk 107 optimal weight: 8.9990 chunk 113 optimal weight: 5.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 405 GLN a 409 ASN ** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.5416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 11244 Z= 0.231 Angle : 0.690 11.046 15226 Z= 0.336 Chirality : 0.046 0.320 1918 Planarity : 0.003 0.044 1803 Dihedral : 7.494 46.744 2929 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 3.11 % Allowed : 14.84 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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 (0.24), residues: 1231 helix: 1.04 (0.27), residues: 373 sheet: 0.91 (0.35), residues: 229 loop : -0.89 (0.24), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 52 HIS 0.013 0.001 HIS A 115 PHE 0.012 0.002 PHE L 87 TYR 0.015 0.001 TYR B 219 ARG 0.013 0.001 ARG c 314 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 139 time to evaluate : 1.250 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.7891 (mtp) cc_final: 0.7585 (mtt) REVERT: A 230 HIS cc_start: 0.7567 (m-70) cc_final: 0.7260 (m-70) REVERT: a 284 MET cc_start: 0.8833 (mtp) cc_final: 0.8338 (mtp) REVERT: a 347 ASP cc_start: 0.8518 (p0) cc_final: 0.8116 (p0) REVERT: a 408 ASP cc_start: 0.8281 (m-30) cc_final: 0.7956 (t70) REVERT: B 134 MET cc_start: 0.8510 (OUTLIER) cc_final: 0.8176 (ttm) REVERT: B 192 MET cc_start: 0.8884 (tpt) cc_final: 0.8547 (tpp) REVERT: b 289 GLU cc_start: 0.7832 (mm-30) cc_final: 0.7499 (mm-30) REVERT: L 87 PHE cc_start: 0.8320 (m-80) cc_final: 0.8050 (m-10) REVERT: L 89 LEU cc_start: 0.8309 (tp) cc_final: 0.8019 (tp) REVERT: L 97 ASP cc_start: 0.8810 (t0) cc_final: 0.8468 (t0) REVERT: C 185 ASN cc_start: 0.8706 (m-40) cc_final: 0.8126 (m-40) REVERT: C 228 GLU cc_start: 0.7738 (pp20) cc_final: 0.7525 (tp30) REVERT: c 348 GLN cc_start: 0.8655 (mm-40) cc_final: 0.8353 (mm-40) REVERT: c 370 TRP cc_start: 0.7825 (m-10) cc_final: 0.7494 (m-10) REVERT: c 414 MET cc_start: 0.9424 (ppp) cc_final: 0.9083 (ppp) outliers start: 35 outliers final: 26 residues processed: 166 average time/residue: 0.2227 time to fit residues: 54.7514 Evaluate side-chains 158 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 131 time to evaluate : 1.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain a residue 301 CYS Chi-restraints excluded: chain a residue 345 ILE Chi-restraints excluded: chain a residue 414 MET Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 114 ASN Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 227 TRP Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain b residue 295 ASN Chi-restraints excluded: chain b residue 408 ASP Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 39 LEU Chi-restraints excluded: chain C residue 90 ASN Chi-restraints excluded: chain C residue 114 ASN Chi-restraints excluded: chain C residue 118 CYS Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 155 CYS Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain c residue 306 ASP Chi-restraints excluded: chain c residue 417 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 6.9990 chunk 110 optimal weight: 5.9990 chunk 113 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 48 optimal weight: 10.0000 chunk 86 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 99 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 116 optimal weight: 4.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.5584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 11244 Z= 0.202 Angle : 0.680 11.750 15226 Z= 0.331 Chirality : 0.045 0.315 1918 Planarity : 0.003 0.042 1803 Dihedral : 7.291 49.582 2929 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.67 % Allowed : 15.64 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.12 (0.24), residues: 1231 helix: 1.05 (0.28), residues: 377 sheet: 1.06 (0.35), residues: 224 loop : -0.89 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP b 370 HIS 0.014 0.001 HIS A 115 PHE 0.011 0.001 PHE b 316 TYR 0.015 0.001 TYR B 219 ARG 0.010 0.000 ARG c 314 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 140 time to evaluate : 1.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.7882 (mtp) cc_final: 0.7588 (mtt) REVERT: A 134 MET cc_start: 0.9102 (tpp) cc_final: 0.7679 (tpp) REVERT: A 230 HIS cc_start: 0.7460 (m-70) cc_final: 0.7254 (m-70) REVERT: a 284 MET cc_start: 0.8833 (mtp) cc_final: 0.8352 (mtp) REVERT: a 408 ASP cc_start: 0.8280 (m-30) cc_final: 0.7963 (t70) REVERT: B 76 GLU cc_start: 0.8664 (tp30) cc_final: 0.8424 (mt-10) REVERT: B 134 MET cc_start: 0.8490 (OUTLIER) cc_final: 0.8172 (ttm) REVERT: B 192 MET cc_start: 0.8937 (tpt) cc_final: 0.8571 (tpp) REVERT: b 289 GLU cc_start: 0.7834 (mm-30) cc_final: 0.7501 (mm-30) REVERT: L 87 PHE cc_start: 0.8301 (m-80) cc_final: 0.8090 (m-10) REVERT: L 97 ASP cc_start: 0.8795 (t0) cc_final: 0.8395 (t0) REVERT: C 185 ASN cc_start: 0.8658 (m-40) cc_final: 0.8068 (m-40) REVERT: c 313 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8672 (mp) REVERT: c 348 GLN cc_start: 0.8617 (mm-40) cc_final: 0.8334 (mm-40) REVERT: c 370 TRP cc_start: 0.7801 (m-10) cc_final: 0.7477 (m-10) REVERT: c 414 MET cc_start: 0.9417 (ppp) cc_final: 0.9018 (ppp) outliers start: 30 outliers final: 28 residues processed: 161 average time/residue: 0.2173 time to fit residues: 51.1841 Evaluate side-chains 162 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 132 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain a residue 301 CYS Chi-restraints excluded: chain a residue 414 MET Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 114 ASN Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 227 TRP Chi-restraints excluded: chain B residue 228 GLU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain b residue 295 ASN Chi-restraints excluded: chain b residue 408 ASP Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 39 LEU Chi-restraints excluded: chain C residue 76 GLU Chi-restraints excluded: chain C residue 90 ASN Chi-restraints excluded: chain C residue 114 ASN Chi-restraints excluded: chain C residue 118 CYS Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 155 CYS Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain c residue 306 ASP Chi-restraints excluded: chain c residue 313 LEU Chi-restraints excluded: chain c residue 359 MET Chi-restraints excluded: chain c residue 417 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 71 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 chunk 81 optimal weight: 0.0770 chunk 122 optimal weight: 0.9980 chunk 112 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 77 optimal weight: 0.7980 chunk 103 optimal weight: 0.9980 overall best weight: 0.7538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 319 ASN ** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 189 GLN ** L 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.5720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11244 Z= 0.188 Angle : 0.681 12.794 15226 Z= 0.328 Chirality : 0.045 0.310 1918 Planarity : 0.003 0.041 1803 Dihedral : 7.116 50.212 2929 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 2.49 % Allowed : 15.47 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.15 (0.24), residues: 1231 helix: 1.07 (0.28), residues: 375 sheet: 0.99 (0.35), residues: 228 loop : -0.84 (0.24), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 227 HIS 0.015 0.001 HIS A 115 PHE 0.011 0.001 PHE b 316 TYR 0.014 0.001 TYR B 219 ARG 0.008 0.000 ARG c 314 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 137 time to evaluate : 1.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.7871 (mtp) cc_final: 0.7595 (mtp) REVERT: a 284 MET cc_start: 0.8832 (mtp) cc_final: 0.8369 (mtt) REVERT: a 408 ASP cc_start: 0.8287 (m-30) cc_final: 0.7989 (t70) REVERT: B 76 GLU cc_start: 0.8644 (tp30) cc_final: 0.8402 (mt-10) REVERT: B 134 MET cc_start: 0.8482 (OUTLIER) cc_final: 0.8183 (ttm) REVERT: B 192 MET cc_start: 0.8943 (tpt) cc_final: 0.8569 (tpp) REVERT: L 97 ASP cc_start: 0.8788 (t0) cc_final: 0.8278 (t0) REVERT: C 185 ASN cc_start: 0.8643 (m-40) cc_final: 0.8066 (m-40) REVERT: c 370 TRP cc_start: 0.7785 (m-10) cc_final: 0.7446 (m-10) REVERT: c 414 MET cc_start: 0.9402 (ppp) cc_final: 0.9013 (ppp) outliers start: 28 outliers final: 23 residues processed: 155 average time/residue: 0.2163 time to fit residues: 49.1170 Evaluate side-chains 152 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 128 time to evaluate : 1.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain a residue 301 CYS Chi-restraints excluded: chain a residue 345 ILE Chi-restraints excluded: chain a residue 414 MET Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 114 ASN Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 227 TRP Chi-restraints excluded: chain B residue 228 GLU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain b residue 408 ASP Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 39 LEU Chi-restraints excluded: chain C residue 90 ASN Chi-restraints excluded: chain C residue 114 ASN Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 155 CYS Chi-restraints excluded: chain c residue 306 ASP Chi-restraints excluded: chain c residue 359 MET Chi-restraints excluded: chain c residue 417 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 29 optimal weight: 10.0000 chunk 89 optimal weight: 7.9990 chunk 14 optimal weight: 5.9990 chunk 27 optimal weight: 0.9980 chunk 97 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 85 optimal weight: 7.9990 chunk 5 optimal weight: 5.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.076887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.062183 restraints weight = 36624.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.064700 restraints weight = 19821.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.066386 restraints weight = 13471.147| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.5832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 11244 Z= 0.203 Angle : 0.677 12.706 15226 Z= 0.328 Chirality : 0.045 0.310 1918 Planarity : 0.003 0.041 1803 Dihedral : 7.035 48.533 2929 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 2.58 % Allowed : 15.73 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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 (0.24), residues: 1231 helix: 1.14 (0.28), residues: 372 sheet: 1.00 (0.35), residues: 228 loop : -0.97 (0.24), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 210 HIS 0.015 0.001 HIS A 115 PHE 0.020 0.001 PHE c 309 TYR 0.014 0.001 TYR B 219 ARG 0.006 0.000 ARG c 314 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2143.04 seconds wall clock time: 41 minutes 15.16 seconds (2475.16 seconds total)