Starting phenix.real_space_refine on Sun Jul 27 04:53:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pvd_13667/07_2025/7pvd_13667.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pvd_13667/07_2025/7pvd_13667.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7pvd_13667/07_2025/7pvd_13667.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pvd_13667/07_2025/7pvd_13667.map" model { file = "/net/cci-nas-00/data/ceres_data/7pvd_13667/07_2025/7pvd_13667.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pvd_13667/07_2025/7pvd_13667.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.016 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-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 6.05, per 1000 atoms: 0.68 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: 3.25 Conformation dependent library (CDL) restraints added in 966.2 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: 0.94 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: 2.21 Time building geometry restraints manager: 3.53 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: 1.140 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: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 24.890 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:3.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.190 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.016 0.002 TRP A 227 HIS 0.005 0.001 HIS a 305 PHE 0.009 0.001 PHE B 191 TYR 0.021 0.002 TYR A 253 ARG 0.003 0.001 ARG B 193 Details of bonding type rmsd link_NAG-ASN : bond 0.00467 ( 21) link_NAG-ASN : angle 1.88325 ( 63) link_BETA1-4 : bond 0.00297 ( 9) link_BETA1-4 : angle 1.93654 ( 27) link_ALPHA1-3 : bond 0.00283 ( 6) link_ALPHA1-3 : angle 1.05867 ( 18) hydrogen bonds : bond 0.15468 ( 356) hydrogen bonds : angle 6.48166 ( 951) SS BOND : bond 0.00434 ( 18) SS BOND : angle 1.71765 ( 36) link_BETA1-3 : bond 0.00854 ( 6) link_BETA1-3 : angle 2.33104 ( 18) covalent geometry : bond 0.00749 ( 9079) covalent geometry : angle 0.82610 (12275) *********************** 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 : 1.034 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: 0.6897 (t0) REVERT: a 417 LYS cc_start: 0.6310 (mptm) cc_final: 0.6076 (mptt) REVERT: b 312 MET cc_start: 0.7583 (mmm) cc_final: 0.7308 (mmt) REVERT: b 357 ASP cc_start: 0.8004 (t0) cc_final: 0.7760 (t0) REVERT: b 414 MET cc_start: 0.6694 (ttm) cc_final: 0.6481 (ttm) REVERT: c 357 ASP cc_start: 0.8182 (t0) cc_final: 0.7845 (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: 0.7088 (t) REVERT: B 255 SER cc_start: 0.7950 (m) cc_final: 0.7693 (t) REVERT: C 68 LEU cc_start: 0.8077 (tp) cc_final: 0.7827 (tp) outliers start: 3 outliers final: 0 residues processed: 288 average time/residue: 0.2502 time to fit residues: 95.0186 Evaluate side-chains 163 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 0.8980 chunk 77 optimal weight: 0.6980 chunk 42 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 41 optimal weight: 0.5980 chunk 79 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 48 optimal weight: 7.9990 chunk 59 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 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 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.158107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.137318 restraints weight = 13713.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.140519 restraints weight = 8906.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.142798 restraints weight = 6622.487| |-----------------------------------------------------------------------------| r_work (final): 0.3774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6767 moved from start: 0.2663 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= 0.161 Angle : 0.823 16.747 12437 Z= 0.390 Chirality : 0.049 0.298 1471 Planarity : 0.004 0.052 1497 Dihedral : 14.790 128.025 1967 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.79 % Allowed : 10.93 % Favored : 86.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.25), residues: 1011 helix: 0.74 (0.28), residues: 324 sheet: -0.88 (0.41), residues: 150 loop : -0.80 (0.24), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP a 370 HIS 0.008 0.001 HIS B 93 PHE 0.012 0.002 PHE a 309 TYR 0.019 0.002 TYR C 62 ARG 0.008 0.001 ARG a 379 Details of bonding type rmsd link_NAG-ASN : bond 0.00400 ( 21) link_NAG-ASN : angle 3.37667 ( 63) link_BETA1-4 : bond 0.00274 ( 9) link_BETA1-4 : angle 1.43597 ( 27) link_ALPHA1-3 : bond 0.00564 ( 6) link_ALPHA1-3 : angle 1.88109 ( 18) hydrogen bonds : bond 0.04638 ( 356) hydrogen bonds : angle 5.51392 ( 951) SS BOND : bond 0.00449 ( 18) SS BOND : angle 1.33351 ( 36) link_BETA1-3 : bond 0.01143 ( 6) link_BETA1-3 : angle 2.94313 ( 18) covalent geometry : bond 0.00363 ( 9079) covalent geometry : angle 0.77417 (12275) *********************** 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 208 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 182 time to evaluate : 1.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 390 ASN cc_start: 0.7277 (t0) cc_final: 0.6881 (t0) REVERT: b 312 MET cc_start: 0.7655 (mmm) cc_final: 0.7450 (mmp) REVERT: b 405 GLN cc_start: 0.7477 (tp40) cc_final: 0.7193 (tt0) REVERT: c 357 ASP cc_start: 0.7984 (t0) cc_final: 0.7757 (t0) REVERT: A 62 TYR cc_start: 0.5330 (m-80) cc_final: 0.4984 (m-80) REVERT: A 255 SER cc_start: 0.7815 (m) cc_final: 0.7428 (t) outliers start: 26 outliers final: 13 residues processed: 193 average time/residue: 0.2266 time to fit residues: 59.7625 Evaluate side-chains 175 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 162 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 263 THR 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 52 optimal weight: 3.9990 chunk 98 optimal weight: 0.7980 chunk 75 optimal weight: 0.6980 chunk 94 optimal weight: 0.9980 chunk 100 optimal weight: 0.8980 chunk 6 optimal weight: 4.9990 chunk 84 optimal weight: 9.9990 chunk 48 optimal weight: 8.9990 chunk 22 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 17 optimal weight: 0.0570 overall best weight: 0.6898 ------------------------------------------------------------------------------- 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 209 ASN ** B 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 HIS C 127 ASN C 146 ASN ** C 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.155795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.134763 restraints weight = 13940.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.138139 restraints weight = 8928.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.140224 restraints weight = 6589.699| |-----------------------------------------------------------------------------| r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6831 moved from start: 0.3230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9139 Z= 0.139 Angle : 0.742 14.515 12437 Z= 0.350 Chirality : 0.047 0.227 1471 Planarity : 0.004 0.031 1497 Dihedral : 11.625 125.276 1967 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.36 % Allowed : 13.18 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.26), residues: 1011 helix: 0.98 (0.29), residues: 324 sheet: -0.67 (0.39), residues: 174 loop : -0.59 (0.26), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP a 386 HIS 0.011 0.001 HIS B 93 PHE 0.023 0.002 PHE C 191 TYR 0.025 0.002 TYR A 94 ARG 0.008 0.001 ARG C 193 Details of bonding type rmsd link_NAG-ASN : bond 0.00442 ( 21) link_NAG-ASN : angle 2.79127 ( 63) link_BETA1-4 : bond 0.00342 ( 9) link_BETA1-4 : angle 1.51213 ( 27) link_ALPHA1-3 : bond 0.00536 ( 6) link_ALPHA1-3 : angle 2.12999 ( 18) hydrogen bonds : bond 0.03935 ( 356) hydrogen bonds : angle 5.31978 ( 951) SS BOND : bond 0.00364 ( 18) SS BOND : angle 1.15191 ( 36) link_BETA1-3 : bond 0.01140 ( 6) link_BETA1-3 : angle 3.05640 ( 18) covalent geometry : bond 0.00313 ( 9079) covalent geometry : angle 0.69921 (12275) *********************** 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 194 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 172 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 390 ASN cc_start: 0.7444 (t0) cc_final: 0.7005 (t0) REVERT: b 402 ASP cc_start: 0.7190 (m-30) cc_final: 0.6871 (t0) REVERT: b 405 GLN cc_start: 0.7682 (tp40) cc_final: 0.7414 (tt0) REVERT: c 284 MET cc_start: 0.5308 (mtp) cc_final: 0.5070 (mtp) REVERT: c 357 ASP cc_start: 0.7983 (t0) cc_final: 0.7762 (t0) REVERT: A 146 ASN cc_start: 0.7510 (m110) cc_final: 0.7251 (m-40) REVERT: A 255 SER cc_start: 0.7722 (m) cc_final: 0.7521 (t) outliers start: 22 outliers final: 12 residues processed: 184 average time/residue: 0.2055 time to fit residues: 52.6043 Evaluate side-chains 167 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 155 time to evaluate : 0.937 ------------------------------------------------------------------------------- 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 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 73 optimal weight: 0.7980 chunk 50 optimal weight: 0.9990 chunk 11 optimal weight: 4.9990 chunk 14 optimal weight: 0.7980 chunk 98 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 5 optimal weight: 0.5980 chunk 40 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 170 HIS C 127 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.153903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.132691 restraints weight = 13724.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.135963 restraints weight = 8855.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.138193 restraints weight = 6601.161| |-----------------------------------------------------------------------------| r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6893 moved from start: 0.3679 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= 0.137 Angle : 0.700 10.897 12437 Z= 0.333 Chirality : 0.045 0.226 1471 Planarity : 0.004 0.042 1497 Dihedral : 10.141 121.868 1967 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.57 % Allowed : 14.90 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.26), residues: 1011 helix: 1.21 (0.30), residues: 324 sheet: -0.65 (0.39), residues: 174 loop : -0.60 (0.27), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 210 HIS 0.010 0.001 HIS B 93 PHE 0.008 0.001 PHE A 191 TYR 0.013 0.001 TYR A 94 ARG 0.010 0.001 ARG a 379 Details of bonding type rmsd link_NAG-ASN : bond 0.00448 ( 21) link_NAG-ASN : angle 2.49041 ( 63) link_BETA1-4 : bond 0.00335 ( 9) link_BETA1-4 : angle 1.47298 ( 27) link_ALPHA1-3 : bond 0.00483 ( 6) link_ALPHA1-3 : angle 1.65584 ( 18) hydrogen bonds : bond 0.03741 ( 356) hydrogen bonds : angle 5.19534 ( 951) SS BOND : bond 0.00384 ( 18) SS BOND : angle 1.24945 ( 36) link_BETA1-3 : bond 0.01188 ( 6) link_BETA1-3 : angle 2.77384 ( 18) covalent geometry : bond 0.00307 ( 9079) covalent geometry : angle 0.66353 (12275) *********************** 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 192 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 168 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 357 ASP cc_start: 0.7171 (t0) cc_final: 0.6898 (t0) REVERT: a 359 MET cc_start: 0.8314 (mtm) cc_final: 0.7882 (mtm) REVERT: b 335 GLN cc_start: 0.7327 (mm-40) cc_final: 0.7098 (mt0) REVERT: b 402 ASP cc_start: 0.7169 (m-30) cc_final: 0.6924 (t0) REVERT: b 405 GLN cc_start: 0.7631 (tp40) cc_final: 0.7428 (tt0) REVERT: c 357 ASP cc_start: 0.8031 (t0) cc_final: 0.7791 (t0) REVERT: A 255 SER cc_start: 0.7852 (m) cc_final: 0.7586 (t) REVERT: B 251 ASP cc_start: 0.7877 (m-30) cc_final: 0.7564 (t0) REVERT: C 156 ASP cc_start: 0.6443 (t0) cc_final: 0.6242 (t0) outliers start: 24 outliers final: 16 residues processed: 182 average time/residue: 0.2024 time to fit residues: 51.3491 Evaluate side-chains 171 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 155 time to evaluate : 1.031 ------------------------------------------------------------------------------- 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 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 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 14 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 18 optimal weight: 5.9990 chunk 93 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 chunk 72 optimal weight: 0.9980 chunk 36 optimal weight: 5.9990 chunk 97 optimal weight: 6.9990 chunk 55 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 overall best weight: 1.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 390 ASN A 146 ASN B 124 HIS B 170 HIS ** C 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 127 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.145361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.123013 restraints weight = 13817.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.126055 restraints weight = 9251.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.128282 restraints weight = 7093.840| |-----------------------------------------------------------------------------| r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7127 moved from start: 0.4579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 9139 Z= 0.206 Angle : 0.783 9.355 12437 Z= 0.379 Chirality : 0.048 0.231 1471 Planarity : 0.004 0.054 1497 Dihedral : 9.734 120.693 1967 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 3.75 % Allowed : 16.40 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.26), residues: 1011 helix: 1.24 (0.29), residues: 324 sheet: -0.49 (0.44), residues: 141 loop : -0.85 (0.26), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 210 HIS 0.008 0.001 HIS B 93 PHE 0.027 0.002 PHE A 191 TYR 0.024 0.002 TYR A 253 ARG 0.009 0.001 ARG a 379 Details of bonding type rmsd link_NAG-ASN : bond 0.00367 ( 21) link_NAG-ASN : angle 2.63303 ( 63) link_BETA1-4 : bond 0.00226 ( 9) link_BETA1-4 : angle 1.88699 ( 27) link_ALPHA1-3 : bond 0.00370 ( 6) link_ALPHA1-3 : angle 2.00893 ( 18) hydrogen bonds : bond 0.04517 ( 356) hydrogen bonds : angle 5.26541 ( 951) SS BOND : bond 0.00806 ( 18) SS BOND : angle 1.79983 ( 36) link_BETA1-3 : bond 0.01244 ( 6) link_BETA1-3 : angle 3.06445 ( 18) covalent geometry : bond 0.00482 ( 9079) covalent geometry : angle 0.74108 (12275) *********************** 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 214 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 179 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 357 ASP cc_start: 0.7412 (t0) cc_final: 0.7181 (t0) REVERT: a 359 MET cc_start: 0.8618 (mtm) cc_final: 0.8259 (mtm) REVERT: b 414 MET cc_start: 0.7264 (ttp) cc_final: 0.6750 (ttm) REVERT: c 357 ASP cc_start: 0.8135 (t0) cc_final: 0.7678 (t0) REVERT: A 146 ASN cc_start: 0.7872 (m110) cc_final: 0.7604 (m-40) REVERT: B 251 ASP cc_start: 0.7961 (OUTLIER) cc_final: 0.7729 (t0) REVERT: C 125 LYS cc_start: 0.8573 (tppt) cc_final: 0.7725 (ttmm) outliers start: 35 outliers final: 19 residues processed: 196 average time/residue: 0.2556 time to fit residues: 69.7182 Evaluate side-chains 176 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 156 time to evaluate : 1.506 ------------------------------------------------------------------------------- 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 290 LEU Chi-restraints excluded: chain b residue 341 VAL Chi-restraints excluded: chain b residue 381 SER Chi-restraints excluded: chain b residue 411 ILE Chi-restraints excluded: chain c residue 332 MET Chi-restraints excluded: chain c residue 358 ILE Chi-restraints excluded: chain c residue 380 THR Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain B residue 70 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 97 VAL Chi-restraints excluded: chain C residue 249 THR 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 88 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 3 optimal weight: 0.3980 chunk 28 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 335 GLN C 127 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.146429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.124242 restraints weight = 13774.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.127347 restraints weight = 9193.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.129490 restraints weight = 7022.280| |-----------------------------------------------------------------------------| r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7106 moved from start: 0.4960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9139 Z= 0.153 Angle : 0.715 13.194 12437 Z= 0.344 Chirality : 0.045 0.211 1471 Planarity : 0.003 0.042 1497 Dihedral : 9.531 118.816 1967 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 3.00 % Allowed : 18.54 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.26), residues: 1011 helix: 1.29 (0.30), residues: 324 sheet: -0.47 (0.45), residues: 144 loop : -0.81 (0.26), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 210 HIS 0.009 0.001 HIS B 93 PHE 0.008 0.002 PHE c 399 TYR 0.012 0.002 TYR B 253 ARG 0.007 0.001 ARG a 379 Details of bonding type rmsd link_NAG-ASN : bond 0.00333 ( 21) link_NAG-ASN : angle 2.35508 ( 63) link_BETA1-4 : bond 0.00282 ( 9) link_BETA1-4 : angle 1.57722 ( 27) link_ALPHA1-3 : bond 0.00457 ( 6) link_ALPHA1-3 : angle 1.77258 ( 18) hydrogen bonds : bond 0.03888 ( 356) hydrogen bonds : angle 5.14361 ( 951) SS BOND : bond 0.00732 ( 18) SS BOND : angle 1.78968 ( 36) link_BETA1-3 : bond 0.01122 ( 6) link_BETA1-3 : angle 2.93159 ( 18) covalent geometry : bond 0.00353 ( 9079) covalent geometry : angle 0.67625 (12275) *********************** 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 194 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 166 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 361 ILE cc_start: 0.8617 (OUTLIER) cc_final: 0.8373 (mt) REVERT: b 405 GLN cc_start: 0.7627 (tp40) cc_final: 0.7421 (tt0) REVERT: b 414 MET cc_start: 0.7311 (ttp) cc_final: 0.6849 (ttm) REVERT: c 357 ASP cc_start: 0.8032 (t0) cc_final: 0.7594 (t0) REVERT: c 390 ASN cc_start: 0.8291 (t0) cc_final: 0.7955 (t0) REVERT: A 146 ASN cc_start: 0.8170 (m110) cc_final: 0.7864 (m-40) REVERT: B 80 MET cc_start: 0.7083 (mtt) cc_final: 0.6860 (mtt) REVERT: B 251 ASP cc_start: 0.7852 (OUTLIER) cc_final: 0.7592 (t0) outliers start: 28 outliers final: 13 residues processed: 185 average time/residue: 0.2163 time to fit residues: 55.7066 Evaluate side-chains 169 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 154 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 265 THR Chi-restraints excluded: chain b residue 341 VAL Chi-restraints excluded: chain b residue 361 ILE Chi-restraints excluded: chain b residue 381 SER Chi-restraints excluded: chain c residue 358 ILE Chi-restraints excluded: chain A residue 73 LEU 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 97 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 29 optimal weight: 0.5980 chunk 98 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 55 optimal weight: 0.8980 chunk 47 optimal weight: 0.5980 chunk 95 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 335 GLN B 124 HIS C 146 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.146853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.124441 restraints weight = 13883.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.127591 restraints weight = 9270.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.129485 restraints weight = 7080.305| |-----------------------------------------------------------------------------| r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7111 moved from start: 0.5181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 9139 Z= 0.145 Angle : 0.732 15.243 12437 Z= 0.346 Chirality : 0.046 0.234 1471 Planarity : 0.003 0.038 1497 Dihedral : 9.466 118.522 1967 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 3.43 % Allowed : 18.97 % Favored : 77.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.27), residues: 1011 helix: 1.40 (0.30), residues: 321 sheet: -0.44 (0.44), residues: 144 loop : -0.82 (0.26), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 210 HIS 0.010 0.001 HIS B 93 PHE 0.036 0.002 PHE A 191 TYR 0.017 0.001 TYR A 94 ARG 0.003 0.000 ARG A 250 Details of bonding type rmsd link_NAG-ASN : bond 0.00466 ( 21) link_NAG-ASN : angle 3.42842 ( 63) link_BETA1-4 : bond 0.00259 ( 9) link_BETA1-4 : angle 1.58400 ( 27) link_ALPHA1-3 : bond 0.00469 ( 6) link_ALPHA1-3 : angle 1.76653 ( 18) hydrogen bonds : bond 0.03869 ( 356) hydrogen bonds : angle 5.10360 ( 951) SS BOND : bond 0.00613 ( 18) SS BOND : angle 1.67729 ( 36) link_BETA1-3 : bond 0.01124 ( 6) link_BETA1-3 : angle 2.90636 ( 18) covalent geometry : bond 0.00337 ( 9079) covalent geometry : angle 0.67212 (12275) *********************** 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 196 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 164 time to evaluate : 1.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 414 MET cc_start: 0.7319 (ttp) cc_final: 0.6853 (ttm) REVERT: c 357 ASP cc_start: 0.8080 (t0) cc_final: 0.7634 (t0) REVERT: A 63 LYS cc_start: 0.6940 (OUTLIER) cc_final: 0.6528 (tptp) REVERT: B 251 ASP cc_start: 0.7744 (OUTLIER) cc_final: 0.7494 (t0) outliers start: 32 outliers final: 18 residues processed: 182 average time/residue: 0.2140 time to fit residues: 53.7464 Evaluate side-chains 176 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 156 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 265 THR Chi-restraints excluded: chain a residue 324 GLN Chi-restraints excluded: chain b residue 341 VAL Chi-restraints excluded: chain b residue 381 SER Chi-restraints excluded: chain c residue 310 CYS Chi-restraints excluded: chain c residue 332 MET Chi-restraints excluded: chain c residue 380 THR Chi-restraints excluded: chain c residue 410 MET Chi-restraints excluded: chain A residue 63 LYS Chi-restraints excluded: chain A residue 73 LEU 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 249 THR Chi-restraints excluded: chain C residue 251 ASP 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 9 optimal weight: 3.9990 chunk 91 optimal weight: 0.2980 chunk 32 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 chunk 67 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 77 optimal weight: 7.9990 chunk 56 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 21 optimal weight: 0.6980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 335 GLN C 146 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.144413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.121790 restraints weight = 14025.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.124808 restraints weight = 9298.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.126677 restraints weight = 7107.206| |-----------------------------------------------------------------------------| r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7173 moved from start: 0.5605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9139 Z= 0.170 Angle : 0.746 10.634 12437 Z= 0.355 Chirality : 0.046 0.214 1471 Planarity : 0.003 0.039 1497 Dihedral : 9.189 117.948 1967 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 3.64 % Allowed : 19.19 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.27), residues: 1011 helix: 1.39 (0.30), residues: 324 sheet: -0.69 (0.40), residues: 174 loop : -0.82 (0.27), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 210 HIS 0.010 0.001 HIS B 93 PHE 0.023 0.002 PHE A 191 TYR 0.015 0.002 TYR B 253 ARG 0.004 0.001 ARG a 379 Details of bonding type rmsd link_NAG-ASN : bond 0.00501 ( 21) link_NAG-ASN : angle 3.11580 ( 63) link_BETA1-4 : bond 0.00248 ( 9) link_BETA1-4 : angle 1.71889 ( 27) link_ALPHA1-3 : bond 0.00451 ( 6) link_ALPHA1-3 : angle 1.76330 ( 18) hydrogen bonds : bond 0.03976 ( 356) hydrogen bonds : angle 5.11716 ( 951) SS BOND : bond 0.00875 ( 18) SS BOND : angle 1.73904 ( 36) link_BETA1-3 : bond 0.01138 ( 6) link_BETA1-3 : angle 2.92533 ( 18) covalent geometry : bond 0.00397 ( 9079) covalent geometry : angle 0.69404 (12275) *********************** 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 200 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 166 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 287 GLU cc_start: 0.7836 (mp0) cc_final: 0.7544 (mp0) REVERT: a 312 MET cc_start: 0.7925 (OUTLIER) cc_final: 0.7650 (mmp) REVERT: b 361 ILE cc_start: 0.8660 (OUTLIER) cc_final: 0.8442 (mt) REVERT: b 414 MET cc_start: 0.7424 (ttp) cc_final: 0.7010 (ttm) REVERT: c 357 ASP cc_start: 0.8055 (t0) cc_final: 0.7640 (t0) REVERT: A 63 LYS cc_start: 0.7052 (OUTLIER) cc_final: 0.6584 (tptp) REVERT: B 251 ASP cc_start: 0.7741 (OUTLIER) cc_final: 0.7526 (t0) REVERT: C 134 MET cc_start: 0.8301 (mmm) cc_final: 0.8029 (tpt) outliers start: 34 outliers final: 17 residues processed: 185 average time/residue: 0.2173 time to fit residues: 55.8695 Evaluate side-chains 178 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 157 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 265 THR Chi-restraints excluded: chain a residue 312 MET 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 310 CYS Chi-restraints excluded: chain c residue 380 THR Chi-restraints excluded: chain c residue 410 MET Chi-restraints excluded: chain A residue 63 LYS 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 B residue 223 GLN 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 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 17 optimal weight: 0.0670 chunk 11 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 24 optimal weight: 0.5980 chunk 47 optimal weight: 5.9990 chunk 22 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 69 optimal weight: 0.1980 chunk 71 optimal weight: 3.9990 overall best weight: 0.5118 ------------------------------------------------------------------------------- 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 = 0.3848 r_free = 0.3848 target = 0.147351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.124849 restraints weight = 13700.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.127962 restraints weight = 9098.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.130121 restraints weight = 6908.833| |-----------------------------------------------------------------------------| r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7097 moved from start: 0.5728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9139 Z= 0.128 Angle : 0.713 11.077 12437 Z= 0.341 Chirality : 0.044 0.234 1471 Planarity : 0.003 0.039 1497 Dihedral : 8.949 116.339 1967 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.14 % Allowed : 21.11 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.27), residues: 1011 helix: 1.45 (0.30), residues: 324 sheet: -0.62 (0.45), residues: 150 loop : -0.82 (0.27), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP c 283 HIS 0.009 0.001 HIS B 93 PHE 0.007 0.001 PHE B 233 TYR 0.012 0.001 TYR A 62 ARG 0.003 0.000 ARG a 379 Details of bonding type rmsd link_NAG-ASN : bond 0.00462 ( 21) link_NAG-ASN : angle 2.78337 ( 63) link_BETA1-4 : bond 0.00330 ( 9) link_BETA1-4 : angle 1.51879 ( 27) link_ALPHA1-3 : bond 0.00441 ( 6) link_ALPHA1-3 : angle 1.70412 ( 18) hydrogen bonds : bond 0.03638 ( 356) hydrogen bonds : angle 5.09156 ( 951) SS BOND : bond 0.00488 ( 18) SS BOND : angle 1.84940 ( 36) link_BETA1-3 : bond 0.01105 ( 6) link_BETA1-3 : angle 2.86619 ( 18) covalent geometry : bond 0.00290 ( 9079) covalent geometry : angle 0.66625 (12275) *********************** 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 181 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 161 time to evaluate : 1.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 414 MET cc_start: 0.7524 (ttp) cc_final: 0.7046 (ttm) REVERT: c 357 ASP cc_start: 0.7982 (t0) cc_final: 0.7596 (t0) REVERT: A 63 LYS cc_start: 0.6869 (OUTLIER) cc_final: 0.6557 (tptp) REVERT: A 129 TYR cc_start: 0.8251 (p90) cc_final: 0.8018 (p90) REVERT: B 251 ASP cc_start: 0.7632 (m-30) cc_final: 0.7385 (t0) REVERT: C 86 CYS cc_start: 0.3050 (p) cc_final: 0.2294 (p) REVERT: C 134 MET cc_start: 0.8204 (mmm) cc_final: 0.7871 (tpt) REVERT: C 193 ARG cc_start: 0.7969 (mmm-85) cc_final: 0.7655 (mtp180) outliers start: 20 outliers final: 12 residues processed: 173 average time/residue: 0.2248 time to fit residues: 54.2225 Evaluate side-chains 165 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 152 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 265 THR Chi-restraints excluded: chain b residue 381 SER Chi-restraints excluded: chain c residue 310 CYS Chi-restraints excluded: chain c residue 380 THR Chi-restraints excluded: chain c residue 410 MET Chi-restraints excluded: chain A residue 63 LYS 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 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 1 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 chunk 79 optimal weight: 0.0970 chunk 37 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 90 optimal weight: 0.9990 chunk 63 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 81 optimal weight: 6.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 127 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.146744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.124150 restraints weight = 13760.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.127216 restraints weight = 9233.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.129395 restraints weight = 7064.664| |-----------------------------------------------------------------------------| r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7125 moved from start: 0.5894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9139 Z= 0.143 Angle : 0.736 11.720 12437 Z= 0.352 Chirality : 0.044 0.230 1471 Planarity : 0.003 0.040 1497 Dihedral : 8.693 116.139 1967 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.04 % Allowed : 21.22 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.27), residues: 1011 helix: 1.44 (0.30), residues: 324 sheet: -0.67 (0.44), residues: 150 loop : -0.81 (0.27), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP a 370 HIS 0.011 0.001 HIS B 93 PHE 0.008 0.001 PHE A 157 TYR 0.012 0.001 TYR b 278 ARG 0.003 0.000 ARG A 193 Details of bonding type rmsd link_NAG-ASN : bond 0.00432 ( 21) link_NAG-ASN : angle 2.74716 ( 63) link_BETA1-4 : bond 0.00277 ( 9) link_BETA1-4 : angle 1.64498 ( 27) link_ALPHA1-3 : bond 0.00460 ( 6) link_ALPHA1-3 : angle 1.69902 ( 18) hydrogen bonds : bond 0.03769 ( 356) hydrogen bonds : angle 5.12185 ( 951) SS BOND : bond 0.00496 ( 18) SS BOND : angle 1.87132 ( 36) link_BETA1-3 : bond 0.01110 ( 6) link_BETA1-3 : angle 2.95436 ( 18) covalent geometry : bond 0.00329 ( 9079) covalent geometry : angle 0.69005 (12275) ********************** 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 178 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 159 time to evaluate : 1.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 410 MET cc_start: 0.6546 (ttt) cc_final: 0.6192 (mtp) REVERT: b 414 MET cc_start: 0.7533 (ttp) cc_final: 0.7093 (ttm) REVERT: c 357 ASP cc_start: 0.7977 (t0) cc_final: 0.7579 (t0) REVERT: A 63 LYS cc_start: 0.6915 (OUTLIER) cc_final: 0.6665 (tptp) REVERT: A 129 TYR cc_start: 0.8288 (p90) cc_final: 0.8034 (p90) REVERT: B 251 ASP cc_start: 0.7673 (m-30) cc_final: 0.7428 (t0) REVERT: C 86 CYS cc_start: 0.3014 (p) cc_final: 0.2346 (p) REVERT: C 125 LYS cc_start: 0.8314 (tppt) cc_final: 0.7570 (ttmm) REVERT: C 134 MET cc_start: 0.8215 (mmm) cc_final: 0.7951 (tpt) REVERT: C 193 ARG cc_start: 0.7962 (mmm-85) cc_final: 0.7663 (mtp180) REVERT: C 244 LEU cc_start: 0.8517 (tp) cc_final: 0.8287 (tp) outliers start: 19 outliers final: 13 residues processed: 171 average time/residue: 0.2439 time to fit residues: 58.7497 Evaluate side-chains 166 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 152 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 265 THR Chi-restraints excluded: chain a residue 290 LEU Chi-restraints excluded: chain b residue 381 SER Chi-restraints excluded: chain c residue 310 CYS Chi-restraints excluded: chain c residue 358 ILE Chi-restraints excluded: chain c residue 380 THR Chi-restraints excluded: chain c residue 410 MET Chi-restraints excluded: chain A residue 63 LYS 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 249 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 96 optimal weight: 0.7980 chunk 68 optimal weight: 0.6980 chunk 94 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 60 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 92 optimal weight: 0.5980 chunk 89 optimal weight: 5.9990 chunk 43 optimal weight: 5.9990 chunk 23 optimal weight: 0.8980 chunk 6 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 335 GLN ** A 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.146503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.124164 restraints weight = 13707.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.127127 restraints weight = 9280.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.129156 restraints weight = 7136.699| |-----------------------------------------------------------------------------| r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 0.6055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 9139 Z= 0.146 Angle : 0.743 11.709 12437 Z= 0.357 Chirality : 0.045 0.225 1471 Planarity : 0.003 0.038 1497 Dihedral : 8.533 115.091 1967 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.04 % Allowed : 21.65 % Favored : 76.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.27), residues: 1011 helix: 1.34 (0.30), residues: 324 sheet: -0.78 (0.44), residues: 150 loop : -0.81 (0.27), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP C 227 HIS 0.010 0.001 HIS B 93 PHE 0.009 0.001 PHE c 293 TYR 0.013 0.001 TYR b 278 ARG 0.005 0.000 ARG C 193 Details of bonding type rmsd link_NAG-ASN : bond 0.00411 ( 21) link_NAG-ASN : angle 2.66502 ( 63) link_BETA1-4 : bond 0.00298 ( 9) link_BETA1-4 : angle 1.63131 ( 27) link_ALPHA1-3 : bond 0.00471 ( 6) link_ALPHA1-3 : angle 1.71679 ( 18) hydrogen bonds : bond 0.03707 ( 356) hydrogen bonds : angle 5.10975 ( 951) SS BOND : bond 0.00791 ( 18) SS BOND : angle 2.24308 ( 36) link_BETA1-3 : bond 0.01113 ( 6) link_BETA1-3 : angle 2.90194 ( 18) covalent geometry : bond 0.00338 ( 9079) covalent geometry : angle 0.69675 (12275) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3220.33 seconds wall clock time: 58 minutes 29.12 seconds (3509.12 seconds total)