Starting phenix.real_space_refine on Sat Dec 9 12:27:39 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eji_28183/12_2023/8eji_28183.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eji_28183/12_2023/8eji_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_28183/12_2023/8eji_28183.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eji_28183/12_2023/8eji_28183.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eji_28183/12_2023/8eji_28183.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eji_28183/12_2023/8eji_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-1.21rc1-5172/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: 6 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: 6 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: 6 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: 6 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: 6 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: 6 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: 6 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: 6 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: 6 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: 6 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: 6 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: 6 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: 6.26, 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: 5.50 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: 1.14 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: 3.38 Time building geometry restraints manager: 5.82 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 - 17.81: 6872 17.81 - 35.62: 237 35.62 - 53.43: 69 53.43 - 71.24: 15 71.24 - 89.04: 10 Dihedral angle restraints: 7203 sinusoidal: 3535 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 7200 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: 2.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.180 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 32.600 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.790 ------------------------------------------------------------------------------- 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 : 10.175 89.045 4772 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 : 1.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 331 average time/residue: 0.2554 time to fit residues: 114.8150 Evaluate side-chains 148 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 1.141 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5211 ------------------------------------------------------------------------------- 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: 7.9990 chunk 49 optimal weight: 1.9990 chunk 96 optimal weight: 0.4980 chunk 37 optimal weight: 0.1980 chunk 58 optimal weight: 0.1980 chunk 71 optimal weight: 0.7980 chunk 111 optimal weight: 3.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.3356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 11244 Z= 0.248 Angle : 0.851 16.280 15226 Z= 0.428 Chirality : 0.050 0.385 1918 Planarity : 0.004 0.042 1803 Dihedral : 6.657 52.699 2435 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.06 % Favored : 95.86 % Rotamer: Outliers : 2.49 % Allowed : 10.40 % Favored : 87.11 % 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: 0.54 (0.26), residues: 369 sheet: 0.99 (0.35), residues: 207 loop : -0.42 (0.23), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 227 HIS 0.008 0.002 HIS A 115 PHE 0.025 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 219 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 191 time to evaluate : 1.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 13 residues processed: 205 average time/residue: 0.2239 time to fit residues: 66.2715 Evaluate side-chains 158 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 145 time to evaluate : 1.337 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1069 time to fit residues: 4.2450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 62 optimal weight: 2.9990 chunk 34 optimal weight: 9.9990 chunk 92 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 111 optimal weight: 5.9990 chunk 120 optimal weight: 1.9990 chunk 99 optimal weight: 7.9990 chunk 110 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 89 optimal weight: 8.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 HIS ** A 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 165 GLN ** a 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 ASN b 319 ASN ** b 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 43 GLN ** C 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 127 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.4426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.080 11244 Z= 0.444 Angle : 0.914 12.084 15226 Z= 0.447 Chirality : 0.050 0.369 1918 Planarity : 0.005 0.043 1803 Dihedral : 7.543 49.320 2435 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 3.47 % Allowed : 12.62 % Favored : 83.91 % 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: -0.40 (0.23), residues: 1231 helix: 0.63 (0.27), residues: 376 sheet: 0.57 (0.34), residues: 210 loop : -1.10 (0.22), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP b 283 HIS 0.009 0.002 HIS A 93 PHE 0.021 0.003 PHE L 87 TYR 0.025 0.003 TYR A 62 ARG 0.008 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 183 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 144 time to evaluate : 1.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 21 residues processed: 175 average time/residue: 0.2328 time to fit residues: 58.5157 Evaluate side-chains 145 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 124 time to evaluate : 1.223 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.1492 time to fit residues: 6.5666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0970 chunk 58 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 chunk 53 optimal weight: 6.9990 chunk 75 optimal weight: 4.9990 chunk 112 optimal weight: 0.6980 chunk 118 optimal weight: 0.8980 chunk 106 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 99 optimal weight: 5.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 247 GLN a 305 HIS a 354 HIS B 93 HIS C 93 HIS ** C 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.4719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11244 Z= 0.184 Angle : 0.723 12.723 15226 Z= 0.354 Chirality : 0.045 0.332 1918 Planarity : 0.004 0.047 1803 Dihedral : 6.743 47.128 2435 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 1.60 % Allowed : 13.87 % Favored : 84.53 % 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: -0.14 (0.23), residues: 1231 helix: 0.82 (0.27), residues: 377 sheet: 0.74 (0.34), residues: 222 loop : -0.96 (0.23), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP c 370 HIS 0.013 0.001 HIS A 115 PHE 0.019 0.002 PHE c 399 TYR 0.020 0.001 TYR c 371 ARG 0.006 0.001 ARG b 314 *********************** 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 181 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 163 time to evaluate : 1.175 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 9 residues processed: 171 average time/residue: 0.2416 time to fit residues: 58.9623 Evaluate side-chains 143 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 134 time to evaluate : 1.147 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1009 time to fit residues: 3.2442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 67 optimal weight: 4.9990 chunk 1 optimal weight: 4.9990 chunk 88 optimal weight: 4.9990 chunk 49 optimal weight: 0.9980 chunk 101 optimal weight: 0.8980 chunk 82 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 106 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 40 optimal weight: 9.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 HIS A 131 HIS ** a 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 335 GLN ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.4974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 11244 Z= 0.235 Angle : 0.724 14.972 15226 Z= 0.352 Chirality : 0.045 0.347 1918 Planarity : 0.004 0.071 1803 Dihedral : 6.630 47.816 2435 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 1.42 % Allowed : 15.56 % Favored : 83.02 % 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 (0.24), residues: 1231 helix: 0.89 (0.27), residues: 375 sheet: 0.76 (0.35), residues: 223 loop : -1.01 (0.23), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP c 370 HIS 0.013 0.001 HIS A 115 PHE 0.021 0.002 PHE L 87 TYR 0.022 0.002 TYR B 241 ARG 0.016 0.001 ARG b 314 *********************** 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 158 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 142 time to evaluate : 1.306 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 9 residues processed: 152 average time/residue: 0.2329 time to fit residues: 51.2356 Evaluate side-chains 134 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 125 time to evaluate : 1.238 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1038 time to fit residues: 3.3849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 107 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 69 optimal weight: 0.6980 chunk 29 optimal weight: 5.9990 chunk 119 optimal weight: 0.8980 chunk 98 optimal weight: 2.9990 chunk 55 optimal weight: 0.0970 chunk 9 optimal weight: 8.9990 chunk 39 optimal weight: 1.9990 chunk 62 optimal weight: 0.4980 chunk 114 optimal weight: 0.8980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 GLN ** a 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 319 ASN ** a 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 185 ASN ** 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: 0.5178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 11244 Z= 0.193 Angle : 0.706 14.738 15226 Z= 0.346 Chirality : 0.044 0.332 1918 Planarity : 0.004 0.046 1803 Dihedral : 6.440 50.742 2435 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 0.98 % Allowed : 16.18 % Favored : 82.84 % 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: 0.82 (0.27), residues: 375 sheet: 0.95 (0.36), residues: 215 loop : -0.95 (0.24), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP c 370 HIS 0.013 0.001 HIS A 115 PHE 0.015 0.001 PHE L 87 TYR 0.016 0.001 TYR B 241 ARG 0.010 0.000 ARG b 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 154 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 143 time to evaluate : 1.419 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 5 residues processed: 148 average time/residue: 0.2214 time to fit residues: 48.3345 Evaluate side-chains 141 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 136 time to evaluate : 1.286 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0939 time to fit residues: 2.3166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 13 optimal weight: 8.9990 chunk 67 optimal weight: 10.0000 chunk 86 optimal weight: 4.9990 chunk 100 optimal weight: 9.9990 chunk 66 optimal weight: 4.9990 chunk 118 optimal weight: 4.9990 chunk 74 optimal weight: 0.2980 chunk 72 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 73 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 overall best weight: 3.0588 ------------------------------------------------------------------------------- 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 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 124 HIS ** L 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 127 ASN ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 189 GLN ** c 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.5405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 11244 Z= 0.390 Angle : 0.810 17.017 15226 Z= 0.394 Chirality : 0.047 0.351 1918 Planarity : 0.004 0.062 1803 Dihedral : 7.125 52.183 2435 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 1.96 % Allowed : 15.91 % Favored : 82.13 % 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: -0.22 (0.24), residues: 1231 helix: 0.98 (0.28), residues: 367 sheet: 0.81 (0.37), residues: 209 loop : -1.15 (0.23), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP c 370 HIS 0.012 0.001 HIS A 115 PHE 0.016 0.002 PHE a 293 TYR 0.022 0.002 TYR L 107 ARG 0.007 0.001 ARG b 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 157 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 135 time to evaluate : 1.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 12 residues processed: 149 average time/residue: 0.2203 time to fit residues: 48.1243 Evaluate side-chains 140 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 128 time to evaluate : 1.219 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1344 time to fit residues: 4.3013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 70 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 11 optimal weight: 9.9990 chunk 93 optimal weight: 0.8980 chunk 107 optimal weight: 0.0670 chunk 113 optimal weight: 0.8980 overall best weight: 0.9120 ------------------------------------------------------------------------------- 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 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 HIS L 95 GLN L 106 GLN ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 189 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.5621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 11244 Z= 0.209 Angle : 0.715 13.660 15226 Z= 0.350 Chirality : 0.044 0.345 1918 Planarity : 0.004 0.039 1803 Dihedral : 6.637 39.944 2435 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 1.24 % Allowed : 16.36 % Favored : 82.40 % 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: -0.16 (0.24), residues: 1231 helix: 0.86 (0.28), residues: 375 sheet: 0.78 (0.37), residues: 215 loop : -1.01 (0.24), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP c 370 HIS 0.014 0.001 HIS A 115 PHE 0.016 0.001 PHE c 262 TYR 0.028 0.001 TYR B 219 ARG 0.010 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 154 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 140 time to evaluate : 1.225 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 9 residues processed: 146 average time/residue: 0.2237 time to fit residues: 47.6841 Evaluate side-chains 131 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 122 time to evaluate : 1.212 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1135 time to fit residues: 3.3511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 8.9990 chunk 110 optimal weight: 0.0000 chunk 113 optimal weight: 0.9990 chunk 66 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 99 optimal weight: 4.9990 chunk 104 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 chunk 116 optimal weight: 3.9990 overall best weight: 1.0988 ------------------------------------------------------------------------------- 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** ** L 106 GLN ** 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: 0.8121 moved from start: 0.5781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 11244 Z= 0.230 Angle : 0.735 18.030 15226 Z= 0.359 Chirality : 0.044 0.348 1918 Planarity : 0.004 0.039 1803 Dihedral : 6.480 39.156 2435 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 0.53 % Allowed : 17.24 % Favored : 82.22 % 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: -0.17 (0.24), residues: 1231 helix: 0.84 (0.28), residues: 377 sheet: 1.00 (0.37), residues: 207 loop : -1.10 (0.24), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP c 370 HIS 0.015 0.001 HIS A 115 PHE 0.023 0.002 PHE c 309 TYR 0.018 0.001 TYR B 219 ARG 0.012 0.001 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 139 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 133 time to evaluate : 1.167 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 135 average time/residue: 0.2180 time to fit residues: 43.2108 Evaluate side-chains 129 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 127 time to evaluate : 1.159 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1357 time to fit residues: 1.9697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 71 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 chunk 81 optimal weight: 0.3980 chunk 122 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 75 optimal weight: 0.8980 chunk 59 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 103 optimal weight: 20.0000 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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** ** L 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 165 GLN ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.5917 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= 0.218 Angle : 0.717 14.536 15226 Z= 0.352 Chirality : 0.044 0.342 1918 Planarity : 0.004 0.040 1803 Dihedral : 6.391 38.372 2435 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 0.53 % Allowed : 17.60 % Favored : 81.87 % 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: -0.20 (0.24), residues: 1231 helix: 0.80 (0.28), residues: 377 sheet: 0.84 (0.37), residues: 211 loop : -1.05 (0.24), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP c 370 HIS 0.016 0.001 HIS A 115 PHE 0.019 0.002 PHE c 309 TYR 0.016 0.001 TYR c 371 ARG 0.005 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 142 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 136 time to evaluate : 1.266 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 136 average time/residue: 0.2243 time to fit residues: 45.0132 Evaluate side-chains 132 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 127 time to evaluate : 1.255 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1208 time to fit residues: 2.7357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 29 optimal weight: 1.9990 chunk 89 optimal weight: 7.9990 chunk 14 optimal weight: 5.9990 chunk 27 optimal weight: 0.7980 chunk 97 optimal weight: 3.9990 chunk 40 optimal weight: 0.6980 chunk 100 optimal weight: 10.0000 chunk 12 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 85 optimal weight: 10.0000 chunk 5 optimal weight: 3.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 165 GLN ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.075833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.061062 restraints weight = 36806.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.063480 restraints weight = 20030.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.065127 restraints weight = 13759.748| |-----------------------------------------------------------------------------| r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.6008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 11244 Z= 0.219 Angle : 0.707 10.526 15226 Z= 0.348 Chirality : 0.044 0.341 1918 Planarity : 0.004 0.039 1803 Dihedral : 6.386 41.934 2435 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 0.36 % Allowed : 18.04 % Favored : 81.60 % 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: -0.16 (0.24), residues: 1231 helix: 0.83 (0.28), residues: 375 sheet: 0.98 (0.37), residues: 205 loop : -1.05 (0.24), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP c 370 HIS 0.015 0.001 HIS A 115 PHE 0.018 0.002 PHE c 309 TYR 0.015 0.001 TYR c 371 ARG 0.005 0.000 ARG c 314 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2102.69 seconds wall clock time: 44 minutes 27.21 seconds (2667.21 seconds total)