Starting phenix.real_space_refine on Fri Mar 14 04:07:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8eje_28179/03_2025/8eje_28179.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eje_28179/03_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_28179/03_2025/8eje_28179.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eje_28179/03_2025/8eje_28179.map" model { file = "/net/cci-nas-00/data/ceres_data/8eje_28179/03_2025/8eje_28179.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eje_28179/03_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 6.63, per 1000 atoms: 0.70 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: 3.53 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.09 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: 2.39 Time building geometry restraints manager: 4.00 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: 0.930 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: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 26.390 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.060 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.390 ------------------------------------------------------------------------------- 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 : 0.023 0.123 9618 Z= 1.470 Angle : 2.139 36.392 13032 Z= 1.262 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 *********************** 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 : 0.984 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: 0.2592 time to fit residues: 120.3253 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 : 0.970 ------------------------------------------------------------------------------- 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 9618 Z= 0.311 Angle : 1.047 12.028 13032 Z= 0.537 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 *********************** 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 : 1.009 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: 0.2678 time to fit residues: 91.3883 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 : 1.086 ------------------------------------------------------------------------------- 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: 9.9990 chunk 25 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 HIS A 217 GLN B 217 GLN C 217 GLN c 334 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.131432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.107375 restraints weight = 19436.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.111171 restraints weight = 12137.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.113672 restraints weight = 9061.791| |-----------------------------------------------------------------------------| r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.4497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 9618 Z= 0.296 Angle : 0.931 9.536 13032 Z= 0.471 Chirality : 0.054 0.294 1632 Planarity : 0.003 0.022 1557 Dihedral : 11.873 76.500 2514 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 5.89 % Allowed : 13.04 % Favored : 81.07 % 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: -0.41 (0.25), residues: 1056 helix: 0.56 (0.27), residues: 333 sheet: 0.11 (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 0.011 0.001 HIS C 123 PHE 0.013 0.002 PHE a 292 TYR 0.018 0.001 TYR B 149 ARG 0.004 0.001 ARG a 355 *********************** 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 269 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 213 time to evaluate : 1.076 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 TYR cc_start: 0.6872 (OUTLIER) cc_final: 0.5323 (p90) REVERT: A 230 CYS cc_start: 0.7539 (OUTLIER) cc_final: 0.7155 (m) REVERT: a 262 THR cc_start: 0.9415 (OUTLIER) cc_final: 0.9189 (m) REVERT: B 152 MET cc_start: 0.7703 (ttt) cc_final: 0.7413 (tmm) REVERT: b 262 THR cc_start: 0.9420 (OUTLIER) cc_final: 0.9089 (m) REVERT: b 401 ASP cc_start: 0.8284 (m-30) cc_final: 0.7885 (m-30) REVERT: C 193 MET cc_start: 0.8392 (tpp) cc_final: 0.7991 (tpp) REVERT: C 229 HIS cc_start: 0.7570 (m-70) cc_final: 0.7111 (m-70) REVERT: C 230 CYS cc_start: 0.7638 (OUTLIER) cc_final: 0.7120 (m) REVERT: c 401 ASP cc_start: 0.8190 (m-30) cc_final: 0.7932 (m-30) REVERT: c 409 MET cc_start: 0.7045 (mtp) cc_final: 0.6812 (mtp) outliers start: 56 outliers final: 35 residues processed: 245 average time/residue: 0.3268 time to fit residues: 106.7176 Evaluate side-chains 218 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 178 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 195 TRP Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain a residue 262 THR Chi-restraints excluded: chain a residue 266 SER Chi-restraints excluded: chain a residue 283 MET Chi-restraints excluded: chain a residue 323 ARG Chi-restraints excluded: chain a residue 376 THR Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 179 CYS Chi-restraints excluded: chain B residue 195 TRP Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain b residue 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 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: 9.9990 chunk 77 optimal weight: 0.9990 chunk 76 optimal weight: 10.0000 chunk 104 optimal weight: 7.9990 chunk 4 optimal weight: 3.9990 chunk 19 optimal weight: 0.0000 chunk 5 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 overall best weight: 1.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 GLN ** b 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 330 GLN 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.129639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.104182 restraints weight = 19404.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.107989 restraints weight = 12147.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.110528 restraints weight = 9129.130| |-----------------------------------------------------------------------------| r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.4975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 9618 Z= 0.304 Angle : 0.893 11.647 13032 Z= 0.449 Chirality : 0.054 0.323 1632 Planarity : 0.003 0.033 1557 Dihedral : 10.913 68.070 2514 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer: Outliers : 5.68 % Allowed : 15.77 % Favored : 78.55 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.47 (0.25), residues: 1056 helix: 0.84 (0.27), residues: 333 sheet: -0.14 (0.44), residues: 144 loop : -1.05 (0.25), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 195 HIS 0.010 0.001 HIS C 123 PHE 0.016 0.002 PHE c 292 TYR 0.021 0.001 TYR B 149 ARG 0.007 0.001 ARG c 355 *********************** 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 247 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 193 time to evaluate : 1.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 LYS cc_start: 0.8382 (mmtm) cc_final: 0.8144 (mmtm) REVERT: A 152 MET cc_start: 0.8199 (tmm) cc_final: 0.7724 (tmm) REVERT: A 171 TYR cc_start: 0.6952 (OUTLIER) cc_final: 0.5198 (p90) REVERT: A 193 MET cc_start: 0.8466 (tpp) cc_final: 0.7821 (tpp) REVERT: B 213 MET cc_start: 0.7396 (pmm) cc_final: 0.7112 (pmm) REVERT: b 310 ASP cc_start: 0.8626 (m-30) cc_final: 0.8209 (t0) REVERT: b 401 ASP cc_start: 0.8277 (m-30) cc_final: 0.7944 (m-30) REVERT: C 148 GLN cc_start: 0.8553 (mm110) cc_final: 0.8050 (tm-30) REVERT: C 191 MET cc_start: 0.8194 (mmm) cc_final: 0.7868 (mmm) REVERT: c 401 ASP cc_start: 0.8242 (m-30) cc_final: 0.8005 (m-30) REVERT: c 409 MET cc_start: 0.7289 (mtp) cc_final: 0.7007 (mtp) outliers start: 54 outliers final: 41 residues processed: 226 average time/residue: 0.4738 time to fit residues: 143.3298 Evaluate side-chains 208 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 166 time to evaluate : 1.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 195 TRP Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain a residue 260 THR Chi-restraints excluded: chain a residue 266 SER Chi-restraints excluded: chain a residue 283 MET Chi-restraints excluded: chain a residue 291 CYS Chi-restraints excluded: chain a residue 360 ILE Chi-restraints excluded: chain a residue 376 THR Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain B residue 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 260 THR Chi-restraints excluded: chain b residue 266 SER Chi-restraints excluded: chain b residue 291 CYS Chi-restraints excluded: chain b residue 360 ILE Chi-restraints excluded: chain b residue 376 THR Chi-restraints excluded: chain b residue 414 LEU Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 116 PHE Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 195 TRP Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain c residue 260 THR Chi-restraints excluded: chain c residue 266 SER Chi-restraints excluded: chain c residue 291 CYS Chi-restraints excluded: chain c residue 323 ARG Chi-restraints excluded: chain c residue 354 LEU Chi-restraints excluded: chain c residue 360 ILE Chi-restraints excluded: chain c residue 376 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 69 optimal weight: 6.9990 chunk 74 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 93 optimal weight: 7.9990 chunk 22 optimal weight: 0.7980 chunk 3 optimal weight: 4.9990 chunk 98 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 54 optimal weight: 6.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 HIS A 169 HIS A 188 GLN B 91 HIS ** b 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.129175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.103729 restraints weight = 19515.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.107531 restraints weight = 12357.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.110024 restraints weight = 9308.751| |-----------------------------------------------------------------------------| r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.5317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 9618 Z= 0.307 Angle : 0.875 12.740 13032 Z= 0.436 Chirality : 0.053 0.342 1632 Planarity : 0.003 0.027 1557 Dihedral : 10.582 62.794 2514 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.43 % Favored : 91.57 % Rotamer: Outliers : 5.78 % Allowed : 17.56 % Favored : 76.66 % 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: -0.64 (0.25), residues: 1056 helix: 0.67 (0.27), residues: 354 sheet: -0.20 (0.43), residues: 144 loop : -1.22 (0.26), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 195 HIS 0.014 0.002 HIS C 130 PHE 0.015 0.002 PHE a 292 TYR 0.022 0.001 TYR A 149 ARG 0.007 0.001 ARG A 234 *********************** 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 255 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 200 time to evaluate : 1.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 LYS cc_start: 0.8122 (mmtm) cc_final: 0.7901 (mmtm) REVERT: A 152 MET cc_start: 0.8244 (tmm) cc_final: 0.7814 (tmm) REVERT: A 171 TYR cc_start: 0.6962 (OUTLIER) cc_final: 0.5267 (p90) REVERT: a 282 TRP cc_start: 0.7602 (m-90) cc_final: 0.7376 (m-90) REVERT: B 74 MET cc_start: 0.8139 (OUTLIER) cc_final: 0.7801 (mtm) REVERT: B 213 MET cc_start: 0.7337 (pmm) cc_final: 0.7001 (pmm) REVERT: b 306 GLU cc_start: 0.8176 (mm-30) cc_final: 0.7888 (mm-30) REVERT: b 310 ASP cc_start: 0.8566 (m-30) cc_final: 0.8300 (t0) REVERT: b 331 MET cc_start: 0.5400 (ptp) cc_final: 0.4892 (ptp) REVERT: b 383 ARG cc_start: 0.7771 (ttm110) cc_final: 0.7568 (mtp85) REVERT: b 401 ASP cc_start: 0.8327 (m-30) cc_final: 0.7920 (m-30) REVERT: C 148 GLN cc_start: 0.8478 (mm110) cc_final: 0.8014 (tm-30) REVERT: C 191 MET cc_start: 0.8171 (mmm) cc_final: 0.7831 (mmm) REVERT: c 334 GLN cc_start: 0.7292 (pt0) cc_final: 0.7058 (mt0) REVERT: c 404 GLN cc_start: 0.8029 (tp40) cc_final: 0.7200 (tp40) REVERT: c 408 ASN cc_start: 0.8636 (m-40) cc_final: 0.8367 (m-40) REVERT: c 409 MET cc_start: 0.7363 (mtp) cc_final: 0.7091 (mtp) outliers start: 55 outliers final: 42 residues processed: 232 average time/residue: 0.2431 time to fit residues: 75.6543 Evaluate side-chains 217 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 173 time to evaluate : 0.864 ------------------------------------------------------------------------------- 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 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 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 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 260 THR Chi-restraints excluded: chain b residue 266 SER Chi-restraints excluded: chain b residue 291 CYS Chi-restraints excluded: chain b residue 304 HIS Chi-restraints excluded: chain b residue 359 CYS Chi-restraints excluded: chain b residue 360 ILE Chi-restraints excluded: chain b residue 376 THR Chi-restraints excluded: chain b residue 414 LEU Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 116 PHE Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 195 TRP Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain c residue 260 THR Chi-restraints excluded: chain c residue 266 SER Chi-restraints excluded: chain c residue 291 CYS Chi-restraints excluded: chain c residue 323 ARG Chi-restraints excluded: chain c residue 336 ILE Chi-restraints excluded: chain c residue 354 LEU Chi-restraints excluded: chain c residue 360 ILE Chi-restraints excluded: chain c residue 376 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 64 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 14 optimal weight: 9.9990 chunk 11 optimal weight: 8.9990 chunk 82 optimal weight: 0.4980 chunk 104 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 overall best weight: 2.6988 ------------------------------------------------------------------------------- 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 130 HIS ** C 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.118646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.093762 restraints weight = 18821.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.096436 restraints weight = 13391.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.098298 restraints weight = 10736.845| |-----------------------------------------------------------------------------| r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.5665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.079 9618 Z= 0.458 Angle : 0.967 11.341 13032 Z= 0.474 Chirality : 0.058 0.376 1632 Planarity : 0.004 0.031 1557 Dihedral : 10.692 56.683 2514 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.75 % Favored : 90.25 % Rotamer: Outliers : 6.52 % Allowed : 17.56 % Favored : 75.92 % Cbeta Deviations : 0.00 % 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: -0.83 (0.25), residues: 1056 helix: 0.79 (0.27), residues: 351 sheet: -0.53 (0.42), residues: 153 loop : -1.47 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 195 HIS 0.008 0.002 HIS c 304 PHE 0.016 0.003 PHE c 292 TYR 0.020 0.002 TYR c 418 ARG 0.007 0.001 ARG A 234 *********************** 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 246 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 184 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 LYS cc_start: 0.8256 (mmtm) cc_final: 0.7973 (mmtm) REVERT: A 152 MET cc_start: 0.8183 (tmm) cc_final: 0.7701 (tmm) REVERT: A 171 TYR cc_start: 0.6865 (OUTLIER) cc_final: 0.5213 (p90) REVERT: A 193 MET cc_start: 0.8662 (tpp) cc_final: 0.8367 (tpp) REVERT: A 199 TYR cc_start: 0.6757 (OUTLIER) cc_final: 0.5363 (m-80) REVERT: a 282 TRP cc_start: 0.7669 (m-90) cc_final: 0.7465 (m-90) REVERT: a 404 GLN cc_start: 0.8024 (tp40) cc_final: 0.7665 (tp40) REVERT: b 306 GLU cc_start: 0.8150 (mm-30) cc_final: 0.7701 (mm-30) REVERT: b 401 ASP cc_start: 0.8347 (m-30) cc_final: 0.7921 (m-30) REVERT: C 148 GLN cc_start: 0.8568 (mm110) cc_final: 0.8019 (tm-30) REVERT: C 191 MET cc_start: 0.8086 (mmm) cc_final: 0.7720 (mmt) outliers start: 62 outliers final: 45 residues processed: 222 average time/residue: 0.2433 time to fit residues: 72.6967 Evaluate side-chains 215 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 168 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 195 TRP Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain a residue 266 SER Chi-restraints excluded: chain a residue 283 MET Chi-restraints excluded: chain a residue 291 CYS Chi-restraints excluded: chain a residue 336 ILE 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 99 GLU Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 130 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 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 70 LEU Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 91 HIS Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 116 PHE Chi-restraints excluded: chain C residue 195 TRP Chi-restraints excluded: chain c residue 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 336 ILE Chi-restraints excluded: chain c residue 354 LEU Chi-restraints excluded: chain c residue 359 CYS Chi-restraints excluded: chain c residue 360 ILE Chi-restraints excluded: chain c residue 376 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 10 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 chunk 97 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 47 optimal weight: 7.9990 chunk 51 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 46 optimal weight: 20.0000 chunk 55 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 123 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 = 0.3798 r_free = 0.3798 target = 0.122192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.097612 restraints weight = 18738.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.100505 restraints weight = 13071.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.102470 restraints weight = 10363.018| |-----------------------------------------------------------------------------| r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.5844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 9618 Z= 0.273 Angle : 0.882 13.620 13032 Z= 0.436 Chirality : 0.053 0.362 1632 Planarity : 0.003 0.028 1557 Dihedral : 9.892 59.245 2514 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.90 % Favored : 91.10 % Rotamer: Outliers : 6.10 % Allowed : 18.93 % Favored : 74.97 % 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: -0.78 (0.26), residues: 1056 helix: 0.80 (0.27), residues: 351 sheet: -0.47 (0.42), residues: 153 loop : -1.43 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 195 HIS 0.010 0.001 HIS C 123 PHE 0.015 0.002 PHE a 292 TYR 0.028 0.001 TYR A 149 ARG 0.006 0.001 ARG A 234 *********************** 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 238 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 180 time to evaluate : 1.173 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: 0.8122 (mmtm) cc_final: 0.7900 (mmtm) REVERT: A 152 MET cc_start: 0.8184 (tmm) cc_final: 0.7780 (tmm) REVERT: A 171 TYR cc_start: 0.6923 (OUTLIER) cc_final: 0.5155 (p90) REVERT: A 193 MET cc_start: 0.8649 (tpp) cc_final: 0.8283 (tpp) REVERT: A 199 TYR cc_start: 0.6644 (OUTLIER) cc_final: 0.5308 (m-80) REVERT: a 282 TRP cc_start: 0.7623 (m-90) cc_final: 0.7418 (m-90) REVERT: a 334 GLN cc_start: 0.7348 (pp30) cc_final: 0.7089 (pp30) REVERT: a 404 GLN cc_start: 0.7966 (tp40) cc_final: 0.7594 (tp40) REVERT: B 213 MET cc_start: 0.7510 (pmm) cc_final: 0.7095 (pmm) REVERT: b 366 SER cc_start: 0.8898 (t) cc_final: 0.8695 (t) REVERT: b 401 ASP cc_start: 0.8245 (m-30) cc_final: 0.7868 (m-30) REVERT: C 152 MET cc_start: 0.7943 (tmm) cc_final: 0.7612 (tmm) REVERT: C 191 MET cc_start: 0.7967 (mmm) cc_final: 0.7663 (mmt) REVERT: C 193 MET cc_start: 0.8183 (tpp) cc_final: 0.7567 (ttm) outliers start: 58 outliers final: 45 residues processed: 217 average time/residue: 0.2488 time to fit residues: 72.4212 Evaluate side-chains 215 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 168 time to evaluate : 1.075 ------------------------------------------------------------------------------- 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 211 CYS 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 292 PHE Chi-restraints excluded: chain a residue 323 ARG Chi-restraints excluded: chain a residue 359 CYS Chi-restraints excluded: chain a residue 376 THR Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 130 HIS Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 195 TRP Chi-restraints excluded: chain B residue 211 CYS Chi-restraints excluded: chain b residue 260 THR Chi-restraints excluded: chain b residue 266 SER Chi-restraints excluded: chain b residue 283 MET Chi-restraints excluded: chain b residue 291 CYS Chi-restraints excluded: chain b residue 304 HIS Chi-restraints excluded: chain b residue 359 CYS Chi-restraints excluded: chain b residue 360 ILE Chi-restraints excluded: chain b residue 376 THR Chi-restraints excluded: chain b residue 387 VAL Chi-restraints excluded: chain b residue 414 LEU Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 116 PHE Chi-restraints excluded: chain C residue 195 TRP Chi-restraints excluded: chain c residue 266 SER Chi-restraints excluded: chain c residue 291 CYS Chi-restraints excluded: chain c residue 323 ARG Chi-restraints excluded: chain c residue 336 ILE Chi-restraints excluded: chain c residue 354 LEU Chi-restraints excluded: chain c residue 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: 20.0000 chunk 52 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 93 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 90 optimal weight: 4.9990 chunk 47 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 114 HIS ** b 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.122334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.097933 restraints weight = 18902.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.100663 restraints weight = 13476.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.102544 restraints weight = 10794.034| |-----------------------------------------------------------------------------| r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.5993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 9618 Z= 0.270 Angle : 0.907 17.332 13032 Z= 0.447 Chirality : 0.054 0.379 1632 Planarity : 0.003 0.039 1557 Dihedral : 9.259 59.873 2514 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.75 % Favored : 90.25 % Rotamer: Outliers : 5.57 % Allowed : 19.14 % Favored : 75.29 % 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: -0.81 (0.26), residues: 1056 helix: 0.76 (0.27), residues: 351 sheet: -0.30 (0.44), residues: 144 loop : -1.48 (0.26), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 195 HIS 0.017 0.001 HIS B 169 PHE 0.013 0.002 PHE a 292 TYR 0.023 0.001 TYR A 149 ARG 0.009 0.001 ARG b 383 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 179 time to evaluate : 1.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 MET cc_start: 0.8192 (tmm) cc_final: 0.7823 (tmm) REVERT: A 171 TYR cc_start: 0.7038 (OUTLIER) cc_final: 0.5308 (p90) REVERT: A 193 MET cc_start: 0.8564 (tpp) cc_final: 0.8184 (tpp) REVERT: A 199 TYR cc_start: 0.6677 (OUTLIER) cc_final: 0.5185 (m-80) REVERT: B 193 MET cc_start: 0.8323 (tpp) cc_final: 0.7844 (ttm) REVERT: b 366 SER cc_start: 0.8862 (t) cc_final: 0.8614 (t) REVERT: b 401 ASP cc_start: 0.8213 (m-30) cc_final: 0.7888 (m-30) REVERT: C 152 MET cc_start: 0.7924 (tmm) cc_final: 0.7683 (tmm) REVERT: C 191 MET cc_start: 0.7867 (mmm) cc_final: 0.7603 (mmt) REVERT: C 210 ASP cc_start: 0.6896 (p0) cc_final: 0.6676 (p0) REVERT: c 409 MET cc_start: 0.7360 (mtp) cc_final: 0.7127 (mtp) outliers start: 53 outliers final: 43 residues processed: 211 average time/residue: 0.2446 time to fit residues: 69.2363 Evaluate side-chains 212 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 167 time to evaluate : 1.020 ------------------------------------------------------------------------------- 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 227 GLU Chi-restraints excluded: chain a residue 266 SER Chi-restraints excluded: chain a residue 291 CYS Chi-restraints excluded: chain a residue 292 PHE Chi-restraints excluded: chain a residue 323 ARG Chi-restraints excluded: chain a residue 359 CYS Chi-restraints excluded: chain a residue 376 THR Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 130 HIS Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 171 TYR Chi-restraints excluded: chain B residue 195 TRP Chi-restraints excluded: chain b residue 260 THR Chi-restraints excluded: chain b residue 266 SER Chi-restraints excluded: chain b residue 291 CYS Chi-restraints excluded: chain b residue 304 HIS Chi-restraints excluded: chain b residue 360 ILE Chi-restraints excluded: chain b residue 376 THR Chi-restraints excluded: chain b residue 387 VAL Chi-restraints excluded: chain b residue 414 LEU Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 116 PHE 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 331 MET Chi-restraints excluded: chain c residue 334 GLN Chi-restraints excluded: chain c residue 336 ILE Chi-restraints excluded: chain c residue 354 LEU Chi-restraints excluded: chain c residue 359 CYS Chi-restraints excluded: chain c residue 360 ILE Chi-restraints excluded: chain c residue 376 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 74 optimal weight: 0.9980 chunk 25 optimal weight: 0.0970 chunk 93 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 80 optimal weight: 5.9990 chunk 99 optimal weight: 0.7980 chunk 70 optimal weight: 5.9990 chunk 4 optimal weight: 0.7980 chunk 9 optimal weight: 10.0000 chunk 56 optimal weight: 2.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- 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 169 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 = 0.3805 r_free = 0.3805 target = 0.122315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.097547 restraints weight = 18675.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.100398 restraints weight = 13017.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.102359 restraints weight = 10347.449| |-----------------------------------------------------------------------------| r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.6166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 9618 Z= 0.267 Angle : 0.893 13.604 13032 Z= 0.438 Chirality : 0.053 0.386 1632 Planarity : 0.003 0.024 1557 Dihedral : 9.060 58.161 2514 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.94 % Favored : 90.06 % Rotamer: Outliers : 4.94 % Allowed : 20.29 % Favored : 74.76 % 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: -0.88 (0.26), residues: 1056 helix: 0.68 (0.27), residues: 354 sheet: -0.58 (0.42), residues: 153 loop : -1.46 (0.27), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 195 HIS 0.007 0.001 HIS C 123 PHE 0.016 0.002 PHE A 116 TYR 0.020 0.001 TYR B 149 ARG 0.005 0.001 ARG A 234 *********************** 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 228 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 181 time to evaluate : 1.004 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: 0.8213 (tmm) cc_final: 0.7858 (tmm) REVERT: A 171 TYR cc_start: 0.7077 (OUTLIER) cc_final: 0.5350 (p90) REVERT: A 193 MET cc_start: 0.8628 (tpp) cc_final: 0.8261 (tpp) REVERT: A 199 TYR cc_start: 0.6706 (OUTLIER) cc_final: 0.5188 (m-80) REVERT: a 334 GLN cc_start: 0.7630 (pp30) cc_final: 0.7055 (pp30) REVERT: a 338 LYS cc_start: 0.8336 (mtmt) cc_final: 0.8106 (mttt) REVERT: a 404 GLN cc_start: 0.7882 (tp40) cc_final: 0.7600 (tp40) REVERT: a 405 GLN cc_start: 0.8388 (tp40) cc_final: 0.7614 (tp40) REVERT: B 152 MET cc_start: 0.7992 (tmm) cc_final: 0.7520 (tmm) REVERT: B 193 MET cc_start: 0.8502 (tpp) cc_final: 0.7949 (ttm) REVERT: b 302 GLU cc_start: 0.7129 (tp30) cc_final: 0.6880 (tp30) REVERT: b 366 SER cc_start: 0.8823 (t) cc_final: 0.8553 (t) REVERT: b 401 ASP cc_start: 0.8286 (m-30) cc_final: 0.8016 (m-30) REVERT: C 152 MET cc_start: 0.8037 (tmm) cc_final: 0.7771 (tmm) REVERT: C 191 MET cc_start: 0.7831 (mmm) cc_final: 0.7608 (mmt) REVERT: C 193 MET cc_start: 0.8051 (tpp) cc_final: 0.7453 (ttm) REVERT: c 409 MET cc_start: 0.7390 (mtp) cc_final: 0.7132 (mtp) outliers start: 47 outliers final: 39 residues processed: 211 average time/residue: 0.2468 time to fit residues: 69.4263 Evaluate side-chains 210 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 169 time to evaluate : 1.027 ------------------------------------------------------------------------------- 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 227 GLU Chi-restraints excluded: chain a residue 266 SER Chi-restraints excluded: chain a residue 291 CYS Chi-restraints excluded: chain a residue 292 PHE Chi-restraints excluded: chain a residue 359 CYS Chi-restraints excluded: chain a residue 376 THR Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain B residue 130 HIS Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 195 TRP Chi-restraints excluded: chain b residue 260 THR Chi-restraints excluded: chain b residue 266 SER Chi-restraints excluded: chain b residue 291 CYS Chi-restraints excluded: chain b residue 304 HIS Chi-restraints excluded: chain b residue 359 CYS Chi-restraints excluded: chain b residue 360 ILE Chi-restraints excluded: chain b residue 376 THR Chi-restraints excluded: chain b residue 387 VAL Chi-restraints excluded: chain b residue 414 LEU Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 116 PHE Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 195 TRP Chi-restraints excluded: chain c residue 266 SER Chi-restraints excluded: chain c residue 291 CYS Chi-restraints excluded: chain c residue 292 PHE Chi-restraints excluded: chain c residue 304 HIS Chi-restraints excluded: chain c residue 323 ARG Chi-restraints excluded: chain c residue 336 ILE Chi-restraints excluded: chain c residue 354 LEU Chi-restraints excluded: chain c residue 359 CYS Chi-restraints excluded: chain c residue 360 ILE Chi-restraints excluded: chain c residue 376 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 20 optimal weight: 6.9990 chunk 64 optimal weight: 0.9980 chunk 35 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 72 optimal weight: 0.5980 chunk 68 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 87 optimal weight: 0.8980 chunk 83 optimal weight: 0.9980 chunk 57 optimal weight: 0.5980 chunk 46 optimal weight: 4.9990 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 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 169 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 = 0.3796 r_free = 0.3796 target = 0.121722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.096558 restraints weight = 19407.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.099333 restraints weight = 13765.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.101203 restraints weight = 11086.308| |-----------------------------------------------------------------------------| r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.6384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 9618 Z= 0.255 Angle : 0.890 12.659 13032 Z= 0.438 Chirality : 0.053 0.375 1632 Planarity : 0.003 0.041 1557 Dihedral : 8.959 59.970 2514 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.94 % Favored : 90.06 % Rotamer: Outliers : 4.31 % Allowed : 21.56 % Favored : 74.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.91 (0.26), residues: 1056 helix: 0.72 (0.28), residues: 348 sheet: -0.67 (0.42), residues: 156 loop : -1.48 (0.27), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 195 HIS 0.008 0.001 HIS B 114 PHE 0.041 0.002 PHE B 116 TYR 0.027 0.001 TYR A 149 ARG 0.010 0.001 ARG b 383 ********************** 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 218 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 177 time to evaluate : 0.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 MET cc_start: 0.8158 (tmm) cc_final: 0.7665 (tmm) REVERT: A 171 TYR cc_start: 0.7241 (OUTLIER) cc_final: 0.5591 (p90) REVERT: A 193 MET cc_start: 0.8630 (tpp) cc_final: 0.8242 (tpp) REVERT: A 199 TYR cc_start: 0.6732 (OUTLIER) cc_final: 0.5258 (m-80) REVERT: a 334 GLN cc_start: 0.7679 (pp30) cc_final: 0.7176 (pp30) REVERT: a 404 GLN cc_start: 0.7727 (tp40) cc_final: 0.7500 (tp40) REVERT: B 152 MET cc_start: 0.8041 (tmm) cc_final: 0.7839 (tmm) REVERT: B 193 MET cc_start: 0.8478 (tpp) cc_final: 0.7927 (ttm) REVERT: b 302 GLU cc_start: 0.6778 (tp30) cc_final: 0.6444 (tp30) REVERT: b 366 SER cc_start: 0.8743 (t) cc_final: 0.8463 (t) REVERT: b 401 ASP cc_start: 0.8314 (m-30) cc_final: 0.7975 (m-30) REVERT: C 152 MET cc_start: 0.8124 (tmm) cc_final: 0.7880 (tmm) REVERT: C 193 MET cc_start: 0.8080 (tpp) cc_final: 0.7441 (ttm) REVERT: c 409 MET cc_start: 0.7345 (mtp) cc_final: 0.7143 (mtp) outliers start: 41 outliers final: 37 residues processed: 209 average time/residue: 0.2455 time to fit residues: 68.5951 Evaluate side-chains 205 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 166 time to evaluate : 1.014 ------------------------------------------------------------------------------- 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 123 HIS Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 195 TRP Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain a residue 266 SER Chi-restraints excluded: chain a residue 291 CYS Chi-restraints excluded: chain a residue 292 PHE Chi-restraints excluded: chain a residue 359 CYS Chi-restraints excluded: chain a residue 376 THR Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain B residue 123 HIS Chi-restraints excluded: chain B residue 130 HIS Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 195 TRP Chi-restraints excluded: chain b residue 260 THR Chi-restraints excluded: chain b residue 266 SER Chi-restraints excluded: chain b residue 291 CYS Chi-restraints excluded: chain b residue 304 HIS Chi-restraints excluded: chain b residue 359 CYS Chi-restraints excluded: chain b residue 360 ILE Chi-restraints excluded: chain b residue 376 THR Chi-restraints excluded: chain b residue 387 VAL Chi-restraints excluded: chain b residue 414 LEU Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 116 PHE Chi-restraints excluded: chain C residue 195 TRP Chi-restraints excluded: chain c residue 266 SER Chi-restraints excluded: chain c residue 291 CYS Chi-restraints excluded: chain c residue 292 PHE Chi-restraints excluded: chain c residue 304 HIS Chi-restraints excluded: chain c residue 336 ILE Chi-restraints excluded: chain c residue 354 LEU Chi-restraints excluded: chain c residue 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: 0.1980 chunk 28 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 52 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 chunk 51 optimal weight: 0.5980 chunk 75 optimal weight: 0.9990 chunk 11 optimal weight: 8.9990 chunk 57 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.122513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.096903 restraints weight = 19644.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.099833 restraints weight = 13659.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.101853 restraints weight = 10873.216| |-----------------------------------------------------------------------------| r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.6539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 9618 Z= 0.255 Angle : 0.884 11.792 13032 Z= 0.436 Chirality : 0.052 0.366 1632 Planarity : 0.003 0.028 1557 Dihedral : 8.883 59.248 2514 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.00 % Favored : 91.00 % Rotamer: Outliers : 3.79 % Allowed : 22.50 % Favored : 73.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.85 (0.26), residues: 1056 helix: 0.70 (0.28), residues: 351 sheet: -0.59 (0.43), residues: 156 loop : -1.41 (0.27), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 195 HIS 0.005 0.001 HIS b 304 PHE 0.021 0.001 PHE B 116 TYR 0.032 0.001 TYR A 149 ARG 0.008 0.001 ARG B 125 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3194.51 seconds wall clock time: 59 minutes 33.36 seconds (3573.36 seconds total)