Starting phenix.real_space_refine on Thu Jul 2 15:14:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7pvd_13667/07_2026/7pvd_13667.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pvd_13667/07_2026/7pvd_13667.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7pvd_13667/07_2026/7pvd_13667.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pvd_13667/07_2026/7pvd_13667.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7pvd_13667/07_2026/7pvd_13667.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7pvd_13667/07_2026/7pvd_13667.cif" model { file = "/net/cci-nas-00/data/ceres_data/7pvd_13667/07_2026/7pvd_13667.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pvd_13667/07_2026/7pvd_13667.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.016 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 84 5.16 5 C 5570 2.51 5 N 1455 2.21 5 O 1793 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8902 Number of models: 1 Model: "" Number of chains: 22 Chain: "a" Number of atoms: 1298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1298 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 3, 'TRANS': 156} Chain: "b" Number of atoms: 1298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1298 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 3, 'TRANS': 156} Chain: "c" Number of atoms: 1298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1298 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 3, 'TRANS': 156} Chain: "A" Number of atoms: 1484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1484 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 4, 'TRANS': 180} Chain breaks: 2 Chain: "B" Number of atoms: 1484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1484 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 4, 'TRANS': 180} Chain breaks: 2 Chain: "C" Number of atoms: 1484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1484 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 4, 'TRANS': 180} Chain breaks: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 136 Unusual residues: {'BDP': 6, 'XYS': 7} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen chiralities: 12 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 2.18, per 1000 atoms: 0.24 Number of scatterers: 8902 At special positions: 0 Unit cell: (86.154, 92.382, 96.534, 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 84 16.00 O 1793 8.00 N 1455 7.00 C 5570 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS a 279 " - pdb=" SG CYS a 292 " distance=2.03 Simple disulfide: pdb=" SG CYS a 301 " - pdb=" SG CYS a 310 " distance=2.02 Simple disulfide: pdb=" SG CYS a 364 " - pdb=" SG CYS a 385 " distance=2.02 Simple disulfide: pdb=" SG CYS b 279 " - pdb=" SG CYS b 292 " distance=2.03 Simple disulfide: pdb=" SG CYS b 301 " - pdb=" SG CYS b 310 " distance=2.03 Simple disulfide: pdb=" SG CYS b 364 " - pdb=" SG CYS b 385 " distance=2.02 Simple disulfide: pdb=" SG CYS c 279 " - pdb=" SG CYS c 292 " distance=2.03 Simple disulfide: pdb=" SG CYS c 301 " - pdb=" SG CYS c 310 " distance=2.02 Simple disulfide: pdb=" SG CYS c 364 " - pdb=" SG CYS c 385 " distance=2.02 Simple disulfide: pdb=" SG CYS A 86 " - pdb=" SG CYS A 231 " distance=2.03 Simple disulfide: pdb=" SG CYS A 118 " - pdb=" SG CYS A 155 " distance=2.03 Simple disulfide: pdb=" SG CYS A 180 " - pdb=" SG CYS A 212 " distance=2.03 Simple disulfide: pdb=" SG CYS B 86 " - pdb=" SG CYS B 231 " distance=2.03 Simple disulfide: pdb=" SG CYS B 118 " - pdb=" SG CYS B 155 " distance=2.03 Simple disulfide: pdb=" SG CYS B 180 " - pdb=" SG CYS B 212 " distance=2.03 Simple disulfide: pdb=" SG CYS C 86 " - pdb=" SG CYS C 231 " distance=2.03 Simple disulfide: pdb=" SG CYS C 118 " - pdb=" SG CYS C 155 " distance=2.03 Simple disulfide: pdb=" SG CYS C 180 " - pdb=" SG CYS C 212 " 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 ALPHA1-3 " BDP M 2 " - " XYS M 3 " " BDP M 4 " - " XYS M 5 " " BDP M 6 " - " XYS M 7 " " BDP M 8 " - " XYS M 9 " " BDP M 10 " - " XYS M 11 " " BDP M 12 " - " XYS M 13 " BETA1-3 " XYS M 1 " - " BDP M 2 " " XYS M 3 " - " BDP M 4 " " XYS M 5 " - " BDP M 6 " " XYS M 7 " - " BDP M 8 " " XYS M 9 " - " BDP M 10 " " XYS M 11 " - " BDP M 12 " 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-ASN " NAG A 301 " - " ASN A 99 " " NAG A 302 " - " ASN A 109 " " NAG B 301 " - " ASN B 99 " " NAG B 302 " - " ASN B 109 " " NAG C 301 " - " ASN C 99 " " NAG C 302 " - " ASN C 109 " " NAG D 1 " - " ASN A 119 " " NAG E 1 " - " ASN A 167 " " NAG F 1 " - " ASN A 79 " " NAG G 1 " - " ASN B 119 " " NAG H 1 " - " ASN B 167 " " NAG I 1 " - " ASN B 79 " " NAG J 1 " - " ASN C 119 " " NAG K 1 " - " ASN C 167 " " NAG L 1 " - " ASN C 79 " " NAG a 601 " - " ASN a 365 " " NAG a 602 " - " ASN a 395 " " NAG b 601 " - " ASN b 365 " " NAG b 602 " - " ASN b 395 " " NAG c 601 " - " ASN c 365 " " NAG c 602 " - " ASN c 395 " Time building additional restraints: 0.96 Conformation dependent library (CDL) restraints added in 413.0 milliseconds 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1950 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 9 sheets defined 38.6% alpha, 15.4% 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 294 through 300 removed outlier: 3.629A pdb=" N VAL a 298 " --> pdb=" O GLY a 294 " (cutoff:3.500A) Processing helix chain 'a' and resid 301 through 303 No H-bonds generated for 'chain 'a' and resid 301 through 303' Processing helix chain 'a' and resid 308 through 325 Processing helix chain 'a' and resid 333 through 345 removed outlier: 4.396A pdb=" N ILE a 337 " --> pdb=" O SER a 333 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N ASN a 342 " --> pdb=" O ASN a 338 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N ALA a 343 " --> pdb=" O LYS a 339 " (cutoff:3.500A) Processing helix chain 'a' and resid 348 through 360 Processing helix chain 'a' and resid 399 through 419 Processing helix chain 'b' and resid 294 through 300 removed outlier: 3.629A pdb=" N VAL b 298 " --> pdb=" O GLY b 294 " (cutoff:3.500A) Processing helix chain 'b' and resid 301 through 303 No H-bonds generated for 'chain 'b' and resid 301 through 303' Processing helix chain 'b' and resid 308 through 325 Processing helix chain 'b' and resid 333 through 345 removed outlier: 4.396A pdb=" N ILE b 337 " --> pdb=" O SER b 333 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N ASN b 342 " --> pdb=" O ASN b 338 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N ALA b 343 " --> pdb=" O LYS b 339 " (cutoff:3.500A) Processing helix chain 'b' and resid 348 through 360 Processing helix chain 'b' and resid 399 through 419 Processing helix chain 'c' and resid 294 through 300 removed outlier: 3.629A pdb=" N VAL c 298 " --> pdb=" O GLY c 294 " (cutoff:3.500A) Processing helix chain 'c' and resid 301 through 303 No H-bonds generated for 'chain 'c' and resid 301 through 303' Processing helix chain 'c' and resid 308 through 325 Processing helix chain 'c' and resid 333 through 345 removed outlier: 4.397A pdb=" N ILE c 337 " --> pdb=" O SER c 333 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N ASN c 342 " --> pdb=" O ASN c 338 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N ALA c 343 " --> pdb=" O LYS c 339 " (cutoff:3.500A) Processing helix chain 'c' and resid 348 through 360 Processing helix chain 'c' and resid 399 through 419 Processing helix chain 'A' and resid 74 through 79 Processing helix chain 'A' and resid 119 through 126 Processing helix chain 'A' and resid 130 through 143 Processing helix chain 'A' and resid 157 through 161 Processing helix chain 'A' and resid 182 through 195 removed outlier: 3.627A pdb=" N GLY A 186 " --> pdb=" O THR A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 248 removed outlier: 3.762A pdb=" N SER A 246 " --> pdb=" O LEU A 242 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLN A 247 " --> pdb=" O GLY A 243 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG A 248 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 79 Processing helix chain 'B' and resid 119 through 126 Processing helix chain 'B' and resid 130 through 143 Processing helix chain 'B' and resid 157 through 161 Processing helix chain 'B' and resid 182 through 195 removed outlier: 3.627A pdb=" N GLY B 186 " --> pdb=" O THR B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 248 removed outlier: 3.763A pdb=" N SER B 246 " --> pdb=" O LEU B 242 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLN B 247 " --> pdb=" O GLY B 243 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG B 248 " --> pdb=" O LEU B 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 79 Processing helix chain 'C' and resid 119 through 126 Processing helix chain 'C' and resid 130 through 143 Processing helix chain 'C' and resid 157 through 161 Processing helix chain 'C' and resid 182 through 195 removed outlier: 3.628A pdb=" N GLY C 186 " --> pdb=" O THR C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 248 removed outlier: 3.762A pdb=" N SER C 246 " --> pdb=" O LEU C 242 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLN C 247 " --> pdb=" O GLY C 243 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG C 248 " --> pdb=" O LEU C 244 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'a' and resid 279 through 280 Processing sheet with id=AA2, first strand: chain 'a' and resid 392 through 393 removed outlier: 9.646A pdb=" N LYS a 384 " --> pdb=" O SER a 367 " (cutoff:3.500A) removed outlier: 8.667A pdb=" N SER a 367 " --> pdb=" O LYS a 384 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N TRP a 386 " --> pdb=" O ASN a 365 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASN a 365 " --> pdb=" O TRP a 386 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'b' and resid 279 through 280 Processing sheet with id=AA4, first strand: chain 'b' and resid 392 through 393 removed outlier: 9.646A pdb=" N LYS b 384 " --> pdb=" O SER b 367 " (cutoff:3.500A) removed outlier: 8.668A pdb=" N SER b 367 " --> pdb=" O LYS b 384 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N TRP b 386 " --> pdb=" O ASN b 365 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASN b 365 " --> pdb=" O TRP b 386 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU B 67 " --> pdb=" O ASN b 373 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'c' and resid 279 through 280 Processing sheet with id=AA6, first strand: chain 'c' and resid 392 through 393 removed outlier: 9.647A pdb=" N LYS c 384 " --> pdb=" O SER c 367 " (cutoff:3.500A) removed outlier: 8.667A pdb=" N SER c 367 " --> pdb=" O LYS c 384 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N TRP c 386 " --> pdb=" O ASN c 365 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASN c 365 " --> pdb=" O TRP c 386 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 84 through 87 removed outlier: 3.623A pdb=" N THR A 101 " --> pdb=" O VAL A 97 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 84 through 87 removed outlier: 3.623A pdb=" N THR B 101 " --> pdb=" O VAL B 97 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 84 through 87 removed outlier: 3.623A pdb=" N THR C 101 " --> pdb=" O VAL C 97 " (cutoff:3.500A) 356 hydrogen bonds defined for protein. 951 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: 1.12 Time building geometry restraints manager: 1.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2784 1.34 - 1.46: 2297 1.46 - 1.58: 3866 1.58 - 1.70: 0 1.70 - 1.82: 132 Bond restraints: 9079 Sorted by residual: bond pdb=" C3 BDP M 6 " pdb=" O3 BDP M 6 " ideal model delta sigma weight residual 1.411 1.520 -0.109 2.00e-02 2.50e+03 2.97e+01 bond pdb=" C3 BDP M 10 " pdb=" O3 BDP M 10 " ideal model delta sigma weight residual 1.411 1.518 -0.107 2.00e-02 2.50e+03 2.88e+01 bond pdb=" C3 BDP M 2 " pdb=" O3 BDP M 2 " ideal model delta sigma weight residual 1.411 1.517 -0.106 2.00e-02 2.50e+03 2.81e+01 bond pdb=" C3 BDP M 4 " pdb=" O3 BDP M 4 " ideal model delta sigma weight residual 1.411 1.517 -0.106 2.00e-02 2.50e+03 2.79e+01 bond pdb=" C3 BDP M 8 " pdb=" O3 BDP M 8 " ideal model delta sigma weight residual 1.411 1.515 -0.104 2.00e-02 2.50e+03 2.72e+01 ... (remaining 9074 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 11743 1.79 - 3.57: 433 3.57 - 5.36: 56 5.36 - 7.15: 39 7.15 - 8.94: 4 Bond angle restraints: 12275 Sorted by residual: angle pdb=" C LEU C 103 " pdb=" N GLU C 104 " pdb=" CA GLU C 104 " ideal model delta sigma weight residual 121.42 127.02 -5.60 1.43e+00 4.89e-01 1.53e+01 angle pdb=" C LEU B 103 " pdb=" N GLU B 104 " pdb=" CA GLU B 104 " ideal model delta sigma weight residual 121.42 126.99 -5.57 1.43e+00 4.89e-01 1.52e+01 angle pdb=" C LEU A 103 " pdb=" N GLU A 104 " pdb=" CA GLU A 104 " ideal model delta sigma weight residual 121.42 126.96 -5.54 1.43e+00 4.89e-01 1.50e+01 angle pdb=" C ILE A 222 " pdb=" N GLN A 223 " pdb=" CA GLN A 223 " ideal model delta sigma weight residual 121.75 115.86 5.89 1.73e+00 3.34e-01 1.16e+01 angle pdb=" C ILE C 222 " pdb=" N GLN C 223 " pdb=" CA GLN C 223 " ideal model delta sigma weight residual 121.75 115.87 5.88 1.73e+00 3.34e-01 1.16e+01 ... (remaining 12270 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.97: 4908 27.97 - 55.95: 184 55.95 - 83.92: 14 83.92 - 111.90: 3 111.90 - 139.87: 7 Dihedral angle restraints: 5116 sinusoidal: 2092 harmonic: 3024 Sorted by residual: dihedral pdb=" CB CYS b 301 " pdb=" SG CYS b 301 " pdb=" SG CYS b 310 " pdb=" CB CYS b 310 " ideal model delta sinusoidal sigma weight residual 93.00 142.75 -49.75 1 1.00e+01 1.00e-02 3.40e+01 dihedral pdb=" CB CYS c 301 " pdb=" SG CYS c 301 " pdb=" SG CYS c 310 " pdb=" CB CYS c 310 " ideal model delta sinusoidal sigma weight residual 93.00 142.74 -49.74 1 1.00e+01 1.00e-02 3.40e+01 dihedral pdb=" CB CYS a 301 " pdb=" SG CYS a 301 " pdb=" SG CYS a 310 " pdb=" CB CYS a 310 " ideal model delta sinusoidal sigma weight residual 93.00 142.71 -49.71 1 1.00e+01 1.00e-02 3.39e+01 ... (remaining 5113 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 1306 0.078 - 0.156: 151 0.156 - 0.234: 11 0.234 - 0.312: 0 0.312 - 0.390: 3 Chirality restraints: 1471 Sorted by residual: chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN B 79 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-01 2.50e+01 3.80e+00 chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN A 79 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-01 2.50e+01 3.72e+00 chirality pdb=" C1 NAG L 1 " pdb=" ND2 ASN C 79 " pdb=" C2 NAG L 1 " pdb=" O5 NAG L 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.68e+00 ... (remaining 1468 not shown) Planarity restraints: 1518 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU C 104 " 0.008 2.00e-02 2.50e+03 1.67e-02 2.78e+00 pdb=" C GLU C 104 " -0.029 2.00e-02 2.50e+03 pdb=" O GLU C 104 " 0.011 2.00e-02 2.50e+03 pdb=" N LEU C 105 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 104 " 0.008 2.00e-02 2.50e+03 1.66e-02 2.76e+00 pdb=" C GLU B 104 " -0.029 2.00e-02 2.50e+03 pdb=" O GLU B 104 " 0.011 2.00e-02 2.50e+03 pdb=" N LEU B 105 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 104 " 0.008 2.00e-02 2.50e+03 1.66e-02 2.76e+00 pdb=" C GLU A 104 " -0.029 2.00e-02 2.50e+03 pdb=" O GLU A 104 " 0.011 2.00e-02 2.50e+03 pdb=" N LEU A 105 " 0.010 2.00e-02 2.50e+03 ... (remaining 1515 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 205 2.69 - 3.24: 8964 3.24 - 3.79: 13728 3.79 - 4.35: 18376 4.35 - 4.90: 29715 Nonbonded interactions: 70988 Sorted by model distance: nonbonded pdb=" OE2 GLU b 396 " pdb=" OH TYR B 62 " model vdw 2.134 3.040 nonbonded pdb=" OE1 GLU C 100 " pdb=" OG1 THR C 101 " model vdw 2.175 3.040 nonbonded pdb=" OE1 GLU B 100 " pdb=" OG1 THR B 101 " model vdw 2.175 3.040 nonbonded pdb=" OE1 GLU A 100 " pdb=" OG1 THR A 101 " model vdw 2.175 3.040 nonbonded pdb=" OD1 ASP c 347 " pdb=" OG SER C 246 " model vdw 2.206 3.040 ... (remaining 70983 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: 0.00 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' } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.250 Find NCS groups from input model: 0.170 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6674 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 : 0.007 0.109 9139 Z= 0.364 Angle : 0.847 8.936 12437 Z= 0.398 Chirality : 0.051 0.390 1471 Planarity : 0.004 0.040 1497 Dihedral : 14.988 139.869 3112 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 0.32 % Allowed : 2.04 % Favored : 97.64 % 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: -1.16 (0.24), residues: 1011 helix: -0.36 (0.27), residues: 351 sheet: -0.45 (0.42), residues: 150 loop : -1.09 (0.24), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 193 TYR 0.021 0.002 TYR A 253 PHE 0.009 0.001 PHE B 191 TRP 0.016 0.002 TRP A 227 HIS 0.005 0.001 HIS a 305 Details of bonding type rmsd/Z covalent geometry : bond 0.00749 / 0.36 ( 9079) covalent geometry : angle 0.82610 / 0.39 (12275) SS BOND : bond 0.00434 / 0.29 ( 18) SS BOND : angle 1.71765 / 1.06 ( 36) hydrogen bonds : bond 0.15468 / 10.35 ( 356) hydrogen bonds : angle 6.48166 / 4.58 ( 951) link_ALPHA1-3 : bond 0.00283 / 0.16 ( 6) link_ALPHA1-3 : angle 1.05867 / 0.61 ( 18) link_BETA1-3 : bond 0.00854 / 0.56 ( 6) link_BETA1-3 : angle 2.33104 / 1.34 ( 18) link_BETA1-4 : bond 0.00297 / 0.20 ( 9) link_BETA1-4 : angle 1.93654 / 1.09 ( 27) link_NAG-ASN : bond 0.00467 / 0.29 ( 21) link_NAG-ASN : angle 1.88325 / 1.35 ( 63) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 286 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 390 ASN cc_start: 0.7114 (t0) cc_final: 0.6902 (t0) REVERT: a 417 LYS cc_start: 0.6310 (mptm) cc_final: 0.6075 (mptt) REVERT: b 312 MET cc_start: 0.7583 (mmm) cc_final: 0.7318 (mmt) REVERT: b 357 ASP cc_start: 0.8004 (t0) cc_final: 0.7759 (t0) REVERT: b 414 MET cc_start: 0.6694 (ttm) cc_final: 0.6477 (ttm) REVERT: c 357 ASP cc_start: 0.8182 (t0) cc_final: 0.7870 (t0) REVERT: A 228 GLU cc_start: 0.6696 (mp0) cc_final: 0.6433 (mt-10) REVERT: A 255 SER cc_start: 0.7468 (m) cc_final: 0.7061 (t) REVERT: B 255 SER cc_start: 0.7950 (m) cc_final: 0.7690 (t) REVERT: C 68 LEU cc_start: 0.8077 (tp) cc_final: 0.7825 (tp) outliers start: 3 outliers final: 0 residues processed: 288 average time/residue: 0.1072 time to fit residues: 41.2744 Evaluate side-chains 162 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 0.8980 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... a 405 GLN A 127 ASN A 146 ASN A 170 HIS B 127 ASN B 131 HIS B 170 HIS ** B 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 127 ASN ** C 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 170 HIS ** C 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.158604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.137829 restraints weight = 13794.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.141027 restraints weight = 8929.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.143205 restraints weight = 6646.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.144895 restraints weight = 5405.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.146056 restraints weight = 4592.356| |-----------------------------------------------------------------------------| r_work (final): 0.3818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6861 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9139 Z= 0.159 Angle : 0.775 17.329 12437 Z= 0.379 Chirality : 0.046 0.224 1471 Planarity : 0.004 0.045 1497 Dihedral : 10.929 138.051 1117 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.68 % Allowed : 10.83 % Favored : 86.50 % 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: -0.47 (0.25), residues: 1011 helix: 0.77 (0.28), residues: 324 sheet: -0.81 (0.41), residues: 150 loop : -0.80 (0.24), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG a 379 TYR 0.018 0.002 TYR C 62 PHE 0.012 0.002 PHE b 318 TRP 0.026 0.002 TRP a 370 HIS 0.008 0.001 HIS B 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 ( 9079) covalent geometry : angle 0.73173 / 0.37 (12275) SS BOND : bond 0.00358 / 0.23 ( 18) SS BOND : angle 1.31821 / 0.81 ( 36) hydrogen bonds : bond 0.04712 / 3.13 ( 356) hydrogen bonds : angle 5.53283 / 3.90 ( 951) link_ALPHA1-3 : bond 0.00682 / 0.45 ( 6) link_ALPHA1-3 : angle 1.19853 / 0.75 ( 18) link_BETA1-3 : bond 0.01137 / 0.75 ( 6) link_BETA1-3 : angle 2.64751 / 1.56 ( 18) link_BETA1-4 : bond 0.00343 / 0.23 ( 9) link_BETA1-4 : angle 1.09865 / 0.63 ( 27) link_NAG-ASN : bond 0.00351 / 0.21 ( 21) link_NAG-ASN : angle 3.22965 / 2.15 ( 63) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 175 time to evaluate : 0.262 Fit side-chains revert: symmetry clash REVERT: a 390 ASN cc_start: 0.7276 (t0) cc_final: 0.6902 (t0) REVERT: b 312 MET cc_start: 0.7691 (mmm) cc_final: 0.7482 (mmt) REVERT: b 405 GLN cc_start: 0.7394 (tp40) cc_final: 0.7159 (tt0) REVERT: b 414 MET cc_start: 0.6816 (ttm) cc_final: 0.6475 (ttp) REVERT: c 357 ASP cc_start: 0.8011 (t0) cc_final: 0.7789 (t0) REVERT: A 62 TYR cc_start: 0.5305 (m-80) cc_final: 0.4991 (m-80) REVERT: A 249 THR cc_start: 0.8910 (p) cc_final: 0.8705 (p) REVERT: A 255 SER cc_start: 0.7702 (m) cc_final: 0.7322 (t) outliers start: 25 outliers final: 13 residues processed: 189 average time/residue: 0.0864 time to fit residues: 22.6426 Evaluate side-chains 164 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 151 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 265 THR Chi-restraints excluded: chain a residue 324 GLN Chi-restraints excluded: chain a residue 381 SER Chi-restraints excluded: chain b residue 381 SER Chi-restraints excluded: chain c residue 358 ILE Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 249 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 30 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 84 optimal weight: 9.9990 chunk 80 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 88 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 chunk 81 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 chunk 35 optimal weight: 6.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 146 ASN B 127 ASN B 170 HIS B 209 ASN ** B 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 HIS C 127 ASN C 146 ASN ** C 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.154660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.133710 restraints weight = 13859.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.136994 restraints weight = 8992.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.139293 restraints weight = 6705.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.140439 restraints weight = 5418.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.141836 restraints weight = 4757.019| |-----------------------------------------------------------------------------| r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6967 moved from start: 0.3214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9139 Z= 0.150 Angle : 0.714 14.040 12437 Z= 0.345 Chirality : 0.045 0.210 1471 Planarity : 0.004 0.031 1497 Dihedral : 10.826 137.983 1117 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.47 % Allowed : 12.33 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.26), residues: 1011 helix: 1.05 (0.29), residues: 324 sheet: -0.66 (0.43), residues: 150 loop : -0.63 (0.25), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG a 379 TYR 0.027 0.002 TYR A 94 PHE 0.023 0.002 PHE C 191 TRP 0.011 0.001 TRP A 210 HIS 0.011 0.001 HIS B 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 ( 9079) covalent geometry : angle 0.67707 / 0.34 (12275) SS BOND : bond 0.00434 / 0.29 ( 18) SS BOND : angle 1.23371 / 0.75 ( 36) hydrogen bonds : bond 0.04030 / 2.68 ( 356) hydrogen bonds : angle 5.30916 / 3.76 ( 951) link_ALPHA1-3 : bond 0.00693 / 0.43 ( 6) link_ALPHA1-3 : angle 1.28246 / 0.80 ( 18) link_BETA1-3 : bond 0.01139 / 0.75 ( 6) link_BETA1-3 : angle 2.65627 / 1.59 ( 18) link_BETA1-4 : bond 0.00299 / 0.19 ( 9) link_BETA1-4 : angle 1.18223 / 0.70 ( 27) link_NAG-ASN : bond 0.00390 / 0.23 ( 21) link_NAG-ASN : angle 2.68818 / 1.79 ( 63) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 168 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 390 ASN cc_start: 0.7465 (t0) cc_final: 0.7017 (t0) REVERT: b 402 ASP cc_start: 0.7184 (m-30) cc_final: 0.6884 (t0) REVERT: b 405 GLN cc_start: 0.7573 (tp40) cc_final: 0.7367 (tt0) REVERT: b 419 TYR cc_start: 0.2686 (OUTLIER) cc_final: 0.1912 (m-10) REVERT: c 357 ASP cc_start: 0.8020 (t0) cc_final: 0.7800 (t0) REVERT: A 255 SER cc_start: 0.7767 (m) cc_final: 0.7545 (t) REVERT: C 227 TRP cc_start: 0.6624 (t60) cc_final: 0.6393 (t60) outliers start: 23 outliers final: 15 residues processed: 181 average time/residue: 0.0898 time to fit residues: 23.1085 Evaluate side-chains 167 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 151 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 265 THR Chi-restraints excluded: chain a residue 324 GLN Chi-restraints excluded: chain a residue 381 SER Chi-restraints excluded: chain b residue 381 SER Chi-restraints excluded: chain b residue 419 TYR Chi-restraints excluded: chain c residue 358 ILE Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 179 HIS Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 258 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 10 optimal weight: 1.9990 chunk 77 optimal weight: 10.0000 chunk 54 optimal weight: 5.9990 chunk 2 optimal weight: 6.9990 chunk 67 optimal weight: 2.9990 chunk 34 optimal weight: 8.9990 chunk 3 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 5 optimal weight: 0.4980 chunk 42 optimal weight: 0.3980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... b 335 GLN ** B 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 170 HIS C 127 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.149092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.126927 restraints weight = 14106.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.130087 restraints weight = 9331.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.132345 restraints weight = 7070.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.133672 restraints weight = 5803.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.134906 restraints weight = 5093.994| |-----------------------------------------------------------------------------| r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7155 moved from start: 0.4029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9139 Z= 0.180 Angle : 0.730 12.610 12437 Z= 0.354 Chirality : 0.045 0.209 1471 Planarity : 0.004 0.045 1497 Dihedral : 10.823 137.416 1117 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.79 % Allowed : 15.97 % Favored : 81.24 % 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: -0.17 (0.26), residues: 1011 helix: 1.14 (0.29), residues: 324 sheet: -0.55 (0.43), residues: 144 loop : -0.74 (0.26), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG a 379 TYR 0.018 0.002 TYR b 363 PHE 0.011 0.002 PHE C 157 TRP 0.038 0.002 TRP B 210 HIS 0.008 0.001 HIS B 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.18 ( 9079) covalent geometry : angle 0.69171 / 0.35 (12275) SS BOND : bond 0.00532 / 0.34 ( 18) SS BOND : angle 1.67471 / 1.02 ( 36) hydrogen bonds : bond 0.04144 / 2.77 ( 356) hydrogen bonds : angle 5.25434 / 3.72 ( 951) link_ALPHA1-3 : bond 0.00668 / 0.41 ( 6) link_ALPHA1-3 : angle 1.30286 / 0.81 ( 18) link_BETA1-3 : bond 0.01130 / 0.75 ( 6) link_BETA1-3 : angle 2.69511 / 1.61 ( 18) link_BETA1-4 : bond 0.00256 / 0.16 ( 9) link_BETA1-4 : angle 1.34724 / 0.80 ( 27) link_NAG-ASN : bond 0.00491 / 0.25 ( 21) link_NAG-ASN : angle 2.64294 / 1.76 ( 63) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 171 time to evaluate : 0.333 Fit side-chains revert: symmetry clash REVERT: a 357 ASP cc_start: 0.7231 (t0) cc_final: 0.6966 (t0) REVERT: a 359 MET cc_start: 0.8491 (mtm) cc_final: 0.8088 (mtm) REVERT: a 372 LEU cc_start: 0.7112 (mm) cc_final: 0.6868 (mm) REVERT: b 419 TYR cc_start: 0.2512 (OUTLIER) cc_final: 0.1613 (m-10) REVERT: c 357 ASP cc_start: 0.8117 (t0) cc_final: 0.7836 (t0) REVERT: A 255 SER cc_start: 0.7916 (m) cc_final: 0.7686 (t) REVERT: B 193 ARG cc_start: 0.7884 (mmm-85) cc_final: 0.7644 (mmm-85) outliers start: 26 outliers final: 14 residues processed: 185 average time/residue: 0.0884 time to fit residues: 23.1616 Evaluate side-chains 171 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 156 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 265 THR Chi-restraints excluded: chain a residue 381 SER Chi-restraints excluded: chain b residue 381 SER Chi-restraints excluded: chain b residue 419 TYR Chi-restraints excluded: chain c residue 358 ILE Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 179 HIS Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 258 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 101 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 79 optimal weight: 0.7980 chunk 90 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 58 optimal weight: 0.7980 chunk 40 optimal weight: 0.9980 chunk 92 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... b 335 GLN c 331 GLN B 170 HIS C 127 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.149558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.127671 restraints weight = 13855.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.130853 restraints weight = 9096.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.133159 restraints weight = 6857.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.134511 restraints weight = 5582.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.135710 restraints weight = 4870.791| |-----------------------------------------------------------------------------| r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7137 moved from start: 0.4384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9139 Z= 0.141 Angle : 0.699 13.030 12437 Z= 0.336 Chirality : 0.044 0.206 1471 Planarity : 0.003 0.035 1497 Dihedral : 10.745 137.087 1117 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 3.32 % Allowed : 16.83 % Favored : 79.85 % 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: -0.02 (0.26), residues: 1011 helix: 1.35 (0.30), residues: 321 sheet: -0.38 (0.44), residues: 144 loop : -0.72 (0.26), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG a 379 TYR 0.022 0.002 TYR A 94 PHE 0.032 0.002 PHE A 191 TRP 0.013 0.001 TRP A 210 HIS 0.009 0.001 HIS B 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 ( 9079) covalent geometry : angle 0.66409 / 0.33 (12275) SS BOND : bond 0.00794 / 0.51 ( 18) SS BOND : angle 1.74249 / 1.00 ( 36) hydrogen bonds : bond 0.03781 / 2.52 ( 356) hydrogen bonds : angle 5.08663 / 3.62 ( 951) link_ALPHA1-3 : bond 0.00638 / 0.39 ( 6) link_ALPHA1-3 : angle 1.28268 / 0.81 ( 18) link_BETA1-3 : bond 0.01090 / 0.73 ( 6) link_BETA1-3 : angle 2.65517 / 1.58 ( 18) link_BETA1-4 : bond 0.00317 / 0.21 ( 9) link_BETA1-4 : angle 1.21778 / 0.74 ( 27) link_NAG-ASN : bond 0.00336 / 0.20 ( 21) link_NAG-ASN : angle 2.35936 / 1.57 ( 63) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 164 time to evaluate : 0.273 Fit side-chains revert: symmetry clash REVERT: a 357 ASP cc_start: 0.7416 (t0) cc_final: 0.7151 (t0) REVERT: a 359 MET cc_start: 0.8606 (mtm) cc_final: 0.8246 (mtm) REVERT: c 357 ASP cc_start: 0.8104 (t0) cc_final: 0.7735 (t0) REVERT: C 125 LYS cc_start: 0.8487 (tppt) cc_final: 0.7697 (ttmm) outliers start: 31 outliers final: 19 residues processed: 179 average time/residue: 0.0911 time to fit residues: 22.9633 Evaluate side-chains 169 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 150 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 265 THR Chi-restraints excluded: chain a residue 324 GLN Chi-restraints excluded: chain b residue 341 VAL Chi-restraints excluded: chain b residue 381 SER Chi-restraints excluded: chain b residue 392 SER Chi-restraints excluded: chain c residue 332 MET Chi-restraints excluded: chain c residue 380 THR Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 179 HIS Chi-restraints excluded: chain B residue 210 TRP Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 179 HIS Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 251 ASP Chi-restraints excluded: chain C residue 258 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 65 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 20 optimal weight: 7.9990 chunk 60 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 21 optimal weight: 0.0770 chunk 39 optimal weight: 4.9990 chunk 98 optimal weight: 0.0470 chunk 22 optimal weight: 0.5980 chunk 92 optimal weight: 5.9990 overall best weight: 0.9440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... c 390 ASN C 127 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.148076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.125951 restraints weight = 13877.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.129150 restraints weight = 9180.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.131392 restraints weight = 6941.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.132681 restraints weight = 5685.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.133787 restraints weight = 4988.794| |-----------------------------------------------------------------------------| r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 moved from start: 0.4766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 9139 Z= 0.151 Angle : 0.696 10.640 12437 Z= 0.336 Chirality : 0.044 0.200 1471 Planarity : 0.003 0.036 1497 Dihedral : 10.711 136.594 1117 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 3.11 % Allowed : 18.22 % Favored : 78.67 % 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: -0.04 (0.27), residues: 1011 helix: 1.38 (0.30), residues: 321 sheet: -0.29 (0.46), residues: 144 loop : -0.79 (0.26), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 250 TYR 0.017 0.001 TYR C 94 PHE 0.009 0.001 PHE A 191 TRP 0.013 0.001 TRP A 210 HIS 0.010 0.001 HIS A 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 ( 9079) covalent geometry : angle 0.66271 / 0.33 (12275) SS BOND : bond 0.00606 / 0.38 ( 18) SS BOND : angle 1.70457 / 0.98 ( 36) hydrogen bonds : bond 0.03774 / 2.51 ( 356) hydrogen bonds : angle 5.05255 / 3.58 ( 951) link_ALPHA1-3 : bond 0.00633 / 0.38 ( 6) link_ALPHA1-3 : angle 1.29346 / 0.81 ( 18) link_BETA1-3 : bond 0.01095 / 0.73 ( 6) link_BETA1-3 : angle 2.66209 / 1.58 ( 18) link_BETA1-4 : bond 0.00262 / 0.17 ( 9) link_BETA1-4 : angle 1.27731 / 0.78 ( 27) link_NAG-ASN : bond 0.00293 / 0.18 ( 21) link_NAG-ASN : angle 2.27929 / 1.51 ( 63) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 163 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 287 GLU cc_start: 0.7854 (mp0) cc_final: 0.7623 (mp0) REVERT: a 312 MET cc_start: 0.7964 (mmt) cc_final: 0.7642 (mmt) REVERT: b 361 ILE cc_start: 0.8579 (OUTLIER) cc_final: 0.8346 (mt) REVERT: c 357 ASP cc_start: 0.8101 (t0) cc_final: 0.7668 (t0) REVERT: C 125 LYS cc_start: 0.8501 (tppt) cc_final: 0.7597 (ttmm) REVERT: C 193 ARG cc_start: 0.7885 (mmm-85) cc_final: 0.7629 (mtp180) outliers start: 29 outliers final: 19 residues processed: 179 average time/residue: 0.0908 time to fit residues: 22.8579 Evaluate side-chains 173 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 153 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 265 THR Chi-restraints excluded: chain b residue 341 VAL Chi-restraints excluded: chain b residue 361 ILE Chi-restraints excluded: chain b residue 381 SER Chi-restraints excluded: chain b residue 392 SER Chi-restraints excluded: chain c residue 332 MET Chi-restraints excluded: chain c residue 358 ILE Chi-restraints excluded: chain c residue 380 THR Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 179 HIS Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 179 HIS Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 258 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 94 optimal weight: 0.6980 chunk 53 optimal weight: 7.9990 chunk 31 optimal weight: 10.0000 chunk 5 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... c 390 ASN C 74 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.147775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.125395 restraints weight = 13969.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.128586 restraints weight = 9247.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.130505 restraints weight = 7008.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.132217 restraints weight = 5839.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.133148 restraints weight = 5045.953| |-----------------------------------------------------------------------------| r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7204 moved from start: 0.5090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9139 Z= 0.139 Angle : 0.689 9.962 12437 Z= 0.330 Chirality : 0.043 0.213 1471 Planarity : 0.003 0.032 1497 Dihedral : 10.688 136.059 1117 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 3.54 % Allowed : 19.51 % Favored : 76.96 % 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: 0.02 (0.27), residues: 1011 helix: 1.46 (0.30), residues: 321 sheet: -0.48 (0.41), residues: 174 loop : -0.70 (0.27), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG a 379 TYR 0.016 0.001 TYR A 94 PHE 0.007 0.001 PHE A 191 TRP 0.014 0.001 TRP A 210 HIS 0.009 0.001 HIS B 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 ( 9079) covalent geometry : angle 0.65844 / 0.32 (12275) SS BOND : bond 0.00547 / 0.35 ( 18) SS BOND : angle 1.59317 / 0.92 ( 36) hydrogen bonds : bond 0.03593 / 2.39 ( 356) hydrogen bonds : angle 4.95348 / 3.52 ( 951) link_ALPHA1-3 : bond 0.00610 / 0.37 ( 6) link_ALPHA1-3 : angle 1.28908 / 0.81 ( 18) link_BETA1-3 : bond 0.01081 / 0.72 ( 6) link_BETA1-3 : angle 2.66165 / 1.57 ( 18) link_BETA1-4 : bond 0.00313 / 0.21 ( 9) link_BETA1-4 : angle 1.25529 / 0.76 ( 27) link_NAG-ASN : bond 0.00283 / 0.17 ( 21) link_NAG-ASN : angle 2.15187 / 1.43 ( 63) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 158 time to evaluate : 0.288 Fit side-chains revert: symmetry clash REVERT: b 361 ILE cc_start: 0.8583 (OUTLIER) cc_final: 0.8346 (mt) REVERT: c 357 ASP cc_start: 0.8098 (t0) cc_final: 0.7676 (t0) REVERT: A 63 LYS cc_start: 0.6903 (OUTLIER) cc_final: 0.6542 (tptp) outliers start: 33 outliers final: 20 residues processed: 178 average time/residue: 0.0924 time to fit residues: 23.2663 Evaluate side-chains 164 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 142 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 265 THR Chi-restraints excluded: chain a residue 324 GLN Chi-restraints excluded: chain b residue 341 VAL Chi-restraints excluded: chain b residue 361 ILE Chi-restraints excluded: chain b residue 381 SER Chi-restraints excluded: chain b residue 392 SER Chi-restraints excluded: chain c residue 332 MET Chi-restraints excluded: chain c residue 358 ILE Chi-restraints excluded: chain c residue 380 THR Chi-restraints excluded: chain A residue 63 LYS Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 179 HIS Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 179 HIS Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 251 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 20 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 chunk 96 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 42 optimal weight: 0.7980 chunk 76 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 52 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 74 ASN C 146 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.147596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.124962 restraints weight = 13795.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.127862 restraints weight = 9237.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.130146 restraints weight = 7114.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.131204 restraints weight = 5862.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.132585 restraints weight = 5237.007| |-----------------------------------------------------------------------------| r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 moved from start: 0.5315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9139 Z= 0.136 Angle : 0.674 9.995 12437 Z= 0.324 Chirality : 0.044 0.200 1471 Planarity : 0.003 0.033 1497 Dihedral : 10.686 135.513 1117 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 3.54 % Allowed : 19.40 % Favored : 77.06 % 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 (0.27), residues: 1011 helix: 1.42 (0.30), residues: 321 sheet: -0.56 (0.41), residues: 174 loop : -0.72 (0.27), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 250 TYR 0.015 0.002 TYR A 94 PHE 0.007 0.001 PHE A 191 TRP 0.013 0.001 TRP A 210 HIS 0.010 0.001 HIS B 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.13 ( 9079) covalent geometry : angle 0.64362 / 0.32 (12275) SS BOND : bond 0.00569 / 0.38 ( 18) SS BOND : angle 1.60279 / 0.93 ( 36) hydrogen bonds : bond 0.03570 / 2.36 ( 356) hydrogen bonds : angle 4.92439 / 3.51 ( 951) link_ALPHA1-3 : bond 0.00627 / 0.37 ( 6) link_ALPHA1-3 : angle 1.27610 / 0.80 ( 18) link_BETA1-3 : bond 0.01082 / 0.72 ( 6) link_BETA1-3 : angle 2.66247 / 1.57 ( 18) link_BETA1-4 : bond 0.00298 / 0.20 ( 9) link_BETA1-4 : angle 1.27816 / 0.77 ( 27) link_NAG-ASN : bond 0.00271 / 0.17 ( 21) link_NAG-ASN : angle 2.10047 / 1.39 ( 63) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 156 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: b 361 ILE cc_start: 0.8595 (OUTLIER) cc_final: 0.8374 (mt) REVERT: c 357 ASP cc_start: 0.8088 (t0) cc_final: 0.7676 (t0) REVERT: c 359 MET cc_start: 0.7588 (mmt) cc_final: 0.7363 (mtt) REVERT: A 63 LYS cc_start: 0.6930 (OUTLIER) cc_final: 0.6499 (tptp) REVERT: C 86 CYS cc_start: 0.3027 (p) cc_final: 0.2286 (p) outliers start: 33 outliers final: 19 residues processed: 173 average time/residue: 0.0900 time to fit residues: 22.2773 Evaluate side-chains 170 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 149 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 265 THR Chi-restraints excluded: chain a residue 324 GLN Chi-restraints excluded: chain b residue 341 VAL Chi-restraints excluded: chain b residue 361 ILE Chi-restraints excluded: chain b residue 381 SER Chi-restraints excluded: chain c residue 332 MET Chi-restraints excluded: chain c residue 358 ILE Chi-restraints excluded: chain c residue 380 THR Chi-restraints excluded: chain A residue 63 LYS Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 179 HIS Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 179 HIS Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 251 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 58 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 100 optimal weight: 0.5980 chunk 1 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 64 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 54 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 127 ASN ** C 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 127 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.142569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.119166 restraints weight = 14039.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.122046 restraints weight = 9619.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.124106 restraints weight = 7516.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.125096 restraints weight = 6322.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.126180 restraints weight = 5711.229| |-----------------------------------------------------------------------------| r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.5795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 9139 Z= 0.212 Angle : 0.775 10.368 12437 Z= 0.374 Chirality : 0.046 0.209 1471 Planarity : 0.003 0.031 1497 Dihedral : 10.880 134.966 1117 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 3.22 % Allowed : 20.04 % Favored : 76.74 % 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: -0.19 (0.27), residues: 1011 helix: 1.32 (0.30), residues: 321 sheet: -0.60 (0.41), residues: 174 loop : -0.86 (0.26), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 193 TYR 0.021 0.002 TYR B 253 PHE 0.013 0.002 PHE b 309 TRP 0.027 0.002 TRP C 227 HIS 0.010 0.001 HIS B 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00500 / 0.21 ( 9079) covalent geometry : angle 0.73929 / 0.37 (12275) SS BOND : bond 0.00769 / 0.47 ( 18) SS BOND : angle 1.95727 / 1.15 ( 36) hydrogen bonds : bond 0.04343 / 2.93 ( 356) hydrogen bonds : angle 5.18579 / 3.68 ( 951) link_ALPHA1-3 : bond 0.00803 / 0.49 ( 6) link_ALPHA1-3 : angle 1.36069 / 0.85 ( 18) link_BETA1-3 : bond 0.01147 / 0.76 ( 6) link_BETA1-3 : angle 2.96531 / 1.76 ( 18) link_BETA1-4 : bond 0.00253 / 0.17 ( 9) link_BETA1-4 : angle 1.61032 / 0.94 ( 27) link_NAG-ASN : bond 0.00272 / 0.16 ( 21) link_NAG-ASN : angle 2.40768 / 1.60 ( 63) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 159 time to evaluate : 0.302 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 287 GLU cc_start: 0.7699 (mp0) cc_final: 0.7339 (mp0) REVERT: c 357 ASP cc_start: 0.8166 (t0) cc_final: 0.7668 (t0) REVERT: A 63 LYS cc_start: 0.6890 (OUTLIER) cc_final: 0.6512 (tptp) REVERT: B 67 GLU cc_start: 0.4538 (tm-30) cc_final: 0.4098 (tm-30) REVERT: C 86 CYS cc_start: 0.3088 (p) cc_final: 0.2460 (p) outliers start: 30 outliers final: 17 residues processed: 177 average time/residue: 0.0876 time to fit residues: 22.1659 Evaluate side-chains 170 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 152 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 265 THR Chi-restraints excluded: chain b residue 341 VAL Chi-restraints excluded: chain b residue 381 SER Chi-restraints excluded: chain c residue 332 MET Chi-restraints excluded: chain c residue 358 ILE Chi-restraints excluded: chain c residue 380 THR Chi-restraints excluded: chain A residue 63 LYS Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 179 HIS Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 179 HIS Chi-restraints excluded: chain C residue 249 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 35 optimal weight: 2.9990 chunk 83 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 42 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 127 ASN C 247 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.144679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.121410 restraints weight = 13807.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.124403 restraints weight = 9417.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.126297 restraints weight = 7311.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.127764 restraints weight = 6175.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.128842 restraints weight = 5442.718| |-----------------------------------------------------------------------------| r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.5995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 9139 Z= 0.154 Angle : 0.746 11.504 12437 Z= 0.357 Chirality : 0.044 0.196 1471 Planarity : 0.003 0.033 1497 Dihedral : 10.824 134.443 1117 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.36 % Allowed : 21.22 % Favored : 76.42 % 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: -0.22 (0.27), residues: 1011 helix: 1.29 (0.30), residues: 324 sheet: -0.69 (0.40), residues: 174 loop : -0.86 (0.27), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 256 TYR 0.013 0.002 TYR B 129 PHE 0.034 0.002 PHE B 191 TRP 0.023 0.001 TRP C 227 HIS 0.005 0.001 HIS B 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 ( 9079) covalent geometry : angle 0.71325 / 0.35 (12275) SS BOND : bond 0.00943 / 0.64 ( 18) SS BOND : angle 2.09591 / 1.28 ( 36) hydrogen bonds : bond 0.03816 / 2.54 ( 356) hydrogen bonds : angle 5.13963 / 3.68 ( 951) link_ALPHA1-3 : bond 0.00691 / 0.44 ( 6) link_ALPHA1-3 : angle 1.32441 / 0.83 ( 18) link_BETA1-3 : bond 0.01154 / 0.77 ( 6) link_BETA1-3 : angle 2.78587 / 1.64 ( 18) link_BETA1-4 : bond 0.00354 / 0.24 ( 9) link_BETA1-4 : angle 1.32112 / 0.78 ( 27) link_NAG-ASN : bond 0.00264 / 0.16 ( 21) link_NAG-ASN : angle 2.17180 / 1.45 ( 63) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 160 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 287 GLU cc_start: 0.7699 (mp0) cc_final: 0.7363 (mp0) REVERT: b 410 MET cc_start: 0.6621 (ttt) cc_final: 0.6218 (mtp) REVERT: c 357 ASP cc_start: 0.8155 (t0) cc_final: 0.7751 (t0) REVERT: A 63 LYS cc_start: 0.7051 (OUTLIER) cc_final: 0.6718 (tptp) REVERT: B 67 GLU cc_start: 0.4459 (tm-30) cc_final: 0.4066 (tm-30) REVERT: C 67 GLU cc_start: 0.6275 (tm-30) cc_final: 0.5603 (tm-30) REVERT: C 86 CYS cc_start: 0.2954 (p) cc_final: 0.2288 (p) REVERT: C 125 LYS cc_start: 0.8327 (tppt) cc_final: 0.7571 (ttmm) REVERT: C 134 MET cc_start: 0.8231 (mmm) cc_final: 0.7933 (tpt) REVERT: C 255 SER cc_start: 0.8508 (m) cc_final: 0.7933 (t) outliers start: 22 outliers final: 16 residues processed: 172 average time/residue: 0.0888 time to fit residues: 21.7517 Evaluate side-chains 164 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 147 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 265 THR Chi-restraints excluded: chain b residue 341 VAL Chi-restraints excluded: chain b residue 381 SER Chi-restraints excluded: chain c residue 332 MET Chi-restraints excluded: chain c residue 358 ILE Chi-restraints excluded: chain c residue 380 THR Chi-restraints excluded: chain A residue 63 LYS Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 179 HIS Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain B residue 223 GLN Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 179 HIS Chi-restraints excluded: chain C residue 249 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 61 optimal weight: 8.9990 chunk 29 optimal weight: 0.6980 chunk 48 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 72 optimal weight: 0.7980 chunk 98 optimal weight: 0.4980 chunk 87 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 4 optimal weight: 0.0970 chunk 28 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... b 335 GLN ** A 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 247 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.146225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.123056 restraints weight = 13719.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.126009 restraints weight = 9291.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.128047 restraints weight = 7196.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.129036 restraints weight = 6035.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.130134 restraints weight = 5429.207| |-----------------------------------------------------------------------------| r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.6124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 9139 Z= 0.139 Angle : 0.741 11.836 12437 Z= 0.355 Chirality : 0.044 0.236 1471 Planarity : 0.004 0.068 1497 Dihedral : 10.792 134.229 1117 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.14 % Allowed : 21.44 % Favored : 76.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.27), residues: 1011 helix: 1.37 (0.30), residues: 324 sheet: -0.71 (0.40), residues: 174 loop : -0.81 (0.27), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 193 TYR 0.013 0.001 TYR C 253 PHE 0.040 0.001 PHE B 191 TRP 0.022 0.001 TRP C 227 HIS 0.005 0.001 HIS A 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 ( 9079) covalent geometry : angle 0.71261 / 0.35 (12275) SS BOND : bond 0.00793 / 0.54 ( 18) SS BOND : angle 1.85807 / 1.11 ( 36) hydrogen bonds : bond 0.03715 / 2.48 ( 356) hydrogen bonds : angle 5.06586 / 3.62 ( 951) link_ALPHA1-3 : bond 0.00595 / 0.36 ( 6) link_ALPHA1-3 : angle 1.24234 / 0.78 ( 18) link_BETA1-3 : bond 0.01089 / 0.72 ( 6) link_BETA1-3 : angle 2.73765 / 1.61 ( 18) link_BETA1-4 : bond 0.00317 / 0.21 ( 9) link_BETA1-4 : angle 1.31042 / 0.78 ( 27) link_NAG-ASN : bond 0.00269 / 0.17 ( 21) link_NAG-ASN : angle 2.03909 / 1.36 ( 63) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1530.90 seconds wall clock time: 27 minutes 29.47 seconds (1649.47 seconds total)