Starting phenix.real_space_refine on Thu Jul 2 09:57:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8dmi_27539/07_2026/8dmi_27539.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dmi_27539/07_2026/8dmi_27539.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dmi_27539/07_2026/8dmi_27539.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dmi_27539/07_2026/8dmi_27539.map" model { file = "/net/cci-nas-00/data/ceres_data/8dmi_27539/07_2026/8dmi_27539.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dmi_27539/07_2026/8dmi_27539.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8dmi_27539/07_2026/8dmi_27539.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8dmi_27539/07_2026/8dmi_27539.cif" } resolution = 3.26 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 81 5.16 5 C 5187 2.51 5 N 1347 2.21 5 O 1644 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8259 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 1357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1357 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 2, 'TRANS': 167} Chain breaks: 3 Chain: "a" Number of atoms: 1200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1200 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 3, 'TRANS': 143} Chain breaks: 1 Chain: "B" Number of atoms: 1357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1357 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 2, 'TRANS': 167} Chain breaks: 3 Chain: "b" Number of atoms: 1200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1200 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 3, 'TRANS': 143} Chain breaks: 1 Chain: "C" Number of atoms: 1357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1357 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 2, 'TRANS': 167} Chain breaks: 3 Chain: "c" Number of atoms: 1200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1200 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 3, 'TRANS': 143} Chain breaks: 1 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "a" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "b" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "c" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.75, per 1000 atoms: 0.21 Number of scatterers: 8259 At special positions: 0 Unit cell: (88.11, 91.08, 92.07, 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 81 16.00 O 1644 8.00 N 1347 7.00 C 5187 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS A 92 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 123 " - pdb=" SG CYS A 160 " distance=2.03 Simple disulfide: pdb=" SG CYS A 184 " - pdb=" SG CYS A 220 " distance=2.03 Simple disulfide: pdb=" SG CYS A 207 " - pdb=" SG CYS a 366 " distance=2.05 Simple disulfide: pdb=" SG CYS a 285 " - pdb=" SG CYS a 298 " distance=2.03 Simple disulfide: pdb=" SG CYS a 307 " - pdb=" SG CYS a 316 " distance=2.03 Simple disulfide: pdb=" SG CYS a 370 " - pdb=" SG CYS a 391 " distance=2.03 Simple disulfide: pdb=" SG CYS B 92 " - pdb=" SG CYS B 239 " distance=2.03 Simple disulfide: pdb=" SG CYS B 123 " - pdb=" SG CYS B 160 " distance=2.03 Simple disulfide: pdb=" SG CYS B 184 " - pdb=" SG CYS B 220 " distance=2.03 Simple disulfide: pdb=" SG CYS B 207 " - pdb=" SG CYS b 366 " distance=2.04 Simple disulfide: pdb=" SG CYS b 285 " - pdb=" SG CYS b 298 " distance=2.03 Simple disulfide: pdb=" SG CYS b 307 " - pdb=" SG CYS b 316 " distance=2.03 Simple disulfide: pdb=" SG CYS b 370 " - pdb=" SG CYS b 391 " distance=2.03 Simple disulfide: pdb=" SG CYS C 92 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 123 " - pdb=" SG CYS C 160 " distance=2.03 Simple disulfide: pdb=" SG CYS C 184 " - pdb=" SG CYS C 220 " distance=2.03 Simple disulfide: pdb=" SG CYS C 207 " - pdb=" SG CYS c 366 " distance=2.07 Simple disulfide: pdb=" SG CYS c 285 " - pdb=" SG CYS c 298 " distance=2.03 Simple disulfide: pdb=" SG CYS c 307 " - pdb=" SG CYS c 316 " distance=2.03 Simple disulfide: pdb=" SG CYS c 370 " - pdb=" SG CYS c 391 " distance=2.03 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 BETA1-4 " NAG D 1 " - " NAG D 2 " " 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 J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " 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 Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " NAG-ASN " NAG A 301 " - " ASN A 124 " " NAG B 301 " - " ASN B 124 " " NAG C 301 " - " ASN C 124 " " NAG D 1 " - " ASN A 85 " " NAG E 1 " - " ASN A 95 " " NAG F 1 " - " ASN A 114 " " NAG G 1 " - " ASN A 171 " " NAG H 1 " - " ASN A 232 " " NAG I 1 " - " ASN a 371 " " NAG J 1 " - " ASN B 85 " " NAG K 1 " - " ASN B 95 " " NAG L 1 " - " ASN B 114 " " NAG M 1 " - " ASN B 171 " " NAG N 1 " - " ASN B 232 " " NAG O 1 " - " ASN b 371 " " NAG P 1 " - " ASN C 85 " " NAG Q 1 " - " ASN C 95 " " NAG R 1 " - " ASN C 114 " " NAG S 1 " - " ASN C 171 " " NAG T 1 " - " ASN C 232 " " NAG U 1 " - " ASN c 371 " " NAG a 701 " - " ASN a 401 " " NAG b 701 " - " ASN b 401 " " NAG c 701 " - " ASN c 401 " Time building additional restraints: 0.75 Conformation dependent library (CDL) restraints added in 287.0 milliseconds 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1818 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 9 sheets defined 35.3% alpha, 12.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'A' and resid 136 through 148 Processing helix chain 'A' and resid 186 through 200 Processing helix chain 'A' and resid 244 through 253 Processing helix chain 'a' and resid 300 through 307 removed outlier: 4.153A pdb=" N VAL a 304 " --> pdb=" O GLY a 300 " (cutoff:3.500A) Processing helix chain 'a' and resid 313 through 330 removed outlier: 4.156A pdb=" N ASP a 317 " --> pdb=" O GLU a 313 " (cutoff:3.500A) Processing helix chain 'a' and resid 335 through 346 Processing helix chain 'a' and resid 352 through 365 Processing helix chain 'a' and resid 405 through 426 Processing helix chain 'B' and resid 136 through 148 Processing helix chain 'B' and resid 186 through 200 Processing helix chain 'B' and resid 244 through 253 Processing helix chain 'b' and resid 300 through 307 removed outlier: 4.154A pdb=" N VAL b 304 " --> pdb=" O GLY b 300 " (cutoff:3.500A) Processing helix chain 'b' and resid 313 through 330 removed outlier: 4.155A pdb=" N ASP b 317 " --> pdb=" O GLU b 313 " (cutoff:3.500A) Processing helix chain 'b' and resid 335 through 346 Processing helix chain 'b' and resid 352 through 365 Processing helix chain 'b' and resid 405 through 426 Processing helix chain 'C' and resid 136 through 148 Processing helix chain 'C' and resid 186 through 200 Processing helix chain 'C' and resid 244 through 253 Processing helix chain 'c' and resid 300 through 307 removed outlier: 4.154A pdb=" N VAL c 304 " --> pdb=" O GLY c 300 " (cutoff:3.500A) Processing helix chain 'c' and resid 313 through 330 removed outlier: 4.156A pdb=" N ASP c 317 " --> pdb=" O GLU c 313 " (cutoff:3.500A) Processing helix chain 'c' and resid 335 through 346 Processing helix chain 'c' and resid 352 through 365 Processing helix chain 'c' and resid 405 through 426 Processing sheet with id=AA1, first strand: chain 'A' and resid 72 through 78 removed outlier: 3.527A pdb=" N GLU a 379 " --> pdb=" O GLN A 73 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 89 through 93 Processing sheet with id=AA3, first strand: chain 'a' and resid 394 through 395 Processing sheet with id=AA4, first strand: chain 'B' and resid 72 through 78 removed outlier: 3.510A pdb=" N GLU b 379 " --> pdb=" O GLN B 73 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 89 through 93 Processing sheet with id=AA6, first strand: chain 'b' and resid 394 through 395 Processing sheet with id=AA7, first strand: chain 'C' and resid 72 through 78 Processing sheet with id=AA8, first strand: chain 'C' and resid 89 through 93 Processing sheet with id=AA9, first strand: chain 'c' and resid 394 through 395 328 hydrogen bonds defined for protein. 939 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: 0.75 Time building geometry restraints manager: 0.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2067 1.33 - 1.45: 1924 1.45 - 1.58: 4307 1.58 - 1.70: 6 1.70 - 1.82: 120 Bond restraints: 8424 Sorted by residual: bond pdb=" CB ASN B 114 " pdb=" CG ASN B 114 " ideal model delta sigma weight residual 1.516 1.609 -0.093 2.50e-02 1.60e+03 1.39e+01 bond pdb=" CB ASN C 114 " pdb=" CG ASN C 114 " ideal model delta sigma weight residual 1.516 1.609 -0.093 2.50e-02 1.60e+03 1.38e+01 bond pdb=" CB ASN A 114 " pdb=" CG ASN A 114 " ideal model delta sigma weight residual 1.516 1.608 -0.092 2.50e-02 1.60e+03 1.37e+01 bond pdb=" CA ASN A 114 " pdb=" CB ASN A 114 " ideal model delta sigma weight residual 1.530 1.565 -0.035 1.54e-02 4.22e+03 5.07e+00 bond pdb=" CA ASN C 114 " pdb=" CB ASN C 114 " ideal model delta sigma weight residual 1.530 1.564 -0.034 1.54e-02 4.22e+03 4.98e+00 ... (remaining 8419 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 11051 2.10 - 4.21: 250 4.21 - 6.31: 54 6.31 - 8.41: 6 8.41 - 10.52: 9 Bond angle restraints: 11370 Sorted by residual: angle pdb=" CA ASN A 114 " pdb=" CB ASN A 114 " pdb=" CG ASN A 114 " ideal model delta sigma weight residual 112.60 119.82 -7.22 1.00e+00 1.00e+00 5.21e+01 angle pdb=" CA ASN B 114 " pdb=" CB ASN B 114 " pdb=" CG ASN B 114 " ideal model delta sigma weight residual 112.60 119.77 -7.17 1.00e+00 1.00e+00 5.14e+01 angle pdb=" CA ASN C 114 " pdb=" CB ASN C 114 " pdb=" CG ASN C 114 " ideal model delta sigma weight residual 112.60 119.76 -7.16 1.00e+00 1.00e+00 5.13e+01 angle pdb=" N ILE C 117 " pdb=" CA ILE C 117 " pdb=" C ILE C 117 " ideal model delta sigma weight residual 113.71 109.94 3.77 9.50e-01 1.11e+00 1.57e+01 angle pdb=" N ILE A 117 " pdb=" CA ILE A 117 " pdb=" C ILE A 117 " ideal model delta sigma weight residual 113.71 109.95 3.76 9.50e-01 1.11e+00 1.57e+01 ... (remaining 11365 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.99: 4113 16.99 - 33.98: 458 33.98 - 50.97: 73 50.97 - 67.96: 36 67.96 - 84.96: 9 Dihedral angle restraints: 4689 sinusoidal: 1890 harmonic: 2799 Sorted by residual: dihedral pdb=" CB CYS B 207 " pdb=" SG CYS B 207 " pdb=" SG CYS b 366 " pdb=" CB CYS b 366 " ideal model delta sinusoidal sigma weight residual -86.00 -170.96 84.96 1 1.00e+01 1.00e-02 8.76e+01 dihedral pdb=" CB CYS B 123 " pdb=" SG CYS B 123 " pdb=" SG CYS B 160 " pdb=" CB CYS B 160 " ideal model delta sinusoidal sigma weight residual 93.00 8.85 84.15 1 1.00e+01 1.00e-02 8.62e+01 dihedral pdb=" CB CYS A 123 " pdb=" SG CYS A 123 " pdb=" SG CYS A 160 " pdb=" CB CYS A 160 " ideal model delta sinusoidal sigma weight residual 93.00 8.87 84.13 1 1.00e+01 1.00e-02 8.62e+01 ... (remaining 4686 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 1245 0.079 - 0.157: 100 0.157 - 0.236: 17 0.236 - 0.315: 6 0.315 - 0.393: 6 Chirality restraints: 1374 Sorted by residual: chirality pdb=" C5 NAG R 1 " pdb=" C4 NAG R 1 " pdb=" C6 NAG R 1 " pdb=" O5 NAG R 1 " both_signs ideal model delta sigma weight residual False -2.41 -2.02 -0.39 2.00e-01 2.50e+01 3.86e+00 chirality pdb=" C5 NAG F 1 " pdb=" C4 NAG F 1 " pdb=" C6 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.41 -2.02 -0.39 2.00e-01 2.50e+01 3.83e+00 chirality pdb=" C5 NAG L 1 " pdb=" C4 NAG L 1 " pdb=" C6 NAG L 1 " pdb=" O5 NAG L 1 " both_signs ideal model delta sigma weight residual False -2.41 -2.02 -0.39 2.00e-01 2.50e+01 3.80e+00 ... (remaining 1371 not shown) Planarity restraints: 1389 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 114 " 0.053 2.00e-02 2.50e+03 6.31e-02 4.98e+01 pdb=" CG ASN C 114 " -0.123 2.00e-02 2.50e+03 pdb=" OD1 ASN C 114 " 0.033 2.00e-02 2.50e+03 pdb=" ND2 ASN C 114 " 0.009 2.00e-02 2.50e+03 pdb=" C1 NAG R 1 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 114 " 0.053 2.00e-02 2.50e+03 6.29e-02 4.95e+01 pdb=" CG ASN B 114 " -0.123 2.00e-02 2.50e+03 pdb=" OD1 ASN B 114 " 0.033 2.00e-02 2.50e+03 pdb=" ND2 ASN B 114 " 0.008 2.00e-02 2.50e+03 pdb=" C1 NAG L 1 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 114 " 0.053 2.00e-02 2.50e+03 6.28e-02 4.92e+01 pdb=" CG ASN A 114 " -0.122 2.00e-02 2.50e+03 pdb=" OD1 ASN A 114 " 0.033 2.00e-02 2.50e+03 pdb=" ND2 ASN A 114 " 0.008 2.00e-02 2.50e+03 pdb=" C1 NAG F 1 " 0.028 2.00e-02 2.50e+03 ... (remaining 1386 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 188 2.67 - 3.23: 7787 3.23 - 3.79: 12362 3.79 - 4.34: 16892 4.34 - 4.90: 28171 Nonbonded interactions: 65400 Sorted by model distance: nonbonded pdb=" ND1 HIS a 380 " pdb=" OG1 THR a 383 " model vdw 2.117 3.120 nonbonded pdb=" ND1 HIS c 380 " pdb=" OG1 THR c 383 " model vdw 2.118 3.120 nonbonded pdb=" ND1 HIS b 380 " pdb=" OG1 THR b 383 " model vdw 2.118 3.120 nonbonded pdb=" OG SER B 82 " pdb=" O7 NAG J 1 " model vdw 2.306 3.040 nonbonded pdb=" OG SER A 82 " pdb=" O7 NAG D 1 " model vdw 2.306 3.040 ... (remaining 65395 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 0.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 7.350 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 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 : 0.004 0.093 8487 Z= 0.197 Angle : 0.885 14.733 11538 Z= 0.461 Chirality : 0.055 0.393 1374 Planarity : 0.009 0.119 1365 Dihedral : 14.295 68.731 2808 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.27), residues: 915 helix: 0.58 (0.28), residues: 351 sheet: -0.12 (0.54), residues: 93 loop : -2.10 (0.25), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.031 0.003 ARG B 188 TYR 0.063 0.002 TYR A 227 PHE 0.016 0.002 PHE B 187 TRP 0.017 0.002 TRP C 219 HIS 0.013 0.002 HIS B 136 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.18 ( 8424) covalent geometry : angle 0.81468 / 0.44 (11370) SS BOND : bond 0.01059 / 0.42 ( 21) SS BOND : angle 4.44360 / 2.17 ( 42) hydrogen bonds : bond 0.14553 / 9.35 ( 328) hydrogen bonds : angle 5.00084 / 3.63 ( 939) link_BETA1-4 : bond 0.00760 / 0.44 ( 18) link_BETA1-4 : angle 1.83548 / 1.63 ( 54) link_NAG-ASN : bond 0.02360 / 1.04 ( 24) link_NAG-ASN : angle 2.58800 / 1.66 ( 72) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 206 time to evaluate : 0.262 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 206 average time/residue: 0.1025 time to fit residues: 27.4285 Evaluate side-chains 141 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 8.9990 chunk 51 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... a 359 ASN C 73 GLN C 237 ASN c 359 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.059099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.046949 restraints weight = 31777.991| |-----------------------------------------------------------------------------| r_work (start): 0.2879 rms_B_bonded: 4.31 r_work: 0.2711 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 8487 Z= 0.226 Angle : 0.748 9.402 11538 Z= 0.373 Chirality : 0.046 0.238 1374 Planarity : 0.004 0.032 1365 Dihedral : 4.697 23.992 1017 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 1.04 % Allowed : 9.84 % Favored : 89.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.27), residues: 915 helix: 1.47 (0.28), residues: 357 sheet: 0.15 (0.55), residues: 93 loop : -1.69 (0.26), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 190 TYR 0.021 0.001 TYR A 227 PHE 0.015 0.002 PHE B 245 TRP 0.013 0.001 TRP c 392 HIS 0.007 0.001 HIS A 238 Details of bonding type rmsd/Z covalent geometry : bond 0.00491 / 0.23 ( 8424) covalent geometry : angle 0.72187 / 0.37 (11370) SS BOND : bond 0.00582 / 0.28 ( 21) SS BOND : angle 2.05065 / 1.21 ( 42) hydrogen bonds : bond 0.04291 / 2.89 ( 328) hydrogen bonds : angle 4.08251 / 2.93 ( 939) link_BETA1-4 : bond 0.00372 / 0.20 ( 18) link_BETA1-4 : angle 1.63449 / 1.35 ( 54) link_NAG-ASN : bond 0.00251 / 0.14 ( 24) link_NAG-ASN : angle 1.70352 / 1.12 ( 72) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 160 time to evaluate : 0.326 Fit side-chains revert: symmetry clash REVERT: A 72 TYR cc_start: 0.8949 (m-80) cc_final: 0.8649 (m-80) REVERT: A 103 MET cc_start: 0.9414 (tpt) cc_final: 0.9024 (tpt) REVERT: A 183 GLN cc_start: 0.7453 (mm110) cc_final: 0.7216 (mm110) REVERT: a 310 ASN cc_start: 0.8487 (t0) cc_final: 0.7364 (t0) REVERT: a 414 ASP cc_start: 0.9132 (m-30) cc_final: 0.8884 (p0) REVERT: B 72 TYR cc_start: 0.9156 (m-80) cc_final: 0.8896 (m-80) REVERT: B 168 ILE cc_start: 0.9530 (mt) cc_final: 0.9314 (mm) REVERT: b 310 ASN cc_start: 0.8218 (t0) cc_final: 0.7313 (t0) REVERT: b 412 GLU cc_start: 0.9012 (tp30) cc_final: 0.8750 (tp30) REVERT: b 416 MET cc_start: 0.9431 (ttp) cc_final: 0.9152 (ttp) REVERT: C 103 MET cc_start: 0.9407 (tpt) cc_final: 0.9153 (tpp) REVERT: C 222 GLN cc_start: 0.9158 (mm110) cc_final: 0.8938 (mm-40) REVERT: c 310 ASN cc_start: 0.8255 (t0) cc_final: 0.7093 (t0) REVERT: c 402 GLU cc_start: 0.9038 (mp0) cc_final: 0.8833 (mp0) outliers start: 9 outliers final: 5 residues processed: 165 average time/residue: 0.0918 time to fit residues: 20.8859 Evaluate side-chains 146 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 141 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain a residue 304 VAL Chi-restraints excluded: chain B residue 109 GLU Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain c residue 299 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 6 optimal weight: 4.9990 chunk 52 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 chunk 76 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 3 optimal weight: 10.0000 chunk 1 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 4 optimal weight: 5.9990 chunk 34 optimal weight: 8.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 164 ASN B 164 ASN C 164 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.057585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.045689 restraints weight = 31492.834| |-----------------------------------------------------------------------------| r_work (start): 0.2841 rms_B_bonded: 4.25 r_work: 0.2675 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.3138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8487 Z= 0.204 Angle : 0.691 9.255 11538 Z= 0.344 Chirality : 0.045 0.231 1374 Planarity : 0.004 0.071 1365 Dihedral : 4.656 21.637 1017 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.04 % Allowed : 11.81 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.28), residues: 915 helix: 1.46 (0.29), residues: 357 sheet: 0.24 (0.58), residues: 96 loop : -1.39 (0.27), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG c 358 TYR 0.017 0.001 TYR A 227 PHE 0.017 0.001 PHE B 245 TRP 0.011 0.001 TRP c 392 HIS 0.006 0.001 HIS A 238 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.20 ( 8424) covalent geometry : angle 0.66749 / 0.34 (11370) SS BOND : bond 0.00468 / 0.26 ( 21) SS BOND : angle 1.95989 / 1.24 ( 42) hydrogen bonds : bond 0.03939 / 2.71 ( 328) hydrogen bonds : angle 3.88554 / 2.76 ( 939) link_BETA1-4 : bond 0.00314 / 0.18 ( 18) link_BETA1-4 : angle 1.47917 / 1.21 ( 54) link_NAG-ASN : bond 0.00268 / 0.15 ( 24) link_NAG-ASN : angle 1.54227 / 1.04 ( 72) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 151 time to evaluate : 0.304 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 103 MET cc_start: 0.9361 (tpt) cc_final: 0.8677 (tpt) REVERT: A 139 MET cc_start: 0.8948 (tpp) cc_final: 0.8652 (tmm) REVERT: A 156 LYS cc_start: 0.9029 (mmmm) cc_final: 0.8625 (mmmm) REVERT: A 256 LYS cc_start: 0.7407 (mmtt) cc_final: 0.7184 (mmtm) REVERT: a 310 ASN cc_start: 0.8564 (t0) cc_final: 0.7386 (t0) REVERT: a 414 ASP cc_start: 0.9156 (m-30) cc_final: 0.8873 (p0) REVERT: B 168 ILE cc_start: 0.9586 (mt) cc_final: 0.9381 (mm) REVERT: b 310 ASN cc_start: 0.8353 (t0) cc_final: 0.7602 (t0) REVERT: b 412 GLU cc_start: 0.9025 (tp30) cc_final: 0.8768 (tp30) REVERT: b 416 MET cc_start: 0.9444 (ttp) cc_final: 0.9075 (ttp) REVERT: C 78 GLU cc_start: 0.8202 (tp30) cc_final: 0.7971 (pm20) REVERT: C 103 MET cc_start: 0.9433 (tpt) cc_final: 0.9015 (tpt) REVERT: C 156 LYS cc_start: 0.8923 (mmtm) cc_final: 0.8621 (mmmm) REVERT: C 222 GLN cc_start: 0.9199 (mm110) cc_final: 0.8425 (mm-40) REVERT: c 310 ASN cc_start: 0.8298 (t0) cc_final: 0.7199 (t0) REVERT: c 362 ARG cc_start: 0.9022 (mmm-85) cc_final: 0.8788 (mtt-85) REVERT: c 372 TYR cc_start: 0.9270 (m-80) cc_final: 0.9019 (m-80) REVERT: c 402 GLU cc_start: 0.9084 (mp0) cc_final: 0.8833 (mp0) outliers start: 9 outliers final: 6 residues processed: 153 average time/residue: 0.0861 time to fit residues: 18.0747 Evaluate side-chains 146 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 140 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain a residue 304 VAL Chi-restraints excluded: chain B residue 109 GLU Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain b residue 304 VAL Chi-restraints excluded: chain c residue 299 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 36 optimal weight: 10.0000 chunk 90 optimal weight: 3.9990 chunk 92 optimal weight: 10.0000 chunk 89 optimal weight: 0.9990 chunk 71 optimal weight: 9.9990 chunk 6 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 70 optimal weight: 0.7980 chunk 83 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 chunk 82 optimal weight: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.057910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.046105 restraints weight = 31980.559| |-----------------------------------------------------------------------------| r_work (start): 0.2850 rms_B_bonded: 4.28 r_work: 0.2678 rms_B_bonded: 4.83 restraints_weight: 0.5000 r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.3356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8487 Z= 0.161 Angle : 0.681 9.309 11538 Z= 0.338 Chirality : 0.044 0.239 1374 Planarity : 0.004 0.065 1365 Dihedral : 4.696 21.683 1017 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 1.85 % Allowed : 12.27 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.28), residues: 915 helix: 1.78 (0.29), residues: 339 sheet: 0.35 (0.59), residues: 96 loop : -1.30 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 205 TYR 0.013 0.001 TYR B 227 PHE 0.012 0.001 PHE B 245 TRP 0.007 0.001 TRP a 392 HIS 0.006 0.001 HIS C 238 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.16 ( 8424) covalent geometry : angle 0.65415 / 0.33 (11370) SS BOND : bond 0.00526 / 0.28 ( 21) SS BOND : angle 2.10133 / 1.25 ( 42) hydrogen bonds : bond 0.03519 / 2.45 ( 328) hydrogen bonds : angle 3.69642 / 2.62 ( 939) link_BETA1-4 : bond 0.00325 / 0.19 ( 18) link_BETA1-4 : angle 1.50785 / 1.25 ( 54) link_NAG-ASN : bond 0.00305 / 0.17 ( 24) link_NAG-ASN : angle 1.56694 / 1.06 ( 72) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 149 time to evaluate : 0.245 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 103 MET cc_start: 0.9376 (tpt) cc_final: 0.8721 (tpt) REVERT: A 156 LYS cc_start: 0.9043 (mmmm) cc_final: 0.8662 (mmmm) REVERT: A 256 LYS cc_start: 0.7322 (mmtt) cc_final: 0.7095 (mmtm) REVERT: a 310 ASN cc_start: 0.8649 (t0) cc_final: 0.7601 (t0) REVERT: a 353 ASP cc_start: 0.8854 (p0) cc_final: 0.8642 (p0) REVERT: a 364 LEU cc_start: 0.9234 (OUTLIER) cc_final: 0.9021 (mm) REVERT: a 416 MET cc_start: 0.9477 (ttp) cc_final: 0.8829 (tmm) REVERT: B 72 TYR cc_start: 0.9092 (m-80) cc_final: 0.8671 (m-80) REVERT: B 222 GLN cc_start: 0.9229 (mm-40) cc_final: 0.9015 (mm-40) REVERT: b 310 ASN cc_start: 0.8305 (t0) cc_final: 0.7571 (t0) REVERT: b 412 GLU cc_start: 0.9014 (tp30) cc_final: 0.8729 (tp30) REVERT: b 416 MET cc_start: 0.9418 (ttp) cc_final: 0.9144 (ttp) REVERT: C 78 GLU cc_start: 0.8229 (tp30) cc_final: 0.8008 (pm20) REVERT: C 103 MET cc_start: 0.9432 (tpt) cc_final: 0.9049 (tpt) REVERT: C 156 LYS cc_start: 0.8906 (mmtm) cc_final: 0.8652 (mmmm) REVERT: c 310 ASN cc_start: 0.8346 (t0) cc_final: 0.7339 (t0) REVERT: c 362 ARG cc_start: 0.9059 (mmm-85) cc_final: 0.8822 (mtt-85) REVERT: c 402 GLU cc_start: 0.9145 (mp0) cc_final: 0.8900 (mp0) outliers start: 16 outliers final: 8 residues processed: 153 average time/residue: 0.0821 time to fit residues: 17.3792 Evaluate side-chains 151 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 142 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain a residue 364 LEU Chi-restraints excluded: chain B residue 109 GLU Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain b residue 304 VAL Chi-restraints excluded: chain C residue 193 ASP Chi-restraints excluded: chain c residue 299 PHE Chi-restraints excluded: chain c residue 364 LEU Chi-restraints excluded: chain c residue 417 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 91 optimal weight: 8.9990 chunk 86 optimal weight: 0.3980 chunk 49 optimal weight: 0.9990 chunk 70 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 27 optimal weight: 8.9990 chunk 17 optimal weight: 6.9990 chunk 60 optimal weight: 6.9990 chunk 64 optimal weight: 0.8980 chunk 88 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 183 GLN C 183 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.057227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.045139 restraints weight = 32123.218| |-----------------------------------------------------------------------------| r_work (start): 0.2828 rms_B_bonded: 4.31 r_work: 0.2661 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.3557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8487 Z= 0.175 Angle : 0.697 11.618 11538 Z= 0.341 Chirality : 0.044 0.239 1374 Planarity : 0.004 0.071 1365 Dihedral : 4.600 20.853 1017 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.20 % Allowed : 12.73 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.28), residues: 915 helix: 1.86 (0.29), residues: 336 sheet: 0.47 (0.59), residues: 96 loop : -1.32 (0.27), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG c 358 TYR 0.012 0.001 TYR C 227 PHE 0.012 0.001 PHE B 245 TRP 0.008 0.001 TRP a 392 HIS 0.005 0.001 HIS C 238 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.18 ( 8424) covalent geometry : angle 0.67135 / 0.33 (11370) SS BOND : bond 0.00452 / 0.25 ( 21) SS BOND : angle 2.03079 / 1.26 ( 42) hydrogen bonds : bond 0.03534 / 2.46 ( 328) hydrogen bonds : angle 3.68567 / 2.62 ( 939) link_BETA1-4 : bond 0.00293 / 0.16 ( 18) link_BETA1-4 : angle 1.56040 / 1.30 ( 54) link_NAG-ASN : bond 0.00269 / 0.15 ( 24) link_NAG-ASN : angle 1.58023 / 1.05 ( 72) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 147 time to evaluate : 0.310 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 103 MET cc_start: 0.9381 (tpt) cc_final: 0.8659 (tpt) REVERT: A 109 GLU cc_start: 0.9365 (OUTLIER) cc_final: 0.8700 (tm-30) REVERT: A 139 MET cc_start: 0.8875 (tpp) cc_final: 0.8592 (tmm) REVERT: a 310 ASN cc_start: 0.8696 (t0) cc_final: 0.7776 (t0) REVERT: a 364 LEU cc_start: 0.9240 (OUTLIER) cc_final: 0.9015 (mm) REVERT: a 379 GLU cc_start: 0.8860 (pt0) cc_final: 0.8553 (pt0) REVERT: a 414 ASP cc_start: 0.9134 (m-30) cc_final: 0.8852 (p0) REVERT: a 416 MET cc_start: 0.9446 (ttp) cc_final: 0.9164 (tmm) REVERT: B 222 GLN cc_start: 0.9257 (mm-40) cc_final: 0.9052 (mm-40) REVERT: b 310 ASN cc_start: 0.8456 (t0) cc_final: 0.7660 (t0) REVERT: b 412 GLU cc_start: 0.9048 (tp30) cc_final: 0.8789 (tp30) REVERT: C 78 GLU cc_start: 0.8250 (tp30) cc_final: 0.8014 (pm20) REVERT: C 103 MET cc_start: 0.9428 (tpt) cc_final: 0.8986 (tpt) REVERT: C 156 LYS cc_start: 0.8996 (mmtm) cc_final: 0.8717 (mmmm) REVERT: C 172 LEU cc_start: 0.9522 (tp) cc_final: 0.9101 (tt) REVERT: c 310 ASN cc_start: 0.8518 (t0) cc_final: 0.7545 (t0) REVERT: c 353 ASP cc_start: 0.8760 (p0) cc_final: 0.8548 (p0) REVERT: c 362 ARG cc_start: 0.9067 (mmm-85) cc_final: 0.8821 (mtt-85) REVERT: c 379 GLU cc_start: 0.8914 (pt0) cc_final: 0.8422 (pt0) REVERT: c 402 GLU cc_start: 0.9155 (mp0) cc_final: 0.8894 (mp0) outliers start: 19 outliers final: 11 residues processed: 155 average time/residue: 0.0800 time to fit residues: 17.1474 Evaluate side-chains 153 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 140 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain a residue 304 VAL Chi-restraints excluded: chain a residue 364 LEU Chi-restraints excluded: chain B residue 109 GLU Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain b residue 304 VAL Chi-restraints excluded: chain b residue 354 GLN Chi-restraints excluded: chain C residue 193 ASP Chi-restraints excluded: chain c residue 291 ILE Chi-restraints excluded: chain c residue 299 PHE Chi-restraints excluded: chain c residue 364 LEU Chi-restraints excluded: chain c residue 417 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 16 optimal weight: 0.8980 chunk 88 optimal weight: 4.9990 chunk 49 optimal weight: 0.3980 chunk 51 optimal weight: 4.9990 chunk 44 optimal weight: 6.9990 chunk 70 optimal weight: 8.9990 chunk 75 optimal weight: 10.0000 chunk 63 optimal weight: 0.7980 chunk 60 optimal weight: 0.0870 chunk 47 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 183 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.058455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.046620 restraints weight = 31784.439| |-----------------------------------------------------------------------------| r_work (start): 0.2865 rms_B_bonded: 4.32 r_work: 0.2694 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.3617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8487 Z= 0.122 Angle : 0.657 9.381 11538 Z= 0.324 Chirality : 0.044 0.245 1374 Planarity : 0.004 0.062 1365 Dihedral : 4.432 19.543 1017 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.39 % Allowed : 15.51 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.29), residues: 915 helix: 1.86 (0.30), residues: 339 sheet: 0.45 (0.59), residues: 96 loop : -1.17 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG c 358 TYR 0.010 0.001 TYR C 227 PHE 0.007 0.001 PHE C 245 TRP 0.007 0.001 TRP B 219 HIS 0.005 0.001 HIS C 238 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 ( 8424) covalent geometry : angle 0.63332 / 0.32 (11370) SS BOND : bond 0.00320 / 0.18 ( 21) SS BOND : angle 1.68893 / 1.06 ( 42) hydrogen bonds : bond 0.03052 / 2.15 ( 328) hydrogen bonds : angle 3.53455 / 2.53 ( 939) link_BETA1-4 : bond 0.00409 / 0.24 ( 18) link_BETA1-4 : angle 1.54503 / 1.33 ( 54) link_NAG-ASN : bond 0.00426 / 0.23 ( 24) link_NAG-ASN : angle 1.55109 / 1.05 ( 72) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 152 time to evaluate : 0.271 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 103 MET cc_start: 0.9352 (tpt) cc_final: 0.8682 (tpt) REVERT: A 109 GLU cc_start: 0.9341 (tt0) cc_final: 0.8704 (tm-30) REVERT: A 139 MET cc_start: 0.8893 (tpp) cc_final: 0.8536 (tmm) REVERT: a 310 ASN cc_start: 0.8692 (t0) cc_final: 0.7810 (t0) REVERT: a 353 ASP cc_start: 0.8828 (p0) cc_final: 0.8618 (p0) REVERT: a 364 LEU cc_start: 0.9208 (OUTLIER) cc_final: 0.8940 (mm) REVERT: a 379 GLU cc_start: 0.8872 (pt0) cc_final: 0.8554 (pt0) REVERT: a 414 ASP cc_start: 0.9141 (m-30) cc_final: 0.8868 (p0) REVERT: a 416 MET cc_start: 0.9389 (ttp) cc_final: 0.8876 (tmm) REVERT: b 310 ASN cc_start: 0.8483 (t0) cc_final: 0.7679 (t0) REVERT: b 379 GLU cc_start: 0.8826 (pt0) cc_final: 0.8509 (pt0) REVERT: b 412 GLU cc_start: 0.8970 (tp30) cc_final: 0.8673 (tp30) REVERT: C 103 MET cc_start: 0.9397 (tpt) cc_final: 0.9071 (tpt) REVERT: C 156 LYS cc_start: 0.8964 (mmtm) cc_final: 0.8682 (mmmm) REVERT: C 172 LEU cc_start: 0.9436 (tp) cc_final: 0.9043 (tt) REVERT: c 310 ASN cc_start: 0.8511 (t0) cc_final: 0.7551 (t0) REVERT: c 362 ARG cc_start: 0.9007 (mmm-85) cc_final: 0.8759 (mtt-85) REVERT: c 379 GLU cc_start: 0.8871 (pt0) cc_final: 0.8551 (pt0) REVERT: c 385 GLU cc_start: 0.8970 (tp30) cc_final: 0.8556 (tp30) REVERT: c 402 GLU cc_start: 0.9164 (mp0) cc_final: 0.8890 (mp0) outliers start: 12 outliers final: 6 residues processed: 159 average time/residue: 0.0834 time to fit residues: 18.4983 Evaluate side-chains 148 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 141 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain a residue 304 VAL Chi-restraints excluded: chain a residue 364 LEU Chi-restraints excluded: chain b residue 354 GLN Chi-restraints excluded: chain c residue 299 PHE Chi-restraints excluded: chain c residue 364 LEU Chi-restraints excluded: chain c residue 417 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 75 optimal weight: 5.9990 chunk 72 optimal weight: 0.9990 chunk 36 optimal weight: 9.9990 chunk 71 optimal weight: 5.9990 chunk 7 optimal weight: 0.0670 chunk 35 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 47 optimal weight: 7.9990 chunk 67 optimal weight: 9.9990 chunk 82 optimal weight: 0.0470 chunk 42 optimal weight: 6.9990 overall best weight: 2.2222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** c 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.056854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.045152 restraints weight = 32356.699| |-----------------------------------------------------------------------------| r_work (start): 0.2823 rms_B_bonded: 4.28 r_work: 0.2655 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.3872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8487 Z= 0.186 Angle : 0.700 9.309 11538 Z= 0.343 Chirality : 0.044 0.261 1374 Planarity : 0.005 0.095 1365 Dihedral : 4.530 20.130 1017 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 1.85 % Allowed : 15.97 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.28), residues: 915 helix: 1.95 (0.29), residues: 336 sheet: -0.05 (0.52), residues: 114 loop : -1.15 (0.27), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 205 TYR 0.010 0.001 TYR B 227 PHE 0.011 0.001 PHE B 245 TRP 0.008 0.001 TRP b 392 HIS 0.006 0.001 HIS C 238 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.19 ( 8424) covalent geometry : angle 0.67427 / 0.34 (11370) SS BOND : bond 0.00478 / 0.26 ( 21) SS BOND : angle 1.93266 / 1.24 ( 42) hydrogen bonds : bond 0.03438 / 2.38 ( 328) hydrogen bonds : angle 3.59646 / 2.56 ( 939) link_BETA1-4 : bond 0.00239 / 0.13 ( 18) link_BETA1-4 : angle 1.63243 / 1.36 ( 54) link_NAG-ASN : bond 0.00219 / 0.12 ( 24) link_NAG-ASN : angle 1.57119 / 1.03 ( 72) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 146 time to evaluate : 0.208 Fit side-chains revert: symmetry clash REVERT: A 78 GLU cc_start: 0.8349 (tp30) cc_final: 0.8050 (pm20) REVERT: A 103 MET cc_start: 0.9348 (tpt) cc_final: 0.8712 (tpt) REVERT: A 109 GLU cc_start: 0.9372 (tt0) cc_final: 0.8720 (tm-30) REVERT: A 256 LYS cc_start: 0.7181 (mmtt) cc_final: 0.6896 (mmtt) REVERT: a 310 ASN cc_start: 0.8796 (t0) cc_final: 0.7939 (t0) REVERT: a 353 ASP cc_start: 0.8973 (p0) cc_final: 0.8738 (p0) REVERT: a 364 LEU cc_start: 0.9263 (OUTLIER) cc_final: 0.8982 (mm) REVERT: a 379 GLU cc_start: 0.8838 (pt0) cc_final: 0.8506 (pt0) REVERT: a 414 ASP cc_start: 0.9157 (m-30) cc_final: 0.8948 (p0) REVERT: B 72 TYR cc_start: 0.8854 (m-80) cc_final: 0.8643 (m-80) REVERT: b 310 ASN cc_start: 0.8619 (t0) cc_final: 0.7674 (t0) REVERT: b 379 GLU cc_start: 0.8774 (pt0) cc_final: 0.8426 (pt0) REVERT: b 412 GLU cc_start: 0.9027 (tp30) cc_final: 0.8728 (tp30) REVERT: C 103 MET cc_start: 0.9426 (tpt) cc_final: 0.9084 (tpt) REVERT: C 156 LYS cc_start: 0.9011 (mmtm) cc_final: 0.8729 (mmmm) REVERT: C 172 LEU cc_start: 0.9524 (tp) cc_final: 0.9156 (tt) REVERT: c 310 ASN cc_start: 0.8557 (t0) cc_final: 0.7642 (t0) REVERT: c 353 ASP cc_start: 0.8750 (p0) cc_final: 0.8441 (p0) REVERT: c 362 ARG cc_start: 0.9160 (mmm-85) cc_final: 0.8923 (mtt-85) REVERT: c 379 GLU cc_start: 0.8874 (pt0) cc_final: 0.8533 (pt0) REVERT: c 402 GLU cc_start: 0.9152 (mp0) cc_final: 0.8869 (mp0) outliers start: 16 outliers final: 11 residues processed: 154 average time/residue: 0.0786 time to fit residues: 16.7452 Evaluate side-chains 153 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 141 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain a residue 304 VAL Chi-restraints excluded: chain a residue 349 SER Chi-restraints excluded: chain a residue 364 LEU Chi-restraints excluded: chain B residue 109 GLU Chi-restraints excluded: chain b residue 354 GLN Chi-restraints excluded: chain C residue 193 ASP Chi-restraints excluded: chain c residue 299 PHE Chi-restraints excluded: chain c residue 347 VAL Chi-restraints excluded: chain c residue 349 SER Chi-restraints excluded: chain c residue 364 LEU Chi-restraints excluded: chain c residue 417 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 0 optimal weight: 8.9990 chunk 87 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 47 optimal weight: 7.9990 chunk 10 optimal weight: 6.9990 chunk 31 optimal weight: 8.9990 chunk 43 optimal weight: 7.9990 chunk 11 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** c 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.056221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.044430 restraints weight = 31978.548| |-----------------------------------------------------------------------------| r_work (start): 0.2806 rms_B_bonded: 4.27 r_work: 0.2637 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.2637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.4026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8487 Z= 0.203 Angle : 0.733 9.301 11538 Z= 0.357 Chirality : 0.044 0.246 1374 Planarity : 0.004 0.063 1365 Dihedral : 4.619 19.769 1017 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 1.85 % Allowed : 16.32 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.28), residues: 915 helix: 1.88 (0.29), residues: 336 sheet: 0.10 (0.53), residues: 114 loop : -1.27 (0.27), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG c 358 TYR 0.009 0.001 TYR A 227 PHE 0.013 0.001 PHE B 245 TRP 0.008 0.001 TRP c 392 HIS 0.005 0.001 HIS c 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.20 ( 8424) covalent geometry : angle 0.70684 / 0.35 (11370) SS BOND : bond 0.00472 / 0.26 ( 21) SS BOND : angle 2.13182 / 1.37 ( 42) hydrogen bonds : bond 0.03615 / 2.52 ( 328) hydrogen bonds : angle 3.66106 / 2.61 ( 939) link_BETA1-4 : bond 0.00280 / 0.16 ( 18) link_BETA1-4 : angle 1.62840 / 1.36 ( 54) link_NAG-ASN : bond 0.00229 / 0.13 ( 24) link_NAG-ASN : angle 1.62385 / 1.07 ( 72) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 144 time to evaluate : 0.301 Fit side-chains REVERT: A 78 GLU cc_start: 0.8347 (tp30) cc_final: 0.8052 (pm20) REVERT: A 103 MET cc_start: 0.9369 (tpt) cc_final: 0.8656 (tpt) REVERT: A 109 GLU cc_start: 0.9386 (tt0) cc_final: 0.8730 (tm-30) REVERT: A 139 MET cc_start: 0.9001 (tpp) cc_final: 0.8278 (ttt) REVERT: A 256 LYS cc_start: 0.7277 (mmtt) cc_final: 0.7011 (mmtt) REVERT: a 310 ASN cc_start: 0.8844 (t0) cc_final: 0.8002 (t0) REVERT: a 354 GLN cc_start: 0.8887 (pt0) cc_final: 0.8657 (mt0) REVERT: a 364 LEU cc_start: 0.9265 (OUTLIER) cc_final: 0.8983 (mm) REVERT: a 379 GLU cc_start: 0.8855 (pt0) cc_final: 0.8541 (pt0) REVERT: a 416 MET cc_start: 0.9432 (ttp) cc_final: 0.9104 (tmm) REVERT: b 310 ASN cc_start: 0.8691 (t0) cc_final: 0.7806 (t0) REVERT: b 379 GLU cc_start: 0.8806 (pt0) cc_final: 0.8474 (pt0) REVERT: b 412 GLU cc_start: 0.9030 (tp30) cc_final: 0.8745 (tp30) REVERT: C 78 GLU cc_start: 0.7942 (pm20) cc_final: 0.7105 (pm20) REVERT: C 103 MET cc_start: 0.9424 (tpt) cc_final: 0.9001 (tpt) REVERT: C 156 LYS cc_start: 0.9039 (mmtm) cc_final: 0.8752 (mmmm) REVERT: C 172 LEU cc_start: 0.9543 (tp) cc_final: 0.9174 (tt) REVERT: c 310 ASN cc_start: 0.8608 (t0) cc_final: 0.7704 (t0) REVERT: c 353 ASP cc_start: 0.8763 (p0) cc_final: 0.8426 (p0) REVERT: c 362 ARG cc_start: 0.9192 (mmm-85) cc_final: 0.8894 (mtt-85) REVERT: c 379 GLU cc_start: 0.8892 (pt0) cc_final: 0.8556 (pt0) REVERT: c 385 GLU cc_start: 0.9023 (tp30) cc_final: 0.8597 (tp30) outliers start: 16 outliers final: 10 residues processed: 153 average time/residue: 0.0796 time to fit residues: 16.7294 Evaluate side-chains 151 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 140 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain a residue 304 VAL Chi-restraints excluded: chain a residue 349 SER Chi-restraints excluded: chain a residue 364 LEU Chi-restraints excluded: chain b residue 354 GLN Chi-restraints excluded: chain b residue 364 LEU Chi-restraints excluded: chain c residue 299 PHE Chi-restraints excluded: chain c residue 347 VAL Chi-restraints excluded: chain c residue 349 SER Chi-restraints excluded: chain c residue 364 LEU Chi-restraints excluded: chain c residue 417 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 77 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 27 optimal weight: 10.0000 chunk 23 optimal weight: 4.9990 chunk 3 optimal weight: 6.9990 chunk 25 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 44 optimal weight: 0.1980 chunk 86 optimal weight: 3.9990 chunk 62 optimal weight: 8.9990 chunk 6 optimal weight: 0.0980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** c 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.057039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.045346 restraints weight = 32023.520| |-----------------------------------------------------------------------------| r_work (start): 0.2831 rms_B_bonded: 4.26 r_work: 0.2662 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.4098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8487 Z= 0.144 Angle : 0.721 10.366 11538 Z= 0.351 Chirality : 0.044 0.247 1374 Planarity : 0.004 0.056 1365 Dihedral : 4.572 21.211 1017 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 1.50 % Allowed : 16.67 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.28), residues: 915 helix: 1.85 (0.29), residues: 336 sheet: 0.14 (0.53), residues: 114 loop : -1.27 (0.27), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG c 358 TYR 0.018 0.001 TYR B 72 PHE 0.009 0.001 PHE B 245 TRP 0.006 0.001 TRP B 219 HIS 0.007 0.001 HIS B 238 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 ( 8424) covalent geometry : angle 0.69629 / 0.34 (11370) SS BOND : bond 0.00375 / 0.21 ( 21) SS BOND : angle 1.93327 / 1.26 ( 42) hydrogen bonds : bond 0.03284 / 2.30 ( 328) hydrogen bonds : angle 3.56632 / 2.55 ( 939) link_BETA1-4 : bond 0.00325 / 0.18 ( 18) link_BETA1-4 : angle 1.63209 / 1.40 ( 54) link_NAG-ASN : bond 0.00342 / 0.19 ( 24) link_NAG-ASN : angle 1.57490 / 1.06 ( 72) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 142 time to evaluate : 0.222 Fit side-chains revert: symmetry clash REVERT: A 103 MET cc_start: 0.9324 (tpt) cc_final: 0.8654 (tpt) REVERT: A 109 GLU cc_start: 0.9375 (tt0) cc_final: 0.8726 (tm-30) REVERT: A 139 MET cc_start: 0.8956 (tpp) cc_final: 0.8236 (ttt) REVERT: a 310 ASN cc_start: 0.8777 (t0) cc_final: 0.7962 (t0) REVERT: a 354 GLN cc_start: 0.8857 (OUTLIER) cc_final: 0.8628 (mt0) REVERT: a 364 LEU cc_start: 0.9227 (OUTLIER) cc_final: 0.8918 (mm) REVERT: a 379 GLU cc_start: 0.8889 (pt0) cc_final: 0.8560 (pt0) REVERT: a 416 MET cc_start: 0.9443 (ttp) cc_final: 0.9167 (ppp) REVERT: b 310 ASN cc_start: 0.8686 (t0) cc_final: 0.7825 (t0) REVERT: b 379 GLU cc_start: 0.8819 (pt0) cc_final: 0.8487 (pt0) REVERT: b 412 GLU cc_start: 0.9000 (tp30) cc_final: 0.8716 (tp30) REVERT: C 103 MET cc_start: 0.9397 (tpt) cc_final: 0.9022 (tpt) REVERT: C 156 LYS cc_start: 0.9021 (mmtm) cc_final: 0.8750 (mmmm) REVERT: C 172 LEU cc_start: 0.9516 (tp) cc_final: 0.9159 (tt) REVERT: c 310 ASN cc_start: 0.8597 (t0) cc_final: 0.7717 (t0) REVERT: c 379 GLU cc_start: 0.8912 (pt0) cc_final: 0.8560 (pt0) REVERT: c 385 GLU cc_start: 0.8962 (tp30) cc_final: 0.8523 (tp30) outliers start: 13 outliers final: 9 residues processed: 148 average time/residue: 0.0733 time to fit residues: 14.9581 Evaluate side-chains 148 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 137 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain a residue 304 VAL Chi-restraints excluded: chain a residue 349 SER Chi-restraints excluded: chain a residue 354 GLN Chi-restraints excluded: chain a residue 364 LEU Chi-restraints excluded: chain B residue 109 GLU Chi-restraints excluded: chain b residue 364 LEU Chi-restraints excluded: chain c residue 299 PHE Chi-restraints excluded: chain c residue 349 SER Chi-restraints excluded: chain c residue 364 LEU Chi-restraints excluded: chain c residue 417 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 53 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 11 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 chunk 74 optimal weight: 7.9990 chunk 2 optimal weight: 0.9990 chunk 29 optimal weight: 8.9990 chunk 82 optimal weight: 6.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 183 GLN ** c 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.055850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.044282 restraints weight = 31578.094| |-----------------------------------------------------------------------------| r_work (start): 0.2799 rms_B_bonded: 4.19 r_work: 0.2632 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.2632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.4244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 8487 Z= 0.210 Angle : 0.782 11.067 11538 Z= 0.380 Chirality : 0.045 0.244 1374 Planarity : 0.004 0.063 1365 Dihedral : 4.734 25.755 1017 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 1.50 % Allowed : 17.01 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.28), residues: 915 helix: 1.79 (0.29), residues: 336 sheet: 0.27 (0.54), residues: 114 loop : -1.38 (0.27), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG c 358 TYR 0.012 0.001 TYR c 284 PHE 0.013 0.001 PHE B 245 TRP 0.008 0.001 TRP a 392 HIS 0.010 0.001 HIS B 238 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.21 ( 8424) covalent geometry : angle 0.75672 / 0.37 (11370) SS BOND : bond 0.00492 / 0.27 ( 21) SS BOND : angle 2.12864 / 1.38 ( 42) hydrogen bonds : bond 0.03679 / 2.57 ( 328) hydrogen bonds : angle 3.69113 / 2.64 ( 939) link_BETA1-4 : bond 0.00256 / 0.14 ( 18) link_BETA1-4 : angle 1.71728 / 1.44 ( 54) link_NAG-ASN : bond 0.00227 / 0.12 ( 24) link_NAG-ASN : angle 1.62041 / 1.07 ( 72) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 140 time to evaluate : 0.284 Fit side-chains revert: symmetry clash REVERT: A 78 GLU cc_start: 0.8363 (tp30) cc_final: 0.8069 (pm20) REVERT: A 103 MET cc_start: 0.9349 (tpt) cc_final: 0.8709 (tpt) REVERT: A 109 GLU cc_start: 0.9382 (tt0) cc_final: 0.8714 (tm-30) REVERT: A 139 MET cc_start: 0.8967 (tpp) cc_final: 0.8228 (ttt) REVERT: a 310 ASN cc_start: 0.8879 (t0) cc_final: 0.8054 (t0) REVERT: a 354 GLN cc_start: 0.8867 (OUTLIER) cc_final: 0.8667 (mt0) REVERT: a 364 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.8954 (mm) REVERT: a 416 MET cc_start: 0.9448 (ttp) cc_final: 0.9229 (ppp) REVERT: B 72 TYR cc_start: 0.8898 (m-80) cc_final: 0.8679 (m-80) REVERT: B 256 LYS cc_start: 0.7554 (mptt) cc_final: 0.6664 (mptt) REVERT: b 310 ASN cc_start: 0.8752 (t0) cc_final: 0.7925 (t0) REVERT: b 412 GLU cc_start: 0.9039 (tp30) cc_final: 0.8756 (tp30) REVERT: b 416 MET cc_start: 0.9486 (ttp) cc_final: 0.9212 (tmm) REVERT: C 78 GLU cc_start: 0.7779 (pm20) cc_final: 0.6972 (pm20) REVERT: C 103 MET cc_start: 0.9422 (tpt) cc_final: 0.9042 (tpt) REVERT: C 156 LYS cc_start: 0.9082 (mmtm) cc_final: 0.8803 (mmmm) REVERT: C 172 LEU cc_start: 0.9540 (tp) cc_final: 0.9193 (tt) REVERT: c 310 ASN cc_start: 0.8603 (t0) cc_final: 0.7751 (t0) REVERT: c 379 GLU cc_start: 0.8883 (pt0) cc_final: 0.8528 (pt0) REVERT: c 385 GLU cc_start: 0.8997 (tp30) cc_final: 0.8571 (tp30) outliers start: 13 outliers final: 11 residues processed: 147 average time/residue: 0.0712 time to fit residues: 14.5576 Evaluate side-chains 150 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 137 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain a residue 304 VAL Chi-restraints excluded: chain a residue 349 SER Chi-restraints excluded: chain a residue 354 GLN Chi-restraints excluded: chain a residue 364 LEU Chi-restraints excluded: chain B residue 109 GLU Chi-restraints excluded: chain b residue 354 GLN Chi-restraints excluded: chain b residue 364 LEU Chi-restraints excluded: chain c residue 299 PHE Chi-restraints excluded: chain c residue 347 VAL Chi-restraints excluded: chain c residue 349 SER Chi-restraints excluded: chain c residue 364 LEU Chi-restraints excluded: chain c residue 417 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 20 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 9 optimal weight: 5.9990 chunk 72 optimal weight: 4.9990 chunk 61 optimal weight: 0.9990 chunk 85 optimal weight: 4.9990 chunk 49 optimal weight: 0.5980 chunk 80 optimal weight: 0.8980 chunk 19 optimal weight: 6.9990 chunk 54 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** c 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.057074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.045456 restraints weight = 31644.302| |-----------------------------------------------------------------------------| r_work (start): 0.2834 rms_B_bonded: 4.25 r_work: 0.2665 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.4275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8487 Z= 0.144 Angle : 0.746 10.026 11538 Z= 0.366 Chirality : 0.044 0.246 1374 Planarity : 0.004 0.052 1365 Dihedral : 4.664 28.896 1017 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.62 % Allowed : 16.55 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.28), residues: 915 helix: 1.77 (0.29), residues: 336 sheet: 0.28 (0.54), residues: 114 loop : -1.34 (0.27), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG c 358 TYR 0.020 0.001 TYR A 72 PHE 0.008 0.001 PHE C 245 TRP 0.007 0.001 TRP B 219 HIS 0.007 0.001 HIS B 238 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 ( 8424) covalent geometry : angle 0.72268 / 0.36 (11370) SS BOND : bond 0.00354 / 0.20 ( 21) SS BOND : angle 1.89652 / 1.23 ( 42) hydrogen bonds : bond 0.03223 / 2.27 ( 328) hydrogen bonds : angle 3.56031 / 2.55 ( 939) link_BETA1-4 : bond 0.00340 / 0.19 ( 18) link_BETA1-4 : angle 1.64634 / 1.43 ( 54) link_NAG-ASN : bond 0.00384 / 0.21 ( 24) link_NAG-ASN : angle 1.57517 / 1.07 ( 72) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1364.45 seconds wall clock time: 24 minutes 20.04 seconds (1460.04 seconds total)