Starting phenix.real_space_refine on Tue Mar 3 22:45:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pvd_13667/03_2026/7pvd_13667.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pvd_13667/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/7pvd_13667/03_2026/7pvd_13667.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pvd_13667/03_2026/7pvd_13667.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7pvd_13667/03_2026/7pvd_13667.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pvd_13667/03_2026/7pvd_13667.map" } 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-5986/lib/python3.9/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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 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 dihedrals: 36 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 2.15, 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: 0.74 Conformation dependent library (CDL) restraints added in 289.9 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: 0.20 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: 0.95 Time building geometry restraints manager: 0.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 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: 5595 27.97 - 55.95: 291 55.95 - 83.92: 22 83.92 - 111.90: 51 111.90 - 139.87: 7 Dihedral angle restraints: 5966 sinusoidal: 2942 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 5963 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: 0.990 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.400 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6515 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 : 18.683 139.869 3962 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 covalent geometry : bond 0.00749 ( 9079) covalent geometry : angle 0.82610 (12275) SS BOND : bond 0.00434 ( 18) SS BOND : angle 1.71765 ( 36) hydrogen bonds : bond 0.15468 ( 356) hydrogen bonds : angle 6.48166 ( 951) link_ALPHA1-3 : bond 0.00283 ( 6) link_ALPHA1-3 : angle 1.05867 ( 18) link_BETA1-3 : bond 0.00854 ( 6) link_BETA1-3 : angle 2.33104 ( 18) link_BETA1-4 : bond 0.00297 ( 9) link_BETA1-4 : angle 1.93654 ( 27) link_NAG-ASN : bond 0.00467 ( 21) link_NAG-ASN : angle 1.88325 ( 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 : 0.330 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: 0.1102 time to fit residues: 41.9773 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 : 0.364 ------------------------------------------------------------------------------- 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: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3969 r_free = 0.3969 target = 0.158018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.137191 restraints weight = 13780.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.140400 restraints weight = 8911.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.142406 restraints weight = 6638.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.144224 restraints weight = 5452.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.145245 restraints weight = 4633.096| |-----------------------------------------------------------------------------| r_work (final): 0.3808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6727 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9139 Z= 0.158 Angle : 0.814 16.803 12437 Z= 0.386 Chirality : 0.048 0.294 1471 Planarity : 0.005 0.052 1497 Dihedral : 14.889 128.435 1967 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.57 % Allowed : 11.25 % Favored : 86.17 % 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: -0.50 (0.25), residues: 1011 helix: 0.75 (0.28), residues: 324 sheet: -0.85 (0.41), residues: 150 loop : -0.81 (0.24), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG a 379 TYR 0.020 0.002 TYR C 62 PHE 0.012 0.002 PHE b 318 TRP 0.022 0.002 TRP a 386 HIS 0.008 0.001 HIS B 93 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 9079) covalent geometry : angle 0.76524 (12275) SS BOND : bond 0.00338 ( 18) SS BOND : angle 1.31406 ( 36) hydrogen bonds : bond 0.04819 ( 356) hydrogen bonds : angle 5.51749 ( 951) link_ALPHA1-3 : bond 0.00693 ( 6) link_ALPHA1-3 : angle 1.95436 ( 18) link_BETA1-3 : bond 0.01294 ( 6) link_BETA1-3 : angle 2.90776 ( 18) link_BETA1-4 : bond 0.00309 ( 9) link_BETA1-4 : angle 1.42950 ( 27) link_NAG-ASN : bond 0.00374 ( 21) link_NAG-ASN : angle 3.38877 ( 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 201 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 177 time to evaluate : 0.279 Fit side-chains revert: symmetry clash REVERT: a 390 ASN cc_start: 0.7259 (t0) cc_final: 0.6876 (t0) REVERT: b 312 MET cc_start: 0.7681 (mmm) cc_final: 0.7473 (mmt) REVERT: b 405 GLN cc_start: 0.7436 (tp40) cc_final: 0.7175 (tt0) REVERT: b 414 MET cc_start: 0.6809 (ttm) cc_final: 0.6475 (ttp) REVERT: c 357 ASP cc_start: 0.8022 (t0) cc_final: 0.7789 (t0) REVERT: A 62 TYR cc_start: 0.5344 (m-80) cc_final: 0.4995 (m-80) REVERT: A 249 THR cc_start: 0.8938 (p) cc_final: 0.8571 (p) REVERT: A 255 SER cc_start: 0.7806 (m) cc_final: 0.7424 (t) outliers start: 24 outliers final: 12 residues processed: 189 average time/residue: 0.0963 time to fit residues: 25.1713 Evaluate side-chains 170 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 158 time to evaluate : 0.290 ------------------------------------------------------------------------------- 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 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: 0.9990 chunk 46 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 84 optimal weight: 0.9990 chunk 80 optimal weight: 4.9990 chunk 14 optimal weight: 0.6980 chunk 88 optimal weight: 4.9990 chunk 57 optimal weight: 0.9980 chunk 81 optimal weight: 6.9990 chunk 7 optimal weight: 0.9990 chunk 35 optimal weight: 6.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 ASN B 127 ASN B 170 HIS ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.153504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.132257 restraints weight = 13860.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.135512 restraints weight = 8964.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.137810 restraints weight = 6672.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.139247 restraints weight = 5424.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.140317 restraints weight = 4695.600| |-----------------------------------------------------------------------------| r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6846 moved from start: 0.3390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9139 Z= 0.156 Angle : 0.761 14.869 12437 Z= 0.359 Chirality : 0.047 0.227 1471 Planarity : 0.004 0.032 1497 Dihedral : 11.591 125.063 1967 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.25 % Allowed : 13.18 % Favored : 84.57 % 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: -0.21 (0.26), residues: 1011 helix: 0.97 (0.29), residues: 324 sheet: -0.65 (0.39), residues: 174 loop : -0.60 (0.26), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG a 379 TYR 0.024 0.002 TYR A 94 PHE 0.023 0.002 PHE C 191 TRP 0.013 0.001 TRP a 386 HIS 0.010 0.001 HIS B 93 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 9079) covalent geometry : angle 0.71595 (12275) SS BOND : bond 0.00428 ( 18) SS BOND : angle 1.29689 ( 36) hydrogen bonds : bond 0.04075 ( 356) hydrogen bonds : angle 5.33936 ( 951) link_ALPHA1-3 : bond 0.00605 ( 6) link_ALPHA1-3 : angle 2.12480 ( 18) link_BETA1-3 : bond 0.01129 ( 6) link_BETA1-3 : angle 3.11492 ( 18) link_BETA1-4 : bond 0.00261 ( 9) link_BETA1-4 : angle 1.62549 ( 27) link_NAG-ASN : bond 0.00414 ( 21) link_NAG-ASN : angle 2.87790 ( 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: 21 poor density : 170 time to evaluate : 0.254 Fit side-chains revert: symmetry clash REVERT: b 402 ASP cc_start: 0.7211 (m-30) cc_final: 0.6942 (t0) REVERT: b 405 GLN cc_start: 0.7569 (tp40) cc_final: 0.7323 (tt0) REVERT: c 357 ASP cc_start: 0.8063 (t0) cc_final: 0.7826 (t0) REVERT: A 255 SER cc_start: 0.7740 (m) cc_final: 0.7502 (t) REVERT: C 227 TRP cc_start: 0.6592 (t60) cc_final: 0.6312 (t60) outliers start: 21 outliers final: 13 residues processed: 182 average time/residue: 0.0864 time to fit residues: 21.9736 Evaluate side-chains 168 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 155 time to evaluate : 0.322 ------------------------------------------------------------------------------- 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 73 LEU Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 179 HIS 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: 3.9990 chunk 77 optimal weight: 0.7980 chunk 54 optimal weight: 5.9990 chunk 2 optimal weight: 6.9990 chunk 67 optimal weight: 0.9980 chunk 34 optimal weight: 7.9990 chunk 3 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 5 optimal weight: 0.5980 chunk 42 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 390 ASN b 335 GLN B 170 HIS B 209 ASN C 127 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.152129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.130568 restraints weight = 14013.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.133819 restraints weight = 9143.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.136175 restraints weight = 6845.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.137540 restraints weight = 5539.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.138687 restraints weight = 4810.721| |-----------------------------------------------------------------------------| r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6896 moved from start: 0.3838 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= 0.143 Angle : 0.704 11.048 12437 Z= 0.336 Chirality : 0.045 0.232 1471 Planarity : 0.004 0.041 1497 Dihedral : 10.215 121.869 1967 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.36 % Allowed : 15.43 % Favored : 82.21 % 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: -0.08 (0.26), residues: 1011 helix: 1.20 (0.29), residues: 324 sheet: -0.64 (0.39), residues: 174 loop : -0.60 (0.27), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG a 379 TYR 0.014 0.001 TYR C 94 PHE 0.009 0.002 PHE A 191 TRP 0.026 0.001 TRP B 210 HIS 0.009 0.001 HIS B 93 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 9079) covalent geometry : angle 0.66665 (12275) SS BOND : bond 0.00375 ( 18) SS BOND : angle 1.28845 ( 36) hydrogen bonds : bond 0.03790 ( 356) hydrogen bonds : angle 5.19453 ( 951) link_ALPHA1-3 : bond 0.00503 ( 6) link_ALPHA1-3 : angle 1.67178 ( 18) link_BETA1-3 : bond 0.01155 ( 6) link_BETA1-3 : angle 2.80832 ( 18) link_BETA1-4 : bond 0.00261 ( 9) link_BETA1-4 : angle 1.44661 ( 27) link_NAG-ASN : bond 0.00440 ( 21) link_NAG-ASN : angle 2.54570 ( 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 187 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 165 time to evaluate : 0.333 Fit side-chains revert: symmetry clash REVERT: a 357 ASP cc_start: 0.7143 (t0) cc_final: 0.6895 (t0) REVERT: a 359 MET cc_start: 0.8419 (mtm) cc_final: 0.8002 (mtm) REVERT: c 284 MET cc_start: 0.5511 (mtp) cc_final: 0.5218 (mtp) REVERT: c 357 ASP cc_start: 0.8094 (t0) cc_final: 0.7764 (t0) REVERT: A 255 SER cc_start: 0.7881 (m) cc_final: 0.7633 (t) REVERT: B 193 ARG cc_start: 0.7866 (mmm-85) cc_final: 0.7622 (mmm-85) REVERT: B 251 ASP cc_start: 0.7850 (m-30) cc_final: 0.7544 (t0) outliers start: 22 outliers final: 15 residues processed: 175 average time/residue: 0.0919 time to fit residues: 22.7197 Evaluate side-chains 168 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 153 time to evaluate : 0.323 ------------------------------------------------------------------------------- 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 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 192 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 C residue 97 VAL Chi-restraints excluded: chain C residue 220 LEU 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: 0.0000 chunk 82 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 79 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 92 optimal weight: 0.7980 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 335 GLN 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 = 0.3905 r_free = 0.3905 target = 0.152101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.130134 restraints weight = 13786.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.133312 restraints weight = 9075.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.135275 restraints weight = 6860.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.136991 restraints weight = 5701.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.138158 restraints weight = 4894.931| |-----------------------------------------------------------------------------| r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6922 moved from start: 0.4167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9139 Z= 0.134 Angle : 0.679 9.009 12437 Z= 0.325 Chirality : 0.044 0.223 1471 Planarity : 0.003 0.044 1497 Dihedral : 9.640 120.224 1967 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.57 % Allowed : 17.36 % Favored : 80.06 % 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: 0.01 (0.27), residues: 1011 helix: 1.33 (0.30), residues: 324 sheet: -0.59 (0.39), residues: 174 loop : -0.59 (0.27), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG a 379 TYR 0.019 0.001 TYR A 94 PHE 0.021 0.002 PHE A 191 TRP 0.012 0.001 TRP A 210 HIS 0.016 0.001 HIS A 93 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 9079) covalent geometry : angle 0.64253 (12275) SS BOND : bond 0.00426 ( 18) SS BOND : angle 1.31629 ( 36) hydrogen bonds : bond 0.03669 ( 356) hydrogen bonds : angle 5.05794 ( 951) link_ALPHA1-3 : bond 0.00507 ( 6) link_ALPHA1-3 : angle 1.83243 ( 18) link_BETA1-3 : bond 0.01129 ( 6) link_BETA1-3 : angle 2.87333 ( 18) link_BETA1-4 : bond 0.00293 ( 9) link_BETA1-4 : angle 1.49822 ( 27) link_NAG-ASN : bond 0.00390 ( 21) link_NAG-ASN : angle 2.28615 ( 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 189 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 165 time to evaluate : 0.202 Fit side-chains revert: symmetry clash REVERT: a 357 ASP cc_start: 0.7286 (t0) cc_final: 0.7024 (t0) REVERT: a 359 MET cc_start: 0.8491 (mtm) cc_final: 0.8097 (mtm) REVERT: c 357 ASP cc_start: 0.8083 (t0) cc_final: 0.7733 (t0) REVERT: A 255 SER cc_start: 0.7881 (m) cc_final: 0.7660 (t) REVERT: B 214 MET cc_start: 0.7024 (mpp) cc_final: 0.6769 (mtm) REVERT: B 251 ASP cc_start: 0.7766 (OUTLIER) cc_final: 0.7478 (t0) REVERT: C 125 LYS cc_start: 0.8474 (tppt) cc_final: 0.7668 (ttmm) REVERT: C 193 ARG cc_start: 0.7970 (mmm-85) cc_final: 0.7684 (mtp180) outliers start: 24 outliers final: 18 residues processed: 178 average time/residue: 0.0918 time to fit residues: 22.9934 Evaluate side-chains 171 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 152 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 265 THR Chi-restraints excluded: chain a residue 278 TYR 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 c residue 380 THR 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 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 251 ASP Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 220 LEU 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: 0.8980 chunk 3 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 76 optimal weight: 0.7980 chunk 71 optimal weight: 0.1980 chunk 21 optimal weight: 0.9990 chunk 39 optimal weight: 4.9990 chunk 98 optimal weight: 0.0060 chunk 22 optimal weight: 3.9990 chunk 92 optimal weight: 0.0970 overall best weight: 0.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 390 ASN 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 = 0.3919 r_free = 0.3919 target = 0.153146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.131318 restraints weight = 13647.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.134572 restraints weight = 8947.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.136704 restraints weight = 6722.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.138349 restraints weight = 5540.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.139399 restraints weight = 4754.805| |-----------------------------------------------------------------------------| r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6901 moved from start: 0.4411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9139 Z= 0.120 Angle : 0.668 9.869 12437 Z= 0.318 Chirality : 0.044 0.225 1471 Planarity : 0.003 0.034 1497 Dihedral : 9.367 119.109 1967 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.79 % Allowed : 17.79 % Favored : 79.42 % 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: 0.08 (0.27), residues: 1011 helix: 1.48 (0.30), residues: 321 sheet: -0.57 (0.40), residues: 174 loop : -0.59 (0.27), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 256 TYR 0.018 0.001 TYR A 94 PHE 0.032 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 covalent geometry : bond 0.00267 ( 9079) covalent geometry : angle 0.63528 (12275) SS BOND : bond 0.00349 ( 18) SS BOND : angle 1.18063 ( 36) hydrogen bonds : bond 0.03433 ( 356) hydrogen bonds : angle 4.98050 ( 951) link_ALPHA1-3 : bond 0.00434 ( 6) link_ALPHA1-3 : angle 1.72567 ( 18) link_BETA1-3 : bond 0.01089 ( 6) link_BETA1-3 : angle 2.80353 ( 18) link_BETA1-4 : bond 0.00314 ( 9) link_BETA1-4 : angle 1.40827 ( 27) link_NAG-ASN : bond 0.00404 ( 21) link_NAG-ASN : angle 2.15881 ( 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 181 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 155 time to evaluate : 0.323 Fit side-chains revert: symmetry clash REVERT: a 390 ASN cc_start: 0.7473 (t0) cc_final: 0.7271 (t0) REVERT: c 357 ASP cc_start: 0.8047 (t0) cc_final: 0.7721 (t0) REVERT: B 251 ASP cc_start: 0.7726 (OUTLIER) cc_final: 0.7445 (t0) REVERT: C 125 LYS cc_start: 0.8460 (tppt) cc_final: 0.7607 (ttmm) REVERT: C 193 ARG cc_start: 0.7956 (mmm-85) cc_final: 0.7577 (mtp180) outliers start: 26 outliers final: 15 residues processed: 166 average time/residue: 0.0931 time to fit residues: 21.4066 Evaluate side-chains 168 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 152 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 265 THR Chi-restraints excluded: chain a residue 290 LEU Chi-restraints excluded: chain a residue 324 GLN Chi-restraints excluded: chain b residue 381 SER Chi-restraints excluded: chain b residue 392 SER Chi-restraints excluded: chain c residue 366 TYR Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 192 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 251 ASP Chi-restraints excluded: chain C residue 82 MET 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 94 optimal weight: 0.9990 chunk 53 optimal weight: 7.9990 chunk 31 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 72 optimal weight: 0.5980 chunk 4 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 29 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 170 HIS C 74 ASN C 127 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.150159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.127734 restraints weight = 13817.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.130920 restraints weight = 9196.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.133144 restraints weight = 6999.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.134445 restraints weight = 5763.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.135580 restraints weight = 5073.586| |-----------------------------------------------------------------------------| r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6993 moved from start: 0.4758 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= 0.139 Angle : 0.671 9.255 12437 Z= 0.322 Chirality : 0.044 0.223 1471 Planarity : 0.003 0.032 1497 Dihedral : 9.081 118.227 1967 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 3.75 % Allowed : 17.36 % Favored : 78.89 % 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: 1.53 (0.30), residues: 321 sheet: -0.33 (0.45), residues: 144 loop : -0.77 (0.26), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG a 379 TYR 0.015 0.001 TYR A 94 PHE 0.029 0.001 PHE A 191 TRP 0.014 0.001 TRP A 210 HIS 0.009 0.001 HIS B 170 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 9079) covalent geometry : angle 0.63616 (12275) SS BOND : bond 0.00400 ( 18) SS BOND : angle 1.34423 ( 36) hydrogen bonds : bond 0.03554 ( 356) hydrogen bonds : angle 4.95826 ( 951) link_ALPHA1-3 : bond 0.00382 ( 6) link_ALPHA1-3 : angle 1.70819 ( 18) link_BETA1-3 : bond 0.01097 ( 6) link_BETA1-3 : angle 2.79629 ( 18) link_BETA1-4 : bond 0.00280 ( 9) link_BETA1-4 : angle 1.57199 ( 27) link_NAG-ASN : bond 0.00347 ( 21) link_NAG-ASN : angle 2.22374 ( 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 198 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 163 time to evaluate : 0.328 Fit side-chains revert: symmetry clash REVERT: b 410 MET cc_start: 0.6310 (ttt) cc_final: 0.6038 (mtp) REVERT: c 357 ASP cc_start: 0.8041 (t0) cc_final: 0.7609 (t0) REVERT: A 63 LYS cc_start: 0.6738 (OUTLIER) cc_final: 0.6453 (tptp) REVERT: B 251 ASP cc_start: 0.7725 (OUTLIER) cc_final: 0.7503 (t0) REVERT: C 125 LYS cc_start: 0.8436 (tppt) cc_final: 0.7616 (ttmm) outliers start: 35 outliers final: 21 residues processed: 182 average time/residue: 0.0949 time to fit residues: 23.9704 Evaluate side-chains 177 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 154 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 265 THR Chi-restraints excluded: chain a residue 290 LEU Chi-restraints excluded: chain a residue 324 GLN Chi-restraints excluded: chain a residue 381 SER Chi-restraints excluded: chain b residue 341 VAL Chi-restraints excluded: chain b residue 381 SER Chi-restraints excluded: chain c residue 280 LEU Chi-restraints excluded: chain c residue 332 MET Chi-restraints excluded: chain A residue 63 LYS 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 82 MET Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 179 HIS Chi-restraints excluded: chain B residue 251 ASP 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 214 MET Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 258 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 20 optimal weight: 0.8980 chunk 1 optimal weight: 0.1980 chunk 96 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 chunk 76 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 13 optimal weight: 6.9990 chunk 52 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 390 ASN C 127 ASN C 146 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.150061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.127664 restraints weight = 13712.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.130775 restraints weight = 9171.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.132840 restraints weight = 6981.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.134510 restraints weight = 5814.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.135267 restraints weight = 5037.513| |-----------------------------------------------------------------------------| r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7000 moved from start: 0.5058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9139 Z= 0.127 Angle : 0.662 9.849 12437 Z= 0.318 Chirality : 0.044 0.215 1471 Planarity : 0.003 0.030 1497 Dihedral : 8.868 116.906 1967 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.43 % Allowed : 18.11 % Favored : 78.46 % 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: 1.48 (0.30), residues: 321 sheet: -0.52 (0.43), residues: 156 loop : -0.79 (0.27), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 193 TYR 0.012 0.001 TYR A 94 PHE 0.024 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 covalent geometry : bond 0.00291 ( 9079) covalent geometry : angle 0.62843 (12275) SS BOND : bond 0.00353 ( 18) SS BOND : angle 1.26357 ( 36) hydrogen bonds : bond 0.03505 ( 356) hydrogen bonds : angle 4.96126 ( 951) link_ALPHA1-3 : bond 0.00446 ( 6) link_ALPHA1-3 : angle 1.71115 ( 18) link_BETA1-3 : bond 0.01079 ( 6) link_BETA1-3 : angle 2.79539 ( 18) link_BETA1-4 : bond 0.00320 ( 9) link_BETA1-4 : angle 1.49054 ( 27) link_NAG-ASN : bond 0.00333 ( 21) link_NAG-ASN : angle 2.14143 ( 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 195 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 163 time to evaluate : 0.329 Fit side-chains revert: symmetry clash REVERT: a 390 ASN cc_start: 0.7625 (t0) cc_final: 0.7419 (t0) REVERT: b 361 ILE cc_start: 0.8530 (OUTLIER) cc_final: 0.8328 (mt) REVERT: c 357 ASP cc_start: 0.8033 (t0) cc_final: 0.7662 (t0) REVERT: c 359 MET cc_start: 0.7551 (mmt) cc_final: 0.7345 (mtt) REVERT: A 63 LYS cc_start: 0.6836 (OUTLIER) cc_final: 0.6465 (tptp) REVERT: C 125 LYS cc_start: 0.8423 (tppt) cc_final: 0.7514 (ttmm) outliers start: 32 outliers final: 18 residues processed: 180 average time/residue: 0.0940 time to fit residues: 23.6022 Evaluate side-chains 169 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 149 time to evaluate : 0.263 ------------------------------------------------------------------------------- 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 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 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 C residue 82 MET Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 214 MET 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: 0.6980 chunk 1 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 89 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.146035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.123203 restraints weight = 13805.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.126218 restraints weight = 9296.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.128359 restraints weight = 7138.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.129594 restraints weight = 5954.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.130682 restraints weight = 5275.294| |-----------------------------------------------------------------------------| r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7106 moved from start: 0.5474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9139 Z= 0.170 Angle : 0.725 10.275 12437 Z= 0.348 Chirality : 0.045 0.216 1471 Planarity : 0.003 0.030 1497 Dihedral : 8.825 117.054 1967 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.79 % Allowed : 19.29 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.27), residues: 1011 helix: 1.40 (0.30), residues: 321 sheet: -0.52 (0.43), residues: 156 loop : -0.92 (0.26), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG a 379 TYR 0.015 0.002 TYR B 253 PHE 0.020 0.002 PHE A 191 TRP 0.016 0.001 TRP A 210 HIS 0.010 0.001 HIS B 93 Details of bonding type rmsd covalent geometry : bond 0.00398 ( 9079) covalent geometry : angle 0.68846 (12275) SS BOND : bond 0.00598 ( 18) SS BOND : angle 1.59749 ( 36) hydrogen bonds : bond 0.03965 ( 356) hydrogen bonds : angle 5.04383 ( 951) link_ALPHA1-3 : bond 0.00549 ( 6) link_ALPHA1-3 : angle 1.79080 ( 18) link_BETA1-3 : bond 0.01185 ( 6) link_BETA1-3 : angle 2.88596 ( 18) link_BETA1-4 : bond 0.00192 ( 9) link_BETA1-4 : angle 1.76914 ( 27) link_NAG-ASN : bond 0.00307 ( 21) link_NAG-ASN : angle 2.31139 ( 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: 26 poor density : 163 time to evaluate : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 287 GLU cc_start: 0.7784 (mp0) cc_final: 0.7404 (mp0) REVERT: c 357 ASP cc_start: 0.8109 (t0) cc_final: 0.7638 (t0) REVERT: A 63 LYS cc_start: 0.6944 (OUTLIER) cc_final: 0.6655 (tptp) REVERT: B 251 ASP cc_start: 0.8251 (t0) cc_final: 0.7824 (t0) REVERT: C 86 CYS cc_start: 0.3024 (p) cc_final: 0.2395 (p) REVERT: C 125 LYS cc_start: 0.8371 (tppt) cc_final: 0.7611 (ttmm) REVERT: C 255 SER cc_start: 0.8362 (m) cc_final: 0.7878 (t) outliers start: 26 outliers final: 17 residues processed: 175 average time/residue: 0.0877 time to fit residues: 21.5619 Evaluate side-chains 172 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 154 time to evaluate : 0.308 ------------------------------------------------------------------------------- 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 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 223 GLN Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 214 MET Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 251 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 35 optimal weight: 7.9990 chunk 83 optimal weight: 4.9990 chunk 5 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 19 optimal weight: 0.0370 chunk 69 optimal weight: 4.9990 chunk 72 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 42 optimal weight: 0.8980 overall best weight: 0.6860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 247 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.147993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.125431 restraints weight = 13589.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.128350 restraints weight = 9176.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.130544 restraints weight = 7060.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.131855 restraints weight = 5852.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.132963 restraints weight = 5155.798| |-----------------------------------------------------------------------------| r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7055 moved from start: 0.5645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9139 Z= 0.132 Angle : 0.694 11.680 12437 Z= 0.332 Chirality : 0.044 0.210 1471 Planarity : 0.003 0.032 1497 Dihedral : 8.652 115.256 1967 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.04 % Allowed : 20.26 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.27), residues: 1011 helix: 1.44 (0.30), residues: 321 sheet: -0.53 (0.43), residues: 156 loop : -0.86 (0.27), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG a 379 TYR 0.021 0.001 TYR B 94 PHE 0.017 0.001 PHE A 191 TRP 0.013 0.001 TRP A 210 HIS 0.011 0.001 HIS B 93 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 9079) covalent geometry : angle 0.66110 (12275) SS BOND : bond 0.00477 ( 18) SS BOND : angle 1.38576 ( 36) hydrogen bonds : bond 0.03544 ( 356) hydrogen bonds : angle 4.98219 ( 951) link_ALPHA1-3 : bond 0.00475 ( 6) link_ALPHA1-3 : angle 1.71256 ( 18) link_BETA1-3 : bond 0.01094 ( 6) link_BETA1-3 : angle 2.82414 ( 18) link_BETA1-4 : bond 0.00338 ( 9) link_BETA1-4 : angle 1.56379 ( 27) link_NAG-ASN : bond 0.00325 ( 21) link_NAG-ASN : angle 2.14923 ( 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 175 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 156 time to evaluate : 0.251 Fit side-chains revert: symmetry clash REVERT: c 357 ASP cc_start: 0.8040 (t0) cc_final: 0.7694 (t0) REVERT: A 63 LYS cc_start: 0.6768 (OUTLIER) cc_final: 0.6462 (tptp) REVERT: B 67 GLU cc_start: 0.4303 (tm-30) cc_final: 0.3731 (tm-30) REVERT: C 67 GLU cc_start: 0.6150 (tm-30) cc_final: 0.5459 (tm-30) REVERT: C 86 CYS cc_start: 0.2974 (p) cc_final: 0.2352 (p) REVERT: C 189 GLN cc_start: 0.7828 (mt0) cc_final: 0.7333 (mt0) outliers start: 19 outliers final: 16 residues processed: 167 average time/residue: 0.0888 time to fit residues: 20.6942 Evaluate side-chains 165 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 148 time to evaluate : 0.217 ------------------------------------------------------------------------------- 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 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 C residue 82 MET Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 214 MET Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 251 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 61 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 48 optimal weight: 10.0000 chunk 9 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 chunk 98 optimal weight: 0.0170 chunk 87 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 28 optimal weight: 0.9980 chunk 59 optimal weight: 0.5980 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.149419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.126746 restraints weight = 13505.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.129811 restraints weight = 9080.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.131762 restraints weight = 6960.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.133445 restraints weight = 5806.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.134202 restraints weight = 5039.424| |-----------------------------------------------------------------------------| r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7043 moved from start: 0.5809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9139 Z= 0.127 Angle : 0.707 11.772 12437 Z= 0.336 Chirality : 0.043 0.212 1471 Planarity : 0.003 0.031 1497 Dihedral : 8.385 114.527 1967 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.93 % Allowed : 20.58 % Favored : 77.49 % 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: 1.44 (0.30), residues: 321 sheet: -0.19 (0.52), residues: 117 loop : -0.85 (0.26), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG a 379 TYR 0.019 0.001 TYR B 94 PHE 0.018 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 covalent geometry : bond 0.00288 ( 9079) covalent geometry : angle 0.66829 (12275) SS BOND : bond 0.00358 ( 18) SS BOND : angle 1.31191 ( 36) hydrogen bonds : bond 0.03457 ( 356) hydrogen bonds : angle 4.97861 ( 951) link_ALPHA1-3 : bond 0.00462 ( 6) link_ALPHA1-3 : angle 1.68174 ( 18) link_BETA1-3 : bond 0.01082 ( 6) link_BETA1-3 : angle 2.89261 ( 18) link_BETA1-4 : bond 0.00325 ( 9) link_BETA1-4 : angle 1.59056 ( 27) link_NAG-ASN : bond 0.00625 ( 21) link_NAG-ASN : angle 2.51081 ( 63) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1475.36 seconds wall clock time: 26 minutes 23.71 seconds (1583.71 seconds total)