Starting phenix.real_space_refine on Tue Mar 3 19:11:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dmi_27539/03_2026/8dmi_27539.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dmi_27539/03_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_27539/03_2026/8dmi_27539.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dmi_27539/03_2026/8dmi_27539.map" model { file = "/net/cci-nas-00/data/ceres_data/8dmi_27539/03_2026/8dmi_27539.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dmi_27539/03_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-5986/lib/python3.9/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 dihedrals: 6 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 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: 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: "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: 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: "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: 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: "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: 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: "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: "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 dihedrals: 3 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 dihedrals: 3 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 dihedrals: 3 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 dihedrals: 3 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 dihedrals: 3 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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.88, per 1000 atoms: 0.23 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: 0.68 Conformation dependent library (CDL) restraints added in 209.4 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: 0.22 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: 1.18 Time building geometry restraints manager: 0.87 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: 4872 16.99 - 33.98: 509 33.98 - 50.97: 126 50.97 - 67.96: 55 67.96 - 84.96: 9 Dihedral angle restraints: 5571 sinusoidal: 2772 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 5568 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: 0.01 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: 0.000 Normalize map: mean=0, sd=1: 0.860 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.060 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 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 : 14.468 68.731 3690 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 covalent geometry : bond 0.00391 ( 8424) covalent geometry : angle 0.81468 (11370) SS BOND : bond 0.01059 ( 21) SS BOND : angle 4.44360 ( 42) hydrogen bonds : bond 0.14553 ( 328) hydrogen bonds : angle 5.00084 ( 939) link_BETA1-4 : bond 0.00760 ( 18) link_BETA1-4 : angle 1.83548 ( 54) link_NAG-ASN : bond 0.02360 ( 24) link_NAG-ASN : angle 2.58800 ( 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 : 0.319 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 206 average time/residue: 0.1081 time to fit residues: 28.8683 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 : 0.225 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3224 r_free = 0.3224 target = 0.058948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.046856 restraints weight = 31759.672| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 4.30 r_work: 0.2710 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 8487 Z= 0.227 Angle : 0.754 9.509 11538 Z= 0.376 Chirality : 0.046 0.237 1374 Planarity : 0.004 0.033 1365 Dihedral : 9.243 56.995 1899 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 1.04 % Allowed : 9.72 % Favored : 89.24 % 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: -0.29 (0.27), residues: 915 helix: 1.48 (0.28), residues: 357 sheet: 0.19 (0.55), residues: 93 loop : -1.71 (0.26), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG c 358 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 covalent geometry : bond 0.00493 ( 8424) covalent geometry : angle 0.72618 (11370) SS BOND : bond 0.00537 ( 21) SS BOND : angle 2.04672 ( 42) hydrogen bonds : bond 0.04191 ( 328) hydrogen bonds : angle 4.09773 ( 939) link_BETA1-4 : bond 0.00430 ( 18) link_BETA1-4 : angle 1.64394 ( 54) link_NAG-ASN : bond 0.00276 ( 24) link_NAG-ASN : angle 1.83907 ( 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 165 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 156 time to evaluate : 0.298 Fit side-chains REVERT: A 72 TYR cc_start: 0.8933 (m-80) cc_final: 0.8598 (m-80) REVERT: A 103 MET cc_start: 0.9416 (tpt) cc_final: 0.9033 (tpt) REVERT: A 183 GLN cc_start: 0.7443 (mm110) cc_final: 0.7184 (mm110) REVERT: a 310 ASN cc_start: 0.8448 (t0) cc_final: 0.7348 (t0) REVERT: a 313 GLU cc_start: 0.8223 (mp0) cc_final: 0.7512 (mp0) REVERT: a 412 GLU cc_start: 0.8982 (tp30) cc_final: 0.8660 (tp30) REVERT: a 414 ASP cc_start: 0.9139 (m-30) cc_final: 0.8835 (p0) REVERT: B 72 TYR cc_start: 0.9120 (m-80) cc_final: 0.8822 (m-80) REVERT: b 310 ASN cc_start: 0.8163 (t0) cc_final: 0.7341 (t0) REVERT: b 412 GLU cc_start: 0.8972 (tp30) cc_final: 0.8683 (tp30) REVERT: b 416 MET cc_start: 0.9437 (ttp) cc_final: 0.9152 (ttp) REVERT: C 103 MET cc_start: 0.9402 (tpt) cc_final: 0.9138 (tpp) REVERT: C 183 GLN cc_start: 0.7566 (mm110) cc_final: 0.7344 (mm110) REVERT: c 310 ASN cc_start: 0.8220 (t0) cc_final: 0.7081 (t0) REVERT: c 353 ASP cc_start: 0.8930 (p0) cc_final: 0.8722 (p0) REVERT: c 357 MET cc_start: 0.9554 (mmt) cc_final: 0.9309 (mmm) REVERT: c 402 GLU cc_start: 0.9023 (mp0) cc_final: 0.8821 (mp0) outliers start: 9 outliers final: 5 residues processed: 161 average time/residue: 0.0921 time to fit residues: 20.2988 Evaluate side-chains 145 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 140 time to evaluate : 0.303 ------------------------------------------------------------------------------- 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: 0.9990 chunk 79 optimal weight: 3.9990 chunk 76 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 3 optimal weight: 9.9990 chunk 1 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 34 optimal weight: 9.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN C 164 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.058222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.046286 restraints weight = 31423.256| |-----------------------------------------------------------------------------| r_work (start): 0.2866 rms_B_bonded: 4.24 r_work: 0.2698 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.3019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8487 Z= 0.172 Angle : 0.667 9.466 11538 Z= 0.335 Chirality : 0.045 0.242 1374 Planarity : 0.003 0.027 1365 Dihedral : 8.393 56.908 1899 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.16 % Allowed : 11.46 % Favored : 87.38 % 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: 1.75 (0.29), residues: 339 sheet: 0.43 (0.58), residues: 93 loop : -1.34 (0.27), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG b 362 TYR 0.016 0.001 TYR A 227 PHE 0.015 0.001 PHE B 245 TRP 0.009 0.001 TRP b 392 HIS 0.006 0.001 HIS A 238 Details of bonding type rmsd covalent geometry : bond 0.00372 ( 8424) covalent geometry : angle 0.64043 (11370) SS BOND : bond 0.00413 ( 21) SS BOND : angle 1.82702 ( 42) hydrogen bonds : bond 0.03805 ( 328) hydrogen bonds : angle 3.85445 ( 939) link_BETA1-4 : bond 0.00306 ( 18) link_BETA1-4 : angle 1.54632 ( 54) link_NAG-ASN : bond 0.00377 ( 24) link_NAG-ASN : angle 1.66013 ( 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 164 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 154 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 103 MET cc_start: 0.9351 (tpt) cc_final: 0.8695 (tpt) REVERT: A 139 MET cc_start: 0.8919 (tpp) cc_final: 0.8639 (tmm) REVERT: A 156 LYS cc_start: 0.8996 (mmmm) cc_final: 0.8600 (mmmm) REVERT: A 256 LYS cc_start: 0.7392 (mmtt) cc_final: 0.7172 (mmtm) REVERT: a 310 ASN cc_start: 0.8608 (t0) cc_final: 0.7445 (t0) REVERT: a 313 GLU cc_start: 0.8413 (mp0) cc_final: 0.7698 (mp0) REVERT: a 412 GLU cc_start: 0.9005 (tp30) cc_final: 0.8750 (tp30) REVERT: a 414 ASP cc_start: 0.9150 (m-30) cc_final: 0.8898 (p0) REVERT: B 72 TYR cc_start: 0.9102 (m-80) cc_final: 0.8721 (m-80) REVERT: B 168 ILE cc_start: 0.9566 (mt) cc_final: 0.9366 (mm) REVERT: B 222 GLN cc_start: 0.9221 (mm-40) cc_final: 0.9010 (mm-40) REVERT: b 310 ASN cc_start: 0.8315 (t0) cc_final: 0.7570 (t0) REVERT: b 323 ASP cc_start: 0.9321 (t0) cc_final: 0.9119 (t0) REVERT: b 412 GLU cc_start: 0.8942 (tp30) cc_final: 0.8678 (tp30) REVERT: b 416 MET cc_start: 0.9418 (ttp) cc_final: 0.9097 (ttp) REVERT: C 103 MET cc_start: 0.9424 (tpt) cc_final: 0.9081 (tpt) REVERT: C 156 LYS cc_start: 0.8977 (mmmm) cc_final: 0.8740 (mmmm) REVERT: c 310 ASN cc_start: 0.8295 (t0) cc_final: 0.7277 (t0) REVERT: c 353 ASP cc_start: 0.8904 (p0) cc_final: 0.8578 (p0) REVERT: c 357 MET cc_start: 0.9554 (mmt) cc_final: 0.9307 (mmm) REVERT: c 362 ARG cc_start: 0.9005 (mmm-85) cc_final: 0.8787 (mtt-85) REVERT: c 402 GLU cc_start: 0.9085 (mp0) cc_final: 0.8848 (mp0) outliers start: 10 outliers final: 6 residues processed: 156 average time/residue: 0.0871 time to fit residues: 18.4270 Evaluate side-chains 150 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 144 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 GLU 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 36 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 92 optimal weight: 10.0000 chunk 89 optimal weight: 9.9990 chunk 71 optimal weight: 5.9990 chunk 6 optimal weight: 5.9990 chunk 49 optimal weight: 6.9990 chunk 70 optimal weight: 0.8980 chunk 83 optimal weight: 5.9990 chunk 67 optimal weight: 0.9980 chunk 82 optimal weight: 0.9980 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 164 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.057746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.045900 restraints weight = 32102.829| |-----------------------------------------------------------------------------| r_work (start): 0.2842 rms_B_bonded: 4.26 r_work: 0.2674 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.3321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8487 Z= 0.183 Angle : 0.688 9.449 11538 Z= 0.342 Chirality : 0.045 0.247 1374 Planarity : 0.004 0.053 1365 Dihedral : 8.014 57.376 1899 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 1.85 % Allowed : 11.92 % Favored : 86.23 % 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: 0.14 (0.28), residues: 915 helix: 1.85 (0.29), residues: 339 sheet: 0.40 (0.59), residues: 96 loop : -1.34 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 205 TYR 0.021 0.001 TYR A 72 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 covalent geometry : bond 0.00399 ( 8424) covalent geometry : angle 0.65986 (11370) SS BOND : bond 0.00463 ( 21) SS BOND : angle 2.04601 ( 42) hydrogen bonds : bond 0.03628 ( 328) hydrogen bonds : angle 3.70857 ( 939) link_BETA1-4 : bond 0.00333 ( 18) link_BETA1-4 : angle 1.54424 ( 54) link_NAG-ASN : bond 0.00268 ( 24) link_NAG-ASN : angle 1.70275 ( 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 : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.9189 (mtp) cc_final: 0.8984 (mtp) REVERT: A 103 MET cc_start: 0.9363 (tpt) cc_final: 0.8669 (tpt) REVERT: A 109 GLU cc_start: 0.9331 (OUTLIER) cc_final: 0.8658 (tm-30) REVERT: A 156 LYS cc_start: 0.9044 (mmmm) cc_final: 0.8661 (mmmm) REVERT: A 256 LYS cc_start: 0.7298 (mmtt) cc_final: 0.7064 (mmtm) REVERT: a 310 ASN cc_start: 0.8586 (t0) cc_final: 0.7419 (t0) REVERT: a 313 GLU cc_start: 0.8408 (mp0) cc_final: 0.7642 (mp0) REVERT: a 364 LEU cc_start: 0.9208 (OUTLIER) cc_final: 0.8989 (mm) REVERT: a 412 GLU cc_start: 0.9005 (tp30) cc_final: 0.8761 (tp30) REVERT: a 416 MET cc_start: 0.9472 (ttp) cc_final: 0.9095 (tmm) REVERT: b 310 ASN cc_start: 0.8322 (t0) cc_final: 0.7543 (t0) REVERT: b 323 ASP cc_start: 0.9369 (t0) cc_final: 0.9141 (t0) REVERT: b 412 GLU cc_start: 0.9029 (tp30) cc_final: 0.8742 (tp30) REVERT: C 103 MET cc_start: 0.9427 (tpt) cc_final: 0.9034 (tpt) REVERT: C 156 LYS cc_start: 0.9028 (mmmm) cc_final: 0.8749 (mmmm) REVERT: c 310 ASN cc_start: 0.8380 (t0) cc_final: 0.7377 (t0) REVERT: c 313 GLU cc_start: 0.8511 (mp0) cc_final: 0.7796 (mp0) REVERT: c 353 ASP cc_start: 0.8891 (p0) cc_final: 0.8650 (p0) REVERT: c 362 ARG cc_start: 0.9052 (mmm-85) cc_final: 0.8819 (mtt-85) REVERT: c 372 TYR cc_start: 0.9255 (m-80) cc_final: 0.9050 (m-80) REVERT: c 402 GLU cc_start: 0.9147 (mp0) cc_final: 0.8891 (mp0) outliers start: 16 outliers final: 8 residues processed: 154 average time/residue: 0.0887 time to fit residues: 18.5003 Evaluate side-chains 151 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 141 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 GLU 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 304 VAL Chi-restraints excluded: chain b residue 349 SER Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 193 ASP Chi-restraints excluded: chain c residue 299 PHE Chi-restraints excluded: chain c residue 364 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 91 optimal weight: 2.9990 chunk 86 optimal weight: 0.1980 chunk 49 optimal weight: 4.9990 chunk 70 optimal weight: 9.9990 chunk 0 optimal weight: 8.9990 chunk 27 optimal weight: 5.9990 chunk 17 optimal weight: 6.9990 chunk 60 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 88 optimal weight: 6.9990 chunk 83 optimal weight: 0.8980 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 183 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.057344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.045538 restraints weight = 31887.194| |-----------------------------------------------------------------------------| r_work (start): 0.2834 rms_B_bonded: 4.25 r_work: 0.2663 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.3628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8487 Z= 0.183 Angle : 0.698 10.640 11538 Z= 0.342 Chirality : 0.045 0.244 1374 Planarity : 0.003 0.029 1365 Dihedral : 7.676 57.319 1899 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 2.43 % Allowed : 13.19 % Favored : 84.38 % 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: 0.15 (0.28), residues: 915 helix: 1.91 (0.29), residues: 336 sheet: 0.54 (0.60), residues: 96 loop : -1.39 (0.27), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG c 358 TYR 0.012 0.001 TYR B 227 PHE 0.015 0.001 PHE B 245 TRP 0.008 0.001 TRP a 392 HIS 0.005 0.001 HIS c 311 Details of bonding type rmsd covalent geometry : bond 0.00398 ( 8424) covalent geometry : angle 0.66820 (11370) SS BOND : bond 0.00459 ( 21) SS BOND : angle 2.08980 ( 42) hydrogen bonds : bond 0.03600 ( 328) hydrogen bonds : angle 3.70432 ( 939) link_BETA1-4 : bond 0.00289 ( 18) link_BETA1-4 : angle 1.59844 ( 54) link_NAG-ASN : bond 0.00283 ( 24) link_NAG-ASN : angle 1.72968 ( 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 170 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 149 time to evaluate : 0.313 Fit side-chains revert: symmetry clash REVERT: A 88 MET cc_start: 0.9219 (OUTLIER) cc_final: 0.8954 (mtt) REVERT: A 103 MET cc_start: 0.9386 (tpt) cc_final: 0.8669 (tpt) REVERT: A 109 GLU cc_start: 0.9366 (OUTLIER) cc_final: 0.8701 (tm-30) REVERT: A 139 MET cc_start: 0.8895 (tpp) cc_final: 0.8594 (tmm) REVERT: a 290 MET cc_start: 0.9046 (mtt) cc_final: 0.8814 (mtt) REVERT: a 310 ASN cc_start: 0.8660 (t0) cc_final: 0.7522 (t0) REVERT: a 313 GLU cc_start: 0.8494 (mp0) cc_final: 0.7723 (mp0) REVERT: a 364 LEU cc_start: 0.9241 (OUTLIER) cc_final: 0.9004 (mm) REVERT: a 379 GLU cc_start: 0.8869 (pt0) cc_final: 0.8564 (pt0) REVERT: a 412 GLU cc_start: 0.9018 (tp30) cc_final: 0.8776 (tp30) REVERT: a 414 ASP cc_start: 0.9160 (m-30) cc_final: 0.8874 (p0) REVERT: a 416 MET cc_start: 0.9393 (ttp) cc_final: 0.9007 (tmm) REVERT: B 72 TYR cc_start: 0.9138 (m-80) cc_final: 0.8870 (m-80) REVERT: b 310 ASN cc_start: 0.8446 (t0) cc_final: 0.7696 (t0) REVERT: b 323 ASP cc_start: 0.9399 (t0) cc_final: 0.9151 (t0) REVERT: b 412 GLU cc_start: 0.9056 (tp30) cc_final: 0.8797 (tp30) REVERT: C 103 MET cc_start: 0.9427 (tpt) cc_final: 0.9031 (tpt) REVERT: C 156 LYS cc_start: 0.9043 (mmmm) cc_final: 0.8706 (mmmm) REVERT: C 172 LEU cc_start: 0.9528 (tp) cc_final: 0.9105 (tt) REVERT: c 310 ASN cc_start: 0.8470 (t0) cc_final: 0.7400 (t0) REVERT: c 313 GLU cc_start: 0.8594 (mp0) cc_final: 0.7855 (mp0) REVERT: c 353 ASP cc_start: 0.8901 (p0) cc_final: 0.8688 (p0) REVERT: c 362 ARG cc_start: 0.9065 (mmm-85) cc_final: 0.8820 (mtt-85) REVERT: c 379 GLU cc_start: 0.8842 (pt0) cc_final: 0.8369 (pt0) REVERT: c 385 GLU cc_start: 0.9042 (tp30) cc_final: 0.8647 (tp30) REVERT: c 402 GLU cc_start: 0.9152 (mp0) cc_final: 0.8895 (mp0) outliers start: 21 outliers final: 12 residues processed: 158 average time/residue: 0.0806 time to fit residues: 17.5897 Evaluate side-chains 156 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 141 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 MET 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 172 LEU Chi-restraints excluded: chain b residue 304 VAL Chi-restraints excluded: chain b residue 349 SER Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 193 ASP Chi-restraints excluded: chain c residue 299 PHE Chi-restraints excluded: chain c residue 351 ILE 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: 1.9990 chunk 88 optimal weight: 6.9990 chunk 49 optimal weight: 6.9990 chunk 51 optimal weight: 4.9990 chunk 44 optimal weight: 6.9990 chunk 70 optimal weight: 10.0000 chunk 75 optimal weight: 4.9990 chunk 63 optimal weight: 0.9980 chunk 60 optimal weight: 7.9990 chunk 47 optimal weight: 0.5980 chunk 1 optimal weight: 2.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.3166 r_free = 0.3166 target = 0.056682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.044976 restraints weight = 31893.346| |-----------------------------------------------------------------------------| r_work (start): 0.2818 rms_B_bonded: 4.24 r_work: 0.2649 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.3810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8487 Z= 0.190 Angle : 0.704 9.431 11538 Z= 0.347 Chirality : 0.045 0.239 1374 Planarity : 0.004 0.079 1365 Dihedral : 7.560 57.275 1899 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 2.78 % Allowed : 14.00 % Favored : 83.22 % 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: 1.87 (0.29), residues: 336 sheet: 0.08 (0.54), residues: 114 loop : -1.28 (0.27), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 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 219 HIS 0.007 0.001 HIS C 238 Details of bonding type rmsd covalent geometry : bond 0.00417 ( 8424) covalent geometry : angle 0.67481 (11370) SS BOND : bond 0.00470 ( 21) SS BOND : angle 2.07068 ( 42) hydrogen bonds : bond 0.03581 ( 328) hydrogen bonds : angle 3.68791 ( 939) link_BETA1-4 : bond 0.00323 ( 18) link_BETA1-4 : angle 1.60706 ( 54) link_NAG-ASN : bond 0.00256 ( 24) link_NAG-ASN : angle 1.74356 ( 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 170 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 146 time to evaluate : 0.293 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 GLU cc_start: 0.8308 (tp30) cc_final: 0.8044 (pm20) REVERT: A 103 MET cc_start: 0.9376 (tpt) cc_final: 0.8606 (tpt) REVERT: A 109 GLU cc_start: 0.9369 (OUTLIER) cc_final: 0.8720 (tm-30) REVERT: a 290 MET cc_start: 0.9121 (mtt) cc_final: 0.8912 (mtt) REVERT: a 310 ASN cc_start: 0.8716 (t0) cc_final: 0.7649 (t0) REVERT: a 313 GLU cc_start: 0.8528 (mp0) cc_final: 0.7734 (mp0) REVERT: a 364 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.8999 (mm) REVERT: a 379 GLU cc_start: 0.8867 (pt0) cc_final: 0.8549 (pt0) REVERT: a 412 GLU cc_start: 0.9037 (tp30) cc_final: 0.8773 (tp30) REVERT: a 416 MET cc_start: 0.9380 (ttp) cc_final: 0.9035 (tmm) REVERT: b 310 ASN cc_start: 0.8567 (t0) cc_final: 0.7721 (t0) REVERT: b 323 ASP cc_start: 0.9415 (t0) cc_final: 0.9154 (t0) REVERT: b 379 GLU cc_start: 0.8778 (pt0) cc_final: 0.8451 (pt0) REVERT: b 412 GLU cc_start: 0.9016 (tp30) cc_final: 0.8728 (tp30) REVERT: C 103 MET cc_start: 0.9433 (tpt) cc_final: 0.8999 (tpt) REVERT: C 156 LYS cc_start: 0.9071 (mmmm) cc_final: 0.8727 (mmmm) REVERT: C 172 LEU cc_start: 0.9536 (tp) cc_final: 0.9135 (tt) REVERT: c 310 ASN cc_start: 0.8511 (t0) cc_final: 0.7443 (t0) REVERT: c 379 GLU cc_start: 0.8851 (pt0) cc_final: 0.8517 (pt0) REVERT: c 385 GLU cc_start: 0.9006 (tp30) cc_final: 0.8615 (tp30) REVERT: c 402 GLU cc_start: 0.9158 (mp0) cc_final: 0.8894 (mp0) outliers start: 24 outliers final: 15 residues processed: 155 average time/residue: 0.0855 time to fit residues: 18.2978 Evaluate side-chains 160 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 143 time to evaluate : 0.242 ------------------------------------------------------------------------------- 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 349 SER Chi-restraints excluded: chain a residue 364 LEU Chi-restraints excluded: chain B residue 109 GLU Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain b residue 349 SER Chi-restraints excluded: chain b residue 354 GLN Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 193 ASP 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 416 MET 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: 9.9990 chunk 72 optimal weight: 2.9990 chunk 36 optimal weight: 20.0000 chunk 71 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 chunk 67 optimal weight: 9.9990 chunk 82 optimal weight: 8.9990 chunk 42 optimal weight: 6.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.055105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.043287 restraints weight = 32672.377| |-----------------------------------------------------------------------------| r_work (start): 0.2766 rms_B_bonded: 4.29 r_work: 0.2594 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.2594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.4128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 8487 Z= 0.279 Angle : 0.784 9.320 11538 Z= 0.382 Chirality : 0.046 0.236 1374 Planarity : 0.004 0.042 1365 Dihedral : 7.689 57.402 1899 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 3.01 % Allowed : 14.47 % Favored : 82.52 % 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: 1.63 (0.29), residues: 336 sheet: 0.17 (0.54), residues: 114 loop : -1.47 (0.27), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 196 TYR 0.010 0.001 TYR B 227 PHE 0.015 0.002 PHE A 245 TRP 0.011 0.001 TRP a 392 HIS 0.006 0.001 HIS c 311 Details of bonding type rmsd covalent geometry : bond 0.00608 ( 8424) covalent geometry : angle 0.75144 (11370) SS BOND : bond 0.00575 ( 21) SS BOND : angle 2.40527 ( 42) hydrogen bonds : bond 0.04151 ( 328) hydrogen bonds : angle 3.88466 ( 939) link_BETA1-4 : bond 0.00299 ( 18) link_BETA1-4 : angle 1.74474 ( 54) link_NAG-ASN : bond 0.00287 ( 24) link_NAG-ASN : angle 1.89837 ( 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 172 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 146 time to evaluate : 0.298 Fit side-chains revert: symmetry clash REVERT: A 78 GLU cc_start: 0.8320 (tp30) cc_final: 0.8015 (pm20) REVERT: A 103 MET cc_start: 0.9388 (tpt) cc_final: 0.8605 (tpt) REVERT: A 139 MET cc_start: 0.9008 (tpp) cc_final: 0.8352 (ttt) REVERT: A 256 LYS cc_start: 0.7237 (mmtt) cc_final: 0.6853 (mmtt) REVERT: a 290 MET cc_start: 0.9162 (mtt) cc_final: 0.8940 (mtt) REVERT: a 310 ASN cc_start: 0.8761 (t0) cc_final: 0.7748 (t0) REVERT: a 313 GLU cc_start: 0.8543 (mp0) cc_final: 0.7760 (mp0) REVERT: a 354 GLN cc_start: 0.8918 (pt0) cc_final: 0.8718 (mt0) REVERT: a 364 LEU cc_start: 0.9269 (OUTLIER) cc_final: 0.9002 (mm) REVERT: a 379 GLU cc_start: 0.8880 (pt0) cc_final: 0.8549 (pt0) REVERT: a 412 GLU cc_start: 0.9116 (tp30) cc_final: 0.8911 (tp30) REVERT: B 72 TYR cc_start: 0.9052 (m-80) cc_final: 0.8796 (m-80) REVERT: b 310 ASN cc_start: 0.8663 (t0) cc_final: 0.7767 (t0) REVERT: b 379 GLU cc_start: 0.8810 (pt0) cc_final: 0.8477 (pt0) REVERT: b 412 GLU cc_start: 0.9073 (tp30) cc_final: 0.8797 (tp30) REVERT: C 78 GLU cc_start: 0.7877 (pm20) cc_final: 0.7127 (pm20) REVERT: C 103 MET cc_start: 0.9453 (tpt) cc_final: 0.8968 (tpt) REVERT: C 156 LYS cc_start: 0.9152 (mmmm) cc_final: 0.8837 (mmmm) REVERT: c 310 ASN cc_start: 0.8625 (t0) cc_final: 0.7732 (t0) REVERT: c 362 ARG cc_start: 0.9219 (mmm-85) cc_final: 0.8969 (mtt-85) REVERT: c 379 GLU cc_start: 0.8883 (pt0) cc_final: 0.8555 (pt0) REVERT: c 402 GLU cc_start: 0.9146 (mp0) cc_final: 0.8870 (mp0) outliers start: 26 outliers final: 17 residues processed: 158 average time/residue: 0.0848 time to fit residues: 18.5113 Evaluate side-chains 159 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 141 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 GLU 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 193 ASP Chi-restraints excluded: chain b residue 304 VAL Chi-restraints excluded: chain b residue 347 VAL Chi-restraints excluded: chain b residue 349 SER Chi-restraints excluded: chain b residue 354 GLN Chi-restraints excluded: chain C residue 109 GLU 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 416 MET 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: 7.9990 chunk 87 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 47 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 31 optimal weight: 7.9990 chunk 43 optimal weight: 5.9990 chunk 11 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.055765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.044106 restraints weight = 31949.489| |-----------------------------------------------------------------------------| r_work (start): 0.2794 rms_B_bonded: 4.23 r_work: 0.2624 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.2624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.4162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8487 Z= 0.183 Angle : 0.732 10.209 11538 Z= 0.358 Chirality : 0.045 0.240 1374 Planarity : 0.003 0.032 1365 Dihedral : 7.606 57.356 1899 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 2.08 % Allowed : 14.81 % 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: -0.03 (0.28), residues: 915 helix: 1.68 (0.29), residues: 336 sheet: 0.21 (0.54), residues: 114 loop : -1.43 (0.27), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG c 358 TYR 0.013 0.001 TYR a 284 PHE 0.011 0.001 PHE B 245 TRP 0.007 0.001 TRP a 392 HIS 0.005 0.001 HIS c 311 Details of bonding type rmsd covalent geometry : bond 0.00402 ( 8424) covalent geometry : angle 0.70065 (11370) SS BOND : bond 0.00456 ( 21) SS BOND : angle 2.23454 ( 42) hydrogen bonds : bond 0.03731 ( 328) hydrogen bonds : angle 3.73442 ( 939) link_BETA1-4 : bond 0.00267 ( 18) link_BETA1-4 : angle 1.68339 ( 54) link_NAG-ASN : bond 0.00290 ( 24) link_NAG-ASN : angle 1.80941 ( 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 168 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 150 time to evaluate : 0.229 Fit side-chains revert: symmetry clash REVERT: A 78 GLU cc_start: 0.8308 (tp30) cc_final: 0.8025 (pm20) REVERT: A 103 MET cc_start: 0.9365 (tpt) cc_final: 0.8523 (tpt) REVERT: A 139 MET cc_start: 0.8974 (tpp) cc_final: 0.8278 (ttt) REVERT: A 256 LYS cc_start: 0.7289 (mmtt) cc_final: 0.6917 (mmtt) REVERT: a 310 ASN cc_start: 0.8760 (t0) cc_final: 0.7703 (t0) REVERT: a 313 GLU cc_start: 0.8540 (mp0) cc_final: 0.7704 (mp0) REVERT: a 354 GLN cc_start: 0.8903 (pt0) cc_final: 0.8689 (mt0) REVERT: a 364 LEU cc_start: 0.9257 (OUTLIER) cc_final: 0.8981 (mm) REVERT: a 379 GLU cc_start: 0.8882 (pt0) cc_final: 0.8561 (pt0) REVERT: a 416 MET cc_start: 0.9457 (ttp) cc_final: 0.9095 (tmm) REVERT: B 72 TYR cc_start: 0.8967 (m-80) cc_final: 0.8668 (m-80) REVERT: b 310 ASN cc_start: 0.8690 (t0) cc_final: 0.7854 (t0) REVERT: b 323 ASP cc_start: 0.9423 (t0) cc_final: 0.9145 (t0) REVERT: b 379 GLU cc_start: 0.8853 (pt0) cc_final: 0.8537 (pt0) REVERT: b 412 GLU cc_start: 0.9031 (tp30) cc_final: 0.8753 (tp30) REVERT: C 78 GLU cc_start: 0.7904 (pm20) cc_final: 0.7702 (pm20) REVERT: C 103 MET cc_start: 0.9426 (tpt) cc_final: 0.8932 (tpt) REVERT: C 156 LYS cc_start: 0.9109 (mmmm) cc_final: 0.8845 (mmmm) REVERT: C 172 LEU cc_start: 0.9543 (tp) cc_final: 0.9175 (tt) REVERT: c 310 ASN cc_start: 0.8645 (t0) cc_final: 0.7807 (t0) REVERT: c 362 ARG cc_start: 0.9196 (mmm-85) cc_final: 0.8946 (mtt-85) REVERT: c 379 GLU cc_start: 0.8885 (pt0) cc_final: 0.8542 (pt0) outliers start: 18 outliers final: 11 residues processed: 156 average time/residue: 0.0875 time to fit residues: 18.8078 Evaluate side-chains 155 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 143 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 193 ASP Chi-restraints excluded: chain b residue 349 SER 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 416 MET 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: 0.1980 chunk 15 optimal weight: 6.9990 chunk 27 optimal weight: 10.0000 chunk 23 optimal weight: 0.3980 chunk 3 optimal weight: 6.9990 chunk 25 optimal weight: 0.0770 chunk 35 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 62 optimal weight: 8.9990 chunk 6 optimal weight: 0.7980 overall best weight: 0.6940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 183 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.057108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.045491 restraints weight = 31847.518| |-----------------------------------------------------------------------------| r_work (start): 0.2838 rms_B_bonded: 4.26 r_work: 0.2670 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.4182 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= 0.131 Angle : 0.707 9.469 11538 Z= 0.349 Chirality : 0.045 0.242 1374 Planarity : 0.003 0.028 1365 Dihedral : 7.408 57.174 1899 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 1.74 % Allowed : 16.32 % Favored : 81.94 % 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: 1.67 (0.29), residues: 339 sheet: 0.19 (0.54), residues: 114 loop : -1.21 (0.27), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG c 358 TYR 0.012 0.001 TYR A 72 PHE 0.008 0.001 PHE C 245 TRP 0.007 0.001 TRP A 219 HIS 0.005 0.001 HIS A 238 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 8424) covalent geometry : angle 0.68114 (11370) SS BOND : bond 0.00303 ( 21) SS BOND : angle 1.83811 ( 42) hydrogen bonds : bond 0.03131 ( 328) hydrogen bonds : angle 3.57913 ( 939) link_BETA1-4 : bond 0.00357 ( 18) link_BETA1-4 : angle 1.66108 ( 54) link_NAG-ASN : bond 0.00417 ( 24) link_NAG-ASN : angle 1.67647 ( 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 160 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 145 time to evaluate : 0.198 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 103 MET cc_start: 0.9298 (tpt) cc_final: 0.8574 (tpt) REVERT: A 139 MET cc_start: 0.8900 (tpp) cc_final: 0.8374 (tmm) REVERT: A 256 LYS cc_start: 0.7333 (mmtt) cc_final: 0.7040 (mmtt) REVERT: a 310 ASN cc_start: 0.8716 (t0) cc_final: 0.7624 (t0) REVERT: a 313 GLU cc_start: 0.8633 (mp0) cc_final: 0.7840 (mp0) REVERT: a 354 GLN cc_start: 0.8864 (pt0) cc_final: 0.8638 (mt0) REVERT: a 364 LEU cc_start: 0.9196 (OUTLIER) cc_final: 0.8836 (mm) REVERT: a 379 GLU cc_start: 0.8893 (pt0) cc_final: 0.8557 (pt0) REVERT: a 416 MET cc_start: 0.9443 (ttp) cc_final: 0.9231 (tmm) REVERT: B 72 TYR cc_start: 0.8886 (m-80) cc_final: 0.8605 (m-80) REVERT: b 310 ASN cc_start: 0.8679 (t0) cc_final: 0.7925 (t0) REVERT: b 323 ASP cc_start: 0.9382 (t0) cc_final: 0.9083 (t0) REVERT: b 379 GLU cc_start: 0.8850 (pt0) cc_final: 0.8519 (pt0) REVERT: b 412 GLU cc_start: 0.8980 (tp30) cc_final: 0.8702 (tp30) REVERT: C 103 MET cc_start: 0.9397 (tpt) cc_final: 0.9025 (tpt) REVERT: C 156 LYS cc_start: 0.9070 (mmmm) cc_final: 0.8807 (mmmm) REVERT: C 172 LEU cc_start: 0.9484 (tp) cc_final: 0.9137 (tt) REVERT: c 310 ASN cc_start: 0.8587 (t0) cc_final: 0.7764 (t0) REVERT: c 362 ARG cc_start: 0.9141 (mmm-85) cc_final: 0.8880 (mtt-85) REVERT: c 379 GLU cc_start: 0.8887 (pt0) cc_final: 0.8563 (pt0) REVERT: c 385 GLU cc_start: 0.8944 (tp30) cc_final: 0.8293 (tp30) outliers start: 15 outliers final: 7 residues processed: 153 average time/residue: 0.0857 time to fit residues: 18.0317 Evaluate side-chains 151 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 143 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 349 SER Chi-restraints excluded: chain c residue 299 PHE Chi-restraints excluded: chain c residue 347 VAL Chi-restraints excluded: chain c residue 364 LEU Chi-restraints excluded: chain c residue 416 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 53 optimal weight: 5.9990 chunk 4 optimal weight: 6.9990 chunk 10 optimal weight: 0.7980 chunk 41 optimal weight: 0.8980 chunk 56 optimal weight: 0.6980 chunk 11 optimal weight: 0.7980 chunk 32 optimal weight: 4.9990 chunk 74 optimal weight: 7.9990 chunk 2 optimal weight: 2.9990 chunk 29 optimal weight: 7.9990 chunk 82 optimal weight: 3.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.056861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.045316 restraints weight = 31523.306| |-----------------------------------------------------------------------------| r_work (start): 0.2829 rms_B_bonded: 4.20 r_work: 0.2667 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.4253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8487 Z= 0.148 Angle : 0.736 9.736 11538 Z= 0.359 Chirality : 0.044 0.242 1374 Planarity : 0.003 0.028 1365 Dihedral : 7.343 57.098 1899 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 1.16 % Allowed : 17.01 % 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: 0.12 (0.28), residues: 915 helix: 1.77 (0.29), residues: 336 sheet: 0.22 (0.53), residues: 114 loop : -1.29 (0.27), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG c 358 TYR 0.009 0.001 TYR A 227 PHE 0.009 0.001 PHE A 245 TRP 0.006 0.001 TRP A 219 HIS 0.011 0.001 HIS B 238 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 8424) covalent geometry : angle 0.71100 (11370) SS BOND : bond 0.00391 ( 21) SS BOND : angle 1.89010 ( 42) hydrogen bonds : bond 0.03259 ( 328) hydrogen bonds : angle 3.56018 ( 939) link_BETA1-4 : bond 0.00290 ( 18) link_BETA1-4 : angle 1.68074 ( 54) link_NAG-ASN : bond 0.00313 ( 24) link_NAG-ASN : angle 1.65297 ( 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 155 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 145 time to evaluate : 0.282 Fit side-chains revert: symmetry clash REVERT: A 78 GLU cc_start: 0.8368 (tp30) cc_final: 0.8055 (pm20) REVERT: A 103 MET cc_start: 0.9314 (tpt) cc_final: 0.8716 (tpt) REVERT: A 139 MET cc_start: 0.8923 (tpp) cc_final: 0.8379 (tmm) REVERT: a 310 ASN cc_start: 0.8763 (t0) cc_final: 0.7678 (t0) REVERT: a 313 GLU cc_start: 0.8623 (mp0) cc_final: 0.7787 (mp0) REVERT: a 354 GLN cc_start: 0.8857 (OUTLIER) cc_final: 0.8632 (mt0) REVERT: a 364 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8831 (mm) REVERT: B 72 TYR cc_start: 0.8889 (m-80) cc_final: 0.8503 (m-80) REVERT: b 310 ASN cc_start: 0.8666 (t0) cc_final: 0.7919 (t0) REVERT: b 323 ASP cc_start: 0.9374 (t0) cc_final: 0.9071 (t0) REVERT: b 379 GLU cc_start: 0.8815 (pt0) cc_final: 0.8469 (pt0) REVERT: b 412 GLU cc_start: 0.9017 (tp30) cc_final: 0.8745 (tp30) REVERT: b 416 MET cc_start: 0.9429 (ttp) cc_final: 0.9222 (tmm) REVERT: C 78 GLU cc_start: 0.8004 (pm20) cc_final: 0.7273 (pm20) REVERT: C 103 MET cc_start: 0.9384 (tpt) cc_final: 0.9011 (tpt) REVERT: C 156 LYS cc_start: 0.9085 (mmmm) cc_final: 0.8815 (mmmm) REVERT: C 172 LEU cc_start: 0.9500 (tp) cc_final: 0.9149 (tt) REVERT: C 204 MET cc_start: 0.8546 (tpt) cc_final: 0.8284 (tpt) REVERT: c 310 ASN cc_start: 0.8554 (t0) cc_final: 0.7787 (t0) REVERT: c 362 ARG cc_start: 0.9142 (mmm-85) cc_final: 0.8893 (mtt-85) REVERT: c 379 GLU cc_start: 0.8875 (pt0) cc_final: 0.8538 (pt0) REVERT: c 385 GLU cc_start: 0.8946 (tp30) cc_final: 0.8494 (tp30) outliers start: 10 outliers final: 6 residues processed: 150 average time/residue: 0.0830 time to fit residues: 17.1377 Evaluate side-chains 150 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 142 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 304 VAL 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 349 SER Chi-restraints excluded: chain c residue 299 PHE Chi-restraints excluded: chain c residue 347 VAL Chi-restraints excluded: chain c residue 364 LEU 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: 4.9990 chunk 9 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 61 optimal weight: 8.9990 chunk 85 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 chunk 80 optimal weight: 4.9990 chunk 19 optimal weight: 0.6980 chunk 54 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.056584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.045059 restraints weight = 31978.992| |-----------------------------------------------------------------------------| r_work (start): 0.2821 rms_B_bonded: 4.21 r_work: 0.2657 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.4338 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= 0.163 Angle : 0.739 10.085 11538 Z= 0.361 Chirality : 0.044 0.241 1374 Planarity : 0.003 0.028 1365 Dihedral : 7.335 57.054 1899 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 1.27 % Allowed : 16.78 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.28), residues: 915 helix: 1.79 (0.29), residues: 336 sheet: 0.25 (0.54), residues: 114 loop : -1.33 (0.27), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG c 358 TYR 0.009 0.001 TYR B 227 PHE 0.010 0.001 PHE A 245 TRP 0.006 0.001 TRP A 219 HIS 0.008 0.001 HIS B 238 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 8424) covalent geometry : angle 0.71400 (11370) SS BOND : bond 0.00404 ( 21) SS BOND : angle 1.91576 ( 42) hydrogen bonds : bond 0.03357 ( 328) hydrogen bonds : angle 3.55558 ( 939) link_BETA1-4 : bond 0.00274 ( 18) link_BETA1-4 : angle 1.66883 ( 54) link_NAG-ASN : bond 0.00284 ( 24) link_NAG-ASN : angle 1.65350 ( 72) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1521.47 seconds wall clock time: 27 minutes 0.45 seconds (1620.45 seconds total)