Starting phenix.real_space_refine on Wed Mar 4 00:28:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8eje_28179/03_2026/8eje_28179.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eje_28179/03_2026/8eje_28179.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8eje_28179/03_2026/8eje_28179.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eje_28179/03_2026/8eje_28179.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8eje_28179/03_2026/8eje_28179.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eje_28179/03_2026/8eje_28179.map" } resolution = 3.69 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= 0.026 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 87 5.16 5 C 5892 2.51 5 N 1497 2.21 5 O 1950 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9426 Number of models: 1 Model: "" Number of chains: 33 Chain: "A" Number of atoms: 1538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1538 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 4, 'TRANS': 190} Chain: "a" Number of atoms: 1308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1308 Classifications: {'peptide': 161} Link IDs: {'PTRANS': 4, 'TRANS': 156} Chain: "B" Number of atoms: 1538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1538 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 4, 'TRANS': 190} Chain: "b" Number of atoms: 1308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1308 Classifications: {'peptide': 161} Link IDs: {'PTRANS': 4, 'TRANS': 156} Chain: "C" Number of atoms: 1538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1538 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 4, 'TRANS': 190} Chain: "c" Number of atoms: 1308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1308 Classifications: {'peptide': 161} Link IDs: {'PTRANS': 4, 'TRANS': 156} Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" 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: "J" 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: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "L" 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: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 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: 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: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 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: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 2.12, per 1000 atoms: 0.22 Number of scatterers: 9426 At special positions: 0 Unit cell: (93.005, 91.96, 100.32, 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 87 16.00 O 1950 8.00 N 1497 7.00 C 5892 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=2.03 Simple disulfide: pdb=" SG CYS A 117 " - pdb=" SG CYS A 154 " distance=2.03 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=2.06 Simple disulfide: pdb=" SG CYS a 278 " - pdb=" SG CYS a 291 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS B 117 " - pdb=" SG CYS B 154 " distance=2.03 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=2.06 Simple disulfide: pdb=" SG CYS b 278 " - pdb=" SG CYS b 291 " distance=2.04 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 85 " - pdb=" SG CYS C 230 " distance=2.03 Simple disulfide: pdb=" SG CYS C 117 " - pdb=" SG CYS C 154 " distance=2.03 Simple disulfide: pdb=" SG CYS C 179 " - pdb=" SG CYS C 211 " distance=2.03 Simple disulfide: pdb=" SG CYS C 206 " - pdb=" SG CYS c 359 " distance=2.06 Simple disulfide: pdb=" SG CYS c 278 " - pdb=" SG CYS c 291 " distance=2.04 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 ALPHA1-3 " BMA I 3 " - " MAN I 4 " " BMA P 3 " - " MAN P 4 " " BMA W 3 " - " MAN W 4 " ALPHA1-6 " BMA I 3 " - " MAN I 5 " " BMA P 3 " - " MAN P 5 " " BMA W 3 " - " MAN W 5 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " NAG-ASN " NAG A 301 " - " ASN A 98 " " NAG A 302 " - " ASN A 223 " " NAG B 301 " - " ASN B 98 " " NAG B 302 " - " ASN B 223 " " NAG C 301 " - " ASN C 98 " " NAG C 302 " - " ASN C 223 " " NAG D 1 " - " ASN A 78 " " NAG E 1 " - " ASN A 88 " " NAG F 1 " - " ASN A 108 " " NAG G 1 " - " ASN A 118 " " NAG H 1 " - " ASN A 166 " " NAG I 1 " - " ASN a 364 " " NAG J 1 " - " ASN a 372 " " NAG K 1 " - " ASN B 78 " " NAG L 1 " - " ASN B 88 " " NAG M 1 " - " ASN B 108 " " NAG N 1 " - " ASN B 118 " " NAG O 1 " - " ASN B 166 " " NAG P 1 " - " ASN b 364 " " NAG Q 1 " - " ASN b 372 " " NAG R 1 " - " ASN C 78 " " NAG S 1 " - " ASN C 88 " " NAG T 1 " - " ASN C 108 " " NAG U 1 " - " ASN C 118 " " NAG V 1 " - " ASN C 166 " " NAG W 1 " - " ASN c 364 " " NAG X 1 " - " ASN c 372 " " NAG a 501 " - " ASN a 394 " " NAG a 502 " - " ASN a 389 " " NAG b 501 " - " ASN b 394 " " NAG b 502 " - " ASN b 389 " " NAG c 501 " - " ASN c 394 " " NAG c 502 " - " ASN c 389 " Time building additional restraints: 0.91 Conformation dependent library (CDL) restraints added in 210.2 milliseconds 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2016 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 12 sheets defined 40.4% alpha, 12.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 73 through 78 Processing helix chain 'A' and resid 118 through 126 Processing helix chain 'A' and resid 129 through 142 Processing helix chain 'A' and resid 168 through 170 No H-bonds generated for 'chain 'A' and resid 168 through 170' Processing helix chain 'A' and resid 171 through 178 Processing helix chain 'A' and resid 182 through 194 removed outlier: 3.733A pdb=" N ARG A 192 " --> pdb=" O GLN A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 205 Processing helix chain 'A' and resid 237 through 246 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 325 removed outlier: 3.805A pdb=" N ASP a 310 " --> pdb=" O GLU a 306 " (cutoff:3.500A) Processing helix chain 'a' and resid 333 through 344 removed outlier: 3.551A pdb=" N ASN a 341 " --> pdb=" O ASN a 337 " (cutoff:3.500A) Processing helix chain 'a' and resid 345 through 357 Processing helix chain 'a' and resid 358 through 360 No H-bonds generated for 'chain 'a' and resid 358 through 360' Processing helix chain 'a' and resid 398 through 415 Processing helix chain 'B' and resid 73 through 78 Processing helix chain 'B' and resid 118 through 126 Processing helix chain 'B' and resid 129 through 142 Processing helix chain 'B' and resid 168 through 170 No H-bonds generated for 'chain 'B' and resid 168 through 170' Processing helix chain 'B' and resid 171 through 178 Processing helix chain 'B' and resid 182 through 194 removed outlier: 3.733A pdb=" N ARG B 192 " --> pdb=" O GLN B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 205 Processing helix chain 'B' and resid 237 through 246 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 325 removed outlier: 3.805A pdb=" N ASP b 310 " --> pdb=" O GLU b 306 " (cutoff:3.500A) Processing helix chain 'b' and resid 333 through 344 removed outlier: 3.551A pdb=" N ASN b 341 " --> pdb=" O ASN b 337 " (cutoff:3.500A) Processing helix chain 'b' and resid 345 through 357 Processing helix chain 'b' and resid 358 through 360 No H-bonds generated for 'chain 'b' and resid 358 through 360' Processing helix chain 'b' and resid 398 through 415 Processing helix chain 'C' and resid 73 through 78 Processing helix chain 'C' and resid 118 through 126 Processing helix chain 'C' and resid 129 through 142 Processing helix chain 'C' and resid 168 through 170 No H-bonds generated for 'chain 'C' and resid 168 through 170' Processing helix chain 'C' and resid 171 through 178 Processing helix chain 'C' and resid 182 through 194 removed outlier: 3.732A pdb=" N ARG C 192 " --> pdb=" O GLN C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 205 Processing helix chain 'C' and resid 237 through 246 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 325 removed outlier: 3.805A pdb=" N ASP c 310 " --> pdb=" O GLU c 306 " (cutoff:3.500A) Processing helix chain 'c' and resid 333 through 344 removed outlier: 3.550A pdb=" N ASN c 341 " --> pdb=" O ASN c 337 " (cutoff:3.500A) Processing helix chain 'c' and resid 345 through 357 Processing helix chain 'c' and resid 358 through 360 No H-bonds generated for 'chain 'c' and resid 358 through 360' Processing helix chain 'c' and resid 398 through 415 Processing sheet with id=AA1, first strand: chain 'A' and resid 65 through 71 Processing sheet with id=AA2, first strand: chain 'A' and resid 83 through 86 Processing sheet with id=AA3, first strand: chain 'a' and resid 277 through 279 Processing sheet with id=AA4, first strand: chain 'a' and resid 387 through 388 Processing sheet with id=AA5, first strand: chain 'B' and resid 65 through 71 Processing sheet with id=AA6, first strand: chain 'B' and resid 83 through 86 Processing sheet with id=AA7, first strand: chain 'b' and resid 277 through 279 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 65 through 71 Processing sheet with id=AB1, first strand: chain 'C' and resid 83 through 86 Processing sheet with id=AB2, first strand: chain 'c' and resid 277 through 279 Processing sheet with id=AB3, first strand: chain 'c' and resid 387 through 388 372 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: 1.37 Time building geometry restraints manager: 1.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.33: 2322 1.33 - 1.47: 3215 1.47 - 1.62: 3946 1.62 - 1.77: 12 1.77 - 1.91: 123 Bond restraints: 9618 Sorted by residual: bond pdb=" CB ILE b 419 " pdb=" CG1 ILE b 419 " ideal model delta sigma weight residual 1.530 1.653 -0.123 2.00e-02 2.50e+03 3.78e+01 bond pdb=" CB ILE a 419 " pdb=" CG1 ILE a 419 " ideal model delta sigma weight residual 1.530 1.653 -0.123 2.00e-02 2.50e+03 3.76e+01 bond pdb=" CB ILE c 419 " pdb=" CG1 ILE c 419 " ideal model delta sigma weight residual 1.530 1.653 -0.123 2.00e-02 2.50e+03 3.76e+01 bond pdb=" NE1 TRP b 385 " pdb=" CE2 TRP b 385 " ideal model delta sigma weight residual 1.370 1.304 0.066 1.10e-02 8.26e+03 3.61e+01 bond pdb=" NE1 TRP c 385 " pdb=" CE2 TRP c 385 " ideal model delta sigma weight residual 1.370 1.304 0.066 1.10e-02 8.26e+03 3.57e+01 ... (remaining 9613 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.28: 12964 7.28 - 14.56: 59 14.56 - 21.84: 0 21.84 - 29.11: 0 29.11 - 36.39: 9 Bond angle restraints: 13032 Sorted by residual: angle pdb=" C2 NAG V 2 " pdb=" N2 NAG V 2 " pdb=" C7 NAG V 2 " ideal model delta sigma weight residual 124.56 160.95 -36.39 3.00e+00 1.11e-01 1.47e+02 angle pdb=" C2 NAG H 2 " pdb=" N2 NAG H 2 " pdb=" C7 NAG H 2 " ideal model delta sigma weight residual 124.56 160.94 -36.38 3.00e+00 1.11e-01 1.47e+02 angle pdb=" C2 NAG A 301 " pdb=" N2 NAG A 301 " pdb=" C7 NAG A 301 " ideal model delta sigma weight residual 124.56 160.94 -36.38 3.00e+00 1.11e-01 1.47e+02 angle pdb=" C2 NAG C 301 " pdb=" N2 NAG C 301 " pdb=" C7 NAG C 301 " ideal model delta sigma weight residual 124.56 160.93 -36.37 3.00e+00 1.11e-01 1.47e+02 angle pdb=" C2 NAG B 301 " pdb=" N2 NAG B 301 " pdb=" C7 NAG B 301 " ideal model delta sigma weight residual 124.56 160.93 -36.37 3.00e+00 1.11e-01 1.47e+02 ... (remaining 13027 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.37: 6246 21.37 - 42.73: 226 42.73 - 64.10: 44 64.10 - 85.47: 45 85.47 - 106.83: 30 Dihedral angle restraints: 6591 sinusoidal: 3456 harmonic: 3135 Sorted by residual: dihedral pdb=" CA CYS B 117 " pdb=" CB CYS B 117 " pdb=" SG CYS B 117 " pdb=" SG CYS B 154 " ideal model delta sinusoidal sigma weight residual 79.00 13.37 65.63 1 2.00e+01 2.50e-03 1.41e+01 dihedral pdb=" CA CYS C 117 " pdb=" CB CYS C 117 " pdb=" SG CYS C 117 " pdb=" SG CYS C 154 " ideal model delta sinusoidal sigma weight residual 79.00 13.39 65.61 1 2.00e+01 2.50e-03 1.41e+01 dihedral pdb=" CA CYS A 117 " pdb=" CB CYS A 117 " pdb=" SG CYS A 117 " pdb=" SG CYS A 154 " ideal model delta sinusoidal sigma weight residual 79.00 13.42 65.58 1 2.00e+01 2.50e-03 1.41e+01 ... (remaining 6588 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.121: 1072 0.121 - 0.242: 359 0.242 - 0.363: 135 0.363 - 0.483: 51 0.483 - 0.604: 15 Chirality restraints: 1632 Sorted by residual: chirality pdb=" C1 BMA D 3 " pdb=" O4 NAG D 2 " pdb=" C2 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.80 -0.60 2.00e-02 2.50e+03 9.13e+02 chirality pdb=" C1 BMA R 3 " pdb=" O4 NAG R 2 " pdb=" C2 BMA R 3 " pdb=" O5 BMA R 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.80 -0.60 2.00e-02 2.50e+03 9.13e+02 chirality pdb=" C1 BMA K 3 " pdb=" O4 NAG K 2 " pdb=" C2 BMA K 3 " pdb=" O5 BMA K 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.80 -0.60 2.00e-02 2.50e+03 9.08e+02 ... (remaining 1629 not shown) Planarity restraints: 1590 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG K 2 " -0.226 2.00e-02 2.50e+03 1.85e-01 4.28e+02 pdb=" C7 NAG K 2 " 0.065 2.00e-02 2.50e+03 pdb=" C8 NAG K 2 " -0.163 2.00e-02 2.50e+03 pdb=" N2 NAG K 2 " 0.298 2.00e-02 2.50e+03 pdb=" O7 NAG K 2 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 2 " -0.226 2.00e-02 2.50e+03 1.85e-01 4.28e+02 pdb=" C7 NAG D 2 " 0.065 2.00e-02 2.50e+03 pdb=" C8 NAG D 2 " -0.163 2.00e-02 2.50e+03 pdb=" N2 NAG D 2 " 0.298 2.00e-02 2.50e+03 pdb=" O7 NAG D 2 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG R 2 " 0.226 2.00e-02 2.50e+03 1.85e-01 4.28e+02 pdb=" C7 NAG R 2 " -0.065 2.00e-02 2.50e+03 pdb=" C8 NAG R 2 " 0.163 2.00e-02 2.50e+03 pdb=" N2 NAG R 2 " -0.298 2.00e-02 2.50e+03 pdb=" O7 NAG R 2 " -0.026 2.00e-02 2.50e+03 ... (remaining 1587 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 2756 2.83 - 3.35: 9323 3.35 - 3.87: 15841 3.87 - 4.38: 19496 4.38 - 4.90: 30060 Nonbonded interactions: 77476 Sorted by model distance: nonbonded pdb=" N ALA B 201 " pdb=" N LEU B 202 " model vdw 2.317 2.560 nonbonded pdb=" N ALA A 201 " pdb=" N LEU A 202 " model vdw 2.317 2.560 nonbonded pdb=" N ALA C 201 " pdb=" N LEU C 202 " model vdw 2.317 2.560 nonbonded pdb=" O GLY B 207 " pdb=" C SER B 208 " model vdw 2.403 3.270 nonbonded pdb=" O GLY C 207 " pdb=" C SER C 208 " model vdw 2.403 3.270 ... (remaining 77471 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 'K' selection = chain 'R' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'Q' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'X' } ncs_group { reference = chain 'I' selection = chain 'P' selection = chain 'W' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.440 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 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:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 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 : 0.024 0.123 9705 Z= 1.287 Angle : 2.242 36.392 13272 Z= 1.276 Chirality : 0.155 0.604 1632 Planarity : 0.012 0.185 1557 Dihedral : 15.070 106.833 4512 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % 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 are not related in a simple way. whole: -0.11 (0.24), residues: 1056 helix: -0.09 (0.24), residues: 339 sheet: 1.95 (0.48), residues: 99 loop : -0.34 (0.24), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 125 TYR 0.043 0.009 TYR B 218 PHE 0.025 0.006 PHE C 146 TRP 0.024 0.005 TRP B 226 HIS 0.009 0.003 HIS C 140 Details of bonding type rmsd covalent geometry : bond 0.02349 ( 9618) covalent geometry : angle 2.13907 (13032) SS BOND : bond 0.01224 ( 21) SS BOND : angle 3.49875 ( 42) hydrogen bonds : bond 0.17248 ( 372) hydrogen bonds : angle 6.30877 ( 990) link_ALPHA1-3 : bond 0.10501 ( 3) link_ALPHA1-3 : angle 7.62833 ( 9) link_ALPHA1-6 : bond 0.04870 ( 3) link_ALPHA1-6 : angle 3.60915 ( 9) link_BETA1-4 : bond 0.07711 ( 27) link_BETA1-4 : angle 6.86572 ( 81) link_NAG-ASN : bond 0.08075 ( 33) link_NAG-ASN : angle 4.59387 ( 99) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 356 time to evaluate : 0.283 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 316 ASP cc_start: 0.8681 (t70) cc_final: 0.8398 (t0) REVERT: a 350 MET cc_start: 0.9295 (mmm) cc_final: 0.9083 (tpp) REVERT: a 401 ASP cc_start: 0.8451 (m-30) cc_final: 0.8054 (m-30) REVERT: B 129 ASP cc_start: 0.8208 (t0) cc_final: 0.7995 (t0) REVERT: B 182 ILE cc_start: 0.8049 (mt) cc_final: 0.7777 (mp) REVERT: b 316 ASP cc_start: 0.8636 (t70) cc_final: 0.8305 (t0) REVERT: b 350 MET cc_start: 0.9260 (mmm) cc_final: 0.9051 (tpp) REVERT: b 401 ASP cc_start: 0.8477 (m-30) cc_final: 0.7987 (m-30) REVERT: C 129 ASP cc_start: 0.8023 (t0) cc_final: 0.7811 (t0) REVERT: C 193 MET cc_start: 0.7915 (tpp) cc_final: 0.7610 (tpp) REVERT: C 210 ASP cc_start: 0.6558 (p0) cc_final: 0.6075 (t0) REVERT: c 316 ASP cc_start: 0.8627 (t70) cc_final: 0.8389 (t0) REVERT: c 401 ASP cc_start: 0.8410 (m-30) cc_final: 0.8076 (m-30) outliers start: 0 outliers final: 0 residues processed: 356 average time/residue: 0.1123 time to fit residues: 52.9721 Evaluate side-chains 195 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 0.369 ------------------------------------------------------------------------------- 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: 1.9990 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 0.7980 chunk 100 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 8.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 GLN ** a 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 415 GLN B 130 HIS b 334 GLN b 415 GLN C 130 HIS c 330 GLN c 353 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.133301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.108825 restraints weight = 19392.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.112728 restraints weight = 12187.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.115220 restraints weight = 9092.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.116862 restraints weight = 7518.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.117942 restraints weight = 6581.511| |-----------------------------------------------------------------------------| r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.3916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 9705 Z= 0.239 Angle : 1.211 13.416 13272 Z= 0.573 Chirality : 0.057 0.305 1632 Planarity : 0.005 0.030 1557 Dihedral : 13.493 84.512 2514 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 4.52 % Allowed : 12.41 % Favored : 83.07 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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 are not related in a simple way. whole: -0.28 (0.25), residues: 1056 helix: 0.53 (0.27), residues: 336 sheet: 0.53 (0.43), residues: 144 loop : -0.79 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 125 TYR 0.020 0.001 TYR B 149 PHE 0.027 0.003 PHE A 116 TRP 0.025 0.002 TRP A 195 HIS 0.021 0.002 HIS C 123 Details of bonding type rmsd covalent geometry : bond 0.00494 ( 9618) covalent geometry : angle 1.05420 (13032) SS BOND : bond 0.00660 ( 21) SS BOND : angle 2.11049 ( 42) hydrogen bonds : bond 0.06509 ( 372) hydrogen bonds : angle 5.44468 ( 990) link_ALPHA1-3 : bond 0.00586 ( 3) link_ALPHA1-3 : angle 4.63034 ( 9) link_ALPHA1-6 : bond 0.00989 ( 3) link_ALPHA1-6 : angle 1.67364 ( 9) link_BETA1-4 : bond 0.02129 ( 27) link_BETA1-4 : angle 5.65714 ( 81) link_NAG-ASN : bond 0.00860 ( 33) link_NAG-ASN : angle 4.49233 ( 99) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 234 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 TYR cc_start: 0.6738 (OUTLIER) cc_final: 0.4977 (p90) REVERT: a 400 ASP cc_start: 0.8020 (OUTLIER) cc_final: 0.7780 (p0) REVERT: a 405 GLN cc_start: 0.8334 (tp40) cc_final: 0.8118 (tp40) REVERT: B 129 ASP cc_start: 0.7941 (t0) cc_final: 0.7718 (m-30) REVERT: b 401 ASP cc_start: 0.8155 (m-30) cc_final: 0.7845 (m-30) REVERT: C 229 HIS cc_start: 0.7660 (m-70) cc_final: 0.7223 (m-70) REVERT: c 401 ASP cc_start: 0.8172 (m-30) cc_final: 0.7959 (m-30) REVERT: c 409 MET cc_start: 0.7092 (mtp) cc_final: 0.6748 (mtp) outliers start: 43 outliers final: 21 residues processed: 256 average time/residue: 0.1074 time to fit residues: 36.8728 Evaluate side-chains 204 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 181 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 195 TRP Chi-restraints excluded: chain a residue 262 THR Chi-restraints excluded: chain a residue 291 CYS Chi-restraints excluded: chain a residue 376 THR Chi-restraints excluded: chain a residue 400 ASP Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 179 CYS Chi-restraints excluded: chain B residue 195 TRP Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain b residue 262 THR Chi-restraints excluded: chain b residue 283 MET Chi-restraints excluded: chain b residue 304 HIS Chi-restraints excluded: chain b residue 376 THR Chi-restraints excluded: chain C residue 116 PHE Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 195 TRP Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain c residue 260 THR Chi-restraints excluded: chain c residue 376 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 78 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 58 optimal weight: 7.9990 chunk 41 optimal weight: 10.0000 chunk 84 optimal weight: 5.9990 chunk 7 optimal weight: 0.4980 chunk 10 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 75 optimal weight: 0.0870 chunk 85 optimal weight: 5.9990 chunk 94 optimal weight: 0.9990 overall best weight: 1.3164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 HIS A 217 GLN B 217 GLN C 217 GLN c 334 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.130236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.105610 restraints weight = 19426.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.109403 restraints weight = 12276.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.111902 restraints weight = 9220.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.113465 restraints weight = 7636.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.114362 restraints weight = 6730.231| |-----------------------------------------------------------------------------| r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.4578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 9705 Z= 0.228 Angle : 1.077 12.196 13272 Z= 0.505 Chirality : 0.055 0.311 1632 Planarity : 0.004 0.021 1557 Dihedral : 11.696 74.154 2514 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 6.10 % Allowed : 13.14 % Favored : 80.76 % Cbeta Deviations : 0.10 % 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 are not related in a simple way. whole: -0.41 (0.25), residues: 1056 helix: 0.62 (0.27), residues: 333 sheet: 0.05 (0.45), residues: 138 loop : -0.86 (0.26), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG a 355 TYR 0.018 0.001 TYR B 149 PHE 0.015 0.002 PHE c 292 TRP 0.021 0.002 TRP A 195 HIS 0.008 0.001 HIS c 304 Details of bonding type rmsd covalent geometry : bond 0.00496 ( 9618) covalent geometry : angle 0.93315 (13032) SS BOND : bond 0.00855 ( 21) SS BOND : angle 2.59722 ( 42) hydrogen bonds : bond 0.05474 ( 372) hydrogen bonds : angle 5.37803 ( 990) link_ALPHA1-3 : bond 0.00597 ( 3) link_ALPHA1-3 : angle 4.79859 ( 9) link_ALPHA1-6 : bond 0.00893 ( 3) link_ALPHA1-6 : angle 1.89059 ( 9) link_BETA1-4 : bond 0.01925 ( 27) link_BETA1-4 : angle 5.01685 ( 81) link_NAG-ASN : bond 0.00897 ( 33) link_NAG-ASN : angle 3.86648 ( 99) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 212 time to evaluate : 0.286 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: A 152 MET cc_start: 0.8112 (tmm) cc_final: 0.7731 (tmm) REVERT: A 171 TYR cc_start: 0.6747 (OUTLIER) cc_final: 0.5183 (p90) REVERT: A 230 CYS cc_start: 0.7600 (OUTLIER) cc_final: 0.7130 (m) REVERT: a 262 THR cc_start: 0.9415 (OUTLIER) cc_final: 0.9204 (m) REVERT: B 152 MET cc_start: 0.7764 (ttt) cc_final: 0.7383 (tmm) REVERT: B 191 MET cc_start: 0.7920 (mmt) cc_final: 0.7688 (mmt) REVERT: B 213 MET cc_start: 0.7175 (pmm) cc_final: 0.6795 (pmm) REVERT: b 262 THR cc_start: 0.9427 (OUTLIER) cc_final: 0.9100 (m) REVERT: b 401 ASP cc_start: 0.8295 (m-30) cc_final: 0.7910 (m-30) REVERT: C 152 MET cc_start: 0.8046 (tmm) cc_final: 0.7664 (tmm) REVERT: C 178 HIS cc_start: 0.6850 (OUTLIER) cc_final: 0.6586 (m-70) REVERT: C 230 CYS cc_start: 0.7718 (OUTLIER) cc_final: 0.7233 (m) REVERT: c 356 ASP cc_start: 0.8195 (t0) cc_final: 0.7983 (t0) REVERT: c 401 ASP cc_start: 0.8232 (m-30) cc_final: 0.7974 (m-30) REVERT: c 409 MET cc_start: 0.7029 (mtp) cc_final: 0.6798 (mtp) outliers start: 58 outliers final: 38 residues processed: 247 average time/residue: 0.1121 time to fit residues: 37.1195 Evaluate side-chains 220 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 176 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 195 TRP Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain a residue 262 THR Chi-restraints excluded: chain a residue 266 SER Chi-restraints excluded: chain a residue 283 MET Chi-restraints excluded: chain a residue 323 ARG Chi-restraints excluded: chain a residue 376 THR Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 179 CYS Chi-restraints excluded: chain B residue 195 TRP Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain b residue 260 THR Chi-restraints excluded: chain b residue 262 THR Chi-restraints excluded: chain b residue 266 SER Chi-restraints excluded: chain b residue 283 MET Chi-restraints excluded: chain b residue 291 CYS Chi-restraints excluded: chain b residue 360 ILE Chi-restraints excluded: chain b residue 376 THR Chi-restraints excluded: chain b residue 414 LEU Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 116 PHE Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 178 HIS Chi-restraints excluded: chain C residue 195 TRP Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain c residue 266 SER Chi-restraints excluded: chain c residue 291 CYS Chi-restraints excluded: chain c residue 323 ARG Chi-restraints excluded: chain c residue 360 ILE Chi-restraints excluded: chain c residue 376 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 66 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 chunk 98 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 93 optimal weight: 5.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 HIS ** A 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 HIS ** c 415 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 = 0.3910 r_free = 0.3910 target = 0.126289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.100377 restraints weight = 19620.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.104099 restraints weight = 12305.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.106505 restraints weight = 9310.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.108082 restraints weight = 7779.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.108943 restraints weight = 6888.565| |-----------------------------------------------------------------------------| r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.5169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 9705 Z= 0.274 Angle : 1.086 12.398 13272 Z= 0.505 Chirality : 0.056 0.358 1632 Planarity : 0.004 0.049 1557 Dihedral : 10.984 61.623 2514 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.43 % Favored : 91.57 % Rotamer: Outliers : 6.10 % Allowed : 15.77 % Favored : 78.13 % Cbeta Deviations : 0.10 % 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 are not related in a simple way. whole: -0.91 (0.25), residues: 1056 helix: 0.50 (0.26), residues: 354 sheet: -0.50 (0.41), residues: 153 loop : -1.39 (0.26), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG c 355 TYR 0.022 0.002 TYR a 418 PHE 0.018 0.003 PHE c 292 TRP 0.018 0.002 TRP A 195 HIS 0.013 0.002 HIS C 123 Details of bonding type rmsd covalent geometry : bond 0.00616 ( 9618) covalent geometry : angle 0.94781 (13032) SS BOND : bond 0.00993 ( 21) SS BOND : angle 3.13108 ( 42) hydrogen bonds : bond 0.05057 ( 372) hydrogen bonds : angle 5.48742 ( 990) link_ALPHA1-3 : bond 0.00674 ( 3) link_ALPHA1-3 : angle 5.07201 ( 9) link_ALPHA1-6 : bond 0.01160 ( 3) link_ALPHA1-6 : angle 2.07331 ( 9) link_BETA1-4 : bond 0.01777 ( 27) link_BETA1-4 : angle 4.92380 ( 81) link_NAG-ASN : bond 0.00788 ( 33) link_NAG-ASN : angle 3.63183 ( 99) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 194 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 MET cc_start: 0.8214 (tmm) cc_final: 0.7752 (tmm) REVERT: A 171 TYR cc_start: 0.6850 (OUTLIER) cc_final: 0.5225 (p90) REVERT: B 149 TYR cc_start: 0.6614 (m-80) cc_final: 0.6323 (m-10) REVERT: B 213 MET cc_start: 0.7429 (pmm) cc_final: 0.7102 (pmm) REVERT: b 310 ASP cc_start: 0.8728 (m-30) cc_final: 0.8300 (t0) REVERT: b 401 ASP cc_start: 0.8406 (m-30) cc_final: 0.8041 (m-30) REVERT: b 405 GLN cc_start: 0.8131 (tt0) cc_final: 0.7887 (tt0) REVERT: C 123 HIS cc_start: 0.7349 (OUTLIER) cc_final: 0.7135 (p-80) REVERT: C 133 MET cc_start: 0.7993 (tmm) cc_final: 0.7779 (tmm) REVERT: C 148 GLN cc_start: 0.8447 (mm110) cc_final: 0.8059 (tm-30) REVERT: C 191 MET cc_start: 0.8143 (mmm) cc_final: 0.7867 (mmm) REVERT: C 193 MET cc_start: 0.8606 (tpp) cc_final: 0.8391 (tpp) REVERT: c 304 HIS cc_start: 0.6847 (OUTLIER) cc_final: 0.6475 (p90) REVERT: c 356 ASP cc_start: 0.8183 (t0) cc_final: 0.7857 (t0) REVERT: c 409 MET cc_start: 0.7290 (mtp) cc_final: 0.7004 (mtp) outliers start: 58 outliers final: 39 residues processed: 229 average time/residue: 0.1088 time to fit residues: 33.8611 Evaluate side-chains 214 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 172 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 195 TRP Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain a residue 260 THR Chi-restraints excluded: chain a residue 266 SER Chi-restraints excluded: chain a residue 291 CYS Chi-restraints excluded: chain a residue 333 ILE Chi-restraints excluded: chain a residue 360 ILE Chi-restraints excluded: chain a residue 376 THR Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 195 TRP Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain b residue 266 SER Chi-restraints excluded: chain b residue 291 CYS Chi-restraints excluded: chain b residue 304 HIS Chi-restraints excluded: chain b residue 360 ILE Chi-restraints excluded: chain b residue 376 THR Chi-restraints excluded: chain b residue 414 LEU Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 116 PHE Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 123 HIS Chi-restraints excluded: chain C residue 171 TYR Chi-restraints excluded: chain C residue 195 TRP Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain c residue 266 SER Chi-restraints excluded: chain c residue 291 CYS Chi-restraints excluded: chain c residue 304 HIS Chi-restraints excluded: chain c residue 323 ARG Chi-restraints excluded: chain c residue 336 ILE Chi-restraints excluded: chain c residue 354 LEU Chi-restraints excluded: chain c residue 360 ILE Chi-restraints excluded: chain c residue 376 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 50 optimal weight: 3.9990 chunk 71 optimal weight: 0.5980 chunk 94 optimal weight: 0.7980 chunk 36 optimal weight: 0.5980 chunk 56 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 GLN ** b 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 415 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 = 0.3791 r_free = 0.3791 target = 0.120894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.095406 restraints weight = 18992.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.098283 restraints weight = 13447.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.100275 restraints weight = 10727.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.101602 restraints weight = 9187.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.102343 restraints weight = 8276.744| |-----------------------------------------------------------------------------| r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.5447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 9705 Z= 0.186 Angle : 0.993 13.649 13272 Z= 0.462 Chirality : 0.052 0.347 1632 Planarity : 0.003 0.027 1557 Dihedral : 10.431 59.956 2514 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.62 % Favored : 91.38 % Rotamer: Outliers : 5.68 % Allowed : 17.35 % Favored : 76.97 % Cbeta Deviations : 0.10 % 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 are not related in a simple way. whole: -0.78 (0.25), residues: 1056 helix: 0.58 (0.26), residues: 357 sheet: -0.33 (0.43), residues: 144 loop : -1.31 (0.26), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG b 383 TYR 0.021 0.001 TYR A 149 PHE 0.016 0.002 PHE c 292 TRP 0.018 0.001 TRP A 195 HIS 0.009 0.001 HIS C 123 Details of bonding type rmsd covalent geometry : bond 0.00413 ( 9618) covalent geometry : angle 0.86466 (13032) SS BOND : bond 0.00739 ( 21) SS BOND : angle 3.09908 ( 42) hydrogen bonds : bond 0.04587 ( 372) hydrogen bonds : angle 5.31180 ( 990) link_ALPHA1-3 : bond 0.00352 ( 3) link_ALPHA1-3 : angle 4.68326 ( 9) link_ALPHA1-6 : bond 0.01243 ( 3) link_ALPHA1-6 : angle 2.21111 ( 9) link_BETA1-4 : bond 0.01747 ( 27) link_BETA1-4 : angle 4.48168 ( 81) link_NAG-ASN : bond 0.00674 ( 33) link_NAG-ASN : angle 3.27400 ( 99) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 197 time to evaluate : 0.283 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: A 152 MET cc_start: 0.8243 (tmm) cc_final: 0.7746 (tmm) REVERT: A 171 TYR cc_start: 0.6881 (OUTLIER) cc_final: 0.5100 (p90) REVERT: a 338 LYS cc_start: 0.8348 (mtmt) cc_final: 0.8076 (mttt) REVERT: a 346 ASP cc_start: 0.7874 (t0) cc_final: 0.7049 (t0) REVERT: a 347 GLN cc_start: 0.8217 (mt0) cc_final: 0.8001 (mt0) REVERT: a 404 GLN cc_start: 0.7870 (tp40) cc_final: 0.7509 (tp40) REVERT: B 213 MET cc_start: 0.7397 (pmm) cc_final: 0.7056 (pmm) REVERT: b 310 ASP cc_start: 0.8524 (m-30) cc_final: 0.8096 (t0) REVERT: b 334 GLN cc_start: 0.7105 (pt0) cc_final: 0.6819 (mp10) REVERT: b 401 ASP cc_start: 0.8321 (m-30) cc_final: 0.8019 (m-30) REVERT: b 405 GLN cc_start: 0.8005 (tt0) cc_final: 0.6963 (tt0) REVERT: C 133 MET cc_start: 0.7983 (tmm) cc_final: 0.7678 (tmm) REVERT: C 148 GLN cc_start: 0.8479 (mm110) cc_final: 0.7987 (tm-30) REVERT: C 152 MET cc_start: 0.7964 (tmm) cc_final: 0.7600 (tmm) REVERT: C 191 MET cc_start: 0.8027 (mmm) cc_final: 0.7691 (mmm) REVERT: c 304 HIS cc_start: 0.6951 (OUTLIER) cc_final: 0.6527 (p90) REVERT: c 356 ASP cc_start: 0.8099 (t0) cc_final: 0.7786 (t0) outliers start: 54 outliers final: 37 residues processed: 230 average time/residue: 0.1154 time to fit residues: 35.5927 Evaluate side-chains 209 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 170 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 195 TRP Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain a residue 266 SER Chi-restraints excluded: chain a residue 283 MET Chi-restraints excluded: chain a residue 323 ARG Chi-restraints excluded: chain a residue 359 CYS Chi-restraints excluded: chain a residue 360 ILE Chi-restraints excluded: chain a residue 376 THR Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 123 HIS Chi-restraints excluded: chain B residue 195 TRP Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain b residue 260 THR Chi-restraints excluded: chain b residue 266 SER Chi-restraints excluded: chain b residue 283 MET Chi-restraints excluded: chain b residue 291 CYS Chi-restraints excluded: chain b residue 304 HIS Chi-restraints excluded: chain b residue 359 CYS Chi-restraints excluded: chain b residue 360 ILE Chi-restraints excluded: chain b residue 376 THR Chi-restraints excluded: chain b residue 414 LEU Chi-restraints excluded: chain C residue 116 PHE Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 195 TRP Chi-restraints excluded: chain c residue 266 SER Chi-restraints excluded: chain c residue 291 CYS Chi-restraints excluded: chain c residue 304 HIS Chi-restraints excluded: chain c residue 323 ARG Chi-restraints excluded: chain c residue 334 GLN Chi-restraints excluded: chain c residue 354 LEU Chi-restraints excluded: chain c residue 360 ILE Chi-restraints excluded: chain c residue 376 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 12 optimal weight: 9.9990 chunk 77 optimal weight: 3.9990 chunk 22 optimal weight: 0.2980 chunk 4 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 69 optimal weight: 0.0670 chunk 84 optimal weight: 8.9990 chunk 8 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 overall best weight: 0.8720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 GLN a 337 ASN b 301 ASN ** b 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 415 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 = 0.3818 r_free = 0.3818 target = 0.123868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.099881 restraints weight = 18525.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.102544 restraints weight = 13379.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.104372 restraints weight = 10771.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.105605 restraints weight = 9272.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.106442 restraints weight = 8362.815| |-----------------------------------------------------------------------------| r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.5678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 9705 Z= 0.188 Angle : 0.994 13.618 13272 Z= 0.463 Chirality : 0.052 0.366 1632 Planarity : 0.003 0.030 1557 Dihedral : 10.031 59.194 2514 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.56 % Favored : 90.44 % Rotamer: Outliers : 6.10 % Allowed : 18.30 % Favored : 75.60 % Cbeta Deviations : 0.10 % 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 are not related in a simple way. whole: -0.84 (0.25), residues: 1056 helix: 0.61 (0.27), residues: 354 sheet: -0.54 (0.41), residues: 153 loop : -1.36 (0.26), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG b 383 TYR 0.026 0.001 TYR B 149 PHE 0.014 0.002 PHE c 292 TRP 0.016 0.002 TRP A 195 HIS 0.007 0.001 HIS C 123 Details of bonding type rmsd covalent geometry : bond 0.00420 ( 9618) covalent geometry : angle 0.86575 (13032) SS BOND : bond 0.00824 ( 21) SS BOND : angle 3.71802 ( 42) hydrogen bonds : bond 0.04415 ( 372) hydrogen bonds : angle 5.23309 ( 990) link_ALPHA1-3 : bond 0.00374 ( 3) link_ALPHA1-3 : angle 4.75052 ( 9) link_ALPHA1-6 : bond 0.01180 ( 3) link_ALPHA1-6 : angle 2.10475 ( 9) link_BETA1-4 : bond 0.01669 ( 27) link_BETA1-4 : angle 4.35489 ( 81) link_NAG-ASN : bond 0.00683 ( 33) link_NAG-ASN : angle 3.13978 ( 99) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 179 time to evaluate : 0.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 MET cc_start: 0.8255 (tmm) cc_final: 0.7877 (tmm) REVERT: A 171 TYR cc_start: 0.6690 (OUTLIER) cc_final: 0.5019 (p90) REVERT: a 334 GLN cc_start: 0.7140 (pp30) cc_final: 0.6831 (pp30) REVERT: a 338 LYS cc_start: 0.8290 (mtmt) cc_final: 0.8089 (mttt) REVERT: b 306 GLU cc_start: 0.8059 (mm-30) cc_final: 0.7654 (mm-30) REVERT: b 310 ASP cc_start: 0.8373 (m-30) cc_final: 0.8105 (t0) REVERT: b 401 ASP cc_start: 0.8274 (m-30) cc_final: 0.7890 (m-30) REVERT: C 148 GLN cc_start: 0.8409 (mm110) cc_final: 0.7998 (tm-30) REVERT: C 152 MET cc_start: 0.7866 (tmm) cc_final: 0.7554 (tmm) REVERT: C 191 MET cc_start: 0.7911 (mmm) cc_final: 0.7669 (mmt) REVERT: C 193 MET cc_start: 0.8199 (tpp) cc_final: 0.7978 (tpp) REVERT: c 304 HIS cc_start: 0.6854 (OUTLIER) cc_final: 0.6467 (p90) REVERT: c 356 ASP cc_start: 0.7961 (t0) cc_final: 0.7707 (t0) REVERT: c 404 GLN cc_start: 0.7845 (tp40) cc_final: 0.7214 (tp40) outliers start: 58 outliers final: 42 residues processed: 217 average time/residue: 0.1020 time to fit residues: 29.8868 Evaluate side-chains 207 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 163 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 CYS Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 195 TRP Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain a residue 266 SER Chi-restraints excluded: chain a residue 291 CYS Chi-restraints excluded: chain a residue 292 PHE Chi-restraints excluded: chain a residue 323 ARG Chi-restraints excluded: chain a residue 337 ASN Chi-restraints excluded: chain a residue 359 CYS Chi-restraints excluded: chain a residue 360 ILE Chi-restraints excluded: chain a residue 376 THR Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 123 HIS Chi-restraints excluded: chain B residue 195 TRP Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain b residue 266 SER Chi-restraints excluded: chain b residue 291 CYS Chi-restraints excluded: chain b residue 304 HIS Chi-restraints excluded: chain b residue 359 CYS Chi-restraints excluded: chain b residue 360 ILE Chi-restraints excluded: chain b residue 376 THR Chi-restraints excluded: chain b residue 387 VAL Chi-restraints excluded: chain b residue 414 LEU Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 91 HIS Chi-restraints excluded: chain C residue 116 PHE Chi-restraints excluded: chain C residue 123 HIS Chi-restraints excluded: chain C residue 171 TYR Chi-restraints excluded: chain C residue 195 TRP Chi-restraints excluded: chain c residue 266 SER Chi-restraints excluded: chain c residue 291 CYS Chi-restraints excluded: chain c residue 304 HIS Chi-restraints excluded: chain c residue 323 ARG Chi-restraints excluded: chain c residue 336 ILE Chi-restraints excluded: chain c residue 354 LEU Chi-restraints excluded: chain c residue 359 CYS Chi-restraints excluded: chain c residue 360 ILE Chi-restraints excluded: chain c residue 376 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 5 optimal weight: 0.8980 chunk 59 optimal weight: 0.6980 chunk 92 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 67 optimal weight: 0.8980 chunk 102 optimal weight: 0.7980 chunk 49 optimal weight: 0.0970 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 337 ASN ** b 304 HIS ** 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 = 0.3824 r_free = 0.3824 target = 0.123712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.099434 restraints weight = 18801.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.102156 restraints weight = 13510.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.104038 restraints weight = 10878.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.105279 restraints weight = 9365.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 16)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.105993 restraints weight = 8448.230| |-----------------------------------------------------------------------------| r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.5901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 9705 Z= 0.182 Angle : 1.003 14.186 13272 Z= 0.467 Chirality : 0.052 0.373 1632 Planarity : 0.003 0.031 1557 Dihedral : 9.370 59.490 2514 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.47 % Favored : 90.44 % Rotamer: Outliers : 5.57 % Allowed : 18.09 % Favored : 76.34 % 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 are not related in a simple way. whole: -0.79 (0.26), residues: 1056 helix: 0.61 (0.27), residues: 357 sheet: -0.26 (0.43), residues: 144 loop : -1.39 (0.26), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG b 383 TYR 0.030 0.001 TYR A 149 PHE 0.017 0.002 PHE A 116 TRP 0.016 0.001 TRP A 195 HIS 0.006 0.001 HIS C 123 Details of bonding type rmsd covalent geometry : bond 0.00411 ( 9618) covalent geometry : angle 0.87451 (13032) SS BOND : bond 0.00612 ( 21) SS BOND : angle 4.26587 ( 42) hydrogen bonds : bond 0.04269 ( 372) hydrogen bonds : angle 5.19755 ( 990) link_ALPHA1-3 : bond 0.00284 ( 3) link_ALPHA1-3 : angle 4.83693 ( 9) link_ALPHA1-6 : bond 0.01284 ( 3) link_ALPHA1-6 : angle 1.58211 ( 9) link_BETA1-4 : bond 0.01669 ( 27) link_BETA1-4 : angle 4.24553 ( 81) link_NAG-ASN : bond 0.00721 ( 33) link_NAG-ASN : angle 3.07488 ( 99) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 176 time to evaluate : 0.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 MET cc_start: 0.8209 (tmm) cc_final: 0.7845 (tmm) REVERT: A 171 TYR cc_start: 0.6723 (OUTLIER) cc_final: 0.5029 (p90) REVERT: A 199 TYR cc_start: 0.6469 (OUTLIER) cc_final: 0.4948 (m-80) REVERT: a 404 GLN cc_start: 0.7814 (tp40) cc_final: 0.7514 (tp40) REVERT: B 152 MET cc_start: 0.7886 (tmm) cc_final: 0.7594 (tmm) REVERT: b 331 MET cc_start: 0.5122 (tpt) cc_final: 0.4819 (ptt) REVERT: b 352 ASN cc_start: 0.8940 (m-40) cc_final: 0.8678 (m-40) REVERT: b 401 ASP cc_start: 0.8255 (m-30) cc_final: 0.7982 (m-30) REVERT: b 405 GLN cc_start: 0.7927 (tt0) cc_final: 0.7340 (tt0) REVERT: C 152 MET cc_start: 0.7938 (tmm) cc_final: 0.7585 (tmm) REVERT: C 193 MET cc_start: 0.8203 (tpp) cc_final: 0.7959 (tpp) REVERT: c 356 ASP cc_start: 0.7934 (t0) cc_final: 0.7700 (t0) outliers start: 53 outliers final: 39 residues processed: 212 average time/residue: 0.1113 time to fit residues: 31.6982 Evaluate side-chains 207 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 166 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 91 HIS Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 195 TRP Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain a residue 266 SER Chi-restraints excluded: chain a residue 291 CYS Chi-restraints excluded: chain a residue 292 PHE Chi-restraints excluded: chain a residue 323 ARG Chi-restraints excluded: chain a residue 360 ILE Chi-restraints excluded: chain a residue 376 THR Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 123 HIS Chi-restraints excluded: chain B residue 195 TRP Chi-restraints excluded: chain B residue 211 CYS Chi-restraints excluded: chain b residue 266 SER Chi-restraints excluded: chain b residue 291 CYS Chi-restraints excluded: chain b residue 304 HIS Chi-restraints excluded: chain b residue 359 CYS Chi-restraints excluded: chain b residue 360 ILE Chi-restraints excluded: chain b residue 387 VAL Chi-restraints excluded: chain b residue 414 LEU Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 116 PHE Chi-restraints excluded: chain C residue 123 HIS Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 171 TYR Chi-restraints excluded: chain C residue 195 TRP Chi-restraints excluded: chain c residue 266 SER Chi-restraints excluded: chain c residue 291 CYS Chi-restraints excluded: chain c residue 292 PHE Chi-restraints excluded: chain c residue 323 ARG Chi-restraints excluded: chain c residue 336 ILE Chi-restraints excluded: chain c residue 354 LEU Chi-restraints excluded: chain c residue 359 CYS Chi-restraints excluded: chain c residue 360 ILE Chi-restraints excluded: chain c residue 376 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 35 optimal weight: 5.9990 chunk 23 optimal weight: 8.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 94 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 49 optimal weight: 5.9990 chunk 17 optimal weight: 0.8980 chunk 56 optimal weight: 0.8980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.122140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.098011 restraints weight = 18740.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.100596 restraints weight = 13582.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.102361 restraints weight = 11016.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.103572 restraints weight = 9544.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.104383 restraints weight = 8637.799| |-----------------------------------------------------------------------------| r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.6039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 9705 Z= 0.202 Angle : 1.015 11.861 13272 Z= 0.475 Chirality : 0.054 0.388 1632 Planarity : 0.003 0.032 1557 Dihedral : 9.030 58.618 2514 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.75 % Favored : 90.25 % Rotamer: Outliers : 5.15 % Allowed : 18.51 % Favored : 76.34 % 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 are not related in a simple way. whole: -0.87 (0.26), residues: 1056 helix: 0.74 (0.27), residues: 354 sheet: -0.61 (0.42), residues: 153 loop : -1.48 (0.27), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG b 383 TYR 0.021 0.001 TYR B 149 PHE 0.014 0.002 PHE B 156 TRP 0.015 0.002 TRP A 195 HIS 0.005 0.001 HIS c 304 Details of bonding type rmsd covalent geometry : bond 0.00463 ( 9618) covalent geometry : angle 0.89256 (13032) SS BOND : bond 0.00597 ( 21) SS BOND : angle 3.93327 ( 42) hydrogen bonds : bond 0.04267 ( 372) hydrogen bonds : angle 5.21496 ( 990) link_ALPHA1-3 : bond 0.00420 ( 3) link_ALPHA1-3 : angle 4.82562 ( 9) link_ALPHA1-6 : bond 0.01441 ( 3) link_ALPHA1-6 : angle 0.93078 ( 9) link_BETA1-4 : bond 0.01583 ( 27) link_BETA1-4 : angle 4.20636 ( 81) link_NAG-ASN : bond 0.00729 ( 33) link_NAG-ASN : angle 3.15991 ( 99) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 173 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 MET cc_start: 0.8160 (tmm) cc_final: 0.7854 (tmm) REVERT: A 171 TYR cc_start: 0.6779 (OUTLIER) cc_final: 0.5171 (p90) REVERT: A 199 TYR cc_start: 0.6570 (OUTLIER) cc_final: 0.5044 (m-80) REVERT: a 331 MET cc_start: 0.4178 (tpt) cc_final: 0.3879 (ptp) REVERT: a 404 GLN cc_start: 0.7897 (tp40) cc_final: 0.7560 (tp40) REVERT: B 123 HIS cc_start: 0.7261 (OUTLIER) cc_final: 0.7042 (p-80) REVERT: B 152 MET cc_start: 0.7914 (tmm) cc_final: 0.7594 (tmm) REVERT: b 306 GLU cc_start: 0.7938 (mm-30) cc_final: 0.7564 (mm-30) REVERT: b 352 ASN cc_start: 0.8960 (m-40) cc_final: 0.8732 (m-40) REVERT: b 401 ASP cc_start: 0.8281 (m-30) cc_final: 0.7909 (m-30) REVERT: C 152 MET cc_start: 0.7978 (tmm) cc_final: 0.7703 (tmm) REVERT: c 409 MET cc_start: 0.7248 (mtp) cc_final: 0.6957 (mtp) REVERT: c 417 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7562 (pm20) outliers start: 49 outliers final: 41 residues processed: 204 average time/residue: 0.1128 time to fit residues: 31.1096 Evaluate side-chains 210 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 165 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 91 HIS Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 123 HIS Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 195 TRP Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain a residue 266 SER Chi-restraints excluded: chain a residue 291 CYS Chi-restraints excluded: chain a residue 292 PHE Chi-restraints excluded: chain a residue 359 CYS Chi-restraints excluded: chain a residue 360 ILE Chi-restraints excluded: chain a residue 376 THR Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain B residue 123 HIS Chi-restraints excluded: chain B residue 195 TRP Chi-restraints excluded: chain b residue 260 THR Chi-restraints excluded: chain b residue 266 SER Chi-restraints excluded: chain b residue 291 CYS Chi-restraints excluded: chain b residue 304 HIS Chi-restraints excluded: chain b residue 359 CYS Chi-restraints excluded: chain b residue 360 ILE Chi-restraints excluded: chain b residue 376 THR Chi-restraints excluded: chain b residue 387 VAL Chi-restraints excluded: chain b residue 414 LEU Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 116 PHE Chi-restraints excluded: chain C residue 123 HIS Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 171 TYR Chi-restraints excluded: chain C residue 195 TRP Chi-restraints excluded: chain c residue 266 SER Chi-restraints excluded: chain c residue 291 CYS Chi-restraints excluded: chain c residue 292 PHE Chi-restraints excluded: chain c residue 304 HIS Chi-restraints excluded: chain c residue 323 ARG Chi-restraints excluded: chain c residue 336 ILE Chi-restraints excluded: chain c residue 354 LEU Chi-restraints excluded: chain c residue 359 CYS Chi-restraints excluded: chain c residue 360 ILE Chi-restraints excluded: chain c residue 376 THR Chi-restraints excluded: chain c residue 417 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 73 optimal weight: 1.9990 chunk 81 optimal weight: 20.0000 chunk 5 optimal weight: 0.7980 chunk 59 optimal weight: 0.6980 chunk 77 optimal weight: 0.8980 chunk 60 optimal weight: 0.0270 chunk 19 optimal weight: 0.0570 chunk 102 optimal weight: 0.7980 chunk 20 optimal weight: 0.5980 chunk 69 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 overall best weight: 0.4356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.123405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.096853 restraints weight = 19261.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.100111 restraints weight = 13093.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.102311 restraints weight = 10267.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.103781 restraints weight = 8732.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.104778 restraints weight = 7813.986| |-----------------------------------------------------------------------------| r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.6256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 9705 Z= 0.175 Angle : 0.981 14.310 13272 Z= 0.460 Chirality : 0.052 0.382 1632 Planarity : 0.003 0.030 1557 Dihedral : 8.773 58.534 2514 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.71 % Favored : 91.29 % Rotamer: Outliers : 4.00 % Allowed : 19.77 % Favored : 76.24 % 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 are not related in a simple way. whole: -0.94 (0.26), residues: 1056 helix: 0.55 (0.27), residues: 360 sheet: -0.70 (0.42), residues: 156 loop : -1.42 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG b 383 TYR 0.022 0.001 TYR B 149 PHE 0.041 0.002 PHE B 116 TRP 0.015 0.001 TRP A 195 HIS 0.004 0.001 HIS c 304 Details of bonding type rmsd covalent geometry : bond 0.00392 ( 9618) covalent geometry : angle 0.86878 (13032) SS BOND : bond 0.00640 ( 21) SS BOND : angle 3.89349 ( 42) hydrogen bonds : bond 0.04126 ( 372) hydrogen bonds : angle 5.12729 ( 990) link_ALPHA1-3 : bond 0.00352 ( 3) link_ALPHA1-3 : angle 4.74828 ( 9) link_ALPHA1-6 : bond 0.01277 ( 3) link_ALPHA1-6 : angle 0.98707 ( 9) link_BETA1-4 : bond 0.01556 ( 27) link_BETA1-4 : angle 3.96564 ( 81) link_NAG-ASN : bond 0.00670 ( 33) link_NAG-ASN : angle 2.85642 ( 99) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 182 time to evaluate : 0.374 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: A 152 MET cc_start: 0.8189 (tmm) cc_final: 0.7675 (tmm) REVERT: A 171 TYR cc_start: 0.7091 (OUTLIER) cc_final: 0.5545 (p90) REVERT: A 199 TYR cc_start: 0.6657 (OUTLIER) cc_final: 0.5156 (m-80) REVERT: a 404 GLN cc_start: 0.7966 (tp40) cc_final: 0.7616 (tp40) REVERT: B 152 MET cc_start: 0.8030 (tmm) cc_final: 0.7826 (tmm) REVERT: B 246 GLN cc_start: 0.7140 (tm-30) cc_final: 0.6287 (tm-30) REVERT: b 331 MET cc_start: 0.5372 (tpt) cc_final: 0.5134 (ppp) REVERT: b 352 ASN cc_start: 0.8925 (m-40) cc_final: 0.8679 (m-40) REVERT: b 401 ASP cc_start: 0.8377 (m-30) cc_final: 0.8091 (m-30) REVERT: C 152 MET cc_start: 0.8073 (tmm) cc_final: 0.7762 (tmm) REVERT: c 404 GLN cc_start: 0.7888 (tp40) cc_final: 0.7573 (tp40) REVERT: c 409 MET cc_start: 0.7373 (mtp) cc_final: 0.7122 (mtp) outliers start: 38 outliers final: 31 residues processed: 208 average time/residue: 0.1107 time to fit residues: 31.1644 Evaluate side-chains 205 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 172 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 HIS Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 123 HIS Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 195 TRP Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain a residue 266 SER Chi-restraints excluded: chain a residue 291 CYS Chi-restraints excluded: chain a residue 292 PHE Chi-restraints excluded: chain a residue 359 CYS Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain B residue 195 TRP Chi-restraints excluded: chain b residue 266 SER Chi-restraints excluded: chain b residue 291 CYS Chi-restraints excluded: chain b residue 359 CYS Chi-restraints excluded: chain b residue 376 THR Chi-restraints excluded: chain b residue 387 VAL Chi-restraints excluded: chain b residue 414 LEU Chi-restraints excluded: chain C residue 116 PHE Chi-restraints excluded: chain C residue 123 HIS Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 171 TYR Chi-restraints excluded: chain C residue 195 TRP Chi-restraints excluded: chain c residue 266 SER Chi-restraints excluded: chain c residue 291 CYS Chi-restraints excluded: chain c residue 292 PHE Chi-restraints excluded: chain c residue 304 HIS Chi-restraints excluded: chain c residue 336 ILE Chi-restraints excluded: chain c residue 354 LEU Chi-restraints excluded: chain c residue 359 CYS Chi-restraints excluded: chain c residue 360 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 51 optimal weight: 0.0170 chunk 87 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 chunk 92 optimal weight: 0.7980 chunk 16 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 93 optimal weight: 6.9990 chunk 52 optimal weight: 0.9980 chunk 99 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.122914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.097054 restraints weight = 19415.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.100046 restraints weight = 13578.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.102086 restraints weight = 10817.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.103408 restraints weight = 9283.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.104270 restraints weight = 8398.911| |-----------------------------------------------------------------------------| r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.6358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 9705 Z= 0.179 Angle : 0.990 13.855 13272 Z= 0.465 Chirality : 0.052 0.367 1632 Planarity : 0.003 0.033 1557 Dihedral : 8.810 58.469 2514 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.28 % Favored : 90.72 % Rotamer: Outliers : 3.79 % Allowed : 20.19 % Favored : 76.03 % 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 are not related in a simple way. whole: -0.92 (0.26), residues: 1056 helix: 0.65 (0.28), residues: 357 sheet: -0.73 (0.42), residues: 156 loop : -1.46 (0.27), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG b 383 TYR 0.021 0.001 TYR B 149 PHE 0.027 0.002 PHE B 116 TRP 0.014 0.001 TRP b 282 HIS 0.004 0.001 HIS C 123 Details of bonding type rmsd covalent geometry : bond 0.00403 ( 9618) covalent geometry : angle 0.88639 (13032) SS BOND : bond 0.00613 ( 21) SS BOND : angle 3.66193 ( 42) hydrogen bonds : bond 0.04057 ( 372) hydrogen bonds : angle 5.09383 ( 990) link_ALPHA1-3 : bond 0.00368 ( 3) link_ALPHA1-3 : angle 4.60128 ( 9) link_ALPHA1-6 : bond 0.01226 ( 3) link_ALPHA1-6 : angle 1.00247 ( 9) link_BETA1-4 : bond 0.01521 ( 27) link_BETA1-4 : angle 3.90351 ( 81) link_NAG-ASN : bond 0.00674 ( 33) link_NAG-ASN : angle 2.77184 ( 99) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 189 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 MET cc_start: 0.8110 (tmm) cc_final: 0.7644 (tmm) REVERT: A 171 TYR cc_start: 0.7073 (OUTLIER) cc_final: 0.5540 (p90) REVERT: A 199 TYR cc_start: 0.6669 (OUTLIER) cc_final: 0.5049 (m-80) REVERT: a 331 MET cc_start: 0.4235 (tpt) cc_final: 0.3785 (ptt) REVERT: a 404 GLN cc_start: 0.7942 (tp40) cc_final: 0.7585 (tp40) REVERT: B 152 MET cc_start: 0.8021 (tmm) cc_final: 0.7756 (tmm) REVERT: b 302 GLU cc_start: 0.7001 (tp30) cc_final: 0.6756 (tp30) REVERT: b 310 ASP cc_start: 0.8023 (t0) cc_final: 0.7823 (t0) REVERT: b 352 ASN cc_start: 0.8913 (m-40) cc_final: 0.8638 (m-40) REVERT: b 401 ASP cc_start: 0.8340 (m-30) cc_final: 0.7967 (m-30) REVERT: C 152 MET cc_start: 0.8067 (tmm) cc_final: 0.7774 (tmm) REVERT: c 409 MET cc_start: 0.7361 (mtp) cc_final: 0.7125 (mtp) outliers start: 36 outliers final: 33 residues processed: 215 average time/residue: 0.1074 time to fit residues: 31.3225 Evaluate side-chains 214 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 179 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 HIS Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 123 HIS Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 195 TRP Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain a residue 266 SER Chi-restraints excluded: chain a residue 291 CYS Chi-restraints excluded: chain a residue 292 PHE Chi-restraints excluded: chain a residue 359 CYS Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain B residue 123 HIS Chi-restraints excluded: chain B residue 195 TRP Chi-restraints excluded: chain b residue 266 SER Chi-restraints excluded: chain b residue 291 CYS Chi-restraints excluded: chain b residue 304 HIS Chi-restraints excluded: chain b residue 359 CYS Chi-restraints excluded: chain b residue 376 THR Chi-restraints excluded: chain b residue 387 VAL Chi-restraints excluded: chain b residue 414 LEU Chi-restraints excluded: chain C residue 116 PHE Chi-restraints excluded: chain C residue 123 HIS Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 171 TYR Chi-restraints excluded: chain C residue 195 TRP Chi-restraints excluded: chain c residue 266 SER Chi-restraints excluded: chain c residue 291 CYS Chi-restraints excluded: chain c residue 292 PHE Chi-restraints excluded: chain c residue 331 MET Chi-restraints excluded: chain c residue 336 ILE Chi-restraints excluded: chain c residue 354 LEU Chi-restraints excluded: chain c residue 359 CYS Chi-restraints excluded: chain c residue 360 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 82 optimal weight: 0.9990 chunk 65 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 14 optimal weight: 0.7980 chunk 18 optimal weight: 4.9990 chunk 29 optimal weight: 0.6980 chunk 68 optimal weight: 0.9990 chunk 26 optimal weight: 0.0370 chunk 22 optimal weight: 3.9990 overall best weight: 0.7062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 405 GLN ** C 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.122975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.097066 restraints weight = 19374.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.099927 restraints weight = 13761.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.101830 restraints weight = 11096.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.103132 restraints weight = 9624.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.103754 restraints weight = 8738.954| |-----------------------------------------------------------------------------| r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.6502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 9705 Z= 0.180 Angle : 0.990 13.095 13272 Z= 0.465 Chirality : 0.052 0.357 1632 Planarity : 0.003 0.029 1557 Dihedral : 8.798 58.859 2514 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.81 % Favored : 91.19 % Rotamer: Outliers : 4.00 % Allowed : 20.93 % Favored : 75.08 % 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 are not related in a simple way. whole: -0.90 (0.26), residues: 1056 helix: 0.73 (0.28), residues: 354 sheet: -0.70 (0.42), residues: 156 loop : -1.48 (0.27), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG a 383 TYR 0.027 0.001 TYR B 149 PHE 0.025 0.002 PHE B 116 TRP 0.013 0.001 TRP b 282 HIS 0.004 0.001 HIS a 304 Details of bonding type rmsd covalent geometry : bond 0.00409 ( 9618) covalent geometry : angle 0.89018 (13032) SS BOND : bond 0.00620 ( 21) SS BOND : angle 3.61445 ( 42) hydrogen bonds : bond 0.04011 ( 372) hydrogen bonds : angle 5.12271 ( 990) link_ALPHA1-3 : bond 0.00413 ( 3) link_ALPHA1-3 : angle 4.54227 ( 9) link_ALPHA1-6 : bond 0.01197 ( 3) link_ALPHA1-6 : angle 1.01853 ( 9) link_BETA1-4 : bond 0.01498 ( 27) link_BETA1-4 : angle 3.85121 ( 81) link_NAG-ASN : bond 0.00629 ( 33) link_NAG-ASN : angle 2.72262 ( 99) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1555.33 seconds wall clock time: 27 minutes 48.22 seconds (1668.22 seconds total)