Starting phenix.real_space_refine on Sun Jul 27 17:10:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8eje_28179/07_2025/8eje_28179.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eje_28179/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8eje_28179/07_2025/8eje_28179.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eje_28179/07_2025/8eje_28179.map" model { file = "/net/cci-nas-00/data/ceres_data/8eje_28179/07_2025/8eje_28179.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eje_28179/07_2025/8eje_28179.cif" } resolution = 3.69 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 6.33, per 1000 atoms: 0.67 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: 3.26 Conformation dependent library (CDL) restraints added in 917.7 milliseconds 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2016 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 12 sheets defined 40.4% alpha, 12.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 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: 2.49 Time building geometry restraints manager: 3.72 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'K' selection = chain 'R' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'Q' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'X' } ncs_group { reference = chain 'I' selection = chain 'P' selection = chain 'W' } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.190 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: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 25.200 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.230 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (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 TRP 0.024 0.005 TRP B 226 HIS 0.009 0.003 HIS C 140 PHE 0.025 0.006 PHE C 146 TYR 0.043 0.009 TYR B 218 ARG 0.006 0.001 ARG C 125 Details of bonding type rmsd link_NAG-ASN : bond 0.08075 ( 33) link_NAG-ASN : angle 4.59387 ( 99) 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_ALPHA1-3 : bond 0.10501 ( 3) link_ALPHA1-3 : angle 7.62833 ( 9) hydrogen bonds : bond 0.17248 ( 372) hydrogen bonds : angle 6.30877 ( 990) SS BOND : bond 0.01224 ( 21) SS BOND : angle 3.49875 ( 42) covalent geometry : bond 0.02349 ( 9618) covalent geometry : angle 2.13907 (13032) *********************** 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 : 0.993 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: 0.7996 (t0) REVERT: B 182 ILE cc_start: 0.8049 (mt) cc_final: 0.7778 (mp) REVERT: b 316 ASP cc_start: 0.8636 (t70) cc_final: 0.8306 (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: 0.7811 (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: 0.6077 (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: 0.8075 (m-30) outliers start: 0 outliers final: 0 residues processed: 356 average time/residue: 0.2632 time to fit residues: 122.7508 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 : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 0.0980 chunk 79 optimal weight: 4.9990 chunk 44 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 chunk 53 optimal weight: 0.7980 chunk 42 optimal weight: 0.5980 chunk 82 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 61 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 334 GLN ** b 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 130 HIS c 330 GLN c 353 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.133446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.108866 restraints weight = 19187.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.112787 restraints weight = 12054.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.115309 restraints weight = 8992.271| |-----------------------------------------------------------------------------| r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.3864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 9705 Z= 0.240 Angle : 1.210 13.302 13272 Z= 0.573 Chirality : 0.056 0.302 1632 Planarity : 0.004 0.029 1557 Dihedral : 13.521 85.208 2514 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 4.42 % Allowed : 12.30 % Favored : 83.28 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.25), residues: 1056 helix: 0.56 (0.27), residues: 336 sheet: 0.58 (0.42), residues: 144 loop : -0.76 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 195 HIS 0.021 0.002 HIS C 123 PHE 0.023 0.003 PHE A 116 TYR 0.020 0.001 TYR B 149 ARG 0.005 0.001 ARG B 125 Details of bonding type rmsd link_NAG-ASN : bond 0.01339 ( 33) link_NAG-ASN : angle 4.54224 ( 99) link_ALPHA1-6 : bond 0.01031 ( 3) link_ALPHA1-6 : angle 1.53379 ( 9) link_BETA1-4 : bond 0.02315 ( 27) link_BETA1-4 : angle 5.67683 ( 81) link_ALPHA1-3 : bond 0.00721 ( 3) link_ALPHA1-3 : angle 4.69009 ( 9) hydrogen bonds : bond 0.06615 ( 372) hydrogen bonds : angle 5.40757 ( 990) SS BOND : bond 0.00981 ( 21) SS BOND : angle 2.47834 ( 42) covalent geometry : bond 0.00491 ( 9618) covalent geometry : angle 1.04715 (13032) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 236 time to evaluate : 0.953 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: 0.7965 (tmm) cc_final: 0.7764 (tmm) REVERT: A 171 TYR cc_start: 0.6899 (OUTLIER) cc_final: 0.5114 (p90) REVERT: a 400 ASP cc_start: 0.8022 (OUTLIER) cc_final: 0.7745 (p0) REVERT: B 129 ASP cc_start: 0.7947 (t0) cc_final: 0.7715 (m-30) REVERT: b 331 MET cc_start: 0.5110 (ptp) cc_final: 0.4857 (ptp) REVERT: b 400 ASP cc_start: 0.8007 (OUTLIER) cc_final: 0.7784 (p0) REVERT: b 401 ASP cc_start: 0.8166 (m-30) cc_final: 0.7889 (m-30) REVERT: C 129 ASP cc_start: 0.7953 (t0) cc_final: 0.7741 (m-30) REVERT: C 152 MET cc_start: 0.7937 (tmm) cc_final: 0.7712 (tmm) REVERT: C 193 MET cc_start: 0.8117 (tpp) cc_final: 0.7679 (tpp) REVERT: C 229 HIS cc_start: 0.7665 (m-70) cc_final: 0.7249 (m-70) REVERT: c 401 ASP cc_start: 0.8173 (m-30) cc_final: 0.7952 (m-30) REVERT: c 409 MET cc_start: 0.7167 (mtp) cc_final: 0.6814 (mtp) outliers start: 42 outliers final: 22 residues processed: 258 average time/residue: 0.2542 time to fit residues: 86.7829 Evaluate side-chains 210 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 185 time to evaluate : 1.031 ------------------------------------------------------------------------------- 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 b residue 400 ASP Chi-restraints excluded: chain C residue 116 PHE Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 195 TRP Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain c residue 260 THR Chi-restraints excluded: chain c residue 357 ILE Chi-restraints excluded: chain c residue 376 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 20 optimal weight: 2.9990 chunk 59 optimal weight: 0.5980 chunk 18 optimal weight: 0.8980 chunk 43 optimal weight: 9.9990 chunk 1 optimal weight: 0.6980 chunk 67 optimal weight: 0.7980 chunk 49 optimal weight: 7.9990 chunk 25 optimal weight: 4.9990 chunk 63 optimal weight: 0.8980 chunk 13 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 HIS A 217 GLN B 217 GLN b 330 GLN C 217 GLN c 334 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.132097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.108157 restraints weight = 19396.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.111978 restraints weight = 12074.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.114518 restraints weight = 8995.432| |-----------------------------------------------------------------------------| r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.4547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 9705 Z= 0.208 Angle : 1.061 11.857 13272 Z= 0.498 Chirality : 0.053 0.293 1632 Planarity : 0.003 0.021 1557 Dihedral : 11.686 75.873 2514 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 5.99 % Allowed : 12.62 % Favored : 81.39 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.25), residues: 1056 helix: 0.54 (0.27), residues: 333 sheet: 0.10 (0.44), residues: 144 loop : -0.85 (0.26), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 195 HIS 0.009 0.001 HIS C 123 PHE 0.014 0.002 PHE a 292 TYR 0.018 0.001 TYR B 149 ARG 0.006 0.001 ARG a 355 Details of bonding type rmsd link_NAG-ASN : bond 0.00907 ( 33) link_NAG-ASN : angle 3.83394 ( 99) link_ALPHA1-6 : bond 0.00875 ( 3) link_ALPHA1-6 : angle 1.77025 ( 9) link_BETA1-4 : bond 0.02017 ( 27) link_BETA1-4 : angle 5.00880 ( 81) link_ALPHA1-3 : bond 0.00372 ( 3) link_ALPHA1-3 : angle 4.66147 ( 9) hydrogen bonds : bond 0.05465 ( 372) hydrogen bonds : angle 5.28120 ( 990) SS BOND : bond 0.00659 ( 21) SS BOND : angle 2.91074 ( 42) covalent geometry : bond 0.00448 ( 9618) covalent geometry : angle 0.91308 (13032) *********************** 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 272 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 215 time to evaluate : 1.023 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: 0.8066 (tmm) cc_final: 0.7443 (tmm) REVERT: A 171 TYR cc_start: 0.6772 (OUTLIER) cc_final: 0.5211 (p90) REVERT: a 262 THR cc_start: 0.9400 (OUTLIER) cc_final: 0.8572 (m) REVERT: B 152 MET cc_start: 0.7756 (ttt) cc_final: 0.7414 (tmm) REVERT: B 213 MET cc_start: 0.7066 (pmm) cc_final: 0.6689 (pmm) REVERT: b 262 THR cc_start: 0.9418 (OUTLIER) cc_final: 0.9020 (m) REVERT: b 401 ASP cc_start: 0.8275 (m-30) cc_final: 0.7899 (m-30) REVERT: C 178 HIS cc_start: 0.6879 (OUTLIER) cc_final: 0.6620 (m-70) REVERT: C 193 MET cc_start: 0.8373 (tpp) cc_final: 0.7975 (tpp) REVERT: C 230 CYS cc_start: 0.7595 (OUTLIER) cc_final: 0.7070 (m) REVERT: c 401 ASP cc_start: 0.8190 (m-30) cc_final: 0.7944 (m-30) REVERT: c 409 MET cc_start: 0.7058 (mtp) cc_final: 0.6843 (mtp) outliers start: 57 outliers final: 35 residues processed: 248 average time/residue: 0.2485 time to fit residues: 81.9242 Evaluate side-chains 213 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 173 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 195 TRP Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain a residue 262 THR Chi-restraints excluded: chain a residue 266 SER Chi-restraints excluded: chain a residue 283 MET Chi-restraints excluded: chain a residue 323 ARG Chi-restraints excluded: chain a residue 376 THR Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 179 CYS Chi-restraints excluded: chain B residue 195 TRP Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain b residue 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 376 THR Chi-restraints excluded: chain b residue 414 LEU Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 116 PHE Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 178 HIS Chi-restraints excluded: chain C residue 195 TRP Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain c residue 266 SER Chi-restraints excluded: chain c residue 291 CYS Chi-restraints excluded: chain c residue 323 ARG Chi-restraints excluded: chain c residue 376 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 14 optimal weight: 7.9990 chunk 43 optimal weight: 6.9990 chunk 77 optimal weight: 0.9980 chunk 76 optimal weight: 10.0000 chunk 104 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 19 optimal weight: 0.0020 chunk 5 optimal weight: 0.9990 chunk 30 optimal weight: 4.9990 chunk 94 optimal weight: 0.9990 chunk 47 optimal weight: 0.2980 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 HIS ** A 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 GLN a 415 GLN B 91 HIS ** b 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 334 GLN 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.132231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.107354 restraints weight = 19301.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.111328 restraints weight = 11996.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.113895 restraints weight = 8929.062| |-----------------------------------------------------------------------------| r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.4984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 9705 Z= 0.186 Angle : 1.001 11.025 13272 Z= 0.467 Chirality : 0.052 0.308 1632 Planarity : 0.003 0.029 1557 Dihedral : 10.802 69.279 2514 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 5.26 % Allowed : 15.46 % Favored : 79.28 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.25), residues: 1056 helix: 0.35 (0.26), residues: 357 sheet: -0.15 (0.43), residues: 144 loop : -1.10 (0.26), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 195 HIS 0.010 0.001 HIS C 123 PHE 0.013 0.002 PHE c 292 TYR 0.021 0.001 TYR B 149 ARG 0.009 0.001 ARG c 355 Details of bonding type rmsd link_NAG-ASN : bond 0.00753 ( 33) link_NAG-ASN : angle 3.54010 ( 99) link_ALPHA1-6 : bond 0.01000 ( 3) link_ALPHA1-6 : angle 1.84769 ( 9) link_BETA1-4 : bond 0.01842 ( 27) link_BETA1-4 : angle 4.70848 ( 81) link_ALPHA1-3 : bond 0.00422 ( 3) link_ALPHA1-3 : angle 4.50048 ( 9) hydrogen bonds : bond 0.04849 ( 372) hydrogen bonds : angle 5.26313 ( 990) SS BOND : bond 0.01061 ( 21) SS BOND : angle 2.77861 ( 42) covalent geometry : bond 0.00401 ( 9618) covalent geometry : angle 0.86374 (13032) *********************** 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 242 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 192 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 LYS cc_start: 0.8340 (mmtm) cc_final: 0.8051 (mmtm) REVERT: A 152 MET cc_start: 0.7954 (tmm) cc_final: 0.7731 (tmm) REVERT: A 171 TYR cc_start: 0.6846 (OUTLIER) cc_final: 0.5139 (p90) REVERT: A 193 MET cc_start: 0.8450 (tpp) cc_final: 0.7842 (tpp) REVERT: a 262 THR cc_start: 0.8948 (OUTLIER) cc_final: 0.8704 (m) REVERT: B 152 MET cc_start: 0.7699 (ttt) cc_final: 0.7278 (tmm) REVERT: B 213 MET cc_start: 0.7303 (pmm) cc_final: 0.7054 (pmm) REVERT: b 310 ASP cc_start: 0.8535 (m-30) cc_final: 0.8041 (t0) REVERT: b 401 ASP cc_start: 0.8292 (m-30) cc_final: 0.7897 (m-30) REVERT: C 148 GLN cc_start: 0.8518 (mm110) cc_final: 0.8033 (tm-30) REVERT: C 191 MET cc_start: 0.8152 (mmm) cc_final: 0.7813 (mmm) REVERT: c 401 ASP cc_start: 0.8225 (m-30) cc_final: 0.8002 (m-30) REVERT: c 409 MET cc_start: 0.7230 (mtp) cc_final: 0.6968 (mtp) outliers start: 50 outliers final: 38 residues processed: 220 average time/residue: 0.2501 time to fit residues: 73.3249 Evaluate side-chains 211 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 171 time to evaluate : 1.054 ------------------------------------------------------------------------------- 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 227 GLU 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 295 THR 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 123 HIS Chi-restraints excluded: chain B residue 195 TRP Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain b residue 266 SER Chi-restraints excluded: chain b residue 291 CYS Chi-restraints excluded: chain b residue 304 HIS Chi-restraints excluded: chain b residue 360 ILE Chi-restraints excluded: chain b residue 376 THR Chi-restraints excluded: chain b residue 414 LEU Chi-restraints excluded: chain C residue 99 GLU 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 260 THR Chi-restraints excluded: chain c residue 266 SER Chi-restraints excluded: chain c residue 291 CYS Chi-restraints excluded: chain c residue 323 ARG Chi-restraints excluded: chain c residue 376 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 69 optimal weight: 6.9990 chunk 74 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 chunk 93 optimal weight: 3.9990 chunk 22 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 54 optimal weight: 4.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 HIS A 188 GLN ** b 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.129858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.104868 restraints weight = 19427.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.108587 restraints weight = 12178.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.111044 restraints weight = 9186.907| |-----------------------------------------------------------------------------| r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.5341 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= 0.207 Angle : 0.987 11.029 13272 Z= 0.458 Chirality : 0.053 0.341 1632 Planarity : 0.003 0.022 1557 Dihedral : 10.435 63.543 2514 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 6.52 % Allowed : 15.56 % Favored : 77.92 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.25), residues: 1056 helix: 0.44 (0.26), residues: 357 sheet: -0.24 (0.43), residues: 144 loop : -1.17 (0.26), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 195 HIS 0.008 0.001 HIS B 123 PHE 0.020 0.002 PHE a 292 TYR 0.024 0.001 TYR A 149 ARG 0.005 0.001 ARG a 355 Details of bonding type rmsd link_NAG-ASN : bond 0.00734 ( 33) link_NAG-ASN : angle 3.37215 ( 99) link_ALPHA1-6 : bond 0.01029 ( 3) link_ALPHA1-6 : angle 1.99964 ( 9) link_BETA1-4 : bond 0.01735 ( 27) link_BETA1-4 : angle 4.53790 ( 81) link_ALPHA1-3 : bond 0.00437 ( 3) link_ALPHA1-3 : angle 4.68871 ( 9) hydrogen bonds : bond 0.04605 ( 372) hydrogen bonds : angle 5.31800 ( 990) SS BOND : bond 0.00695 ( 21) SS BOND : angle 3.01533 ( 42) covalent geometry : bond 0.00468 ( 9618) covalent geometry : angle 0.85438 (13032) *********************** 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 257 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 195 time to evaluate : 1.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 LYS cc_start: 0.8215 (mmtm) cc_final: 0.7914 (mmtm) REVERT: A 152 MET cc_start: 0.7947 (tmm) cc_final: 0.7708 (tmm) REVERT: A 171 TYR cc_start: 0.6856 (OUTLIER) cc_final: 0.5195 (p90) REVERT: A 199 TYR cc_start: 0.6638 (OUTLIER) cc_final: 0.5041 (m-80) REVERT: a 262 THR cc_start: 0.8924 (OUTLIER) cc_final: 0.8684 (m) REVERT: B 74 MET cc_start: 0.8138 (OUTLIER) cc_final: 0.7781 (mtm) REVERT: B 213 MET cc_start: 0.7290 (pmm) cc_final: 0.6939 (pmm) REVERT: b 310 ASP cc_start: 0.8565 (m-30) cc_final: 0.8304 (t0) REVERT: b 334 GLN cc_start: 0.7148 (pt0) cc_final: 0.6847 (mp10) REVERT: b 401 ASP cc_start: 0.8315 (m-30) cc_final: 0.7994 (m-30) REVERT: b 405 GLN cc_start: 0.8012 (tt0) cc_final: 0.7745 (tt0) REVERT: C 148 GLN cc_start: 0.8454 (mm110) cc_final: 0.7989 (tm-30) REVERT: C 191 MET cc_start: 0.8120 (mmm) cc_final: 0.7765 (mmm) REVERT: C 210 ASP cc_start: 0.6616 (p0) cc_final: 0.6094 (p0) REVERT: c 303 LYS cc_start: 0.7728 (mmtt) cc_final: 0.7479 (mmmt) REVERT: c 401 ASP cc_start: 0.8274 (m-30) cc_final: 0.8059 (m-30) REVERT: c 404 GLN cc_start: 0.7987 (tp40) cc_final: 0.7574 (tp40) outliers start: 62 outliers final: 41 residues processed: 232 average time/residue: 0.3006 time to fit residues: 93.0496 Evaluate side-chains 217 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 172 time to evaluate : 1.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 123 HIS Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 195 TRP Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain A residue 245 SER 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 360 ILE Chi-restraints excluded: chain a residue 376 THR Chi-restraints excluded: chain B residue 74 MET 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 123 HIS Chi-restraints excluded: chain B residue 195 TRP Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain b residue 266 SER Chi-restraints excluded: chain b residue 283 MET Chi-restraints excluded: chain b residue 291 CYS Chi-restraints excluded: chain b residue 304 HIS Chi-restraints excluded: chain b residue 359 CYS Chi-restraints excluded: chain b residue 360 ILE Chi-restraints excluded: chain b residue 376 THR Chi-restraints excluded: chain b residue 414 LEU Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 91 HIS Chi-restraints excluded: chain C residue 116 PHE Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 123 HIS Chi-restraints excluded: chain C residue 171 TYR Chi-restraints excluded: chain C residue 195 TRP Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain c residue 266 SER Chi-restraints excluded: chain c residue 291 CYS Chi-restraints excluded: chain c residue 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 64 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 62 optimal weight: 0.0050 chunk 83 optimal weight: 4.9990 chunk 14 optimal weight: 10.0000 chunk 11 optimal weight: 9.9990 chunk 82 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 chunk 102 optimal weight: 0.9980 overall best weight: 0.7998 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.130235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.104752 restraints weight = 19427.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.108648 restraints weight = 11993.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.111195 restraints weight = 8953.553| |-----------------------------------------------------------------------------| r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.5584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 9705 Z= 0.183 Angle : 0.957 10.523 13272 Z= 0.446 Chirality : 0.052 0.341 1632 Planarity : 0.003 0.029 1557 Dihedral : 10.091 61.052 2514 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.62 % Favored : 91.38 % Rotamer: Outliers : 5.26 % Allowed : 17.67 % Favored : 77.08 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.25), residues: 1056 helix: 0.56 (0.26), residues: 357 sheet: -0.26 (0.43), residues: 144 loop : -1.16 (0.26), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 195 HIS 0.009 0.001 HIS B 123 PHE 0.014 0.002 PHE A 116 TYR 0.018 0.001 TYR c 418 ARG 0.007 0.001 ARG A 234 Details of bonding type rmsd link_NAG-ASN : bond 0.00679 ( 33) link_NAG-ASN : angle 3.21400 ( 99) link_ALPHA1-6 : bond 0.01105 ( 3) link_ALPHA1-6 : angle 2.02746 ( 9) link_BETA1-4 : bond 0.01654 ( 27) link_BETA1-4 : angle 4.33318 ( 81) link_ALPHA1-3 : bond 0.00353 ( 3) link_ALPHA1-3 : angle 4.54166 ( 9) hydrogen bonds : bond 0.04405 ( 372) hydrogen bonds : angle 5.21412 ( 990) SS BOND : bond 0.00695 ( 21) SS BOND : angle 2.86689 ( 42) covalent geometry : bond 0.00408 ( 9618) covalent geometry : angle 0.83275 (13032) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 187 time to evaluate : 1.635 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 95 MET cc_start: 0.7063 (ttt) cc_final: 0.6728 (ttt) REVERT: A 115 LYS cc_start: 0.8330 (mmtm) cc_final: 0.8106 (mmtm) REVERT: A 171 TYR cc_start: 0.6907 (OUTLIER) cc_final: 0.5185 (p90) REVERT: A 199 TYR cc_start: 0.6598 (OUTLIER) cc_final: 0.5050 (m-80) REVERT: A 245 SER cc_start: 0.7979 (OUTLIER) cc_final: 0.7754 (t) REVERT: a 404 GLN cc_start: 0.7762 (tp40) cc_final: 0.7401 (tp40) REVERT: B 193 MET cc_start: 0.8278 (tpp) cc_final: 0.7507 (ttm) REVERT: B 213 MET cc_start: 0.7379 (pmm) cc_final: 0.6983 (pmm) REVERT: b 306 GLU cc_start: 0.8180 (mm-30) cc_final: 0.7694 (mm-30) REVERT: b 311 MET cc_start: 0.8413 (mmm) cc_final: 0.8188 (tpt) REVERT: b 401 ASP cc_start: 0.8355 (m-30) cc_final: 0.7988 (m-30) REVERT: C 148 GLN cc_start: 0.8481 (mm110) cc_final: 0.7907 (tm-30) REVERT: C 152 MET cc_start: 0.7865 (tmm) cc_final: 0.7558 (tmm) REVERT: C 191 MET cc_start: 0.8090 (mmm) cc_final: 0.7862 (mmt) REVERT: C 210 ASP cc_start: 0.6407 (p0) cc_final: 0.6141 (p0) REVERT: c 303 LYS cc_start: 0.7691 (mmtt) cc_final: 0.7445 (mmmt) REVERT: c 404 GLN cc_start: 0.7984 (tp40) cc_final: 0.7226 (tp40) REVERT: c 408 ASN cc_start: 0.8605 (m-40) cc_final: 0.8364 (m-40) outliers start: 50 outliers final: 37 residues processed: 216 average time/residue: 0.3784 time to fit residues: 109.4333 Evaluate side-chains 208 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 168 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 HIS Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 123 HIS Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 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 266 SER Chi-restraints excluded: chain a residue 291 CYS Chi-restraints excluded: chain a residue 323 ARG Chi-restraints excluded: chain a residue 360 ILE Chi-restraints excluded: chain a residue 376 THR Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 123 HIS Chi-restraints excluded: chain B residue 195 TRP Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain b residue 266 SER Chi-restraints excluded: chain b residue 283 MET 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 10 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 chunk 97 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 46 optimal weight: 6.9990 chunk 55 optimal weight: 0.9990 chunk 12 optimal weight: 5.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 91 HIS ** C 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.121738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.096065 restraints weight = 18891.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.098856 restraints weight = 13344.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.100770 restraints weight = 10699.160| |-----------------------------------------------------------------------------| r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.5770 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= 0.188 Angle : 0.976 13.466 13272 Z= 0.451 Chirality : 0.054 0.377 1632 Planarity : 0.003 0.029 1557 Dihedral : 9.965 59.555 2514 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer: Outliers : 5.26 % Allowed : 16.93 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.26), residues: 1056 helix: 0.73 (0.27), residues: 354 sheet: -0.57 (0.42), residues: 153 loop : -1.27 (0.26), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 195 HIS 0.008 0.001 HIS C 123 PHE 0.019 0.002 PHE A 116 TYR 0.025 0.001 TYR B 149 ARG 0.007 0.001 ARG A 234 Details of bonding type rmsd link_NAG-ASN : bond 0.00668 ( 33) link_NAG-ASN : angle 3.17283 ( 99) link_ALPHA1-6 : bond 0.01071 ( 3) link_ALPHA1-6 : angle 2.05420 ( 9) link_BETA1-4 : bond 0.01593 ( 27) link_BETA1-4 : angle 4.23365 ( 81) link_ALPHA1-3 : bond 0.00422 ( 3) link_ALPHA1-3 : angle 4.51026 ( 9) hydrogen bonds : bond 0.04333 ( 372) hydrogen bonds : angle 5.21039 ( 990) SS BOND : bond 0.00683 ( 21) SS BOND : angle 3.47840 ( 42) covalent geometry : bond 0.00421 ( 9618) covalent geometry : angle 0.85167 (13032) *********************** 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 223 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 173 time to evaluate : 1.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 TYR cc_start: 0.6963 (OUTLIER) cc_final: 0.5253 (p90) REVERT: A 193 MET cc_start: 0.8346 (tpp) cc_final: 0.7708 (ttm) REVERT: A 199 TYR cc_start: 0.6588 (OUTLIER) cc_final: 0.5042 (m-80) REVERT: A 245 SER cc_start: 0.8096 (OUTLIER) cc_final: 0.7814 (t) REVERT: a 262 THR cc_start: 0.8893 (OUTLIER) cc_final: 0.8628 (m) REVERT: B 213 MET cc_start: 0.7188 (pmm) cc_final: 0.6931 (pmm) REVERT: b 311 MET cc_start: 0.8465 (mmm) cc_final: 0.8230 (tpt) REVERT: b 401 ASP cc_start: 0.8319 (m-30) cc_final: 0.8054 (m-30) REVERT: b 405 GLN cc_start: 0.8059 (tt0) cc_final: 0.6794 (tt0) REVERT: C 152 MET cc_start: 0.7887 (tmm) cc_final: 0.7601 (tmm) REVERT: C 191 MET cc_start: 0.7977 (mmm) cc_final: 0.7734 (mmt) REVERT: c 303 LYS cc_start: 0.7662 (mmtt) cc_final: 0.7409 (mmmt) REVERT: c 404 GLN cc_start: 0.7939 (tp40) cc_final: 0.7216 (tp40) REVERT: c 408 ASN cc_start: 0.8629 (m-40) cc_final: 0.8367 (m-40) outliers start: 50 outliers final: 37 residues processed: 204 average time/residue: 0.2564 time to fit residues: 69.9565 Evaluate side-chains 204 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 163 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 HIS Chi-restraints excluded: chain A residue 99 GLU 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 245 SER 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 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 123 HIS Chi-restraints excluded: chain B residue 171 TYR 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 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 359 CYS Chi-restraints excluded: chain b residue 360 ILE Chi-restraints excluded: chain b residue 376 THR Chi-restraints excluded: chain b residue 414 LEU Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 116 PHE Chi-restraints excluded: chain C residue 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 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 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 81 optimal weight: 9.9990 chunk 52 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 93 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 chunk 90 optimal weight: 0.0470 chunk 47 optimal weight: 7.9990 chunk 26 optimal weight: 5.9990 chunk 87 optimal weight: 0.9990 overall best weight: 0.8082 ------------------------------------------------------------------------------- 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 91 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.124750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.100686 restraints weight = 18677.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.103372 restraints weight = 13382.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.105212 restraints weight = 10766.086| |-----------------------------------------------------------------------------| r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.5932 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= 0.184 Angle : 0.998 12.492 13272 Z= 0.464 Chirality : 0.054 0.367 1632 Planarity : 0.003 0.032 1557 Dihedral : 9.911 59.949 2514 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.56 % Favored : 90.44 % Rotamer: Outliers : 4.84 % Allowed : 18.51 % Favored : 76.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.26), residues: 1056 helix: 0.72 (0.27), residues: 354 sheet: -0.55 (0.42), residues: 153 loop : -1.32 (0.27), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 195 HIS 0.012 0.001 HIS C 91 PHE 0.022 0.002 PHE A 116 TYR 0.024 0.001 TYR B 149 ARG 0.010 0.001 ARG b 383 Details of bonding type rmsd link_NAG-ASN : bond 0.00663 ( 33) link_NAG-ASN : angle 3.04911 ( 99) link_ALPHA1-6 : bond 0.01094 ( 3) link_ALPHA1-6 : angle 2.04368 ( 9) link_BETA1-4 : bond 0.01551 ( 27) link_BETA1-4 : angle 4.10756 ( 81) link_ALPHA1-3 : bond 0.00269 ( 3) link_ALPHA1-3 : angle 4.56342 ( 9) hydrogen bonds : bond 0.04310 ( 372) hydrogen bonds : angle 5.15572 ( 990) SS BOND : bond 0.00627 ( 21) SS BOND : angle 4.18445 ( 42) covalent geometry : bond 0.00422 ( 9618) covalent geometry : angle 0.87423 (13032) *********************** 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 217 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 171 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.7019 (ttt) cc_final: 0.6689 (ttt) REVERT: A 171 TYR cc_start: 0.7039 (OUTLIER) cc_final: 0.5349 (p90) REVERT: A 199 TYR cc_start: 0.6526 (OUTLIER) cc_final: 0.5010 (m-80) REVERT: a 262 THR cc_start: 0.8903 (OUTLIER) cc_final: 0.8672 (m) REVERT: a 331 MET cc_start: 0.3865 (tpt) cc_final: 0.3551 (ptp) REVERT: a 404 GLN cc_start: 0.7689 (tp40) cc_final: 0.7327 (tp40) REVERT: B 193 MET cc_start: 0.8199 (tpp) cc_final: 0.7656 (ttm) REVERT: b 306 GLU cc_start: 0.7898 (mm-30) cc_final: 0.7681 (mm-30) REVERT: b 401 ASP cc_start: 0.8173 (m-30) cc_final: 0.7799 (m-30) REVERT: C 152 MET cc_start: 0.7920 (tmm) cc_final: 0.7684 (tmm) REVERT: C 191 MET cc_start: 0.7798 (mmm) cc_final: 0.7595 (mmt) REVERT: C 193 MET cc_start: 0.8022 (tpp) cc_final: 0.7386 (ttm) REVERT: c 404 GLN cc_start: 0.7782 (tp40) cc_final: 0.7455 (tp40) outliers start: 46 outliers final: 36 residues processed: 200 average time/residue: 0.2672 time to fit residues: 70.8032 Evaluate side-chains 203 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 164 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 HIS Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 123 HIS Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 195 TRP Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain a residue 262 THR Chi-restraints excluded: chain a residue 266 SER Chi-restraints excluded: chain a residue 291 CYS Chi-restraints excluded: chain a residue 359 CYS Chi-restraints excluded: chain a residue 360 ILE Chi-restraints excluded: chain a residue 376 THR Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain B residue 123 HIS Chi-restraints excluded: chain B residue 171 TYR Chi-restraints excluded: chain B residue 195 TRP Chi-restraints excluded: chain b residue 266 SER Chi-restraints excluded: chain b residue 283 MET Chi-restraints excluded: chain b residue 291 CYS Chi-restraints excluded: chain b residue 304 HIS Chi-restraints excluded: chain b residue 359 CYS Chi-restraints excluded: chain b residue 360 ILE Chi-restraints excluded: chain b residue 376 THR Chi-restraints excluded: chain b residue 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 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 Chi-restraints excluded: chain c residue 376 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 74 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 93 optimal weight: 7.9990 chunk 27 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 80 optimal weight: 5.9990 chunk 99 optimal weight: 0.8980 chunk 70 optimal weight: 5.9990 chunk 4 optimal weight: 0.9990 chunk 9 optimal weight: 7.9990 chunk 56 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 405 GLN ** C 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.122411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.098018 restraints weight = 18638.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.100640 restraints weight = 13370.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.102443 restraints weight = 10783.833| |-----------------------------------------------------------------------------| r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.6094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.102 9705 Z= 0.223 Angle : 1.026 15.941 13272 Z= 0.477 Chirality : 0.057 0.403 1632 Planarity : 0.003 0.033 1557 Dihedral : 10.037 59.575 2514 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.75 % Favored : 90.25 % Rotamer: Outliers : 4.73 % Allowed : 17.98 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.26), residues: 1056 helix: 0.80 (0.28), residues: 351 sheet: -0.55 (0.42), residues: 153 loop : -1.35 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 195 HIS 0.009 0.001 HIS A 123 PHE 0.027 0.002 PHE B 116 TYR 0.024 0.001 TYR B 149 ARG 0.006 0.001 ARG a 383 Details of bonding type rmsd link_NAG-ASN : bond 0.00664 ( 33) link_NAG-ASN : angle 2.98277 ( 99) link_ALPHA1-6 : bond 0.01023 ( 3) link_ALPHA1-6 : angle 2.05138 ( 9) link_BETA1-4 : bond 0.01469 ( 27) link_BETA1-4 : angle 4.12742 ( 81) link_ALPHA1-3 : bond 0.00344 ( 3) link_ALPHA1-3 : angle 4.57994 ( 9) hydrogen bonds : bond 0.04310 ( 372) hydrogen bonds : angle 5.24700 ( 990) SS BOND : bond 0.00742 ( 21) SS BOND : angle 4.14098 ( 42) covalent geometry : bond 0.00515 ( 9618) covalent geometry : angle 0.90907 (13032) *********************** 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 219 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 174 time to evaluate : 1.068 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 95 MET cc_start: 0.7154 (ttt) cc_final: 0.6821 (ttt) REVERT: A 171 TYR cc_start: 0.7036 (OUTLIER) cc_final: 0.5332 (p90) REVERT: A 193 MET cc_start: 0.8233 (tpp) cc_final: 0.7644 (ttm) REVERT: A 199 TYR cc_start: 0.6643 (OUTLIER) cc_final: 0.5145 (m-80) REVERT: a 262 THR cc_start: 0.8910 (OUTLIER) cc_final: 0.8707 (m) REVERT: a 334 GLN cc_start: 0.7303 (pp30) cc_final: 0.6943 (pp30) REVERT: a 404 GLN cc_start: 0.7783 (tp40) cc_final: 0.7397 (tp40) REVERT: B 193 MET cc_start: 0.8317 (tpp) cc_final: 0.7695 (ttm) REVERT: B 213 MET cc_start: 0.7573 (pmm) cc_final: 0.7112 (pmm) REVERT: b 306 GLU cc_start: 0.7889 (mm-30) cc_final: 0.7638 (mm-30) REVERT: b 401 ASP cc_start: 0.8296 (m-30) cc_final: 0.7981 (m-30) REVERT: C 152 MET cc_start: 0.7964 (tmm) cc_final: 0.7722 (tmm) REVERT: C 193 MET cc_start: 0.8114 (tpp) cc_final: 0.7413 (ttm) REVERT: c 404 GLN cc_start: 0.7907 (tp40) cc_final: 0.7567 (tp40) outliers start: 45 outliers final: 39 residues processed: 202 average time/residue: 0.2602 time to fit residues: 70.6154 Evaluate side-chains 207 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 165 time to evaluate : 1.024 ------------------------------------------------------------------------------- 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 99 GLU Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 195 TRP Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain a residue 262 THR Chi-restraints excluded: chain a residue 266 SER Chi-restraints excluded: chain a residue 283 MET Chi-restraints excluded: chain a residue 291 CYS Chi-restraints excluded: chain a residue 359 CYS Chi-restraints excluded: chain a residue 360 ILE Chi-restraints excluded: chain a residue 376 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 81 MET 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 266 SER Chi-restraints excluded: chain b residue 283 MET Chi-restraints excluded: chain b residue 291 CYS Chi-restraints excluded: chain b residue 304 HIS Chi-restraints excluded: chain b residue 359 CYS Chi-restraints excluded: chain b residue 360 ILE Chi-restraints excluded: chain b residue 376 THR Chi-restraints excluded: chain b residue 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 136 ILE Chi-restraints excluded: chain C residue 171 TYR Chi-restraints excluded: chain C residue 195 TRP Chi-restraints excluded: chain c residue 266 SER Chi-restraints excluded: chain c residue 291 CYS Chi-restraints excluded: chain c residue 292 PHE Chi-restraints excluded: chain c residue 323 ARG Chi-restraints excluded: chain c residue 336 ILE Chi-restraints excluded: chain c residue 354 LEU Chi-restraints excluded: chain c residue 359 CYS Chi-restraints excluded: chain c residue 360 ILE Chi-restraints excluded: chain c residue 376 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 20 optimal weight: 8.9990 chunk 64 optimal weight: 0.8980 chunk 35 optimal weight: 4.9990 chunk 47 optimal weight: 6.9990 chunk 72 optimal weight: 0.5980 chunk 68 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 chunk 87 optimal weight: 0.7980 chunk 83 optimal weight: 0.8980 chunk 57 optimal weight: 0.6980 chunk 46 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 130 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.123022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.097593 restraints weight = 19251.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.100380 restraints weight = 13817.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.102344 restraints weight = 11139.188| |-----------------------------------------------------------------------------| r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.6277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 9705 Z= 0.182 Angle : 1.004 14.753 13272 Z= 0.471 Chirality : 0.053 0.358 1632 Planarity : 0.003 0.029 1557 Dihedral : 9.683 59.940 2514 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.90 % Favored : 91.00 % Rotamer: Outliers : 3.68 % Allowed : 19.45 % Favored : 76.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.26), residues: 1056 helix: 0.67 (0.28), residues: 351 sheet: -0.17 (0.48), residues: 123 loop : -1.45 (0.25), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP c 282 HIS 0.004 0.001 HIS b 304 PHE 0.032 0.002 PHE B 116 TYR 0.024 0.001 TYR B 149 ARG 0.007 0.001 ARG b 383 Details of bonding type rmsd link_NAG-ASN : bond 0.00612 ( 33) link_NAG-ASN : angle 2.73020 ( 99) link_ALPHA1-6 : bond 0.01102 ( 3) link_ALPHA1-6 : angle 1.89656 ( 9) link_BETA1-4 : bond 0.01534 ( 27) link_BETA1-4 : angle 3.99521 ( 81) link_ALPHA1-3 : bond 0.00253 ( 3) link_ALPHA1-3 : angle 4.65941 ( 9) hydrogen bonds : bond 0.04187 ( 372) hydrogen bonds : angle 5.16695 ( 990) SS BOND : bond 0.00676 ( 21) SS BOND : angle 3.75674 ( 42) covalent geometry : bond 0.00415 ( 9618) covalent geometry : angle 0.89849 (13032) ********************** 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 217 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 182 time to evaluate : 0.995 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 95 MET cc_start: 0.7068 (ttt) cc_final: 0.6749 (ttt) REVERT: A 152 MET cc_start: 0.8148 (tmm) cc_final: 0.7798 (tmm) REVERT: A 171 TYR cc_start: 0.7222 (OUTLIER) cc_final: 0.5567 (p90) REVERT: A 193 MET cc_start: 0.8337 (tpp) cc_final: 0.7964 (ttm) REVERT: a 331 MET cc_start: 0.4516 (tpt) cc_final: 0.3723 (ptt) REVERT: a 334 GLN cc_start: 0.7469 (pp30) cc_final: 0.7130 (pp30) REVERT: a 404 GLN cc_start: 0.7871 (tp40) cc_final: 0.7490 (tp40) REVERT: B 193 MET cc_start: 0.8359 (tpp) cc_final: 0.7795 (ttm) REVERT: b 310 ASP cc_start: 0.8092 (t0) cc_final: 0.7884 (t0) REVERT: b 401 ASP cc_start: 0.8345 (m-30) cc_final: 0.8098 (m-30) REVERT: C 152 MET cc_start: 0.8050 (tmm) cc_final: 0.7821 (tmm) REVERT: C 193 MET cc_start: 0.8064 (tpp) cc_final: 0.7445 (ttm) REVERT: c 404 GLN cc_start: 0.7957 (tp40) cc_final: 0.7616 (tp40) outliers start: 35 outliers final: 32 residues processed: 207 average time/residue: 0.3291 time to fit residues: 90.7264 Evaluate side-chains 201 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 168 time to evaluate : 1.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 HIS Chi-restraints excluded: chain A residue 99 GLU 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 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 81 MET 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 266 SER Chi-restraints excluded: chain b residue 291 CYS Chi-restraints excluded: chain b residue 359 CYS Chi-restraints excluded: chain b residue 360 ILE Chi-restraints excluded: chain b residue 387 VAL Chi-restraints excluded: chain b residue 414 LEU Chi-restraints excluded: chain C residue 116 PHE 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 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 1 optimal weight: 0.5980 chunk 28 optimal weight: 0.8980 chunk 35 optimal weight: 4.9990 chunk 52 optimal weight: 0.6980 chunk 38 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 75 optimal weight: 0.9990 chunk 11 optimal weight: 7.9990 chunk 57 optimal weight: 0.6980 chunk 10 optimal weight: 6.9990 chunk 69 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 405 GLN ** 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 = 0.3818 r_free = 0.3818 target = 0.123009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.097253 restraints weight = 19342.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.100044 restraints weight = 13925.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.101930 restraints weight = 11276.392| |-----------------------------------------------------------------------------| r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.6417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 9705 Z= 0.180 Angle : 0.985 13.969 13272 Z= 0.459 Chirality : 0.053 0.363 1632 Planarity : 0.003 0.028 1557 Dihedral : 9.357 59.398 2514 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.47 % Favored : 90.44 % Rotamer: Outliers : 3.79 % Allowed : 19.77 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.26), residues: 1056 helix: 0.68 (0.28), residues: 351 sheet: -0.38 (0.47), residues: 126 loop : -1.51 (0.26), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 195 HIS 0.007 0.001 HIS C 123 PHE 0.028 0.002 PHE B 116 TYR 0.025 0.001 TYR B 149 ARG 0.011 0.001 ARG b 383 Details of bonding type rmsd link_NAG-ASN : bond 0.00598 ( 33) link_NAG-ASN : angle 2.69629 ( 99) link_ALPHA1-6 : bond 0.01151 ( 3) link_ALPHA1-6 : angle 1.58082 ( 9) link_BETA1-4 : bond 0.01487 ( 27) link_BETA1-4 : angle 3.91288 ( 81) link_ALPHA1-3 : bond 0.00267 ( 3) link_ALPHA1-3 : angle 4.64084 ( 9) hydrogen bonds : bond 0.04144 ( 372) hydrogen bonds : angle 5.13972 ( 990) SS BOND : bond 0.00662 ( 21) SS BOND : angle 3.58326 ( 42) covalent geometry : bond 0.00407 ( 9618) covalent geometry : angle 0.88288 (13032) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3290.10 seconds wall clock time: 60 minutes 15.52 seconds (3615.52 seconds total)