Starting phenix.real_space_refine on Thu Jul 2 17:47:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8eje_28179/07_2026/8eje_28179.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eje_28179/07_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_28179/07_2026/8eje_28179.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eje_28179/07_2026/8eje_28179.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8eje_28179/07_2026/8eje_28179.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eje_28179/07_2026/8eje_28179.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8eje_28179/07_2026/8eje_28179.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8eje_28179/07_2026/8eje_28179.cif" } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 chiralities: 2 Time building chain proxies: 1.62, per 1000 atoms: 0.17 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: 1.05 Conformation dependent library (CDL) restraints added in 271.4 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: 0.27 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: 1.40 Time building geometry restraints manager: 1.27 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 - 16.94: 4986 16.94 - 33.89: 177 33.89 - 50.83: 33 50.83 - 67.78: 21 67.78 - 84.72: 12 Dihedral angle restraints: 5229 sinusoidal: 2094 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 5226 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: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 8.530 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 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 : 11.053 84.721 3150 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/Z covalent geometry : bond 0.02349 / 1.25 ( 9618) covalent geometry : angle 2.13907 / 1.26 (13032) SS BOND : bond 0.01224 / 0.70 ( 21) SS BOND : angle 3.49875 / 2.26 ( 42) hydrogen bonds : bond 0.17248 / 11.35 ( 372) hydrogen bonds : angle 6.30877 / 4.56 ( 990) link_ALPHA1-3 : bond 0.10501 / 4.85 ( 3) link_ALPHA1-3 : angle 7.62833 / 4.39 ( 9) link_ALPHA1-6 : bond 0.04870 / 2.25 ( 3) link_ALPHA1-6 : angle 3.60915 / 2.07 ( 9) link_BETA1-4 : bond 0.07711 / 4.46 ( 27) link_BETA1-4 : angle 6.86572 / 4.26 ( 81) link_NAG-ASN : bond 0.08075 / 4.70 ( 33) link_NAG-ASN : angle 4.59387 / 2.59 ( 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 : 0.314 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: 0.1012 time to fit residues: 48.1217 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 : 0.367 ------------------------------------------------------------------------------- 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... A 188 GLN ** a 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 415 GLN B 130 HIS b 330 GLN b 334 GLN b 415 GLN C 130 HIS c 330 GLN c 353 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.133267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.108798 restraints weight = 19434.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.112689 restraints weight = 12195.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.115250 restraints weight = 9118.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.116893 restraints weight = 7509.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.117989 restraints weight = 6572.404| |-----------------------------------------------------------------------------| r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.3914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 9705 Z= 0.245 Angle : 1.209 13.035 13272 Z= 0.571 Chirality : 0.055 0.295 1632 Planarity : 0.005 0.029 1557 Dihedral : 6.149 31.559 1152 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 4.63 % Allowed : 12.41 % Favored : 82.97 % 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: -0.29 (0.25), residues: 1056 helix: 0.52 (0.27), residues: 336 sheet: 0.55 (0.43), residues: 144 loop : -0.80 (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 0.023 0.003 PHE A 116 TRP 0.024 0.002 TRP A 195 HIS 0.023 0.003 HIS C 123 Details of bonding type rmsd/Z covalent geometry : bond 0.00508 / 0.24 ( 9618) covalent geometry : angle 1.05587 / 0.54 (13032) SS BOND : bond 0.00549 / 0.27 ( 21) SS BOND : angle 2.59957 / 1.44 ( 42) hydrogen bonds : bond 0.06608 / 4.29 ( 372) hydrogen bonds : angle 5.43661 / 3.86 ( 990) link_ALPHA1-3 : bond 0.01196 / 0.55 ( 3) link_ALPHA1-3 : angle 3.23767 / 1.84 ( 9) link_ALPHA1-6 : bond 0.00971 / 0.45 ( 3) link_ALPHA1-6 : angle 1.17221 / 0.70 ( 9) link_BETA1-4 : bond 0.02053 / 1.17 ( 27) link_BETA1-4 : angle 5.51967 / 3.36 ( 81) link_NAG-ASN : bond 0.01307 / 0.67 ( 33) link_NAG-ASN : angle 4.49480 / 2.70 ( 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 278 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 234 time to evaluate : 0.208 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 171 TYR cc_start: 0.6653 (OUTLIER) cc_final: 0.4914 (p90) REVERT: a 400 ASP cc_start: 0.8015 (OUTLIER) cc_final: 0.7777 (p0) REVERT: B 129 ASP cc_start: 0.7933 (t0) cc_final: 0.7712 (m-30) REVERT: b 383 ARG cc_start: 0.7850 (ttm110) cc_final: 0.7647 (ttm110) REVERT: b 401 ASP cc_start: 0.8158 (m-30) cc_final: 0.7864 (m-30) REVERT: C 149 TYR cc_start: 0.6644 (m-80) cc_final: 0.6146 (m-10) REVERT: C 229 HIS cc_start: 0.7650 (m-70) cc_final: 0.7225 (m-70) REVERT: c 401 ASP cc_start: 0.8171 (m-30) cc_final: 0.7947 (m-30) REVERT: c 409 MET cc_start: 0.7086 (mtp) cc_final: 0.6743 (mtp) outliers start: 44 outliers final: 24 residues processed: 258 average time/residue: 0.0980 time to fit residues: 34.2103 Evaluate side-chains 210 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 184 time to evaluate : 0.251 ------------------------------------------------------------------------------- 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 266 SER 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 266 SER 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 357 ILE 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: 6.9990 chunk 45 optimal weight: 4.9990 chunk 58 optimal weight: 8.9990 chunk 41 optimal weight: 20.0000 chunk 84 optimal weight: 5.9990 chunk 7 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 75 optimal weight: 0.5980 chunk 85 optimal weight: 4.9990 chunk 94 optimal weight: 0.9980 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 169 HIS A 217 GLN B 217 GLN b 330 GLN C 217 GLN c 334 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.127792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.103275 restraints weight = 19164.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.107090 restraints weight = 11756.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.109543 restraints weight = 8711.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.111098 restraints weight = 7166.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.112158 restraints weight = 6275.188| |-----------------------------------------------------------------------------| r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.4615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 9705 Z= 0.261 Angle : 1.098 12.395 13272 Z= 0.515 Chirality : 0.054 0.268 1632 Planarity : 0.004 0.025 1557 Dihedral : 6.076 26.689 1152 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 6.62 % Allowed : 13.67 % Favored : 79.71 % 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: -0.39 (0.25), residues: 1056 helix: 0.76 (0.27), residues: 333 sheet: -0.05 (0.44), residues: 144 loop : -0.91 (0.26), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG a 355 TYR 0.021 0.002 TYR c 418 PHE 0.015 0.002 PHE a 292 TRP 0.021 0.002 TRP A 195 HIS 0.009 0.001 HIS c 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00582 / 0.25 ( 9618) covalent geometry : angle 0.96173 / 0.48 (13032) SS BOND : bond 0.00810 / 0.41 ( 21) SS BOND : angle 2.95767 / 1.77 ( 42) hydrogen bonds : bond 0.05515 / 3.56 ( 372) hydrogen bonds : angle 5.47244 / 3.84 ( 990) link_ALPHA1-3 : bond 0.01160 / 0.54 ( 3) link_ALPHA1-3 : angle 3.57014 / 2.04 ( 9) link_ALPHA1-6 : bond 0.00801 / 0.37 ( 3) link_ALPHA1-6 : angle 1.36855 / 0.78 ( 9) link_BETA1-4 : bond 0.01927 / 1.11 ( 27) link_BETA1-4 : angle 4.97295 / 3.00 ( 81) link_NAG-ASN : bond 0.00884 / 0.44 ( 33) link_NAG-ASN : angle 3.83228 / 2.34 ( 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: 63 poor density : 207 time to evaluate : 0.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 MET cc_start: 0.8135 (tmm) cc_final: 0.7721 (tmm) REVERT: A 171 TYR cc_start: 0.6827 (OUTLIER) cc_final: 0.5277 (p90) REVERT: A 230 CYS cc_start: 0.7608 (OUTLIER) cc_final: 0.7168 (m) REVERT: a 262 THR cc_start: 0.9444 (OUTLIER) cc_final: 0.9154 (m) REVERT: B 152 MET cc_start: 0.7743 (ttt) cc_final: 0.7343 (tmm) REVERT: B 191 MET cc_start: 0.7944 (mmt) cc_final: 0.7739 (mmt) REVERT: b 262 THR cc_start: 0.9443 (OUTLIER) cc_final: 0.9132 (m) REVERT: b 383 ARG cc_start: 0.7849 (ttm110) cc_final: 0.7550 (ttm110) REVERT: b 401 ASP cc_start: 0.8324 (m-30) cc_final: 0.8002 (m-30) REVERT: C 152 MET cc_start: 0.8035 (tmm) cc_final: 0.7659 (tmm) REVERT: C 191 MET cc_start: 0.8127 (mmt) cc_final: 0.7818 (mmt) REVERT: C 230 CYS cc_start: 0.7757 (OUTLIER) cc_final: 0.7265 (m) REVERT: c 401 ASP cc_start: 0.8308 (m-30) cc_final: 0.8054 (m-30) REVERT: c 409 MET cc_start: 0.7147 (mtp) cc_final: 0.6907 (mtp) outliers start: 63 outliers final: 43 residues processed: 245 average time/residue: 0.1044 time to fit residues: 34.4823 Evaluate side-chains 218 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 170 time to evaluate : 0.246 ------------------------------------------------------------------------------- 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 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 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 388 SER Chi-restraints excluded: chain b residue 414 LEU Chi-restraints excluded: chain C residue 81 MET 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 195 TRP Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain c residue 260 THR 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 354 LEU 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: 1.9990 chunk 38 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 99 optimal weight: 0.8980 chunk 6 optimal weight: 5.9990 chunk 98 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 34 optimal weight: 7.9990 chunk 52 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 93 optimal weight: 4.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 353 HIS ** 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 = 0.3946 r_free = 0.3946 target = 0.128748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.103874 restraints weight = 19493.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.107562 restraints weight = 12361.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.109983 restraints weight = 9340.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.111543 restraints weight = 7797.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.112614 restraints weight = 6896.034| |-----------------------------------------------------------------------------| r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.5001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 9705 Z= 0.212 Angle : 1.037 12.441 13272 Z= 0.484 Chirality : 0.051 0.274 1632 Planarity : 0.003 0.024 1557 Dihedral : 6.011 25.765 1152 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 5.78 % Allowed : 15.35 % Favored : 78.86 % 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: -0.70 (0.25), residues: 1056 helix: 0.55 (0.27), residues: 357 sheet: -0.10 (0.44), residues: 144 loop : -1.26 (0.26), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG c 355 TYR 0.021 0.001 TYR B 149 PHE 0.018 0.002 PHE a 292 TRP 0.019 0.002 TRP A 195 HIS 0.011 0.002 HIS B 123 Details of bonding type rmsd/Z covalent geometry : bond 0.00479 / 0.20 ( 9618) covalent geometry : angle 0.90788 / 0.45 (13032) SS BOND : bond 0.01104 / 0.64 ( 21) SS BOND : angle 3.23511 / 1.96 ( 42) hydrogen bonds : bond 0.04889 / 3.14 ( 372) hydrogen bonds : angle 5.35872 / 3.77 ( 990) link_ALPHA1-3 : bond 0.01001 / 0.47 ( 3) link_ALPHA1-3 : angle 3.03606 / 1.72 ( 9) link_ALPHA1-6 : bond 0.00877 / 0.41 ( 3) link_ALPHA1-6 : angle 1.37967 / 0.79 ( 9) link_BETA1-4 : bond 0.01796 / 1.03 ( 27) link_BETA1-4 : angle 4.72516 / 2.87 ( 81) link_NAG-ASN : bond 0.00718 / 0.36 ( 33) link_NAG-ASN : angle 3.44242 / 2.11 ( 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 253 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 198 time to evaluate : 0.352 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 115 LYS cc_start: 0.8365 (mmtm) cc_final: 0.8155 (mmtm) REVERT: A 152 MET cc_start: 0.8217 (tmm) cc_final: 0.7555 (tmm) REVERT: A 171 TYR cc_start: 0.6781 (OUTLIER) cc_final: 0.5066 (p90) REVERT: a 262 THR cc_start: 0.9387 (OUTLIER) cc_final: 0.9172 (m) REVERT: B 213 MET cc_start: 0.7353 (pmm) cc_final: 0.7025 (pmm) REVERT: b 310 ASP cc_start: 0.8572 (m-30) cc_final: 0.8067 (t0) REVERT: b 383 ARG cc_start: 0.7716 (ttm110) cc_final: 0.7497 (ttm110) REVERT: b 401 ASP cc_start: 0.8323 (m-30) cc_final: 0.8033 (m-30) REVERT: C 193 MET cc_start: 0.8510 (tpp) cc_final: 0.8231 (tpp) REVERT: c 401 ASP cc_start: 0.8261 (m-30) cc_final: 0.8034 (m-30) REVERT: c 409 MET cc_start: 0.7239 (mtp) cc_final: 0.6986 (mtp) outliers start: 55 outliers final: 38 residues processed: 229 average time/residue: 0.1028 time to fit residues: 31.5565 Evaluate side-chains 218 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 178 time to evaluate : 0.251 ------------------------------------------------------------------------------- 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 245 SER Chi-restraints excluded: chain a residue 260 THR 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 291 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 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 99 GLU 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 266 SER Chi-restraints excluded: chain c residue 291 CYS Chi-restraints excluded: chain c residue 323 ARG 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: 0.8980 chunk 94 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 62 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 5 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 169 HIS A 188 GLN ** B 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 415 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.128941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.103374 restraints weight = 19679.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.107227 restraints weight = 12253.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.109730 restraints weight = 9227.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.111358 restraints weight = 7659.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.112433 restraints weight = 6751.320| |-----------------------------------------------------------------------------| r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.5354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 9705 Z= 0.197 Angle : 0.989 12.744 13272 Z= 0.461 Chirality : 0.050 0.298 1632 Planarity : 0.003 0.028 1557 Dihedral : 5.864 25.918 1152 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.43 % Favored : 91.57 % Rotamer: Outliers : 5.78 % Allowed : 15.98 % Favored : 78.23 % 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: -0.75 (0.25), residues: 1056 helix: 0.63 (0.27), residues: 357 sheet: -0.27 (0.43), residues: 144 loop : -1.34 (0.26), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 234 TYR 0.024 0.001 TYR A 149 PHE 0.015 0.002 PHE c 292 TRP 0.018 0.001 TRP A 195 HIS 0.010 0.001 HIS B 123 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.19 ( 9618) covalent geometry : angle 0.87012 / 0.43 (13032) SS BOND : bond 0.00701 / 0.42 ( 21) SS BOND : angle 2.90757 / 1.70 ( 42) hydrogen bonds : bond 0.04491 / 2.91 ( 372) hydrogen bonds : angle 5.34788 / 3.80 ( 990) link_ALPHA1-3 : bond 0.00937 / 0.44 ( 3) link_ALPHA1-3 : angle 3.05803 / 1.72 ( 9) link_ALPHA1-6 : bond 0.00803 / 0.37 ( 3) link_ALPHA1-6 : angle 1.45316 / 0.82 ( 9) link_BETA1-4 : bond 0.01730 / 1.00 ( 27) link_BETA1-4 : angle 4.49495 / 2.74 ( 81) link_NAG-ASN : bond 0.00678 / 0.34 ( 33) link_NAG-ASN : angle 3.20142 / 1.96 ( 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 246 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 191 time to evaluate : 0.365 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 115 LYS cc_start: 0.8244 (mmtm) cc_final: 0.7981 (mmtm) REVERT: A 152 MET cc_start: 0.7977 (tmm) cc_final: 0.7762 (tmm) REVERT: A 154 CYS cc_start: 0.5680 (m) cc_final: 0.5461 (m) REVERT: A 171 TYR cc_start: 0.6809 (OUTLIER) cc_final: 0.5154 (p90) REVERT: A 193 MET cc_start: 0.8313 (tpp) cc_final: 0.7644 (ttm) REVERT: a 262 THR cc_start: 0.9403 (OUTLIER) cc_final: 0.9191 (m) REVERT: a 310 ASP cc_start: 0.8605 (OUTLIER) cc_final: 0.8300 (t0) REVERT: a 334 GLN cc_start: 0.7086 (OUTLIER) cc_final: 0.6855 (pp30) REVERT: a 338 LYS cc_start: 0.8273 (mtmt) cc_final: 0.7961 (mttt) REVERT: a 346 ASP cc_start: 0.7920 (t0) cc_final: 0.7101 (t0) REVERT: a 347 GLN cc_start: 0.8267 (mt0) cc_final: 0.8055 (mt0) REVERT: B 213 MET cc_start: 0.7345 (pmm) cc_final: 0.7012 (pmm) REVERT: b 310 ASP cc_start: 0.8510 (m-30) cc_final: 0.8159 (t0) REVERT: b 401 ASP cc_start: 0.8376 (m-30) cc_final: 0.8073 (m-30) REVERT: C 191 MET cc_start: 0.8096 (mmm) cc_final: 0.7793 (mmm) REVERT: c 404 GLN cc_start: 0.7998 (tp40) cc_final: 0.7608 (tp40) outliers start: 55 outliers final: 38 residues processed: 223 average time/residue: 0.1015 time to fit residues: 30.7255 Evaluate side-chains 211 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 169 time to evaluate : 0.363 ------------------------------------------------------------------------------- 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 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 262 THR Chi-restraints excluded: chain a residue 266 SER Chi-restraints excluded: chain a residue 291 CYS Chi-restraints excluded: chain a residue 310 ASP Chi-restraints excluded: chain a residue 323 ARG Chi-restraints excluded: chain a residue 334 GLN 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 291 CYS 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 81 MET Chi-restraints excluded: chain C residue 116 PHE Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 136 ILE 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 12 optimal weight: 7.9990 chunk 77 optimal weight: 5.9990 chunk 22 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 chunk 83 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 GLN ** b 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 130 HIS c 415 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.128934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.103969 restraints weight = 19513.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.107786 restraints weight = 12313.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.110268 restraints weight = 9256.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.111874 restraints weight = 7662.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.112936 restraints weight = 6749.382| |-----------------------------------------------------------------------------| r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.5575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 9705 Z= 0.187 Angle : 0.973 13.519 13272 Z= 0.454 Chirality : 0.049 0.289 1632 Planarity : 0.003 0.028 1557 Dihedral : 5.777 25.427 1152 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer: Outliers : 5.68 % Allowed : 17.98 % Favored : 76.34 % 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: -0.77 (0.26), residues: 1056 helix: 0.69 (0.27), residues: 357 sheet: -0.41 (0.42), residues: 153 loop : -1.38 (0.27), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG b 383 TYR 0.016 0.001 TYR C 149 PHE 0.015 0.002 PHE c 292 TRP 0.017 0.002 TRP A 195 HIS 0.012 0.001 HIS B 123 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.18 ( 9618) covalent geometry : angle 0.85684 / 0.42 (13032) SS BOND : bond 0.00678 / 0.41 ( 21) SS BOND : angle 3.13981 / 1.74 ( 42) hydrogen bonds : bond 0.04343 / 2.78 ( 372) hydrogen bonds : angle 5.24215 / 3.73 ( 990) link_ALPHA1-3 : bond 0.00903 / 0.42 ( 3) link_ALPHA1-3 : angle 2.92879 / 1.64 ( 9) link_ALPHA1-6 : bond 0.00789 / 0.37 ( 3) link_ALPHA1-6 : angle 1.44919 / 0.81 ( 9) link_BETA1-4 : bond 0.01700 / 0.99 ( 27) link_BETA1-4 : angle 4.36205 / 2.66 ( 81) link_NAG-ASN : bond 0.00642 / 0.33 ( 33) link_NAG-ASN : angle 3.07676 / 1.89 ( 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 242 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 188 time to evaluate : 0.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 LYS cc_start: 0.8148 (mmtm) cc_final: 0.7929 (mmtm) REVERT: A 133 MET cc_start: 0.7941 (OUTLIER) cc_final: 0.7702 (tmm) REVERT: A 171 TYR cc_start: 0.6740 (OUTLIER) cc_final: 0.4999 (p90) REVERT: a 262 THR cc_start: 0.9366 (OUTLIER) cc_final: 0.9130 (m) REVERT: a 310 ASP cc_start: 0.8600 (m-30) cc_final: 0.8314 (t0) REVERT: a 334 GLN cc_start: 0.7156 (OUTLIER) cc_final: 0.6920 (pp30) REVERT: b 272 GLU cc_start: 0.6011 (pt0) cc_final: 0.5808 (pm20) REVERT: b 306 GLU cc_start: 0.8087 (mm-30) cc_final: 0.7718 (mm-30) REVERT: b 310 ASP cc_start: 0.8437 (m-30) cc_final: 0.8191 (t0) REVERT: b 346 ASP cc_start: 0.7691 (t0) cc_final: 0.7104 (t0) REVERT: b 401 ASP cc_start: 0.8367 (m-30) cc_final: 0.8020 (m-30) REVERT: C 152 MET cc_start: 0.7888 (tmm) cc_final: 0.7609 (tmm) REVERT: C 191 MET cc_start: 0.8090 (mmm) cc_final: 0.7728 (mmm) REVERT: C 210 ASP cc_start: 0.6413 (p0) cc_final: 0.6156 (p0) REVERT: c 404 GLN cc_start: 0.7999 (tp40) cc_final: 0.7275 (tp40) REVERT: c 408 ASN cc_start: 0.8592 (m-40) cc_final: 0.8326 (m-40) outliers start: 54 outliers final: 38 residues processed: 221 average time/residue: 0.0967 time to fit residues: 29.2297 Evaluate side-chains 211 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 169 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 123 HIS Chi-restraints excluded: chain A residue 133 MET 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 262 THR Chi-restraints excluded: chain a residue 266 SER Chi-restraints excluded: chain a residue 334 GLN Chi-restraints excluded: chain a residue 359 CYS 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 195 TRP Chi-restraints excluded: chain B residue 241 LEU 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 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 136 ILE 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 323 ARG Chi-restraints excluded: chain c residue 334 GLN 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: 0.3980 chunk 59 optimal weight: 0.5980 chunk 92 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 chunk 94 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 chunk 102 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** a 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 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 = 0.3820 r_free = 0.3820 target = 0.123057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.097558 restraints weight = 19195.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.100606 restraints weight = 13254.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.102650 restraints weight = 10444.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.104021 restraints weight = 8927.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.104952 restraints weight = 8012.733| |-----------------------------------------------------------------------------| r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.5816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 9705 Z= 0.185 Angle : 1.001 13.065 13272 Z= 0.466 Chirality : 0.051 0.342 1632 Planarity : 0.003 0.030 1557 Dihedral : 5.896 30.228 1152 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.28 % Favored : 90.72 % Rotamer: Outliers : 5.36 % Allowed : 17.88 % Favored : 76.76 % Cbeta Deviations : 0.00 % 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: -0.80 (0.26), residues: 1056 helix: 0.77 (0.27), residues: 354 sheet: -0.51 (0.41), residues: 153 loop : -1.44 (0.27), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 234 TYR 0.027 0.001 TYR C 149 PHE 0.036 0.002 PHE A 116 TRP 0.017 0.002 TRP A 195 HIS 0.005 0.001 HIS c 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.18 ( 9618) covalent geometry : angle 0.88089 / 0.43 (13032) SS BOND : bond 0.00666 / 0.39 ( 21) SS BOND : angle 4.03796 / 2.25 ( 42) hydrogen bonds : bond 0.04309 / 2.76 ( 372) hydrogen bonds : angle 5.20768 / 3.73 ( 990) link_ALPHA1-3 : bond 0.00875 / 0.41 ( 3) link_ALPHA1-3 : angle 2.89832 / 1.62 ( 9) link_ALPHA1-6 : bond 0.00760 / 0.35 ( 3) link_ALPHA1-6 : angle 1.46140 / 0.82 ( 9) link_BETA1-4 : bond 0.01688 / 0.98 ( 27) link_BETA1-4 : angle 4.24513 / 2.60 ( 81) link_NAG-ASN : bond 0.00655 / 0.34 ( 33) link_NAG-ASN : angle 3.08593 / 1.88 ( 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 235 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 184 time to evaluate : 0.373 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 155 ASP cc_start: 0.6549 (OUTLIER) cc_final: 0.6313 (m-30) REVERT: A 171 TYR cc_start: 0.6794 (OUTLIER) cc_final: 0.5105 (p90) REVERT: A 193 MET cc_start: 0.8283 (tpp) cc_final: 0.7706 (ttm) REVERT: A 199 TYR cc_start: 0.6631 (OUTLIER) cc_final: 0.5064 (m-80) REVERT: a 310 ASP cc_start: 0.8600 (m-30) cc_final: 0.8301 (t0) REVERT: a 404 GLN cc_start: 0.7908 (tp40) cc_final: 0.7552 (tp40) REVERT: B 213 MET cc_start: 0.7434 (pmm) cc_final: 0.7058 (pmm) REVERT: b 310 ASP cc_start: 0.8399 (m-30) cc_final: 0.8193 (t0) REVERT: b 331 MET cc_start: 0.5259 (tpt) cc_final: 0.4788 (ptt) REVERT: b 401 ASP cc_start: 0.8357 (m-30) cc_final: 0.8048 (m-30) REVERT: C 152 MET cc_start: 0.7951 (tmm) cc_final: 0.7723 (tmm) REVERT: C 191 MET cc_start: 0.8034 (mmm) cc_final: 0.7768 (mmt) REVERT: C 193 MET cc_start: 0.8280 (tpp) cc_final: 0.7323 (ttt) REVERT: c 404 GLN cc_start: 0.8028 (tp40) cc_final: 0.7268 (tp40) REVERT: c 408 ASN cc_start: 0.8647 (m-40) cc_final: 0.8305 (m-40) outliers start: 51 outliers final: 40 residues processed: 216 average time/residue: 0.0977 time to fit residues: 28.8339 Evaluate side-chains 209 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 166 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 GLU 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 155 ASP 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 211 CYS 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 359 CYS 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 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 376 THR 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 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 334 GLN 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: 4.9990 chunk 23 optimal weight: 0.0670 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 49 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** b 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 = 0.3815 r_free = 0.3815 target = 0.122672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.097548 restraints weight = 19119.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.100420 restraints weight = 13557.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.102384 restraints weight = 10843.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.103482 restraints weight = 9345.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.104481 restraints weight = 8511.039| |-----------------------------------------------------------------------------| r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.5989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 9705 Z= 0.178 Angle : 1.005 12.143 13272 Z= 0.468 Chirality : 0.051 0.414 1632 Planarity : 0.003 0.032 1557 Dihedral : 5.887 26.565 1152 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.38 % Favored : 90.62 % Rotamer: Outliers : 4.63 % Allowed : 19.66 % Favored : 75.71 % 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: 0.71 (0.27), residues: 354 sheet: -0.25 (0.48), residues: 123 loop : -1.53 (0.26), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG b 383 TYR 0.024 0.001 TYR C 149 PHE 0.018 0.002 PHE A 116 TRP 0.016 0.001 TRP A 195 HIS 0.004 0.001 HIS C 229 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.17 ( 9618) covalent geometry : angle 0.89389 / 0.44 (13032) SS BOND : bond 0.00674 / 0.42 ( 21) SS BOND : angle 4.03919 / 2.25 ( 42) hydrogen bonds : bond 0.04206 / 2.65 ( 372) hydrogen bonds : angle 5.19158 / 3.76 ( 990) link_ALPHA1-3 : bond 0.00847 / 0.39 ( 3) link_ALPHA1-3 : angle 2.83763 / 1.58 ( 9) link_ALPHA1-6 : bond 0.00733 / 0.34 ( 3) link_ALPHA1-6 : angle 1.44788 / 0.80 ( 9) link_BETA1-4 : bond 0.01549 / 0.91 ( 27) link_BETA1-4 : angle 4.10033 / 2.52 ( 81) link_NAG-ASN : bond 0.00639 / 0.32 ( 33) link_NAG-ASN : angle 2.94341 / 1.78 ( 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 232 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 188 time to evaluate : 0.295 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 133 MET cc_start: 0.7988 (OUTLIER) cc_final: 0.7722 (tmm) REVERT: A 171 TYR cc_start: 0.6965 (OUTLIER) cc_final: 0.5307 (p90) REVERT: A 193 MET cc_start: 0.8340 (tpp) cc_final: 0.7828 (ttm) REVERT: A 199 TYR cc_start: 0.6665 (OUTLIER) cc_final: 0.5155 (m-80) REVERT: a 331 MET cc_start: 0.3923 (tpt) cc_final: 0.3485 (ptt) REVERT: a 404 GLN cc_start: 0.7855 (tp40) cc_final: 0.7517 (tp40) REVERT: B 152 MET cc_start: 0.7958 (tmm) cc_final: 0.7728 (tmm) REVERT: B 213 MET cc_start: 0.7437 (pmm) cc_final: 0.6920 (pmm) REVERT: b 306 GLU cc_start: 0.8140 (mm-30) cc_final: 0.7873 (mm-30) REVERT: b 401 ASP cc_start: 0.8341 (m-30) cc_final: 0.7953 (m-30) REVERT: C 152 MET cc_start: 0.7992 (tmm) cc_final: 0.7785 (tmm) REVERT: C 191 MET cc_start: 0.7960 (mmm) cc_final: 0.7703 (mmt) REVERT: C 193 MET cc_start: 0.8334 (tpp) cc_final: 0.7380 (ttt) REVERT: C 210 ASP cc_start: 0.7150 (p0) cc_final: 0.6948 (p0) REVERT: c 404 GLN cc_start: 0.7946 (tp40) cc_final: 0.7603 (tp40) outliers start: 44 outliers final: 34 residues processed: 215 average time/residue: 0.0928 time to fit residues: 27.5404 Evaluate side-chains 209 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 172 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 123 HIS Chi-restraints excluded: chain A residue 133 MET 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 359 CYS 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 130 HIS Chi-restraints excluded: chain B residue 171 TYR 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 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 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 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=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: 0.5980 chunk 77 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 19 optimal weight: 0.0070 chunk 102 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 69 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 overall best weight: 0.6800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 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 = 0.3821 r_free = 0.3821 target = 0.123220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.096736 restraints weight = 19226.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.099995 restraints weight = 13063.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.102052 restraints weight = 10190.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.103537 restraints weight = 8730.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.104542 restraints weight = 7809.787| |-----------------------------------------------------------------------------| r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.6154 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 : 0.999 13.937 13272 Z= 0.466 Chirality : 0.052 0.458 1632 Planarity : 0.003 0.031 1557 Dihedral : 5.857 27.328 1152 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.47 % Favored : 90.53 % Rotamer: Outliers : 4.63 % Allowed : 19.77 % Favored : 75.60 % 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: 0.83 (0.28), residues: 351 sheet: -0.42 (0.48), residues: 126 loop : -1.63 (0.26), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG a 383 TYR 0.032 0.001 TYR B 149 PHE 0.031 0.002 PHE B 116 TRP 0.016 0.001 TRP A 195 HIS 0.004 0.001 HIS C 229 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.17 ( 9618) covalent geometry : angle 0.90008 / 0.44 (13032) SS BOND : bond 0.00667 / 0.41 ( 21) SS BOND : angle 3.66123 / 2.13 ( 42) hydrogen bonds : bond 0.04151 / 2.65 ( 372) hydrogen bonds : angle 5.17327 / 3.75 ( 990) link_ALPHA1-3 : bond 0.00858 / 0.40 ( 3) link_ALPHA1-3 : angle 2.83705 / 1.58 ( 9) link_ALPHA1-6 : bond 0.00705 / 0.33 ( 3) link_ALPHA1-6 : angle 1.43537 / 0.80 ( 9) link_BETA1-4 : bond 0.01522 / 0.88 ( 27) link_BETA1-4 : angle 4.02850 / 2.48 ( 81) link_NAG-ASN : bond 0.00575 / 0.28 ( 33) link_NAG-ASN : angle 2.70727 / 1.66 ( 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 225 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 181 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 TYR cc_start: 0.7105 (OUTLIER) cc_final: 0.5511 (p90) REVERT: A 193 MET cc_start: 0.8422 (tpp) cc_final: 0.7976 (ttm) REVERT: A 199 TYR cc_start: 0.6677 (OUTLIER) cc_final: 0.5135 (m-80) REVERT: a 334 GLN cc_start: 0.7122 (pp30) cc_final: 0.6819 (pp30) REVERT: a 404 GLN cc_start: 0.7966 (tp40) cc_final: 0.7610 (tp40) REVERT: B 152 MET cc_start: 0.7942 (tmm) cc_final: 0.7691 (tmm) REVERT: B 246 GLN cc_start: 0.7098 (tm-30) cc_final: 0.6217 (tm-30) REVERT: b 401 ASP cc_start: 0.8397 (m-30) cc_final: 0.8014 (m-30) REVERT: b 404 GLN cc_start: 0.8102 (tp40) cc_final: 0.7813 (tp40) REVERT: C 152 MET cc_start: 0.8115 (tmm) cc_final: 0.7724 (tmm) REVERT: C 191 MET cc_start: 0.7932 (mmm) cc_final: 0.7671 (mmt) REVERT: C 193 MET cc_start: 0.8373 (tpp) cc_final: 0.7476 (ttt) REVERT: C 246 GLN cc_start: 0.7296 (tm-30) cc_final: 0.7041 (tm-30) REVERT: c 404 GLN cc_start: 0.8000 (tp40) cc_final: 0.7661 (tp40) outliers start: 44 outliers final: 39 residues processed: 210 average time/residue: 0.1001 time to fit residues: 28.7151 Evaluate side-chains 215 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 174 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 99 GLU 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 292 PHE Chi-restraints excluded: chain a residue 323 ARG Chi-restraints excluded: chain a residue 359 CYS 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 130 HIS Chi-restraints excluded: chain B residue 171 TYR 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 51 optimal weight: 0.8980 chunk 87 optimal weight: 0.5980 chunk 97 optimal weight: 8.9990 chunk 35 optimal weight: 4.9990 chunk 92 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 52 optimal weight: 0.5980 chunk 99 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 334 GLN ** 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 = 0.3821 r_free = 0.3821 target = 0.123234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.097182 restraints weight = 19298.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.100131 restraints weight = 13514.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.102117 restraints weight = 10785.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.103415 restraints weight = 9279.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.104216 restraints weight = 8376.418| |-----------------------------------------------------------------------------| r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.6348 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 13.430 13272 Z= 0.463 Chirality : 0.051 0.283 1632 Planarity : 0.003 0.027 1557 Dihedral : 5.818 29.028 1152 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.28 % Favored : 90.72 % Rotamer: Outliers : 4.42 % Allowed : 20.93 % Favored : 74.66 % 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: -0.98 (0.26), residues: 1056 helix: 0.71 (0.28), residues: 357 sheet: -0.60 (0.47), residues: 126 loop : -1.60 (0.26), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG b 383 TYR 0.026 0.001 TYR C 149 PHE 0.032 0.002 PHE B 116 TRP 0.015 0.001 TRP A 195 HIS 0.004 0.001 HIS C 229 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.17 ( 9618) covalent geometry : angle 0.89626 / 0.44 (13032) SS BOND : bond 0.00673 / 0.41 ( 21) SS BOND : angle 3.42675 / 2.03 ( 42) hydrogen bonds : bond 0.04130 / 2.64 ( 372) hydrogen bonds : angle 5.19546 / 3.78 ( 990) link_ALPHA1-3 : bond 0.00883 / 0.41 ( 3) link_ALPHA1-3 : angle 2.83352 / 1.58 ( 9) link_ALPHA1-6 : bond 0.00688 / 0.32 ( 3) link_ALPHA1-6 : angle 1.43053 / 0.79 ( 9) link_BETA1-4 : bond 0.01502 / 0.87 ( 27) link_BETA1-4 : angle 3.97544 / 2.44 ( 81) link_NAG-ASN : bond 0.00615 / 0.29 ( 33) link_NAG-ASN : angle 2.59075 / 1.64 ( 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: 42 poor density : 183 time to evaluate : 0.350 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 99 GLU cc_start: 0.7381 (OUTLIER) cc_final: 0.7141 (mp0) REVERT: A 171 TYR cc_start: 0.7127 (OUTLIER) cc_final: 0.5498 (p90) REVERT: A 193 MET cc_start: 0.8425 (tpp) cc_final: 0.7948 (ttm) REVERT: A 199 TYR cc_start: 0.6679 (OUTLIER) cc_final: 0.5182 (m-80) REVERT: a 331 MET cc_start: 0.4243 (tpt) cc_final: 0.3368 (ptt) REVERT: a 404 GLN cc_start: 0.7966 (tp40) cc_final: 0.7624 (tp40) REVERT: a 409 MET cc_start: 0.8004 (mtp) cc_final: 0.7660 (mtp) REVERT: B 152 MET cc_start: 0.7895 (tmm) cc_final: 0.7645 (tmm) REVERT: b 302 GLU cc_start: 0.7195 (tp30) cc_final: 0.6669 (tp30) REVERT: b 331 MET cc_start: 0.5608 (tpt) cc_final: 0.4806 (ppp) REVERT: b 401 ASP cc_start: 0.8376 (m-30) cc_final: 0.8071 (m-30) REVERT: C 152 MET cc_start: 0.8185 (tmm) cc_final: 0.7951 (tmm) REVERT: C 191 MET cc_start: 0.7867 (mmm) cc_final: 0.7625 (mmt) REVERT: C 193 MET cc_start: 0.8372 (tpp) cc_final: 0.7462 (ttt) REVERT: c 404 GLN cc_start: 0.8044 (tp40) cc_final: 0.7723 (tp40) outliers start: 42 outliers final: 38 residues processed: 212 average time/residue: 0.0972 time to fit residues: 28.0046 Evaluate side-chains 221 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 180 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 99 GLU 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 292 PHE Chi-restraints excluded: chain a residue 359 CYS 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 130 HIS Chi-restraints excluded: chain B residue 171 TYR 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 82 optimal weight: 8.9990 chunk 65 optimal weight: 0.7980 chunk 97 optimal weight: 8.9990 chunk 16 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 18 optimal weight: 0.4980 chunk 29 optimal weight: 0.9980 chunk 68 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 334 GLN ** 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 = 0.3813 r_free = 0.3813 target = 0.122457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.096522 restraints weight = 19195.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.099409 restraints weight = 13473.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.101397 restraints weight = 10745.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.102763 restraints weight = 9241.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.103487 restraints weight = 8318.324| |-----------------------------------------------------------------------------| r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.6481 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= 0.178 Angle : 0.985 12.845 13272 Z= 0.460 Chirality : 0.050 0.305 1632 Planarity : 0.003 0.033 1557 Dihedral : 5.679 23.966 1152 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.81 % Favored : 91.10 % Rotamer: Outliers : 4.42 % Allowed : 21.56 % Favored : 74.03 % 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: -0.96 (0.26), residues: 1056 helix: 0.71 (0.28), residues: 357 sheet: -0.54 (0.48), residues: 126 loop : -1.59 (0.26), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 125 TYR 0.023 0.001 TYR C 149 PHE 0.028 0.002 PHE B 116 TRP 0.014 0.001 TRP A 195 HIS 0.005 0.001 HIS b 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.17 ( 9618) covalent geometry : angle 0.89452 / 0.44 (13032) SS BOND : bond 0.00700 / 0.41 ( 21) SS BOND : angle 3.38681 / 2.03 ( 42) hydrogen bonds : bond 0.04060 / 2.61 ( 372) hydrogen bonds : angle 5.20548 / 3.79 ( 990) link_ALPHA1-3 : bond 0.00926 / 0.43 ( 3) link_ALPHA1-3 : angle 2.84638 / 1.59 ( 9) link_ALPHA1-6 : bond 0.00712 / 0.33 ( 3) link_ALPHA1-6 : angle 1.44604 / 0.80 ( 9) link_BETA1-4 : bond 0.01457 / 0.85 ( 27) link_BETA1-4 : angle 3.92622 / 2.41 ( 81) link_NAG-ASN : bond 0.00579 / 0.28 ( 33) link_NAG-ASN : angle 2.52494 / 1.56 ( 99) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1459.01 seconds wall clock time: 26 minutes 12.68 seconds (1572.68 seconds total)