Starting phenix.real_space_refine on Sat Aug 23 03:53:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8eje_28179/08_2025/8eje_28179.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eje_28179/08_2025/8eje_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_28179/08_2025/8eje_28179.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eje_28179/08_2025/8eje_28179.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8eje_28179/08_2025/8eje_28179.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eje_28179/08_2025/8eje_28179.map" } resolution = 3.69 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 87 5.16 5 C 5892 2.51 5 N 1497 2.21 5 O 1950 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9426 Number of models: 1 Model: "" Number of chains: 33 Chain: "A" Number of atoms: 1538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1538 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 4, 'TRANS': 190} Chain: "a" Number of atoms: 1308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1308 Classifications: {'peptide': 161} Link IDs: {'PTRANS': 4, 'TRANS': 156} Chain: "B" Number of atoms: 1538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1538 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 4, 'TRANS': 190} Chain: "b" Number of atoms: 1308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1308 Classifications: {'peptide': 161} Link IDs: {'PTRANS': 4, 'TRANS': 156} Chain: "C" Number of atoms: 1538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1538 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 4, 'TRANS': 190} Chain: "c" Number of atoms: 1308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1308 Classifications: {'peptide': 161} Link IDs: {'PTRANS': 4, 'TRANS': 156} Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 2.63, per 1000 atoms: 0.28 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: 1.20 Conformation dependent library (CDL) restraints added in 324.7 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.32 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: 1.48 Time building geometry restraints manager: 1.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.33: 2322 1.33 - 1.47: 3215 1.47 - 1.62: 3946 1.62 - 1.77: 12 1.77 - 1.91: 123 Bond restraints: 9618 Sorted by residual: bond pdb=" CB ILE b 419 " pdb=" CG1 ILE b 419 " ideal model delta sigma weight residual 1.530 1.653 -0.123 2.00e-02 2.50e+03 3.78e+01 bond pdb=" CB ILE a 419 " pdb=" CG1 ILE a 419 " ideal model delta sigma weight residual 1.530 1.653 -0.123 2.00e-02 2.50e+03 3.76e+01 bond pdb=" CB ILE c 419 " pdb=" CG1 ILE c 419 " ideal model delta sigma weight residual 1.530 1.653 -0.123 2.00e-02 2.50e+03 3.76e+01 bond pdb=" NE1 TRP b 385 " pdb=" CE2 TRP b 385 " ideal model delta sigma weight residual 1.370 1.304 0.066 1.10e-02 8.26e+03 3.61e+01 bond pdb=" NE1 TRP c 385 " pdb=" CE2 TRP c 385 " ideal model delta sigma weight residual 1.370 1.304 0.066 1.10e-02 8.26e+03 3.57e+01 ... (remaining 9613 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.28: 12964 7.28 - 14.56: 59 14.56 - 21.84: 0 21.84 - 29.11: 0 29.11 - 36.39: 9 Bond angle restraints: 13032 Sorted by residual: angle pdb=" C2 NAG V 2 " pdb=" N2 NAG V 2 " pdb=" C7 NAG V 2 " ideal model delta sigma weight residual 124.56 160.95 -36.39 3.00e+00 1.11e-01 1.47e+02 angle pdb=" C2 NAG H 2 " pdb=" N2 NAG H 2 " pdb=" C7 NAG H 2 " ideal model delta sigma weight residual 124.56 160.94 -36.38 3.00e+00 1.11e-01 1.47e+02 angle pdb=" C2 NAG A 301 " pdb=" N2 NAG A 301 " pdb=" C7 NAG A 301 " ideal model delta sigma weight residual 124.56 160.94 -36.38 3.00e+00 1.11e-01 1.47e+02 angle pdb=" C2 NAG C 301 " pdb=" N2 NAG C 301 " pdb=" C7 NAG C 301 " ideal model delta sigma weight residual 124.56 160.93 -36.37 3.00e+00 1.11e-01 1.47e+02 angle pdb=" C2 NAG B 301 " pdb=" N2 NAG B 301 " pdb=" C7 NAG B 301 " ideal model delta sigma weight residual 124.56 160.93 -36.37 3.00e+00 1.11e-01 1.47e+02 ... (remaining 13027 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.37: 6246 21.37 - 42.73: 226 42.73 - 64.10: 44 64.10 - 85.47: 45 85.47 - 106.83: 30 Dihedral angle restraints: 6591 sinusoidal: 3456 harmonic: 3135 Sorted by residual: dihedral pdb=" CA CYS B 117 " pdb=" CB CYS B 117 " pdb=" SG CYS B 117 " pdb=" SG CYS B 154 " ideal model delta sinusoidal sigma weight residual 79.00 13.37 65.63 1 2.00e+01 2.50e-03 1.41e+01 dihedral pdb=" CA CYS C 117 " pdb=" CB CYS C 117 " pdb=" SG CYS C 117 " pdb=" SG CYS C 154 " ideal model delta sinusoidal sigma weight residual 79.00 13.39 65.61 1 2.00e+01 2.50e-03 1.41e+01 dihedral pdb=" CA CYS A 117 " pdb=" CB CYS A 117 " pdb=" SG CYS A 117 " pdb=" SG CYS A 154 " ideal model delta sinusoidal sigma weight residual 79.00 13.42 65.58 1 2.00e+01 2.50e-03 1.41e+01 ... (remaining 6588 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.121: 1072 0.121 - 0.242: 359 0.242 - 0.363: 135 0.363 - 0.483: 51 0.483 - 0.604: 15 Chirality restraints: 1632 Sorted by residual: chirality pdb=" C1 BMA D 3 " pdb=" O4 NAG D 2 " pdb=" C2 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.80 -0.60 2.00e-02 2.50e+03 9.13e+02 chirality pdb=" C1 BMA R 3 " pdb=" O4 NAG R 2 " pdb=" C2 BMA R 3 " pdb=" O5 BMA R 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.80 -0.60 2.00e-02 2.50e+03 9.13e+02 chirality pdb=" C1 BMA K 3 " pdb=" O4 NAG K 2 " pdb=" C2 BMA K 3 " pdb=" O5 BMA K 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.80 -0.60 2.00e-02 2.50e+03 9.08e+02 ... (remaining 1629 not shown) Planarity restraints: 1590 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG K 2 " -0.226 2.00e-02 2.50e+03 1.85e-01 4.28e+02 pdb=" C7 NAG K 2 " 0.065 2.00e-02 2.50e+03 pdb=" C8 NAG K 2 " -0.163 2.00e-02 2.50e+03 pdb=" N2 NAG K 2 " 0.298 2.00e-02 2.50e+03 pdb=" O7 NAG K 2 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 2 " -0.226 2.00e-02 2.50e+03 1.85e-01 4.28e+02 pdb=" C7 NAG D 2 " 0.065 2.00e-02 2.50e+03 pdb=" C8 NAG D 2 " -0.163 2.00e-02 2.50e+03 pdb=" N2 NAG D 2 " 0.298 2.00e-02 2.50e+03 pdb=" O7 NAG D 2 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG R 2 " 0.226 2.00e-02 2.50e+03 1.85e-01 4.28e+02 pdb=" C7 NAG R 2 " -0.065 2.00e-02 2.50e+03 pdb=" C8 NAG R 2 " 0.163 2.00e-02 2.50e+03 pdb=" N2 NAG R 2 " -0.298 2.00e-02 2.50e+03 pdb=" O7 NAG R 2 " -0.026 2.00e-02 2.50e+03 ... (remaining 1587 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 2756 2.83 - 3.35: 9323 3.35 - 3.87: 15841 3.87 - 4.38: 19496 4.38 - 4.90: 30060 Nonbonded interactions: 77476 Sorted by model distance: nonbonded pdb=" N ALA B 201 " pdb=" N LEU B 202 " model vdw 2.317 2.560 nonbonded pdb=" N ALA A 201 " pdb=" N LEU A 202 " model vdw 2.317 2.560 nonbonded pdb=" N ALA C 201 " pdb=" N LEU C 202 " model vdw 2.317 2.560 nonbonded pdb=" O GLY B 207 " pdb=" C SER B 208 " model vdw 2.403 3.270 nonbonded pdb=" O GLY C 207 " pdb=" C SER C 208 " model vdw 2.403 3.270 ... (remaining 77471 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'K' selection = chain 'R' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'Q' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'X' } ncs_group { reference = chain 'I' selection = chain 'P' selection = chain 'W' } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 1.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.660 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 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:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.024 0.123 9705 Z= 1.287 Angle : 2.242 36.392 13272 Z= 1.276 Chirality : 0.155 0.604 1632 Planarity : 0.012 0.185 1557 Dihedral : 15.070 106.833 4512 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.11 (0.24), residues: 1056 helix: -0.09 (0.24), residues: 339 sheet: 1.95 (0.48), residues: 99 loop : -0.34 (0.24), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 125 TYR 0.043 0.009 TYR B 218 PHE 0.025 0.006 PHE C 146 TRP 0.024 0.005 TRP B 226 HIS 0.009 0.003 HIS C 140 Details of bonding type rmsd covalent geometry : bond 0.02349 ( 9618) covalent geometry : angle 2.13907 (13032) SS BOND : bond 0.01224 ( 21) SS BOND : angle 3.49875 ( 42) hydrogen bonds : bond 0.17248 ( 372) hydrogen bonds : angle 6.30877 ( 990) link_ALPHA1-3 : bond 0.10501 ( 3) link_ALPHA1-3 : angle 7.62833 ( 9) link_ALPHA1-6 : bond 0.04870 ( 3) link_ALPHA1-6 : angle 3.60915 ( 9) link_BETA1-4 : bond 0.07711 ( 27) link_BETA1-4 : angle 6.86572 ( 81) link_NAG-ASN : bond 0.08075 ( 33) link_NAG-ASN : angle 4.59387 ( 99) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 356 time to evaluate : 0.364 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: 0.7988 (m-30) REVERT: C 129 ASP cc_start: 0.8023 (t0) cc_final: 0.7812 (t0) REVERT: C 193 MET cc_start: 0.7914 (tpp) cc_final: 0.7609 (tpp) REVERT: C 210 ASP cc_start: 0.6558 (p0) cc_final: 0.6076 (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: 0.1227 time to fit residues: 57.6875 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 : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 0.7980 chunk 100 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 8.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 GLN ** a 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 415 GLN B 130 HIS b 334 GLN b 415 GLN C 130 HIS c 330 GLN c 353 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.133301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.108825 restraints weight = 19392.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.112728 restraints weight = 12187.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.115220 restraints weight = 9092.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.116862 restraints weight = 7518.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.117942 restraints weight = 6581.511| |-----------------------------------------------------------------------------| r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.3916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 9705 Z= 0.239 Angle : 1.211 13.416 13272 Z= 0.573 Chirality : 0.057 0.305 1632 Planarity : 0.005 0.030 1557 Dihedral : 13.493 84.512 2514 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 4.52 % Allowed : 12.41 % Favored : 83.07 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.28 (0.25), residues: 1056 helix: 0.53 (0.27), residues: 336 sheet: 0.53 (0.43), residues: 144 loop : -0.79 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 125 TYR 0.020 0.001 TYR B 149 PHE 0.027 0.003 PHE A 116 TRP 0.025 0.002 TRP A 195 HIS 0.021 0.002 HIS C 123 Details of bonding type rmsd covalent geometry : bond 0.00494 ( 9618) covalent geometry : angle 1.05420 (13032) SS BOND : bond 0.00660 ( 21) SS BOND : angle 2.11049 ( 42) hydrogen bonds : bond 0.06509 ( 372) hydrogen bonds : angle 5.44468 ( 990) link_ALPHA1-3 : bond 0.00586 ( 3) link_ALPHA1-3 : angle 4.63034 ( 9) link_ALPHA1-6 : bond 0.00989 ( 3) link_ALPHA1-6 : angle 1.67364 ( 9) link_BETA1-4 : bond 0.02129 ( 27) link_BETA1-4 : angle 5.65714 ( 81) link_NAG-ASN : bond 0.00860 ( 33) link_NAG-ASN : angle 4.49233 ( 99) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 234 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 TYR cc_start: 0.6739 (OUTLIER) cc_final: 0.4977 (p90) REVERT: a 400 ASP cc_start: 0.8020 (OUTLIER) cc_final: 0.7780 (p0) REVERT: a 405 GLN cc_start: 0.8333 (tp40) cc_final: 0.8118 (tp40) REVERT: B 129 ASP cc_start: 0.7941 (t0) cc_final: 0.7717 (m-30) REVERT: b 383 ARG cc_start: 0.7849 (ttm110) cc_final: 0.7648 (ttm110) REVERT: b 401 ASP cc_start: 0.8155 (m-30) cc_final: 0.7845 (m-30) REVERT: C 229 HIS cc_start: 0.7660 (m-70) cc_final: 0.7223 (m-70) REVERT: c 401 ASP cc_start: 0.8172 (m-30) cc_final: 0.7959 (m-30) REVERT: c 409 MET cc_start: 0.7092 (mtp) cc_final: 0.6748 (mtp) outliers start: 43 outliers final: 21 residues processed: 256 average time/residue: 0.1186 time to fit residues: 40.5799 Evaluate side-chains 205 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 182 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 195 TRP Chi-restraints excluded: chain a residue 262 THR Chi-restraints excluded: chain a residue 291 CYS Chi-restraints excluded: chain a residue 376 THR Chi-restraints excluded: chain a residue 400 ASP Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 179 CYS Chi-restraints excluded: chain B residue 195 TRP Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain b residue 262 THR Chi-restraints excluded: chain b residue 283 MET Chi-restraints excluded: chain b residue 304 HIS Chi-restraints excluded: chain b residue 376 THR Chi-restraints excluded: chain C residue 116 PHE Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 195 TRP Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain c residue 260 THR Chi-restraints excluded: chain c residue 376 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 78 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 58 optimal weight: 7.9990 chunk 41 optimal weight: 10.0000 chunk 84 optimal weight: 5.9990 chunk 7 optimal weight: 0.4980 chunk 10 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 75 optimal weight: 0.0870 chunk 85 optimal weight: 5.9990 chunk 94 optimal weight: 0.9990 overall best weight: 1.3164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 HIS A 217 GLN B 217 GLN C 217 GLN c 334 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.129358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.105107 restraints weight = 19065.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.108959 restraints weight = 11587.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.111486 restraints weight = 8540.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.113052 restraints weight = 6979.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.113968 restraints weight = 6108.195| |-----------------------------------------------------------------------------| r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.4638 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= 0.226 Angle : 1.067 12.160 13272 Z= 0.500 Chirality : 0.055 0.317 1632 Planarity : 0.004 0.022 1557 Dihedral : 11.526 72.697 2514 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 5.99 % Allowed : 13.56 % Favored : 80.44 % 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 aren not related in a simple way. whole: -0.37 (0.25), residues: 1056 helix: 0.70 (0.27), residues: 333 sheet: 0.04 (0.45), residues: 138 loop : -0.86 (0.26), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG a 355 TYR 0.019 0.001 TYR c 418 PHE 0.015 0.002 PHE a 292 TRP 0.021 0.002 TRP A 195 HIS 0.007 0.001 HIS c 304 Details of bonding type rmsd covalent geometry : bond 0.00496 ( 9618) covalent geometry : angle 0.92485 (13032) SS BOND : bond 0.00839 ( 21) SS BOND : angle 2.68917 ( 42) hydrogen bonds : bond 0.05410 ( 372) hydrogen bonds : angle 5.38972 ( 990) link_ALPHA1-3 : bond 0.00351 ( 3) link_ALPHA1-3 : angle 4.89777 ( 9) link_ALPHA1-6 : bond 0.00920 ( 3) link_ALPHA1-6 : angle 1.89488 ( 9) link_BETA1-4 : bond 0.01906 ( 27) link_BETA1-4 : angle 4.95089 ( 81) link_NAG-ASN : bond 0.00906 ( 33) link_NAG-ASN : angle 3.77681 ( 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 266 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 209 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 MET cc_start: 0.8113 (tmm) cc_final: 0.7725 (tmm) REVERT: A 171 TYR cc_start: 0.6800 (OUTLIER) cc_final: 0.5202 (p90) REVERT: A 230 CYS cc_start: 0.7600 (OUTLIER) cc_final: 0.7122 (m) REVERT: a 262 THR cc_start: 0.9417 (OUTLIER) cc_final: 0.9208 (m) REVERT: B 152 MET cc_start: 0.7752 (ttt) cc_final: 0.7391 (tmm) REVERT: B 213 MET cc_start: 0.7238 (pmm) cc_final: 0.6857 (pmm) REVERT: b 262 THR cc_start: 0.9430 (OUTLIER) cc_final: 0.9097 (m) REVERT: b 383 ARG cc_start: 0.7826 (ttm110) cc_final: 0.7564 (ttm110) REVERT: b 401 ASP cc_start: 0.8357 (m-30) cc_final: 0.8032 (m-30) REVERT: C 152 MET cc_start: 0.8050 (tmm) cc_final: 0.7661 (tmm) REVERT: C 230 CYS cc_start: 0.7740 (OUTLIER) cc_final: 0.7251 (m) REVERT: c 356 ASP cc_start: 0.8264 (t0) cc_final: 0.8046 (t0) REVERT: c 401 ASP cc_start: 0.8271 (m-30) cc_final: 0.7999 (m-30) REVERT: c 409 MET cc_start: 0.7061 (mtp) cc_final: 0.6845 (mtp) outliers start: 57 outliers final: 37 residues processed: 244 average time/residue: 0.1174 time to fit residues: 38.2686 Evaluate side-chains 219 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 177 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 195 TRP Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain a residue 262 THR Chi-restraints excluded: chain a residue 266 SER Chi-restraints excluded: chain a residue 283 MET Chi-restraints excluded: chain a residue 323 ARG Chi-restraints excluded: chain a residue 376 THR Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 179 CYS Chi-restraints excluded: chain B residue 195 TRP Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain b residue 260 THR Chi-restraints excluded: chain b residue 262 THR Chi-restraints excluded: chain b residue 266 SER Chi-restraints excluded: chain b residue 283 MET Chi-restraints excluded: chain b residue 291 CYS Chi-restraints excluded: chain b residue 360 ILE Chi-restraints excluded: chain b residue 376 THR Chi-restraints excluded: chain b residue 414 LEU Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 116 PHE Chi-restraints excluded: chain C residue 195 TRP Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain c residue 266 SER Chi-restraints excluded: chain c residue 291 CYS Chi-restraints excluded: chain c residue 323 ARG Chi-restraints excluded: chain c residue 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: 0.9990 chunk 38 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 99 optimal weight: 0.9990 chunk 6 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 HIS ** c 337 ASN ** 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 = 0.3920 r_free = 0.3920 target = 0.126844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.101044 restraints weight = 19568.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.104762 restraints weight = 12232.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.107236 restraints weight = 9256.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.108793 restraints weight = 7709.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.109650 restraints weight = 6829.782| |-----------------------------------------------------------------------------| r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.5165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 9705 Z= 0.259 Angle : 1.075 12.196 13272 Z= 0.500 Chirality : 0.056 0.347 1632 Planarity : 0.004 0.027 1557 Dihedral : 10.919 61.799 2514 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.62 % Favored : 91.38 % Rotamer: Outliers : 5.78 % Allowed : 15.77 % Favored : 78.44 % 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 aren not related in a simple way. whole: -0.89 (0.25), residues: 1056 helix: 0.52 (0.26), residues: 354 sheet: -0.51 (0.41), residues: 153 loop : -1.36 (0.26), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG c 355 TYR 0.021 0.002 TYR B 149 PHE 0.019 0.002 PHE a 292 TRP 0.018 0.002 TRP A 195 HIS 0.013 0.002 HIS C 123 Details of bonding type rmsd covalent geometry : bond 0.00583 ( 9618) covalent geometry : angle 0.93776 (13032) SS BOND : bond 0.00754 ( 21) SS BOND : angle 3.09358 ( 42) hydrogen bonds : bond 0.04993 ( 372) hydrogen bonds : angle 5.44950 ( 990) link_ALPHA1-3 : bond 0.00701 ( 3) link_ALPHA1-3 : angle 5.02777 ( 9) link_ALPHA1-6 : bond 0.01168 ( 3) link_ALPHA1-6 : angle 2.04719 ( 9) link_BETA1-4 : bond 0.01773 ( 27) link_BETA1-4 : angle 4.88778 ( 81) link_NAG-ASN : bond 0.00790 ( 33) link_NAG-ASN : angle 3.58546 ( 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 251 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 196 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 LYS cc_start: 0.8375 (mmtm) cc_final: 0.8158 (mmtm) REVERT: A 152 MET cc_start: 0.8189 (tmm) cc_final: 0.7648 (tmm) REVERT: A 171 TYR cc_start: 0.6899 (OUTLIER) cc_final: 0.5179 (p90) REVERT: B 149 TYR cc_start: 0.6686 (m-80) cc_final: 0.6434 (m-10) REVERT: b 310 ASP cc_start: 0.8692 (m-30) cc_final: 0.8288 (t0) REVERT: b 383 ARG cc_start: 0.7757 (ttm110) cc_final: 0.7493 (ttm110) REVERT: b 401 ASP cc_start: 0.8384 (m-30) cc_final: 0.8044 (m-30) REVERT: C 115 LYS cc_start: 0.8226 (mmtm) cc_final: 0.8013 (mmtm) REVERT: C 133 MET cc_start: 0.7999 (tmm) cc_final: 0.7797 (tmm) REVERT: C 148 GLN cc_start: 0.8453 (mm110) cc_final: 0.8056 (tm-30) REVERT: C 191 MET cc_start: 0.8134 (mmm) cc_final: 0.7856 (mmm) REVERT: C 193 MET cc_start: 0.8637 (tpp) cc_final: 0.8345 (tpp) REVERT: c 304 HIS cc_start: 0.6860 (OUTLIER) cc_final: 0.6468 (p90) REVERT: c 356 ASP cc_start: 0.8171 (t0) cc_final: 0.7844 (t0) REVERT: c 404 GLN cc_start: 0.8160 (tp40) cc_final: 0.7702 (tp40) REVERT: c 409 MET cc_start: 0.7283 (mtp) cc_final: 0.6992 (mtp) outliers start: 55 outliers final: 36 residues processed: 228 average time/residue: 0.1171 time to fit residues: 35.8898 Evaluate side-chains 214 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 176 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 195 TRP Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain a residue 260 THR Chi-restraints excluded: chain a residue 266 SER Chi-restraints excluded: chain a residue 291 CYS Chi-restraints excluded: chain a residue 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 195 TRP Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain b residue 266 SER Chi-restraints excluded: chain b residue 291 CYS Chi-restraints excluded: chain b residue 304 HIS Chi-restraints excluded: chain b residue 360 ILE Chi-restraints excluded: chain b residue 376 THR Chi-restraints excluded: chain b residue 414 LEU Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 116 PHE Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 171 TYR Chi-restraints excluded: chain C residue 195 TRP Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain c residue 266 SER Chi-restraints excluded: chain c residue 291 CYS Chi-restraints excluded: chain c residue 304 HIS Chi-restraints excluded: chain c residue 323 ARG Chi-restraints excluded: chain c residue 336 ILE Chi-restraints excluded: chain c residue 354 LEU Chi-restraints excluded: chain c residue 360 ILE Chi-restraints excluded: chain c residue 376 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 50 optimal weight: 5.9990 chunk 71 optimal weight: 0.6980 chunk 94 optimal weight: 0.7980 chunk 36 optimal weight: 0.6980 chunk 56 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 353 HIS ** b 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 337 ASN ** 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 = 0.3799 r_free = 0.3799 target = 0.121202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.095726 restraints weight = 18859.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.098613 restraints weight = 13316.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.100581 restraints weight = 10614.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.101725 restraints weight = 9104.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.102786 restraints weight = 8254.813| |-----------------------------------------------------------------------------| r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.5424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 9705 Z= 0.183 Angle : 0.981 13.522 13272 Z= 0.456 Chirality : 0.052 0.347 1632 Planarity : 0.003 0.026 1557 Dihedral : 10.417 59.945 2514 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.43 % Favored : 91.48 % Rotamer: Outliers : 5.05 % Allowed : 18.40 % Favored : 76.55 % 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 aren not related in a simple way. whole: -0.75 (0.25), residues: 1056 helix: 0.59 (0.26), residues: 357 sheet: -0.35 (0.43), residues: 144 loop : -1.28 (0.26), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 234 TYR 0.025 0.001 TYR A 149 PHE 0.015 0.002 PHE a 292 TRP 0.018 0.001 TRP A 195 HIS 0.008 0.001 HIS C 130 Details of bonding type rmsd covalent geometry : bond 0.00409 ( 9618) covalent geometry : angle 0.85216 (13032) SS BOND : bond 0.00702 ( 21) SS BOND : angle 3.17822 ( 42) hydrogen bonds : bond 0.04493 ( 372) hydrogen bonds : angle 5.28841 ( 990) link_ALPHA1-3 : bond 0.00385 ( 3) link_ALPHA1-3 : angle 4.68119 ( 9) link_ALPHA1-6 : bond 0.01214 ( 3) link_ALPHA1-6 : angle 2.20697 ( 9) link_BETA1-4 : bond 0.01728 ( 27) link_BETA1-4 : angle 4.46579 ( 81) link_NAG-ASN : bond 0.00682 ( 33) link_NAG-ASN : angle 3.23286 ( 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 244 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 196 time to evaluate : 0.385 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: 0.8109 (mmtm) cc_final: 0.7861 (mmtm) REVERT: A 152 MET cc_start: 0.8236 (tmm) cc_final: 0.7709 (tmm) REVERT: A 171 TYR cc_start: 0.6855 (OUTLIER) cc_final: 0.5082 (p90) REVERT: a 338 LYS cc_start: 0.8340 (mtmt) cc_final: 0.8009 (mttt) REVERT: a 346 ASP cc_start: 0.7876 (t0) cc_final: 0.7054 (t0) REVERT: b 310 ASP cc_start: 0.8503 (m-30) cc_final: 0.8104 (t0) REVERT: b 334 GLN cc_start: 0.7205 (pt0) cc_final: 0.6940 (mp10) REVERT: b 401 ASP cc_start: 0.8315 (m-30) cc_final: 0.8022 (m-30) REVERT: C 133 MET cc_start: 0.7959 (tmm) cc_final: 0.7654 (tmm) REVERT: C 148 GLN cc_start: 0.8464 (mm110) cc_final: 0.7985 (tm-30) REVERT: C 152 MET cc_start: 0.7954 (tmm) cc_final: 0.7582 (tmm) REVERT: C 191 MET cc_start: 0.8013 (mmm) cc_final: 0.7692 (mmt) REVERT: c 304 HIS cc_start: 0.6957 (OUTLIER) cc_final: 0.6538 (p90) REVERT: c 356 ASP cc_start: 0.8084 (t0) cc_final: 0.7769 (t0) REVERT: c 404 GLN cc_start: 0.8042 (tp40) cc_final: 0.7727 (tp40) outliers start: 48 outliers final: 36 residues processed: 224 average time/residue: 0.1199 time to fit residues: 35.8676 Evaluate side-chains 209 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 171 time to evaluate : 0.355 ------------------------------------------------------------------------------- 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 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 266 SER Chi-restraints excluded: chain a residue 283 MET Chi-restraints excluded: chain a residue 323 ARG Chi-restraints excluded: chain a residue 359 CYS Chi-restraints excluded: chain a residue 360 ILE Chi-restraints excluded: chain a residue 376 THR Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 123 HIS Chi-restraints excluded: chain B residue 195 TRP Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain b residue 260 THR Chi-restraints excluded: chain b residue 266 SER Chi-restraints excluded: chain b residue 283 MET Chi-restraints excluded: chain b residue 291 CYS Chi-restraints excluded: chain b residue 359 CYS Chi-restraints excluded: chain b residue 376 THR Chi-restraints excluded: chain b residue 414 LEU Chi-restraints excluded: chain C residue 116 PHE Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 123 HIS Chi-restraints excluded: chain C residue 195 TRP Chi-restraints excluded: chain c residue 266 SER Chi-restraints excluded: chain c residue 291 CYS Chi-restraints excluded: chain c residue 304 HIS Chi-restraints excluded: chain c residue 323 ARG Chi-restraints excluded: chain c residue 334 GLN Chi-restraints excluded: chain c residue 360 ILE Chi-restraints excluded: chain c residue 376 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 12 optimal weight: 9.9990 chunk 77 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 4 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 69 optimal weight: 0.5980 chunk 84 optimal weight: 7.9990 chunk 8 optimal weight: 0.1980 chunk 83 optimal weight: 0.9980 chunk 64 optimal weight: 0.0770 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 HIS ** A 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 GLN ** b 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 130 HIS ** C 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.125483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.101594 restraints weight = 18385.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.104259 restraints weight = 13178.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.106142 restraints weight = 10596.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.107167 restraints weight = 9100.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.108158 restraints weight = 8277.668| |-----------------------------------------------------------------------------| r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.5664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 9705 Z= 0.175 Angle : 0.981 13.065 13272 Z= 0.457 Chirality : 0.052 0.362 1632 Planarity : 0.003 0.027 1557 Dihedral : 9.990 59.958 2514 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.28 % Favored : 90.72 % Rotamer: Outliers : 5.68 % Allowed : 19.14 % Favored : 75.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.78 (0.25), residues: 1056 helix: 0.58 (0.27), residues: 354 sheet: -0.34 (0.43), residues: 144 loop : -1.31 (0.26), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG b 383 TYR 0.017 0.001 TYR B 149 PHE 0.014 0.001 PHE c 292 TRP 0.018 0.002 TRP A 195 HIS 0.009 0.001 HIS B 123 Details of bonding type rmsd covalent geometry : bond 0.00385 ( 9618) covalent geometry : angle 0.85466 (13032) SS BOND : bond 0.00687 ( 21) SS BOND : angle 3.65694 ( 42) hydrogen bonds : bond 0.04306 ( 372) hydrogen bonds : angle 5.21006 ( 990) link_ALPHA1-3 : bond 0.00283 ( 3) link_ALPHA1-3 : angle 4.65447 ( 9) link_ALPHA1-6 : bond 0.01171 ( 3) link_ALPHA1-6 : angle 2.17198 ( 9) link_BETA1-4 : bond 0.01679 ( 27) link_BETA1-4 : angle 4.30235 ( 81) link_NAG-ASN : bond 0.00667 ( 33) link_NAG-ASN : angle 3.09055 ( 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 238 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 184 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 LYS cc_start: 0.8002 (mmtm) cc_final: 0.7772 (mmtm) REVERT: A 171 TYR cc_start: 0.6611 (OUTLIER) cc_final: 0.4965 (p90) REVERT: A 193 MET cc_start: 0.8283 (tpp) cc_final: 0.7661 (ttm) REVERT: a 334 GLN cc_start: 0.7088 (pp30) cc_final: 0.6771 (pp30) REVERT: a 338 LYS cc_start: 0.8248 (mtmt) cc_final: 0.8031 (mttt) REVERT: a 404 GLN cc_start: 0.7756 (tp40) cc_final: 0.7416 (tp40) REVERT: b 306 GLU cc_start: 0.7834 (mm-30) cc_final: 0.7454 (mm-30) REVERT: b 310 ASP cc_start: 0.8366 (m-30) cc_final: 0.8097 (t0) REVERT: b 352 ASN cc_start: 0.8960 (m-40) cc_final: 0.8738 (m-40) REVERT: b 401 ASP cc_start: 0.8148 (m-30) cc_final: 0.7844 (m-30) REVERT: C 152 MET cc_start: 0.7885 (tmm) cc_final: 0.7606 (tmm) REVERT: c 356 ASP cc_start: 0.7910 (t0) cc_final: 0.7667 (t0) REVERT: c 404 GLN cc_start: 0.7965 (tp40) cc_final: 0.7756 (tp40) outliers start: 54 outliers final: 37 residues processed: 220 average time/residue: 0.1153 time to fit residues: 34.1141 Evaluate side-chains 203 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 165 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 211 CYS Chi-restraints excluded: chain a residue 266 SER Chi-restraints excluded: chain a residue 291 CYS Chi-restraints excluded: chain a residue 292 PHE Chi-restraints excluded: chain a residue 376 THR 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 211 CYS Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain b residue 266 SER Chi-restraints excluded: chain b residue 291 CYS Chi-restraints excluded: chain b residue 304 HIS Chi-restraints excluded: chain b residue 359 CYS Chi-restraints excluded: chain b residue 360 ILE Chi-restraints excluded: chain b residue 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 121 ASP Chi-restraints excluded: chain C residue 123 HIS Chi-restraints excluded: chain C residue 171 TYR Chi-restraints excluded: chain C residue 195 TRP Chi-restraints excluded: chain c residue 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 360 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 5 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 92 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 17 optimal weight: 0.0170 chunk 67 optimal weight: 3.9990 chunk 102 optimal weight: 0.9980 chunk 49 optimal weight: 9.9990 overall best weight: 1.3822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 HIS A 123 HIS ** A 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 HIS ** b 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.122374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.097390 restraints weight = 18857.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.100194 restraints weight = 13284.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.102160 restraints weight = 10579.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.103455 restraints weight = 9061.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.104330 restraints weight = 8139.357| |-----------------------------------------------------------------------------| r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.5901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 9705 Z= 0.213 Angle : 1.024 12.105 13272 Z= 0.477 Chirality : 0.054 0.370 1632 Planarity : 0.003 0.032 1557 Dihedral : 9.808 59.900 2514 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.94 % Favored : 90.06 % Rotamer: Outliers : 5.36 % Allowed : 18.51 % Favored : 76.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.84 (0.26), residues: 1056 helix: 0.60 (0.27), residues: 357 sheet: -0.56 (0.42), residues: 153 loop : -1.35 (0.27), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 234 TYR 0.023 0.001 TYR B 149 PHE 0.017 0.002 PHE B 156 TRP 0.017 0.002 TRP A 195 HIS 0.008 0.001 HIS A 123 Details of bonding type rmsd covalent geometry : bond 0.00484 ( 9618) covalent geometry : angle 0.88880 (13032) SS BOND : bond 0.00649 ( 21) SS BOND : angle 4.53514 ( 42) hydrogen bonds : bond 0.04291 ( 372) hydrogen bonds : angle 5.28027 ( 990) link_ALPHA1-3 : bond 0.00348 ( 3) link_ALPHA1-3 : angle 4.74854 ( 9) link_ALPHA1-6 : bond 0.01192 ( 3) link_ALPHA1-6 : angle 1.85222 ( 9) link_BETA1-4 : bond 0.01616 ( 27) link_BETA1-4 : angle 4.31150 ( 81) link_NAG-ASN : bond 0.00761 ( 33) link_NAG-ASN : angle 3.19163 ( 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 224 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 173 time to evaluate : 0.351 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 115 LYS cc_start: 0.8167 (mmtm) cc_final: 0.7956 (mmtm) REVERT: A 152 MET cc_start: 0.8149 (tmm) cc_final: 0.7791 (tmm) REVERT: A 171 TYR cc_start: 0.6797 (OUTLIER) cc_final: 0.5097 (p90) REVERT: A 199 TYR cc_start: 0.6623 (OUTLIER) cc_final: 0.5075 (m-80) REVERT: a 404 GLN cc_start: 0.7841 (tp40) cc_final: 0.7529 (tp40) REVERT: B 152 MET cc_start: 0.7915 (tmm) cc_final: 0.7594 (tmm) REVERT: b 306 GLU cc_start: 0.7887 (mm-30) cc_final: 0.7606 (mm-30) REVERT: b 310 ASP cc_start: 0.8460 (m-30) cc_final: 0.8218 (t0) REVERT: b 331 MET cc_start: 0.5284 (tpt) cc_final: 0.5007 (ptt) REVERT: b 346 ASP cc_start: 0.7320 (t0) cc_final: 0.7086 (t0) REVERT: b 352 ASN cc_start: 0.9017 (m-40) cc_final: 0.8772 (m-40) REVERT: b 401 ASP cc_start: 0.8291 (m-30) cc_final: 0.7940 (m-30) REVERT: C 152 MET cc_start: 0.7910 (tmm) cc_final: 0.7637 (tmm) REVERT: C 193 MET cc_start: 0.8167 (tpp) cc_final: 0.7127 (ttm) REVERT: c 404 GLN cc_start: 0.8000 (tp40) cc_final: 0.7792 (tp40) outliers start: 51 outliers final: 40 residues processed: 206 average time/residue: 0.1174 time to fit residues: 32.5957 Evaluate side-chains 209 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 167 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 91 HIS Chi-restraints excluded: chain A residue 117 CYS 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 283 MET Chi-restraints excluded: chain a residue 291 CYS Chi-restraints excluded: chain a residue 359 CYS Chi-restraints excluded: chain a residue 376 THR Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 123 HIS Chi-restraints excluded: chain B residue 195 TRP Chi-restraints excluded: chain b residue 266 SER Chi-restraints excluded: chain b residue 291 CYS Chi-restraints excluded: chain b residue 304 HIS Chi-restraints excluded: chain b residue 359 CYS Chi-restraints excluded: chain b residue 360 ILE Chi-restraints excluded: chain b residue 376 THR Chi-restraints excluded: chain b residue 387 VAL Chi-restraints excluded: chain b residue 414 LEU Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 116 PHE Chi-restraints excluded: chain C residue 123 HIS Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 171 TYR Chi-restraints excluded: chain C residue 195 TRP Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain c residue 266 SER Chi-restraints excluded: chain c residue 291 CYS Chi-restraints excluded: chain c residue 304 HIS Chi-restraints excluded: chain c residue 323 ARG Chi-restraints excluded: chain c residue 334 GLN Chi-restraints excluded: chain c residue 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: 5.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 94 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 HIS ** a 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 178 HIS ** b 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.121075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.096290 restraints weight = 18659.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.099128 restraints weight = 12927.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.101082 restraints weight = 10228.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.102387 restraints weight = 8735.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.103277 restraints weight = 7835.974| |-----------------------------------------------------------------------------| r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.6002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 9705 Z= 0.239 Angle : 1.040 12.672 13272 Z= 0.483 Chirality : 0.054 0.383 1632 Planarity : 0.003 0.031 1557 Dihedral : 9.500 59.980 2514 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.85 % Favored : 90.15 % Rotamer: Outliers : 5.05 % Allowed : 19.14 % Favored : 75.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.89 (0.26), residues: 1056 helix: 0.64 (0.27), residues: 354 sheet: -0.56 (0.42), residues: 153 loop : -1.46 (0.26), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG b 383 TYR 0.022 0.001 TYR B 149 PHE 0.015 0.002 PHE B 156 TRP 0.016 0.002 TRP A 195 HIS 0.033 0.002 HIS A 91 Details of bonding type rmsd covalent geometry : bond 0.00548 ( 9618) covalent geometry : angle 0.91843 (13032) SS BOND : bond 0.00661 ( 21) SS BOND : angle 3.83422 ( 42) hydrogen bonds : bond 0.04348 ( 372) hydrogen bonds : angle 5.33400 ( 990) link_ALPHA1-3 : bond 0.00401 ( 3) link_ALPHA1-3 : angle 4.93439 ( 9) link_ALPHA1-6 : bond 0.01389 ( 3) link_ALPHA1-6 : angle 1.11609 ( 9) link_BETA1-4 : bond 0.01571 ( 27) link_BETA1-4 : angle 4.32930 ( 81) link_NAG-ASN : bond 0.00726 ( 33) link_NAG-ASN : angle 3.18145 ( 99) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 174 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 MET cc_start: 0.8149 (tmm) cc_final: 0.7812 (tmm) REVERT: A 171 TYR cc_start: 0.6946 (OUTLIER) cc_final: 0.5263 (p90) REVERT: A 193 MET cc_start: 0.8471 (tpp) cc_final: 0.7967 (ttm) REVERT: A 199 TYR cc_start: 0.6727 (OUTLIER) cc_final: 0.5192 (m-80) REVERT: a 404 GLN cc_start: 0.7987 (tp40) cc_final: 0.7641 (tp40) REVERT: B 152 MET cc_start: 0.7925 (tmm) cc_final: 0.7529 (tmm) REVERT: b 352 ASN cc_start: 0.9086 (m-40) cc_final: 0.8851 (m-40) REVERT: b 401 ASP cc_start: 0.8388 (m-30) cc_final: 0.8015 (m-30) REVERT: C 193 MET cc_start: 0.8313 (tpp) cc_final: 0.7202 (ttm) REVERT: c 409 MET cc_start: 0.7415 (mtp) cc_final: 0.7208 (mtp) REVERT: c 417 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7561 (pm20) outliers start: 48 outliers final: 43 residues processed: 208 average time/residue: 0.1159 time to fit residues: 32.5349 Evaluate side-chains 212 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 166 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 117 CYS Chi-restraints excluded: chain A residue 123 HIS Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 195 TRP Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain a residue 262 THR 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 333 ILE Chi-restraints excluded: chain a residue 359 CYS Chi-restraints excluded: chain a residue 376 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 123 HIS Chi-restraints excluded: chain B residue 195 TRP Chi-restraints excluded: chain b residue 266 SER Chi-restraints excluded: chain b residue 291 CYS Chi-restraints excluded: chain b residue 304 HIS Chi-restraints excluded: chain b residue 359 CYS Chi-restraints excluded: chain b residue 360 ILE Chi-restraints excluded: chain b residue 376 THR Chi-restraints excluded: chain b residue 387 VAL Chi-restraints excluded: chain b residue 414 LEU Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 116 PHE Chi-restraints excluded: chain C residue 123 HIS Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 171 TYR Chi-restraints excluded: chain C residue 195 TRP Chi-restraints excluded: chain C residue 245 SER 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 Chi-restraints excluded: chain c residue 417 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 73 optimal weight: 0.9990 chunk 81 optimal weight: 20.0000 chunk 5 optimal weight: 0.6980 chunk 59 optimal weight: 0.7980 chunk 77 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 chunk 19 optimal weight: 0.0170 chunk 102 optimal weight: 0.0470 chunk 20 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.123522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.099333 restraints weight = 18543.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.101995 restraints weight = 13397.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.103814 restraints weight = 10840.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.105019 restraints weight = 9367.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.105728 restraints weight = 8480.951| |-----------------------------------------------------------------------------| r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.6132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 9705 Z= 0.175 Angle : 0.983 13.458 13272 Z= 0.459 Chirality : 0.052 0.383 1632 Planarity : 0.003 0.032 1557 Dihedral : 9.058 59.854 2514 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.00 % Favored : 91.00 % Rotamer: Outliers : 4.42 % Allowed : 19.98 % 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 aren not related in a simple way. whole: -0.94 (0.26), residues: 1056 helix: 0.61 (0.27), residues: 354 sheet: -0.74 (0.42), residues: 156 loop : -1.43 (0.27), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 125 TYR 0.021 0.001 TYR B 149 PHE 0.015 0.001 PHE B 116 TRP 0.017 0.002 TRP A 195 HIS 0.006 0.001 HIS c 304 Details of bonding type rmsd covalent geometry : bond 0.00394 ( 9618) covalent geometry : angle 0.86988 (13032) SS BOND : bond 0.00639 ( 21) SS BOND : angle 3.63029 ( 42) hydrogen bonds : bond 0.04094 ( 372) hydrogen bonds : angle 5.19916 ( 990) link_ALPHA1-3 : bond 0.00404 ( 3) link_ALPHA1-3 : angle 4.82112 ( 9) link_ALPHA1-6 : bond 0.01357 ( 3) link_ALPHA1-6 : angle 0.98893 ( 9) link_BETA1-4 : bond 0.01599 ( 27) link_BETA1-4 : angle 4.05173 ( 81) link_NAG-ASN : bond 0.00669 ( 33) link_NAG-ASN : angle 2.95371 ( 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 222 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 180 time to evaluate : 0.292 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: 0.8023 (mmtm) cc_final: 0.7810 (mmtm) REVERT: A 152 MET cc_start: 0.8183 (tmm) cc_final: 0.7923 (tmm) REVERT: A 171 TYR cc_start: 0.7002 (OUTLIER) cc_final: 0.5449 (p90) REVERT: A 193 MET cc_start: 0.8303 (tpp) cc_final: 0.7751 (ttm) REVERT: A 199 TYR cc_start: 0.6553 (OUTLIER) cc_final: 0.5085 (m-80) REVERT: a 404 GLN cc_start: 0.7759 (tp40) cc_final: 0.7457 (tp40) REVERT: B 152 MET cc_start: 0.8017 (tmm) cc_final: 0.7753 (tmm) REVERT: B 199 TYR cc_start: 0.6438 (OUTLIER) cc_final: 0.5187 (m-80) REVERT: b 331 MET cc_start: 0.5370 (tpt) cc_final: 0.4804 (ptt) REVERT: b 352 ASN cc_start: 0.8959 (m-40) cc_final: 0.8695 (m-40) REVERT: b 401 ASP cc_start: 0.8236 (m-30) cc_final: 0.7918 (m-30) REVERT: C 193 MET cc_start: 0.8142 (tpp) cc_final: 0.7242 (ttt) REVERT: c 404 GLN cc_start: 0.7760 (tp40) cc_final: 0.7400 (tp40) REVERT: c 409 MET cc_start: 0.7146 (mtp) cc_final: 0.6902 (mtp) outliers start: 42 outliers final: 35 residues processed: 209 average time/residue: 0.0951 time to fit residues: 26.7961 Evaluate side-chains 204 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 166 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 CYS Chi-restraints excluded: chain A residue 123 HIS Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 195 TRP Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain a residue 262 THR 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 B residue 116 PHE Chi-restraints excluded: chain B residue 123 HIS Chi-restraints excluded: chain B residue 171 TYR Chi-restraints excluded: chain B residue 195 TRP Chi-restraints excluded: chain B residue 199 TYR 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 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 354 LEU Chi-restraints excluded: chain c residue 359 CYS Chi-restraints excluded: chain c residue 360 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 51 optimal weight: 0.7980 chunk 87 optimal weight: 0.0370 chunk 97 optimal weight: 0.9980 chunk 35 optimal weight: 5.9990 chunk 92 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 18 optimal weight: 5.9990 chunk 93 optimal weight: 2.9990 chunk 52 optimal weight: 0.1980 chunk 99 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 HIS ** b 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 337 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 = 0.3820 r_free = 0.3820 target = 0.123292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.098123 restraints weight = 18895.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.100942 restraints weight = 13391.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.102731 restraints weight = 10755.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.104055 restraints weight = 9334.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.104940 restraints weight = 8425.022| |-----------------------------------------------------------------------------| r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.6300 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= 0.175 Angle : 0.980 12.398 13272 Z= 0.459 Chirality : 0.052 0.374 1632 Planarity : 0.003 0.036 1557 Dihedral : 8.798 58.922 2514 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer: Outliers : 3.89 % Allowed : 20.29 % Favored : 75.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.86 (0.26), residues: 1056 helix: 0.61 (0.27), residues: 357 sheet: -0.66 (0.42), residues: 156 loop : -1.35 (0.27), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 125 TYR 0.021 0.001 TYR B 149 PHE 0.013 0.001 PHE a 292 TRP 0.015 0.001 TRP A 195 HIS 0.006 0.001 HIS c 304 Details of bonding type rmsd covalent geometry : bond 0.00393 ( 9618) covalent geometry : angle 0.87506 (13032) SS BOND : bond 0.00640 ( 21) SS BOND : angle 3.51931 ( 42) hydrogen bonds : bond 0.03971 ( 372) hydrogen bonds : angle 5.14968 ( 990) link_ALPHA1-3 : bond 0.00374 ( 3) link_ALPHA1-3 : angle 4.68737 ( 9) link_ALPHA1-6 : bond 0.01263 ( 3) link_ALPHA1-6 : angle 0.98930 ( 9) link_BETA1-4 : bond 0.01552 ( 27) link_BETA1-4 : angle 3.93298 ( 81) link_NAG-ASN : bond 0.00673 ( 33) link_NAG-ASN : angle 2.79948 ( 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 221 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 184 time to evaluate : 0.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 LYS cc_start: 0.8083 (mmtm) cc_final: 0.7868 (mmtm) REVERT: A 152 MET cc_start: 0.8038 (tmm) cc_final: 0.7592 (tmm) REVERT: A 171 TYR cc_start: 0.6902 (OUTLIER) cc_final: 0.5378 (p90) REVERT: A 193 MET cc_start: 0.8358 (tpp) cc_final: 0.7853 (ttm) REVERT: A 199 TYR cc_start: 0.6579 (OUTLIER) cc_final: 0.5124 (m-80) REVERT: a 404 GLN cc_start: 0.7851 (tp40) cc_final: 0.7511 (tp40) REVERT: B 152 MET cc_start: 0.7946 (tmm) cc_final: 0.7697 (tmm) REVERT: B 199 TYR cc_start: 0.6449 (OUTLIER) cc_final: 0.5236 (m-80) REVERT: b 331 MET cc_start: 0.5372 (tpt) cc_final: 0.5153 (ppp) REVERT: b 352 ASN cc_start: 0.8941 (m-40) cc_final: 0.8694 (m-40) REVERT: b 401 ASP cc_start: 0.8250 (m-30) cc_final: 0.7970 (m-30) REVERT: C 152 MET cc_start: 0.7937 (tmm) cc_final: 0.7713 (tmm) REVERT: C 193 MET cc_start: 0.8177 (tpp) cc_final: 0.7317 (ttt) REVERT: c 409 MET cc_start: 0.7153 (mtp) cc_final: 0.6944 (mtp) outliers start: 37 outliers final: 32 residues processed: 210 average time/residue: 0.0901 time to fit residues: 25.6347 Evaluate side-chains 203 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 168 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 195 TRP Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain a residue 266 SER Chi-restraints excluded: chain a residue 291 CYS Chi-restraints excluded: chain a residue 292 PHE Chi-restraints excluded: chain a residue 359 CYS Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 123 HIS Chi-restraints excluded: chain B residue 171 TYR Chi-restraints excluded: chain B residue 195 TRP Chi-restraints excluded: chain B residue 199 TYR 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 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 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: 0.9990 chunk 65 optimal weight: 0.8980 chunk 97 optimal weight: 7.9990 chunk 16 optimal weight: 0.8980 chunk 20 optimal weight: 10.0000 chunk 14 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 HIS A 123 HIS ** a 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.122794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.098056 restraints weight = 18787.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.100635 restraints weight = 13689.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.102416 restraints weight = 11170.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.103594 restraints weight = 9718.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.104248 restraints weight = 8837.930| |-----------------------------------------------------------------------------| r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.6437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 9705 Z= 0.187 Angle : 0.977 11.789 13272 Z= 0.458 Chirality : 0.052 0.361 1632 Planarity : 0.003 0.033 1557 Dihedral : 8.788 59.844 2514 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.62 % Favored : 91.38 % Rotamer: Outliers : 4.42 % Allowed : 21.03 % Favored : 74.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.84 (0.26), residues: 1056 helix: 0.64 (0.27), residues: 357 sheet: -0.65 (0.42), residues: 156 loop : -1.34 (0.27), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG b 383 TYR 0.020 0.001 TYR B 149 PHE 0.014 0.001 PHE B 156 TRP 0.015 0.001 TRP A 195 HIS 0.006 0.001 HIS c 304 Details of bonding type rmsd covalent geometry : bond 0.00431 ( 9618) covalent geometry : angle 0.87473 (13032) SS BOND : bond 0.00649 ( 21) SS BOND : angle 3.47579 ( 42) hydrogen bonds : bond 0.04004 ( 372) hydrogen bonds : angle 5.16222 ( 990) link_ALPHA1-3 : bond 0.00397 ( 3) link_ALPHA1-3 : angle 4.60230 ( 9) link_ALPHA1-6 : bond 0.01223 ( 3) link_ALPHA1-6 : angle 1.01770 ( 9) link_BETA1-4 : bond 0.01510 ( 27) link_BETA1-4 : angle 3.90670 ( 81) link_NAG-ASN : bond 0.00658 ( 33) link_NAG-ASN : angle 2.75764 ( 99) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1593.76 seconds wall clock time: 28 minutes 40.91 seconds (1720.91 seconds total)