Starting phenix.real_space_refine on Sat Aug 23 05:55:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ejg_28181/08_2025/8ejg_28181.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ejg_28181/08_2025/8ejg_28181.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ejg_28181/08_2025/8ejg_28181.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ejg_28181/08_2025/8ejg_28181.map" model { file = "/net/cci-nas-00/data/ceres_data/8ejg_28181/08_2025/8ejg_28181.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ejg_28181/08_2025/8ejg_28181.cif" } resolution = 3.13 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.001 sd= 0.025 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 90 5.16 5 C 6174 2.51 5 N 1530 2.21 5 O 2172 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 49 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9966 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 1551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1551 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 4, 'TRANS': 191} Chain: "a" Number of atoms: 1337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1337 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 4, 'TRANS': 160} Chain: "B" Number of atoms: 1551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1551 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 4, 'TRANS': 191} Chain: "C" Number of atoms: 1551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1551 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 4, 'TRANS': 191} Chain: "b" Number of atoms: 1337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1337 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 4, 'TRANS': 160} Chain: "c" Number of atoms: 1337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1337 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 4, 'TRANS': 160} Chain: "D" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "E" Number of atoms: 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: "F" 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: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BGC': 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: "H" 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: "I" 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: "J" 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: "K" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "L" 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: 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: "P" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BGC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Q" Number of atoms: 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: "R" 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: "S" 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: "T" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "U" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BGC': 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: "X" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Y" Number of atoms: 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: "Z" 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: "d" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "e" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "f" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "g" 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: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 3.02, per 1000 atoms: 0.30 Number of scatterers: 9966 At special positions: 0 Unit cell: (101.2, 102.35, 104.65, 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 90 16.00 O 2172 8.00 N 1530 7.00 C 6174 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS A 85 " - pdb=" SG CYS A 230 " distance=2.04 Simple disulfide: pdb=" SG CYS A 117 " - pdb=" SG CYS A 154 " distance=2.16 Simple disulfide: pdb=" SG CYS A 179 " - pdb=" SG CYS A 211 " distance=2.03 Simple disulfide: pdb=" SG CYS A 206 " - pdb=" SG CYS a 359 " distance=2.02 Simple disulfide: pdb=" SG CYS a 278 " - pdb=" SG CYS a 291 " distance=2.03 Simple disulfide: pdb=" SG CYS a 300 " - pdb=" SG CYS a 309 " distance=2.03 Simple disulfide: pdb=" SG CYS a 363 " - pdb=" SG CYS a 384 " distance=2.01 Simple disulfide: pdb=" SG CYS B 85 " - pdb=" SG CYS B 230 " distance=2.04 Simple disulfide: pdb=" SG CYS B 117 " - pdb=" SG CYS B 154 " distance=2.16 Simple disulfide: pdb=" SG CYS B 179 " - pdb=" SG CYS B 211 " distance=2.03 Simple disulfide: pdb=" SG CYS B 206 " - pdb=" SG CYS b 359 " distance=2.02 Simple disulfide: pdb=" SG CYS C 85 " - pdb=" SG CYS C 230 " distance=2.04 Simple disulfide: pdb=" SG CYS C 117 " - pdb=" SG CYS C 154 " distance=2.16 Simple disulfide: pdb=" SG CYS C 179 " - pdb=" SG CYS C 211 " distance=2.04 Simple disulfide: pdb=" SG CYS C 206 " - pdb=" SG CYS c 359 " distance=2.02 Simple disulfide: pdb=" SG CYS b 278 " - pdb=" SG CYS b 291 " distance=2.03 Simple disulfide: pdb=" SG CYS b 300 " - pdb=" SG CYS b 309 " distance=2.03 Simple disulfide: pdb=" SG CYS b 363 " - pdb=" SG CYS b 384 " distance=2.01 Simple disulfide: pdb=" SG CYS c 278 " - pdb=" SG CYS c 291 " distance=2.03 Simple disulfide: pdb=" SG CYS c 300 " - pdb=" SG CYS c 309 " distance=2.03 Simple disulfide: pdb=" SG CYS c 363 " - pdb=" SG CYS c 384 " distance=2.01 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 K 4 " - " MAN K 5 " " MAN d 4 " - " MAN d 5 " " MAN f 4 " - " MAN f 5 " ALPHA1-3 " BMA D 3 " - " MAN D 4 " " BMA K 3 " - " MAN K 4 " " MAN K 6 " - " MAN K 7 " " BMA M 3 " - " MAN M 4 " " BMA T 3 " - " MAN T 4 " " BMA d 3 " - " MAN d 4 " " MAN d 6 " - " MAN d 7 " " BMA f 3 " - " MAN f 4 " " MAN f 6 " - " MAN f 7 " ALPHA1-6 " BMA D 3 " - " MAN D 5 " " BMA K 3 " - " MAN K 6 " " BMA M 3 " - " MAN M 5 " " BMA T 3 " - " MAN T 5 " " BMA d 3 " - " MAN d 6 " " BMA f 3 " - " MAN f 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 G 1 " - " NAG G 2 " " NAG G 2 " - " BGC G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " 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 L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 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 P 1 " - " NAG P 2 " " NAG P 2 " - " BGC P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BGC W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " 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-ASN " NAG D 1 " - " ASN A 78 " " NAG E 1 " - " ASN A 88 " " NAG F 1 " - " ASN A 98 " " NAG G 1 " - " ASN A 108 " " NAG H 1 " - " ASN A 118 " " NAG I 1 " - " ASN A 166 " " NAG J 1 " - " ASN A 223 " " NAG K 1 " - " ASN a 364 " " NAG L 1 " - " ASN a 372 " " NAG M 1 " - " ASN B 78 " " NAG N 1 " - " ASN B 88 " " NAG O 1 " - " ASN B 98 " " NAG P 1 " - " ASN B 108 " " NAG Q 1 " - " ASN B 118 " " NAG R 1 " - " ASN B 166 " " NAG S 1 " - " ASN B 223 " " NAG T 1 " - " ASN C 78 " " NAG U 1 " - " ASN C 88 " " NAG V 1 " - " ASN C 98 " " NAG W 1 " - " ASN C 108 " " NAG X 1 " - " ASN C 118 " " NAG Y 1 " - " ASN C 166 " " NAG Z 1 " - " ASN C 223 " " NAG a 501 " - " ASN a 389 " " NAG a 502 " - " ASN a 394 " " NAG b 501 " - " ASN b 389 " " NAG b 502 " - " ASN b 394 " " NAG c 501 " - " ASN c 389 " " NAG c 502 " - " ASN c 394 " " NAG d 1 " - " ASN b 364 " " NAG e 1 " - " ASN b 372 " " NAG f 1 " - " ASN c 364 " " NAG g 1 " - " ASN c 372 " Time building additional restraints: 1.69 Conformation dependent library (CDL) restraints added in 362.2 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2040 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 9 sheets defined 41.0% alpha, 13.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 73 through 78 removed outlier: 3.680A pdb=" N THR A 76 " --> pdb=" O ASN A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 126 Processing helix chain 'A' and resid 129 through 142 Processing helix chain 'A' and resid 148 through 150 No H-bonds generated for 'chain 'A' and resid 148 through 150' Processing helix chain 'A' and resid 156 through 160 Processing helix chain 'A' and resid 181 through 194 Processing helix chain 'A' and resid 197 through 201 Processing helix chain 'A' and resid 237 through 245 Processing helix chain 'a' and resid 263 through 269 Processing helix chain 'a' and resid 293 through 298 Processing helix chain 'a' and resid 299 through 302 Processing helix chain 'a' and resid 306 through 324 Processing helix chain 'a' and resid 335 through 340 Processing helix chain 'a' and resid 341 through 343 No H-bonds generated for 'chain 'a' and resid 341 through 343' Processing helix chain 'a' and resid 345 through 358 removed outlier: 3.649A pdb=" N ILE a 349 " --> pdb=" O ASN a 345 " (cutoff:3.500A) Processing helix chain 'a' and resid 398 through 421 Processing helix chain 'B' and resid 73 through 78 removed outlier: 3.682A pdb=" N THR B 76 " --> pdb=" O ASN B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 126 Processing helix chain 'B' and resid 129 through 142 Processing helix chain 'B' and resid 148 through 150 No H-bonds generated for 'chain 'B' and resid 148 through 150' Processing helix chain 'B' and resid 156 through 160 Processing helix chain 'B' and resid 181 through 194 Processing helix chain 'B' and resid 197 through 201 Processing helix chain 'B' and resid 237 through 245 Processing helix chain 'C' and resid 73 through 78 removed outlier: 3.681A pdb=" N THR C 76 " --> pdb=" O ASN C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 126 Processing helix chain 'C' and resid 129 through 142 Processing helix chain 'C' and resid 148 through 150 No H-bonds generated for 'chain 'C' and resid 148 through 150' Processing helix chain 'C' and resid 156 through 160 Processing helix chain 'C' and resid 181 through 194 Processing helix chain 'C' and resid 197 through 201 Processing helix chain 'C' and resid 237 through 245 Processing helix chain 'b' and resid 263 through 269 Processing helix chain 'b' and resid 293 through 298 Processing helix chain 'b' and resid 299 through 302 Processing helix chain 'b' and resid 306 through 324 Processing helix chain 'b' and resid 335 through 340 Processing helix chain 'b' and resid 341 through 343 No H-bonds generated for 'chain 'b' and resid 341 through 343' Processing helix chain 'b' and resid 345 through 358 removed outlier: 3.648A pdb=" N ILE b 349 " --> pdb=" O ASN b 345 " (cutoff:3.500A) Processing helix chain 'b' and resid 398 through 421 Processing helix chain 'c' and resid 263 through 269 Processing helix chain 'c' and resid 293 through 298 Processing helix chain 'c' and resid 299 through 302 Processing helix chain 'c' and resid 306 through 324 Processing helix chain 'c' and resid 335 through 340 Processing helix chain 'c' and resid 341 through 343 No H-bonds generated for 'chain 'c' and resid 341 through 343' Processing helix chain 'c' and resid 345 through 358 removed outlier: 3.648A pdb=" N ILE c 349 " --> pdb=" O ASN c 345 " (cutoff:3.500A) Processing helix chain 'c' and resid 398 through 421 Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 61 Processing sheet with id=AA2, first strand: chain 'A' and resid 152 through 154 removed outlier: 6.854A pdb=" N HIS A 91 " --> pdb=" O LYS A 87 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N THR A 86 " --> pdb=" O ARG A 234 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N ARG A 234 " --> pdb=" O THR A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'a' and resid 387 through 388 Processing sheet with id=AA4, first strand: chain 'B' and resid 60 through 61 Processing sheet with id=AA5, first strand: chain 'B' and resid 152 through 154 removed outlier: 6.854A pdb=" N HIS B 91 " --> pdb=" O LYS B 87 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N THR B 86 " --> pdb=" O ARG B 234 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N ARG B 234 " --> pdb=" O THR B 86 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 60 through 61 Processing sheet with id=AA7, first strand: chain 'C' and resid 152 through 154 removed outlier: 6.854A pdb=" N HIS C 91 " --> pdb=" O LYS C 87 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N THR C 86 " --> pdb=" O ARG C 234 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N ARG C 234 " --> pdb=" O THR C 86 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'b' and resid 387 through 388 Processing sheet with id=AA9, first strand: chain 'c' and resid 387 through 388 378 hydrogen bonds defined for protein. 990 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: 1.65 Time building geometry restraints manager: 2.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 2577 1.33 - 1.47: 3187 1.47 - 1.60: 4251 1.60 - 1.74: 11 1.74 - 1.88: 132 Bond restraints: 10158 Sorted by residual: bond pdb=" NE1 TRP c 385 " pdb=" CE2 TRP c 385 " ideal model delta sigma weight residual 1.370 1.284 0.086 1.10e-02 8.26e+03 6.15e+01 bond pdb=" NE1 TRP a 385 " pdb=" CE2 TRP a 385 " ideal model delta sigma weight residual 1.370 1.284 0.086 1.10e-02 8.26e+03 6.15e+01 bond pdb=" NE1 TRP b 385 " pdb=" CE2 TRP b 385 " ideal model delta sigma weight residual 1.370 1.284 0.086 1.10e-02 8.26e+03 6.13e+01 bond pdb=" CB LEU A 59 " pdb=" CG LEU A 59 " ideal model delta sigma weight residual 1.530 1.668 -0.138 2.00e-02 2.50e+03 4.77e+01 bond pdb=" CB LEU C 59 " pdb=" CG LEU C 59 " ideal model delta sigma weight residual 1.530 1.668 -0.138 2.00e-02 2.50e+03 4.75e+01 ... (remaining 10153 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.42: 13719 7.42 - 14.84: 30 14.84 - 22.26: 3 22.26 - 29.67: 0 29.67 - 37.09: 3 Bond angle restraints: 13755 Sorted by residual: angle pdb=" C2 NAG b 502 " pdb=" N2 NAG b 502 " pdb=" C7 NAG b 502 " ideal model delta sigma weight residual 124.56 161.65 -37.09 3.00e+00 1.11e-01 1.53e+02 angle pdb=" C2 NAG c 502 " pdb=" N2 NAG c 502 " pdb=" C7 NAG c 502 " ideal model delta sigma weight residual 124.56 161.59 -37.03 3.00e+00 1.11e-01 1.52e+02 angle pdb=" C2 NAG a 502 " pdb=" N2 NAG a 502 " pdb=" C7 NAG a 502 " ideal model delta sigma weight residual 124.56 161.59 -37.03 3.00e+00 1.11e-01 1.52e+02 angle pdb=" CA PHE a 398 " pdb=" CB PHE a 398 " pdb=" CG PHE a 398 " ideal model delta sigma weight residual 113.80 122.30 -8.50 1.00e+00 1.00e+00 7.23e+01 angle pdb=" CA PHE b 398 " pdb=" CB PHE b 398 " pdb=" CG PHE b 398 " ideal model delta sigma weight residual 113.80 122.30 -8.50 1.00e+00 1.00e+00 7.22e+01 ... (remaining 13750 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.44: 6813 21.44 - 42.88: 264 42.88 - 64.33: 79 64.33 - 85.77: 134 85.77 - 107.21: 84 Dihedral angle restraints: 7374 sinusoidal: 4200 harmonic: 3174 Sorted by residual: dihedral pdb=" C PHE a 398 " pdb=" N PHE a 398 " pdb=" CA PHE a 398 " pdb=" CB PHE a 398 " ideal model delta harmonic sigma weight residual -122.60 -111.92 -10.68 0 2.50e+00 1.60e-01 1.83e+01 dihedral pdb=" C PHE b 398 " pdb=" N PHE b 398 " pdb=" CA PHE b 398 " pdb=" CB PHE b 398 " ideal model delta harmonic sigma weight residual -122.60 -111.94 -10.66 0 2.50e+00 1.60e-01 1.82e+01 dihedral pdb=" C PHE c 398 " pdb=" N PHE c 398 " pdb=" CA PHE c 398 " pdb=" CB PHE c 398 " ideal model delta harmonic sigma weight residual -122.60 -111.95 -10.65 0 2.50e+00 1.60e-01 1.82e+01 ... (remaining 7371 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.108: 1047 0.108 - 0.216: 410 0.216 - 0.325: 211 0.325 - 0.433: 100 0.433 - 0.541: 44 Chirality restraints: 1812 Sorted by residual: chirality pdb=" C1 NAG V 2 " pdb=" O4 NAG V 1 " pdb=" C2 NAG V 2 " pdb=" O5 NAG V 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.65 0.25 2.00e-02 2.50e+03 1.61e+02 chirality pdb=" C1 NAG O 2 " pdb=" O4 NAG O 1 " pdb=" C2 NAG O 2 " pdb=" O5 NAG O 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.65 0.25 2.00e-02 2.50e+03 1.59e+02 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.65 0.25 2.00e-02 2.50e+03 1.58e+02 ... (remaining 1809 not shown) Planarity restraints: 1629 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 98 " -0.038 2.00e-02 2.50e+03 4.19e-02 2.19e+01 pdb=" CG ASN C 98 " 0.013 2.00e-02 2.50e+03 pdb=" OD1 ASN C 98 " 0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN C 98 " 0.067 2.00e-02 2.50e+03 pdb=" C1 NAG V 1 " -0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 98 " -0.038 2.00e-02 2.50e+03 4.19e-02 2.19e+01 pdb=" CG ASN A 98 " 0.013 2.00e-02 2.50e+03 pdb=" OD1 ASN A 98 " 0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN A 98 " 0.068 2.00e-02 2.50e+03 pdb=" C1 NAG F 1 " -0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 98 " -0.038 2.00e-02 2.50e+03 4.18e-02 2.18e+01 pdb=" CG ASN B 98 " 0.013 2.00e-02 2.50e+03 pdb=" OD1 ASN B 98 " 0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN B 98 " 0.067 2.00e-02 2.50e+03 pdb=" C1 NAG O 1 " -0.050 2.00e-02 2.50e+03 ... (remaining 1626 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.66: 303 2.66 - 3.22: 9737 3.22 - 3.78: 15061 3.78 - 4.34: 21516 4.34 - 4.90: 33333 Nonbonded interactions: 79950 Sorted by model distance: nonbonded pdb=" NH1 ARG a 378 " pdb=" O THR a 379 " model vdw 2.106 3.120 nonbonded pdb=" NH1 ARG b 378 " pdb=" O THR b 379 " model vdw 2.107 3.120 nonbonded pdb=" NH1 ARG c 378 " pdb=" O THR c 379 " model vdw 2.109 3.120 nonbonded pdb=" N HIS c 397 " pdb=" O HIS c 397 " model vdw 2.286 2.496 nonbonded pdb=" N HIS a 397 " pdb=" O HIS a 397 " model vdw 2.286 2.496 ... (remaining 79945 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'M' selection = chain 'T' } ncs_group { reference = (chain 'E' and resid 1 through 2) selection = (chain 'G' and resid 1 through 2) selection = (chain 'H' and resid 1 through 2) selection = (chain 'I' and resid 1 through 2) selection = (chain 'J' and resid 1 through 2) selection = (chain 'L' and resid 1 through 2) selection = (chain 'N' and resid 1 through 2) selection = (chain 'P' and resid 1 through 2) selection = (chain 'Q' and resid 1 through 2) selection = (chain 'R' and resid 1 through 2) selection = (chain 'S' and resid 1 through 2) selection = (chain 'U' and resid 1 through 2) selection = (chain 'W' and resid 1 through 2) selection = (chain 'X' and resid 1 through 2) selection = (chain 'Y' and resid 1 through 2) selection = (chain 'Z' and resid 1 through 2) selection = (chain 'e' and resid 1 through 2) selection = (chain 'g' and resid 1 through 2) } ncs_group { reference = chain 'F' selection = chain 'O' selection = chain 'V' } ncs_group { reference = chain 'K' selection = chain 'd' selection = chain 'f' } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.530 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.960 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.020 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 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 : 0.026 0.138 10281 Z= 1.388 Angle : 2.059 37.092 14103 Z= 1.161 Chirality : 0.172 0.541 1812 Planarity : 0.009 0.051 1596 Dihedral : 20.946 107.210 5271 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 0.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Cbeta Deviations : 0.29 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.09 (0.24), residues: 1071 helix: -1.09 (0.22), residues: 423 sheet: 1.26 (0.50), residues: 102 loop : -0.71 (0.26), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 95 TYR 0.055 0.008 TYR A 240 PHE 0.024 0.006 PHE b 261 TRP 0.027 0.007 TRP A 226 HIS 0.008 0.002 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.02537 (10158) covalent geometry : angle 1.94434 (13755) SS BOND : bond 0.04909 ( 21) SS BOND : angle 3.77771 ( 42) hydrogen bonds : bond 0.16477 ( 378) hydrogen bonds : angle 7.06040 ( 990) link_ALPHA1-2 : bond 0.07660 ( 3) link_ALPHA1-2 : angle 4.26510 ( 9) link_ALPHA1-3 : bond 0.07983 ( 9) link_ALPHA1-3 : angle 4.50889 ( 27) link_ALPHA1-6 : bond 0.05259 ( 6) link_ALPHA1-6 : angle 3.46290 ( 18) link_BETA1-4 : bond 0.07505 ( 51) link_BETA1-4 : angle 6.04600 ( 153) link_NAG-ASN : bond 0.07530 ( 33) link_NAG-ASN : angle 2.60422 ( 99) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 322 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 305 ASP cc_start: 0.6570 (p0) cc_final: 0.6359 (p0) REVERT: a 330 GLN cc_start: 0.7109 (mp10) cc_final: 0.6559 (pp30) REVERT: b 305 ASP cc_start: 0.6440 (p0) cc_final: 0.6091 (p0) REVERT: c 305 ASP cc_start: 0.6753 (p0) cc_final: 0.6429 (p0) outliers start: 0 outliers final: 0 residues processed: 322 average time/residue: 0.1348 time to fit residues: 57.2026 Evaluate side-chains 180 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 49 optimal weight: 7.9990 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 HIS A 222 GLN a 304 HIS ** a 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 341 ASN ** a 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 HIS C 91 HIS b 304 HIS b 404 GLN c 304 HIS c 347 GLN c 404 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.090409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.064637 restraints weight = 28063.177| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 4.33 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.3533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 10281 Z= 0.219 Angle : 1.131 19.172 14103 Z= 0.498 Chirality : 0.056 0.412 1812 Planarity : 0.005 0.039 1596 Dihedral : 17.643 85.809 3228 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.98 % Favored : 93.84 % Rotamer: Outliers : 2.17 % Allowed : 11.80 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.72 (0.25), residues: 1071 helix: -0.31 (0.25), residues: 426 sheet: 1.62 (0.50), residues: 120 loop : -1.08 (0.27), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG c 378 TYR 0.021 0.002 TYR c 277 PHE 0.022 0.002 PHE b 261 TRP 0.022 0.002 TRP c 263 HIS 0.006 0.002 HIS B 123 Details of bonding type rmsd covalent geometry : bond 0.00433 (10158) covalent geometry : angle 0.97292 (13755) SS BOND : bond 0.00441 ( 21) SS BOND : angle 1.56661 ( 42) hydrogen bonds : bond 0.05555 ( 378) hydrogen bonds : angle 5.25120 ( 990) link_ALPHA1-2 : bond 0.00287 ( 3) link_ALPHA1-2 : angle 1.81307 ( 9) link_ALPHA1-3 : bond 0.01549 ( 9) link_ALPHA1-3 : angle 1.32438 ( 27) link_ALPHA1-6 : bond 0.00586 ( 6) link_ALPHA1-6 : angle 1.71457 ( 18) link_BETA1-4 : bond 0.01906 ( 51) link_BETA1-4 : angle 5.12288 ( 153) link_NAG-ASN : bond 0.00697 ( 33) link_NAG-ASN : angle 2.78048 ( 99) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 217 time to evaluate : 0.499 Fit side-chains revert: symmetry clash REVERT: A 99 GLU cc_start: 0.8241 (tp30) cc_final: 0.7743 (mm-30) REVERT: A 152 MET cc_start: 0.7992 (ttt) cc_final: 0.7683 (ttt) REVERT: A 178 HIS cc_start: 0.8024 (p90) cc_final: 0.7640 (p90) REVERT: a 330 GLN cc_start: 0.7665 (mp10) cc_final: 0.7426 (pp30) REVERT: a 355 ARG cc_start: 0.8560 (mtt180) cc_final: 0.8327 (mtt180) REVERT: B 62 LYS cc_start: 0.9217 (mmmm) cc_final: 0.9007 (mmmm) REVERT: B 94 ILE cc_start: 0.9059 (mt) cc_final: 0.8846 (tt) REVERT: B 133 MET cc_start: 0.9241 (tpt) cc_final: 0.9027 (tpt) REVERT: C 94 ILE cc_start: 0.8963 (mt) cc_final: 0.8729 (tt) REVERT: C 99 GLU cc_start: 0.8406 (tp30) cc_final: 0.8150 (mm-30) REVERT: C 193 MET cc_start: 0.8801 (mmm) cc_final: 0.8523 (tpp) REVERT: C 227 GLU cc_start: 0.7949 (mm-30) cc_final: 0.7734 (mm-30) REVERT: b 326 LYS cc_start: 0.8001 (tppt) cc_final: 0.7658 (tppt) REVERT: b 341 ASN cc_start: 0.9182 (m-40) cc_final: 0.8761 (m-40) REVERT: b 404 GLN cc_start: 0.8693 (tp40) cc_final: 0.8420 (tp-100) REVERT: c 305 ASP cc_start: 0.7567 (p0) cc_final: 0.7266 (p0) REVERT: c 378 ARG cc_start: 0.7961 (ttm-80) cc_final: 0.7597 (ttm-80) REVERT: c 401 ASP cc_start: 0.8953 (m-30) cc_final: 0.8743 (m-30) REVERT: c 407 ASP cc_start: 0.8656 (m-30) cc_final: 0.8370 (m-30) outliers start: 21 outliers final: 9 residues processed: 231 average time/residue: 0.1156 time to fit residues: 36.8218 Evaluate side-chains 186 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 177 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain a residue 341 ASN Chi-restraints excluded: chain a residue 398 PHE Chi-restraints excluded: chain B residue 211 CYS Chi-restraints excluded: chain C residue 211 CYS Chi-restraints excluded: chain b residue 288 GLU Chi-restraints excluded: chain b residue 375 SER Chi-restraints excluded: chain b residue 398 PHE Chi-restraints excluded: chain c residue 375 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 87 optimal weight: 0.9990 chunk 60 optimal weight: 0.0070 chunk 54 optimal weight: 6.9990 chunk 69 optimal weight: 5.9990 chunk 35 optimal weight: 6.9990 chunk 79 optimal weight: 1.9990 chunk 4 optimal weight: 7.9990 chunk 9 optimal weight: 2.9990 chunk 11 optimal weight: 30.0000 chunk 29 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 overall best weight: 1.2006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 145 ASN ** B 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 145 ASN ** C 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 422 GLN c 422 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.090136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.064425 restraints weight = 28443.926| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 4.37 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.4117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10281 Z= 0.189 Angle : 1.016 18.434 14103 Z= 0.438 Chirality : 0.053 0.398 1812 Planarity : 0.004 0.053 1596 Dihedral : 13.929 74.534 3228 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.66 % Favored : 92.06 % Rotamer: Outliers : 3.11 % Allowed : 13.15 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.75 (0.25), residues: 1071 helix: 0.00 (0.25), residues: 414 sheet: 2.41 (0.53), residues: 96 loop : -1.45 (0.25), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG c 421 TYR 0.013 0.001 TYR A 149 PHE 0.017 0.002 PHE b 398 TRP 0.017 0.001 TRP a 263 HIS 0.006 0.001 HIS B 92 Details of bonding type rmsd covalent geometry : bond 0.00372 (10158) covalent geometry : angle 0.86102 (13755) SS BOND : bond 0.00587 ( 21) SS BOND : angle 1.62039 ( 42) hydrogen bonds : bond 0.04531 ( 378) hydrogen bonds : angle 5.13678 ( 990) link_ALPHA1-2 : bond 0.00213 ( 3) link_ALPHA1-2 : angle 1.69427 ( 9) link_ALPHA1-3 : bond 0.01468 ( 9) link_ALPHA1-3 : angle 1.32648 ( 27) link_ALPHA1-6 : bond 0.00901 ( 6) link_ALPHA1-6 : angle 1.58354 ( 18) link_BETA1-4 : bond 0.01787 ( 51) link_BETA1-4 : angle 4.69326 ( 153) link_NAG-ASN : bond 0.00611 ( 33) link_NAG-ASN : angle 2.76287 ( 99) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 199 time to evaluate : 0.415 Fit side-chains REVERT: A 99 GLU cc_start: 0.8237 (tp30) cc_final: 0.7723 (mm-30) REVERT: A 155 ASP cc_start: 0.8426 (p0) cc_final: 0.7987 (p0) REVERT: A 178 HIS cc_start: 0.8018 (p90) cc_final: 0.7646 (p90) REVERT: A 188 GLN cc_start: 0.8702 (mm-40) cc_final: 0.8420 (mm-40) REVERT: a 323 GLN cc_start: 0.8081 (tm-30) cc_final: 0.7830 (tm-30) REVERT: a 400 ASP cc_start: 0.8332 (p0) cc_final: 0.7878 (p0) REVERT: B 79 MET cc_start: 0.8534 (mmm) cc_final: 0.8136 (mmm) REVERT: B 99 GLU cc_start: 0.8426 (tp30) cc_final: 0.8099 (mm-30) REVERT: B 133 MET cc_start: 0.9254 (OUTLIER) cc_final: 0.9015 (tpt) REVERT: B 249 ARG cc_start: 0.7032 (ttm-80) cc_final: 0.6493 (mtm-85) REVERT: C 94 ILE cc_start: 0.8964 (mt) cc_final: 0.8689 (tt) REVERT: C 99 GLU cc_start: 0.8479 (tp30) cc_final: 0.8193 (mm-30) REVERT: C 193 MET cc_start: 0.8757 (mmm) cc_final: 0.8348 (tpp) REVERT: C 213 MET cc_start: 0.8032 (mmt) cc_final: 0.7686 (mmp) REVERT: C 227 GLU cc_start: 0.8004 (mm-30) cc_final: 0.7744 (mm-30) REVERT: C 246 GLN cc_start: 0.7928 (pp30) cc_final: 0.7646 (pp30) REVERT: b 341 ASN cc_start: 0.9233 (m-40) cc_final: 0.8857 (m-40) REVERT: b 404 GLN cc_start: 0.8864 (tp40) cc_final: 0.8401 (tp-100) REVERT: c 305 ASP cc_start: 0.7432 (p0) cc_final: 0.7165 (p0) REVERT: c 330 GLN cc_start: 0.8852 (mp10) cc_final: 0.8476 (mp10) REVERT: c 331 MET cc_start: 0.6693 (mmp) cc_final: 0.6354 (mmp) REVERT: c 378 ARG cc_start: 0.8141 (ttm-80) cc_final: 0.7912 (ttm-80) REVERT: c 400 ASP cc_start: 0.8717 (p0) cc_final: 0.8318 (p0) REVERT: c 409 MET cc_start: 0.8442 (mtp) cc_final: 0.8133 (mtp) outliers start: 30 outliers final: 13 residues processed: 220 average time/residue: 0.1109 time to fit residues: 33.8412 Evaluate side-chains 190 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 176 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain a residue 322 ILE Chi-restraints excluded: chain a residue 398 PHE Chi-restraints excluded: chain B residue 133 MET Chi-restraints excluded: chain B residue 211 CYS Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain C residue 211 CYS Chi-restraints excluded: chain b residue 288 GLU Chi-restraints excluded: chain b residue 332 SER Chi-restraints excluded: chain b residue 375 SER Chi-restraints excluded: chain c residue 322 ILE Chi-restraints excluded: chain c residue 341 ASN Chi-restraints excluded: chain c residue 375 SER Chi-restraints excluded: chain c residue 398 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 71 optimal weight: 8.9990 chunk 56 optimal weight: 10.0000 chunk 1 optimal weight: 0.0010 chunk 67 optimal weight: 5.9990 chunk 77 optimal weight: 9.9990 chunk 13 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 82 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 27 optimal weight: 10.0000 chunk 38 optimal weight: 6.9990 overall best weight: 4.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 HIS A 169 HIS ** a 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 422 GLN B 140 HIS B 145 ASN ** B 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 145 ASN ** C 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 GLN ** b 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.085973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.059911 restraints weight = 29255.090| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 4.34 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.4681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 10281 Z= 0.324 Angle : 1.068 18.198 14103 Z= 0.469 Chirality : 0.055 0.377 1812 Planarity : 0.005 0.065 1596 Dihedral : 11.436 67.094 3228 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.28 % Allowed : 8.87 % Favored : 90.85 % Rotamer: Outliers : 3.31 % Allowed : 14.70 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.14 (0.24), residues: 1071 helix: -0.17 (0.25), residues: 408 sheet: 1.67 (0.51), residues: 96 loop : -1.69 (0.24), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 192 TYR 0.013 0.002 TYR a 277 PHE 0.020 0.002 PHE b 398 TRP 0.019 0.002 TRP a 385 HIS 0.007 0.002 HIS b 397 Details of bonding type rmsd covalent geometry : bond 0.00695 (10158) covalent geometry : angle 0.92449 (13755) SS BOND : bond 0.00629 ( 21) SS BOND : angle 1.58480 ( 42) hydrogen bonds : bond 0.04944 ( 378) hydrogen bonds : angle 5.04145 ( 990) link_ALPHA1-2 : bond 0.00208 ( 3) link_ALPHA1-2 : angle 1.80804 ( 9) link_ALPHA1-3 : bond 0.01184 ( 9) link_ALPHA1-3 : angle 1.61012 ( 27) link_ALPHA1-6 : bond 0.00944 ( 6) link_ALPHA1-6 : angle 2.04564 ( 18) link_BETA1-4 : bond 0.01709 ( 51) link_BETA1-4 : angle 4.63409 ( 153) link_NAG-ASN : bond 0.00794 ( 33) link_NAG-ASN : angle 2.76141 ( 99) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 193 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 GLU cc_start: 0.8408 (tp30) cc_final: 0.7845 (mm-30) REVERT: A 188 GLN cc_start: 0.8639 (mm-40) cc_final: 0.8222 (mm-40) REVERT: a 323 GLN cc_start: 0.8344 (tm-30) cc_final: 0.7980 (tm-30) REVERT: a 326 LYS cc_start: 0.8378 (tppt) cc_final: 0.8138 (tptp) REVERT: a 331 MET cc_start: 0.7241 (tmm) cc_final: 0.6226 (tmm) REVERT: a 346 ASP cc_start: 0.9118 (p0) cc_final: 0.8882 (p0) REVERT: a 400 ASP cc_start: 0.8530 (p0) cc_final: 0.8225 (p0) REVERT: a 418 TYR cc_start: 0.5458 (t80) cc_final: 0.5080 (t80) REVERT: B 124 LYS cc_start: 0.8854 (mtmm) cc_final: 0.8637 (mtmm) REVERT: B 227 GLU cc_start: 0.7910 (mm-30) cc_final: 0.7696 (mm-30) REVERT: C 94 ILE cc_start: 0.9096 (mt) cc_final: 0.8728 (tt) REVERT: C 99 GLU cc_start: 0.8495 (tp30) cc_final: 0.8190 (mm-30) REVERT: C 150 GLU cc_start: 0.8464 (pm20) cc_final: 0.8247 (tm-30) REVERT: C 193 MET cc_start: 0.8915 (mmm) cc_final: 0.8524 (tpp) REVERT: C 227 GLU cc_start: 0.8102 (mm-30) cc_final: 0.7782 (mm-30) REVERT: C 246 GLN cc_start: 0.7841 (OUTLIER) cc_final: 0.7490 (pp30) REVERT: b 326 LYS cc_start: 0.8309 (tppt) cc_final: 0.8084 (tppt) REVERT: b 341 ASN cc_start: 0.9292 (m-40) cc_final: 0.8930 (m-40) REVERT: b 400 ASP cc_start: 0.8779 (p0) cc_final: 0.8506 (p0) REVERT: b 404 GLN cc_start: 0.8970 (tp40) cc_final: 0.8493 (tp-100) REVERT: c 330 GLN cc_start: 0.8822 (mp10) cc_final: 0.8491 (mp10) REVERT: c 338 LYS cc_start: 0.9194 (mtmm) cc_final: 0.8849 (mptt) REVERT: c 400 ASP cc_start: 0.8872 (p0) cc_final: 0.8609 (p0) REVERT: c 401 ASP cc_start: 0.8925 (m-30) cc_final: 0.8657 (m-30) REVERT: c 409 MET cc_start: 0.8475 (mtp) cc_final: 0.8236 (mtp) outliers start: 32 outliers final: 23 residues processed: 211 average time/residue: 0.1155 time to fit residues: 33.5698 Evaluate side-chains 197 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 173 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain a residue 295 THR Chi-restraints excluded: chain a residue 322 ILE Chi-restraints excluded: chain a residue 375 SER Chi-restraints excluded: chain a residue 398 PHE Chi-restraints excluded: chain a residue 420 ASP Chi-restraints excluded: chain B residue 145 ASN Chi-restraints excluded: chain B residue 211 CYS Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain C residue 178 HIS Chi-restraints excluded: chain C residue 211 CYS Chi-restraints excluded: chain C residue 246 GLN Chi-restraints excluded: chain b residue 347 GLN Chi-restraints excluded: chain b residue 348 LEU Chi-restraints excluded: chain b residue 375 SER Chi-restraints excluded: chain b residue 398 PHE Chi-restraints excluded: chain c residue 295 THR Chi-restraints excluded: chain c residue 322 ILE Chi-restraints excluded: chain c residue 341 ASN Chi-restraints excluded: chain c residue 348 LEU Chi-restraints excluded: chain c residue 375 SER Chi-restraints excluded: chain c residue 398 PHE Chi-restraints excluded: chain c residue 420 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 84 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 72 optimal weight: 0.6980 chunk 5 optimal weight: 8.9990 chunk 63 optimal weight: 5.9990 chunk 15 optimal weight: 0.9990 chunk 86 optimal weight: 5.9990 chunk 46 optimal weight: 30.0000 chunk 10 optimal weight: 3.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 145 ASN B 178 HIS C 169 HIS ** b 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.087968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.061944 restraints weight = 28621.223| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 4.36 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.4904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 10281 Z= 0.172 Angle : 0.937 18.151 14103 Z= 0.408 Chirality : 0.050 0.375 1812 Planarity : 0.004 0.042 1596 Dihedral : 10.441 61.985 3228 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.28 % Allowed : 8.31 % Favored : 91.41 % Rotamer: Outliers : 2.59 % Allowed : 16.15 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.92 (0.25), residues: 1071 helix: 0.13 (0.26), residues: 417 sheet: 1.53 (0.52), residues: 96 loop : -1.62 (0.25), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 125 TYR 0.015 0.001 TYR B 65 PHE 0.016 0.002 PHE b 398 TRP 0.016 0.001 TRP a 263 HIS 0.004 0.001 HIS A 123 Details of bonding type rmsd covalent geometry : bond 0.00333 (10158) covalent geometry : angle 0.79367 (13755) SS BOND : bond 0.00445 ( 21) SS BOND : angle 1.21163 ( 42) hydrogen bonds : bond 0.04123 ( 378) hydrogen bonds : angle 4.90602 ( 990) link_ALPHA1-2 : bond 0.00058 ( 3) link_ALPHA1-2 : angle 1.94625 ( 9) link_ALPHA1-3 : bond 0.01448 ( 9) link_ALPHA1-3 : angle 1.56859 ( 27) link_ALPHA1-6 : bond 0.01132 ( 6) link_ALPHA1-6 : angle 1.74109 ( 18) link_BETA1-4 : bond 0.01734 ( 51) link_BETA1-4 : angle 4.37784 ( 153) link_NAG-ASN : bond 0.00361 ( 33) link_NAG-ASN : angle 2.42134 ( 99) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 185 time to evaluate : 0.384 Fit side-chains revert: symmetry clash REVERT: A 99 GLU cc_start: 0.8332 (tp30) cc_final: 0.7811 (mm-30) REVERT: A 188 GLN cc_start: 0.8622 (mm-40) cc_final: 0.8250 (mm-40) REVERT: a 323 GLN cc_start: 0.8385 (tm-30) cc_final: 0.8114 (tm-30) REVERT: a 331 MET cc_start: 0.7212 (tmm) cc_final: 0.6091 (tmm) REVERT: a 346 ASP cc_start: 0.9130 (p0) cc_final: 0.8842 (p0) REVERT: a 400 ASP cc_start: 0.8550 (p0) cc_final: 0.8259 (p0) REVERT: B 99 GLU cc_start: 0.8483 (tp30) cc_final: 0.8144 (mm-30) REVERT: B 124 LYS cc_start: 0.8900 (mtmm) cc_final: 0.8661 (mtmm) REVERT: B 227 GLU cc_start: 0.7906 (mm-30) cc_final: 0.7641 (mm-30) REVERT: C 94 ILE cc_start: 0.8974 (mt) cc_final: 0.8650 (tt) REVERT: C 99 GLU cc_start: 0.8460 (tp30) cc_final: 0.8175 (mm-30) REVERT: C 142 SER cc_start: 0.9113 (OUTLIER) cc_final: 0.8607 (p) REVERT: C 178 HIS cc_start: 0.7983 (p90) cc_final: 0.7687 (p90) REVERT: C 193 MET cc_start: 0.8851 (mmm) cc_final: 0.8488 (tpp) REVERT: C 213 MET cc_start: 0.7836 (mmt) cc_final: 0.7404 (mmp) REVERT: C 227 GLU cc_start: 0.8139 (mm-30) cc_final: 0.7832 (mm-30) REVERT: b 341 ASN cc_start: 0.9152 (m-40) cc_final: 0.8818 (m-40) REVERT: b 400 ASP cc_start: 0.8688 (p0) cc_final: 0.8479 (p0) REVERT: b 404 GLN cc_start: 0.8984 (tp40) cc_final: 0.8498 (tp-100) REVERT: b 418 TYR cc_start: 0.5549 (t80) cc_final: 0.5294 (t80) REVERT: c 326 LYS cc_start: 0.8406 (tppt) cc_final: 0.7751 (tppt) REVERT: c 338 LYS cc_start: 0.9167 (mtmm) cc_final: 0.8776 (mptt) REVERT: c 400 ASP cc_start: 0.8796 (p0) cc_final: 0.8380 (p0) REVERT: c 401 ASP cc_start: 0.8899 (m-30) cc_final: 0.8559 (m-30) REVERT: c 409 MET cc_start: 0.8394 (mtp) cc_final: 0.7971 (mtp) outliers start: 25 outliers final: 15 residues processed: 200 average time/residue: 0.1174 time to fit residues: 32.3418 Evaluate side-chains 186 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 170 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain a residue 303 LYS Chi-restraints excluded: chain a residue 322 ILE Chi-restraints excluded: chain a residue 398 PHE Chi-restraints excluded: chain B residue 211 CYS Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain C residue 211 CYS Chi-restraints excluded: chain b residue 323 GLN Chi-restraints excluded: chain b residue 332 SER Chi-restraints excluded: chain b residue 398 PHE Chi-restraints excluded: chain c residue 322 ILE Chi-restraints excluded: chain c residue 341 ASN Chi-restraints excluded: chain c residue 375 SER Chi-restraints excluded: chain c residue 398 PHE Chi-restraints excluded: chain c residue 420 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 99 optimal weight: 0.9980 chunk 68 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 31 optimal weight: 9.9990 chunk 3 optimal weight: 0.9980 chunk 102 optimal weight: 2.9990 chunk 73 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 145 ASN B 169 HIS B 178 HIS C 140 HIS C 169 HIS c 330 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.088252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.062495 restraints weight = 28818.904| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 4.37 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.5106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10281 Z= 0.166 Angle : 0.915 18.034 14103 Z= 0.398 Chirality : 0.050 0.369 1812 Planarity : 0.004 0.042 1596 Dihedral : 9.719 57.383 3228 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.28 % Allowed : 8.12 % Favored : 91.60 % Rotamer: Outliers : 2.59 % Allowed : 17.08 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.85 (0.25), residues: 1071 helix: 0.26 (0.26), residues: 417 sheet: 1.44 (0.52), residues: 96 loop : -1.63 (0.25), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG b 421 TYR 0.014 0.001 TYR B 65 PHE 0.016 0.001 PHE b 398 TRP 0.015 0.001 TRP c 263 HIS 0.004 0.001 HIS C 123 Details of bonding type rmsd covalent geometry : bond 0.00316 (10158) covalent geometry : angle 0.77230 (13755) SS BOND : bond 0.00435 ( 21) SS BOND : angle 1.22261 ( 42) hydrogen bonds : bond 0.03924 ( 378) hydrogen bonds : angle 4.70500 ( 990) link_ALPHA1-2 : bond 0.00071 ( 3) link_ALPHA1-2 : angle 1.87352 ( 9) link_ALPHA1-3 : bond 0.01474 ( 9) link_ALPHA1-3 : angle 1.60987 ( 27) link_ALPHA1-6 : bond 0.01220 ( 6) link_ALPHA1-6 : angle 1.76955 ( 18) link_BETA1-4 : bond 0.01718 ( 51) link_BETA1-4 : angle 4.26897 ( 153) link_NAG-ASN : bond 0.00304 ( 33) link_NAG-ASN : angle 2.44483 ( 99) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 193 time to evaluate : 0.360 Fit side-chains revert: symmetry clash REVERT: A 99 GLU cc_start: 0.8361 (tp30) cc_final: 0.7845 (mm-30) REVERT: A 188 GLN cc_start: 0.8617 (mm-40) cc_final: 0.8241 (mm-40) REVERT: A 192 ARG cc_start: 0.8861 (mtp85) cc_final: 0.8631 (mtp85) REVERT: a 331 MET cc_start: 0.7359 (tmm) cc_final: 0.6211 (tmm) REVERT: a 346 ASP cc_start: 0.9116 (p0) cc_final: 0.8766 (p0) REVERT: a 400 ASP cc_start: 0.8507 (p0) cc_final: 0.8039 (p0) REVERT: B 74 MET cc_start: 0.8923 (mmt) cc_final: 0.8574 (mmm) REVERT: B 99 GLU cc_start: 0.8520 (tp30) cc_final: 0.8156 (mm-30) REVERT: B 156 PHE cc_start: 0.9163 (m-80) cc_final: 0.8903 (m-80) REVERT: B 188 GLN cc_start: 0.8864 (mm-40) cc_final: 0.8534 (mm-40) REVERT: B 227 GLU cc_start: 0.7885 (mm-30) cc_final: 0.7613 (mm-30) REVERT: C 94 ILE cc_start: 0.8979 (mt) cc_final: 0.8681 (tt) REVERT: C 99 GLU cc_start: 0.8467 (tp30) cc_final: 0.8037 (mm-30) REVERT: C 142 SER cc_start: 0.9086 (OUTLIER) cc_final: 0.8603 (p) REVERT: C 178 HIS cc_start: 0.8028 (p90) cc_final: 0.7626 (p90) REVERT: C 193 MET cc_start: 0.8818 (mmm) cc_final: 0.8459 (tpp) REVERT: C 213 MET cc_start: 0.7703 (mmt) cc_final: 0.7365 (mmp) REVERT: C 227 GLU cc_start: 0.8178 (mm-30) cc_final: 0.7860 (mm-30) REVERT: C 246 GLN cc_start: 0.7607 (pp30) cc_final: 0.7332 (pp30) REVERT: C 249 ARG cc_start: 0.6389 (mtt90) cc_final: 0.6126 (mtt90) REVERT: b 341 ASN cc_start: 0.9157 (m-40) cc_final: 0.8839 (m-40) REVERT: b 400 ASP cc_start: 0.8676 (p0) cc_final: 0.8471 (p0) REVERT: b 404 GLN cc_start: 0.8946 (tp40) cc_final: 0.8496 (tp-100) REVERT: b 418 TYR cc_start: 0.5845 (t80) cc_final: 0.5643 (t80) REVERT: c 326 LYS cc_start: 0.8498 (tppt) cc_final: 0.8278 (tppt) REVERT: c 330 GLN cc_start: 0.8741 (mm110) cc_final: 0.8473 (mm110) REVERT: c 338 LYS cc_start: 0.9159 (mtmm) cc_final: 0.8744 (mptt) REVERT: c 400 ASP cc_start: 0.8756 (p0) cc_final: 0.8214 (p0) REVERT: c 401 ASP cc_start: 0.8972 (m-30) cc_final: 0.8574 (m-30) REVERT: c 409 MET cc_start: 0.8439 (mtp) cc_final: 0.8149 (mtp) outliers start: 25 outliers final: 16 residues processed: 207 average time/residue: 0.1163 time to fit residues: 32.8448 Evaluate side-chains 190 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 173 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain a residue 303 LYS Chi-restraints excluded: chain a residue 304 HIS Chi-restraints excluded: chain a residue 322 ILE Chi-restraints excluded: chain a residue 341 ASN Chi-restraints excluded: chain B residue 213 MET Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain C residue 211 CYS Chi-restraints excluded: chain b residue 323 GLN Chi-restraints excluded: chain b residue 332 SER Chi-restraints excluded: chain c residue 295 THR Chi-restraints excluded: chain c residue 341 ASN Chi-restraints excluded: chain c residue 375 SER Chi-restraints excluded: chain c residue 398 PHE Chi-restraints excluded: chain c residue 420 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 13 optimal weight: 5.9990 chunk 6 optimal weight: 7.9990 chunk 102 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 69 optimal weight: 0.0670 chunk 12 optimal weight: 4.9990 chunk 18 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 61 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 overall best weight: 2.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN B 178 HIS C 169 HIS b 373 HIS ** c 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 373 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.086827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.060913 restraints weight = 28925.368| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 4.37 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.5267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 10281 Z= 0.232 Angle : 0.973 17.949 14103 Z= 0.432 Chirality : 0.051 0.370 1812 Planarity : 0.004 0.042 1596 Dihedral : 9.412 56.389 3228 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.28 % Allowed : 9.15 % Favored : 90.57 % Rotamer: Outliers : 3.73 % Allowed : 16.87 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.99 (0.25), residues: 1071 helix: 0.23 (0.26), residues: 411 sheet: 0.69 (0.51), residues: 114 loop : -1.70 (0.26), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 192 TYR 0.018 0.001 TYR B 65 PHE 0.030 0.002 PHE C 116 TRP 0.010 0.001 TRP a 263 HIS 0.005 0.001 HIS A 123 Details of bonding type rmsd covalent geometry : bond 0.00487 (10158) covalent geometry : angle 0.83647 (13755) SS BOND : bond 0.00801 ( 21) SS BOND : angle 2.15080 ( 42) hydrogen bonds : bond 0.04145 ( 378) hydrogen bonds : angle 4.70918 ( 990) link_ALPHA1-2 : bond 0.00129 ( 3) link_ALPHA1-2 : angle 1.86170 ( 9) link_ALPHA1-3 : bond 0.01341 ( 9) link_ALPHA1-3 : angle 1.73612 ( 27) link_ALPHA1-6 : bond 0.01173 ( 6) link_ALPHA1-6 : angle 1.95434 ( 18) link_BETA1-4 : bond 0.01662 ( 51) link_BETA1-4 : angle 4.24259 ( 153) link_NAG-ASN : bond 0.00453 ( 33) link_NAG-ASN : angle 2.44506 ( 99) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 180 time to evaluate : 0.391 Fit side-chains revert: symmetry clash REVERT: A 99 GLU cc_start: 0.8388 (tp30) cc_final: 0.7877 (mm-30) REVERT: A 188 GLN cc_start: 0.8639 (mm-40) cc_final: 0.8262 (mm-40) REVERT: A 192 ARG cc_start: 0.8906 (mtp85) cc_final: 0.8692 (mtp85) REVERT: A 249 ARG cc_start: 0.6376 (mtt90) cc_final: 0.5998 (mpt90) REVERT: a 331 MET cc_start: 0.7603 (tmm) cc_final: 0.6749 (tmm) REVERT: a 346 ASP cc_start: 0.9149 (p0) cc_final: 0.8825 (p0) REVERT: a 400 ASP cc_start: 0.8494 (p0) cc_final: 0.8013 (p0) REVERT: B 188 GLN cc_start: 0.8896 (mm-40) cc_final: 0.8535 (mm-40) REVERT: B 227 GLU cc_start: 0.7914 (mm-30) cc_final: 0.7643 (mm-30) REVERT: C 94 ILE cc_start: 0.9081 (mt) cc_final: 0.8770 (tt) REVERT: C 99 GLU cc_start: 0.8444 (tp30) cc_final: 0.7984 (mm-30) REVERT: C 150 GLU cc_start: 0.8692 (pm20) cc_final: 0.7984 (tm-30) REVERT: C 178 HIS cc_start: 0.8008 (OUTLIER) cc_final: 0.7754 (p90) REVERT: b 341 ASN cc_start: 0.9122 (m-40) cc_final: 0.8823 (m-40) REVERT: b 400 ASP cc_start: 0.8797 (p0) cc_final: 0.8516 (p0) REVERT: b 404 GLN cc_start: 0.8966 (tp40) cc_final: 0.8506 (tp-100) REVERT: b 418 TYR cc_start: 0.5656 (t80) cc_final: 0.5095 (t80) REVERT: c 338 LYS cc_start: 0.9178 (mtmm) cc_final: 0.8734 (mptt) REVERT: c 400 ASP cc_start: 0.8850 (p0) cc_final: 0.8355 (p0) REVERT: c 401 ASP cc_start: 0.8979 (m-30) cc_final: 0.8563 (m-30) REVERT: c 409 MET cc_start: 0.8496 (mtp) cc_final: 0.8210 (mtp) outliers start: 36 outliers final: 24 residues processed: 201 average time/residue: 0.1211 time to fit residues: 33.2158 Evaluate side-chains 197 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 172 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 213 MET Chi-restraints excluded: chain a residue 295 THR Chi-restraints excluded: chain a residue 303 LYS Chi-restraints excluded: chain a residue 304 HIS Chi-restraints excluded: chain a residue 322 ILE Chi-restraints excluded: chain a residue 341 ASN Chi-restraints excluded: chain a residue 375 SER Chi-restraints excluded: chain a residue 398 PHE Chi-restraints excluded: chain B residue 213 MET Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain C residue 178 HIS Chi-restraints excluded: chain C residue 211 CYS Chi-restraints excluded: chain b residue 295 THR Chi-restraints excluded: chain b residue 323 GLN Chi-restraints excluded: chain b residue 348 LEU Chi-restraints excluded: chain b residue 398 PHE Chi-restraints excluded: chain c residue 295 THR Chi-restraints excluded: chain c residue 304 HIS Chi-restraints excluded: chain c residue 341 ASN Chi-restraints excluded: chain c residue 398 PHE Chi-restraints excluded: chain c residue 420 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 24 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 chunk 81 optimal weight: 9.9990 chunk 92 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 93 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 97 optimal weight: 8.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 373 HIS B 178 HIS ** c 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.087686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.062163 restraints weight = 28418.132| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 4.30 r_work: 0.2906 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.5435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.113 10281 Z= 0.190 Angle : 0.964 17.890 14103 Z= 0.426 Chirality : 0.051 0.364 1812 Planarity : 0.004 0.043 1596 Dihedral : 9.079 53.613 3228 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.28 % Allowed : 8.03 % Favored : 91.69 % Rotamer: Outliers : 2.59 % Allowed : 18.74 % Favored : 78.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.98 (0.26), residues: 1071 helix: 0.23 (0.26), residues: 417 sheet: 0.57 (0.52), residues: 114 loop : -1.66 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 192 TYR 0.044 0.001 TYR c 418 PHE 0.022 0.002 PHE A 156 TRP 0.013 0.001 TRP c 263 HIS 0.007 0.001 HIS C 169 Details of bonding type rmsd covalent geometry : bond 0.00401 (10158) covalent geometry : angle 0.82340 (13755) SS BOND : bond 0.00606 ( 21) SS BOND : angle 2.67422 ( 42) hydrogen bonds : bond 0.03914 ( 378) hydrogen bonds : angle 4.73273 ( 990) link_ALPHA1-2 : bond 0.00078 ( 3) link_ALPHA1-2 : angle 1.91749 ( 9) link_ALPHA1-3 : bond 0.01452 ( 9) link_ALPHA1-3 : angle 1.70235 ( 27) link_ALPHA1-6 : bond 0.01246 ( 6) link_ALPHA1-6 : angle 1.85502 ( 18) link_BETA1-4 : bond 0.01671 ( 51) link_BETA1-4 : angle 4.12148 ( 153) link_NAG-ASN : bond 0.00274 ( 33) link_NAG-ASN : angle 2.65871 ( 99) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 183 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 99 GLU cc_start: 0.8791 (tp30) cc_final: 0.8273 (mm-30) REVERT: A 188 GLN cc_start: 0.8914 (mm-40) cc_final: 0.8591 (mm-40) REVERT: A 249 ARG cc_start: 0.6455 (mtt90) cc_final: 0.6075 (mpt90) REVERT: a 331 MET cc_start: 0.7649 (tmm) cc_final: 0.6733 (tmm) REVERT: a 346 ASP cc_start: 0.9265 (p0) cc_final: 0.8965 (p0) REVERT: a 400 ASP cc_start: 0.8598 (p0) cc_final: 0.8252 (p0) REVERT: B 62 LYS cc_start: 0.8977 (mmmm) cc_final: 0.8671 (mmmm) REVERT: B 74 MET cc_start: 0.9222 (mmt) cc_final: 0.8993 (mmm) REVERT: B 99 GLU cc_start: 0.8874 (tp30) cc_final: 0.8521 (mm-30) REVERT: B 156 PHE cc_start: 0.9174 (m-80) cc_final: 0.8967 (m-80) REVERT: B 188 GLN cc_start: 0.9038 (mm-40) cc_final: 0.8719 (mm-40) REVERT: B 227 GLU cc_start: 0.8173 (mm-30) cc_final: 0.7878 (mm-30) REVERT: C 94 ILE cc_start: 0.9189 (mt) cc_final: 0.8858 (tt) REVERT: C 99 GLU cc_start: 0.8817 (tp30) cc_final: 0.8374 (mm-30) REVERT: C 150 GLU cc_start: 0.8701 (pm20) cc_final: 0.7944 (tm-30) REVERT: C 178 HIS cc_start: 0.7921 (OUTLIER) cc_final: 0.7620 (p90) REVERT: C 193 MET cc_start: 0.9323 (tpp) cc_final: 0.9031 (tpp) REVERT: C 227 GLU cc_start: 0.8348 (mm-30) cc_final: 0.8048 (mm-30) REVERT: b 341 ASN cc_start: 0.9269 (m-40) cc_final: 0.8990 (m-40) REVERT: b 400 ASP cc_start: 0.8809 (p0) cc_final: 0.8571 (p0) REVERT: b 404 GLN cc_start: 0.9145 (tp40) cc_final: 0.8734 (tp-100) REVERT: c 338 LYS cc_start: 0.9286 (mtmm) cc_final: 0.8845 (mptt) REVERT: c 400 ASP cc_start: 0.8838 (p0) cc_final: 0.8386 (p0) REVERT: c 401 ASP cc_start: 0.8981 (m-30) cc_final: 0.8649 (m-30) REVERT: c 409 MET cc_start: 0.8338 (mtp) cc_final: 0.8011 (mtp) outliers start: 25 outliers final: 18 residues processed: 196 average time/residue: 0.1210 time to fit residues: 32.1450 Evaluate side-chains 187 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 168 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 213 MET Chi-restraints excluded: chain a residue 303 LYS Chi-restraints excluded: chain a residue 304 HIS Chi-restraints excluded: chain a residue 322 ILE Chi-restraints excluded: chain a residue 398 PHE Chi-restraints excluded: chain B residue 213 MET Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain C residue 178 HIS Chi-restraints excluded: chain C residue 211 CYS Chi-restraints excluded: chain b residue 323 GLN Chi-restraints excluded: chain b residue 348 LEU Chi-restraints excluded: chain b residue 415 GLN Chi-restraints excluded: chain c residue 304 HIS Chi-restraints excluded: chain c residue 332 SER Chi-restraints excluded: chain c residue 341 ASN Chi-restraints excluded: chain c residue 398 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 79 optimal weight: 0.5980 chunk 74 optimal weight: 6.9990 chunk 76 optimal weight: 7.9990 chunk 55 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 7 optimal weight: 9.9990 chunk 20 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 21 optimal weight: 0.5980 chunk 28 optimal weight: 4.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 178 HIS ** b 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 334 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.088371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.062726 restraints weight = 28566.567| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 4.34 r_work: 0.2927 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.5610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 10281 Z= 0.169 Angle : 0.942 17.860 14103 Z= 0.415 Chirality : 0.050 0.362 1812 Planarity : 0.004 0.044 1596 Dihedral : 8.673 53.283 3228 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.28 % Allowed : 8.31 % Favored : 91.41 % Rotamer: Outliers : 2.17 % Allowed : 19.36 % Favored : 78.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.89 (0.26), residues: 1071 helix: 0.34 (0.26), residues: 417 sheet: 0.53 (0.52), residues: 114 loop : -1.62 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 192 TYR 0.027 0.001 TYR c 418 PHE 0.020 0.002 PHE b 398 TRP 0.015 0.001 TRP c 263 HIS 0.005 0.001 HIS B 123 Details of bonding type rmsd covalent geometry : bond 0.00343 (10158) covalent geometry : angle 0.80939 (13755) SS BOND : bond 0.00583 ( 21) SS BOND : angle 2.25583 ( 42) hydrogen bonds : bond 0.03594 ( 378) hydrogen bonds : angle 4.68980 ( 990) link_ALPHA1-2 : bond 0.00021 ( 3) link_ALPHA1-2 : angle 1.91385 ( 9) link_ALPHA1-3 : bond 0.01508 ( 9) link_ALPHA1-3 : angle 1.69138 ( 27) link_ALPHA1-6 : bond 0.01306 ( 6) link_ALPHA1-6 : angle 1.79227 ( 18) link_BETA1-4 : bond 0.01674 ( 51) link_BETA1-4 : angle 4.06510 ( 153) link_NAG-ASN : bond 0.00349 ( 33) link_NAG-ASN : angle 2.45310 ( 99) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 179 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 GLU cc_start: 0.8786 (tp30) cc_final: 0.8317 (mm-30) REVERT: A 150 GLU cc_start: 0.8629 (pm20) cc_final: 0.7816 (tm-30) REVERT: A 188 GLN cc_start: 0.8898 (mm-40) cc_final: 0.8578 (mm-40) REVERT: A 249 ARG cc_start: 0.6587 (mtt90) cc_final: 0.6274 (mpt90) REVERT: a 331 MET cc_start: 0.7543 (tmm) cc_final: 0.6629 (tmm) REVERT: a 346 ASP cc_start: 0.9220 (p0) cc_final: 0.8918 (p0) REVERT: a 400 ASP cc_start: 0.8642 (p0) cc_final: 0.8339 (p0) REVERT: B 74 MET cc_start: 0.9219 (mmt) cc_final: 0.8992 (mmm) REVERT: B 99 GLU cc_start: 0.8892 (tp30) cc_final: 0.8567 (mm-30) REVERT: B 156 PHE cc_start: 0.9174 (m-80) cc_final: 0.8935 (m-80) REVERT: B 188 GLN cc_start: 0.9027 (mm-40) cc_final: 0.8716 (mm-40) REVERT: B 227 GLU cc_start: 0.8217 (mm-30) cc_final: 0.7937 (mm-30) REVERT: C 94 ILE cc_start: 0.9181 (mt) cc_final: 0.8862 (tt) REVERT: C 99 GLU cc_start: 0.8820 (tp30) cc_final: 0.8451 (mm-30) REVERT: C 142 SER cc_start: 0.8971 (OUTLIER) cc_final: 0.8515 (p) REVERT: C 150 GLU cc_start: 0.8711 (pm20) cc_final: 0.7952 (tm-30) REVERT: C 193 MET cc_start: 0.9302 (tpp) cc_final: 0.8875 (tpp) REVERT: C 227 GLU cc_start: 0.8408 (mm-30) cc_final: 0.8107 (mm-30) REVERT: b 316 ASP cc_start: 0.8700 (t70) cc_final: 0.8293 (t0) REVERT: b 341 ASN cc_start: 0.9265 (m-40) cc_final: 0.8996 (m-40) REVERT: b 400 ASP cc_start: 0.8771 (p0) cc_final: 0.8550 (p0) REVERT: c 338 LYS cc_start: 0.9273 (mtmm) cc_final: 0.8840 (mptt) REVERT: c 365 TYR cc_start: 0.9579 (m-80) cc_final: 0.9334 (m-80) REVERT: c 400 ASP cc_start: 0.8815 (p0) cc_final: 0.8402 (p0) REVERT: c 401 ASP cc_start: 0.8947 (m-30) cc_final: 0.8640 (m-30) REVERT: c 409 MET cc_start: 0.8338 (mtp) cc_final: 0.7984 (mtp) outliers start: 21 outliers final: 15 residues processed: 189 average time/residue: 0.1237 time to fit residues: 31.7462 Evaluate side-chains 187 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 171 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 213 MET Chi-restraints excluded: chain a residue 304 HIS Chi-restraints excluded: chain a residue 322 ILE Chi-restraints excluded: chain B residue 213 MET Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain b residue 295 THR Chi-restraints excluded: chain b residue 323 GLN Chi-restraints excluded: chain b residue 348 LEU Chi-restraints excluded: chain c residue 295 THR Chi-restraints excluded: chain c residue 304 HIS Chi-restraints excluded: chain c residue 332 SER Chi-restraints excluded: chain c residue 341 ASN Chi-restraints excluded: chain c residue 398 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 90 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 98 optimal weight: 5.9990 chunk 96 optimal weight: 7.9990 chunk 70 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 34 optimal weight: 9.9990 chunk 20 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 29 optimal weight: 5.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 178 HIS ** C 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 334 GLN ** 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 = 0.3704 r_free = 0.3704 target = 0.087052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.061270 restraints weight = 28532.373| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 4.34 r_work: 0.2878 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.5674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 10281 Z= 0.241 Angle : 0.980 17.808 14103 Z= 0.435 Chirality : 0.051 0.361 1812 Planarity : 0.004 0.043 1596 Dihedral : 8.736 53.671 3228 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.28 % Allowed : 8.50 % Favored : 91.22 % Rotamer: Outliers : 2.28 % Allowed : 19.36 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.95 (0.26), residues: 1071 helix: 0.41 (0.26), residues: 411 sheet: 0.41 (0.52), residues: 114 loop : -1.73 (0.26), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 192 TYR 0.021 0.002 TYR c 418 PHE 0.015 0.002 PHE b 398 TRP 0.017 0.002 TRP A 209 HIS 0.005 0.001 HIS B 123 Details of bonding type rmsd covalent geometry : bond 0.00519 (10158) covalent geometry : angle 0.85138 (13755) SS BOND : bond 0.00589 ( 21) SS BOND : angle 2.17728 ( 42) hydrogen bonds : bond 0.04065 ( 378) hydrogen bonds : angle 4.70533 ( 990) link_ALPHA1-2 : bond 0.00169 ( 3) link_ALPHA1-2 : angle 1.88604 ( 9) link_ALPHA1-3 : bond 0.01286 ( 9) link_ALPHA1-3 : angle 1.80626 ( 27) link_ALPHA1-6 : bond 0.01218 ( 6) link_ALPHA1-6 : angle 1.96676 ( 18) link_BETA1-4 : bond 0.01643 ( 51) link_BETA1-4 : angle 4.07575 ( 153) link_NAG-ASN : bond 0.00419 ( 33) link_NAG-ASN : angle 2.53681 ( 99) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 175 time to evaluate : 0.382 Fit side-chains revert: symmetry clash REVERT: A 99 GLU cc_start: 0.8798 (tp30) cc_final: 0.8299 (mm-30) REVERT: A 188 GLN cc_start: 0.8928 (mm-40) cc_final: 0.8599 (mm-40) REVERT: A 249 ARG cc_start: 0.6512 (mtt90) cc_final: 0.6169 (mpt90) REVERT: a 331 MET cc_start: 0.7664 (tmm) cc_final: 0.6995 (tmm) REVERT: a 346 ASP cc_start: 0.9219 (p0) cc_final: 0.8942 (p0) REVERT: a 400 ASP cc_start: 0.8689 (p0) cc_final: 0.8142 (p0) REVERT: B 188 GLN cc_start: 0.9068 (mm-40) cc_final: 0.8749 (mm-40) REVERT: B 227 GLU cc_start: 0.8225 (mm-30) cc_final: 0.7939 (mm-30) REVERT: C 94 ILE cc_start: 0.9238 (mt) cc_final: 0.8851 (tt) REVERT: C 99 GLU cc_start: 0.8842 (tp30) cc_final: 0.8358 (mm-30) REVERT: C 193 MET cc_start: 0.9334 (tpp) cc_final: 0.8994 (tpp) REVERT: C 249 ARG cc_start: 0.7413 (mtt90) cc_final: 0.6476 (mmt-90) REVERT: b 341 ASN cc_start: 0.9271 (m-40) cc_final: 0.9003 (m-40) REVERT: b 400 ASP cc_start: 0.8884 (p0) cc_final: 0.8616 (p0) REVERT: b 404 GLN cc_start: 0.9102 (tt0) cc_final: 0.8699 (tp-100) REVERT: b 421 ARG cc_start: 0.8850 (ttp80) cc_final: 0.8590 (ttp80) REVERT: c 334 GLN cc_start: 0.8803 (mm110) cc_final: 0.8587 (mm-40) REVERT: c 338 LYS cc_start: 0.9288 (mtmm) cc_final: 0.8844 (mptt) REVERT: c 400 ASP cc_start: 0.8897 (p0) cc_final: 0.8469 (p0) REVERT: c 401 ASP cc_start: 0.8977 (m-30) cc_final: 0.8654 (m-30) REVERT: c 409 MET cc_start: 0.8354 (mtp) cc_final: 0.8044 (mtp) outliers start: 22 outliers final: 19 residues processed: 188 average time/residue: 0.1174 time to fit residues: 30.2446 Evaluate side-chains 188 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 169 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 213 MET Chi-restraints excluded: chain a residue 295 THR Chi-restraints excluded: chain a residue 303 LYS Chi-restraints excluded: chain a residue 304 HIS Chi-restraints excluded: chain a residue 322 ILE Chi-restraints excluded: chain a residue 398 PHE Chi-restraints excluded: chain B residue 213 MET Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain C residue 211 CYS Chi-restraints excluded: chain b residue 295 THR Chi-restraints excluded: chain b residue 323 GLN Chi-restraints excluded: chain b residue 348 LEU Chi-restraints excluded: chain b residue 398 PHE Chi-restraints excluded: chain b residue 420 ASP Chi-restraints excluded: chain c residue 295 THR Chi-restraints excluded: chain c residue 341 ASN Chi-restraints excluded: chain c residue 398 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 59 optimal weight: 5.9990 chunk 81 optimal weight: 6.9990 chunk 49 optimal weight: 0.8980 chunk 16 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 chunk 54 optimal weight: 6.9990 chunk 76 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 178 HIS ** b 334 GLN ** 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 = 0.3714 r_free = 0.3714 target = 0.087755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.061893 restraints weight = 28871.287| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 4.37 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.5764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 10281 Z= 0.187 Angle : 0.969 18.082 14103 Z= 0.430 Chirality : 0.050 0.359 1812 Planarity : 0.005 0.044 1596 Dihedral : 8.529 52.958 3228 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.28 % Allowed : 8.22 % Favored : 91.50 % Rotamer: Outliers : 2.07 % Allowed : 19.88 % Favored : 78.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.91 (0.26), residues: 1071 helix: 0.41 (0.26), residues: 417 sheet: 0.48 (0.52), residues: 114 loop : -1.70 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG b 421 TYR 0.023 0.001 TYR c 418 PHE 0.018 0.002 PHE b 398 TRP 0.012 0.001 TRP a 263 HIS 0.004 0.001 HIS B 123 Details of bonding type rmsd covalent geometry : bond 0.00388 (10158) covalent geometry : angle 0.84614 (13755) SS BOND : bond 0.00528 ( 21) SS BOND : angle 1.96495 ( 42) hydrogen bonds : bond 0.03785 ( 378) hydrogen bonds : angle 4.69505 ( 990) link_ALPHA1-2 : bond 0.00105 ( 3) link_ALPHA1-2 : angle 1.94680 ( 9) link_ALPHA1-3 : bond 0.01422 ( 9) link_ALPHA1-3 : angle 1.74176 ( 27) link_ALPHA1-6 : bond 0.01272 ( 6) link_ALPHA1-6 : angle 1.84094 ( 18) link_BETA1-4 : bond 0.01665 ( 51) link_BETA1-4 : angle 4.01815 ( 153) link_NAG-ASN : bond 0.00294 ( 33) link_NAG-ASN : angle 2.41559 ( 99) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2254.45 seconds wall clock time: 39 minutes 52.83 seconds (2392.83 seconds total)