Starting phenix.real_space_refine on Thu Mar 13 17:36:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pvd_13667/03_2025/7pvd_13667.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pvd_13667/03_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_13667/03_2025/7pvd_13667.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pvd_13667/03_2025/7pvd_13667.map" model { file = "/net/cci-nas-00/data/ceres_data/7pvd_13667/03_2025/7pvd_13667.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pvd_13667/03_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-5624/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: 5.62, per 1000 atoms: 0.63 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: 2.81 Conformation dependent library (CDL) restraints added in 903.5 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: 0.90 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: 2.22 Time building geometry restraints manager: 3.04 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: 1.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 22.700 Find NCS groups from input model: 0.390 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.610 ------------------------------------------------------------------------------- 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 9079 Z= 0.484 Angle : 0.826 8.936 12275 Z= 0.393 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 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 286 time to evaluate : 0.946 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: 0.2384 time to fit residues: 90.2635 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 : 0.884 ------------------------------------------------------------------------------- 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: 0.9990 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: 0.8182 ------------------------------------------------------------------------------- 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 = 0.3969 r_free = 0.3969 target = 0.158014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.137265 restraints weight = 13716.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.140478 restraints weight = 8870.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.142779 restraints weight = 6611.662| |-----------------------------------------------------------------------------| r_work (final): 0.3776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6767 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9079 Z= 0.234 Angle : 0.772 10.278 12275 Z= 0.379 Chirality : 0.048 0.297 1471 Planarity : 0.004 0.047 1497 Dihedral : 15.091 128.514 1967 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % 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 (0.24), residues: 1011 helix: 0.75 (0.28), residues: 324 sheet: -0.86 (0.41), residues: 150 loop : -0.80 (0.24), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP a 370 HIS 0.009 0.001 HIS B 93 PHE 0.012 0.002 PHE a 309 TYR 0.018 0.002 TYR C 62 ARG 0.009 0.001 ARG a 379 *********************** 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 205 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 179 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 390 ASN cc_start: 0.7278 (t0) cc_final: 0.6878 (t0) REVERT: b 405 GLN cc_start: 0.7474 (tp40) cc_final: 0.7188 (tt0) REVERT: b 414 MET cc_start: 0.6754 (ttm) cc_final: 0.6398 (ttp) REVERT: c 357 ASP cc_start: 0.7992 (t0) cc_final: 0.7763 (t0) REVERT: A 62 TYR cc_start: 0.5331 (m-80) cc_final: 0.4982 (m-80) REVERT: A 249 THR cc_start: 0.8915 (p) cc_final: 0.8708 (p) REVERT: A 255 SER cc_start: 0.7809 (m) cc_final: 0.7423 (t) outliers start: 26 outliers final: 13 residues processed: 192 average time/residue: 0.2218 time to fit residues: 57.9188 Evaluate side-chains 168 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 155 time to evaluate : 0.901 ------------------------------------------------------------------------------- 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: 1.9990 chunk 98 optimal weight: 0.4980 chunk 75 optimal weight: 3.9990 chunk 94 optimal weight: 0.7980 chunk 100 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 84 optimal weight: 10.0000 chunk 48 optimal weight: 8.9990 chunk 22 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 chunk 17 optimal weight: 0.0670 overall best weight: 0.8720 ------------------------------------------------------------------------------- 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 = 0.3928 r_free = 0.3928 target = 0.154391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.133139 restraints weight = 13932.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.136491 restraints weight = 8999.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.138827 restraints weight = 6647.432| |-----------------------------------------------------------------------------| r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6864 moved from start: 0.3299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9079 Z= 0.221 Angle : 0.714 10.315 12275 Z= 0.347 Chirality : 0.047 0.229 1471 Planarity : 0.004 0.031 1497 Dihedral : 11.808 125.374 1967 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.47 % Allowed : 13.08 % 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: -0.20 (0.26), residues: 1011 helix: 1.00 (0.29), residues: 324 sheet: -0.68 (0.39), residues: 174 loop : -0.61 (0.26), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP a 386 HIS 0.011 0.001 HIS B 93 PHE 0.024 0.002 PHE C 191 TYR 0.025 0.002 TYR A 94 ARG 0.007 0.001 ARG C 193 *********************** 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 195 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 172 time to evaluate : 0.889 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 390 ASN cc_start: 0.7535 (t0) cc_final: 0.7084 (t0) REVERT: b 335 GLN cc_start: 0.7370 (mm-40) cc_final: 0.7062 (mt0) REVERT: b 402 ASP cc_start: 0.7211 (m-30) cc_final: 0.6934 (t0) REVERT: b 405 GLN cc_start: 0.7592 (tp40) cc_final: 0.7340 (tt0) REVERT: b 419 TYR cc_start: 0.2737 (OUTLIER) cc_final: 0.1957 (m-10) REVERT: c 357 ASP cc_start: 0.8006 (t0) cc_final: 0.7758 (t0) REVERT: A 146 ASN cc_start: 0.7598 (m110) cc_final: 0.7394 (m-40) REVERT: A 255 SER cc_start: 0.7734 (m) cc_final: 0.7524 (t) REVERT: C 96 MET cc_start: 0.6510 (ttt) cc_final: 0.5992 (ttt) REVERT: C 227 TRP cc_start: 0.6609 (t60) cc_final: 0.6344 (t60) outliers start: 23 outliers final: 14 residues processed: 185 average time/residue: 0.2000 time to fit residues: 51.4849 Evaluate side-chains 171 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 156 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 265 THR Chi-restraints excluded: chain a residue 324 GLN Chi-restraints excluded: chain a residue 381 SER Chi-restraints excluded: chain b residue 381 SER Chi-restraints excluded: chain b residue 419 TYR Chi-restraints excluded: chain c residue 358 ILE Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 179 HIS Chi-restraints excluded: chain 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: 2.9990 chunk 50 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 14 optimal weight: 0.8980 chunk 98 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 5 optimal weight: 0.5980 chunk 40 optimal weight: 3.9990 chunk 87 optimal weight: 6.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 = 0.3889 r_free = 0.3889 target = 0.151036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.129197 restraints weight = 13779.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.132383 restraints weight = 9016.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.134364 restraints weight = 6802.727| |-----------------------------------------------------------------------------| r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6992 moved from start: 0.3938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9079 Z= 0.240 Angle : 0.693 9.174 12275 Z= 0.339 Chirality : 0.046 0.242 1471 Planarity : 0.004 0.044 1497 Dihedral : 10.149 121.462 1967 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.68 % Allowed : 15.86 % Favored : 81.46 % 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: -0.11 (0.26), residues: 1011 helix: 1.15 (0.29), 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 0.028 0.001 TRP B 210 HIS 0.010 0.001 HIS B 93 PHE 0.010 0.002 PHE A 191 TYR 0.014 0.002 TYR A 253 ARG 0.009 0.001 ARG a 379 *********************** 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 202 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 177 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 359 MET cc_start: 0.8417 (mtm) cc_final: 0.8004 (mtm) REVERT: b 405 GLN cc_start: 0.7753 (tp40) cc_final: 0.7487 (tt0) REVERT: b 419 TYR cc_start: 0.2537 (OUTLIER) cc_final: 0.1651 (m-10) REVERT: c 357 ASP cc_start: 0.8062 (t0) cc_final: 0.7780 (t0) REVERT: A 153 MET cc_start: 0.6122 (mtp) cc_final: 0.5896 (ttt) REVERT: A 255 SER cc_start: 0.7872 (m) cc_final: 0.7632 (t) REVERT: B 193 ARG cc_start: 0.7870 (mmm-85) cc_final: 0.7629 (mmm-85) outliers start: 25 outliers final: 13 residues processed: 189 average time/residue: 0.2110 time to fit residues: 55.1160 Evaluate side-chains 177 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 163 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 265 THR Chi-restraints excluded: chain a residue 381 SER Chi-restraints excluded: chain b residue 381 SER Chi-restraints excluded: chain b residue 419 TYR Chi-restraints excluded: chain c residue 358 ILE Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 179 HIS Chi-restraints excluded: chain B residue 223 GLN Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 258 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 14 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 18 optimal weight: 6.9990 chunk 93 optimal weight: 0.3980 chunk 74 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 chunk 36 optimal weight: 6.9990 chunk 97 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 335 GLN A 146 ASN B 170 HIS C 127 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.149225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.126904 restraints weight = 13779.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.130032 restraints weight = 9134.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.132228 restraints weight = 6959.657| |-----------------------------------------------------------------------------| r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7044 moved from start: 0.4419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9079 Z= 0.233 Angle : 0.674 11.883 12275 Z= 0.336 Chirality : 0.045 0.224 1471 Planarity : 0.004 0.044 1497 Dihedral : 9.710 120.189 1967 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 3.00 % Allowed : 16.61 % Favored : 80.39 % 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 (0.26), residues: 1011 helix: 1.24 (0.29), residues: 324 sheet: -0.51 (0.43), residues: 144 loop : -0.71 (0.26), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 227 HIS 0.017 0.001 HIS A 93 PHE 0.016 0.002 PHE A 191 TYR 0.018 0.002 TYR A 94 ARG 0.008 0.000 ARG a 379 *********************** 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 193 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 165 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 359 MET cc_start: 0.8582 (mtm) cc_final: 0.8242 (mtm) REVERT: c 357 ASP cc_start: 0.8077 (t0) cc_final: 0.7693 (t0) REVERT: A 255 SER cc_start: 0.7876 (m) cc_final: 0.7661 (t) REVERT: C 125 LYS cc_start: 0.8487 (tppt) cc_final: 0.7678 (ttmm) outliers start: 28 outliers final: 20 residues processed: 180 average time/residue: 0.2021 time to fit residues: 50.6080 Evaluate side-chains 178 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 158 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 265 THR Chi-restraints excluded: chain a residue 290 LEU Chi-restraints excluded: chain a residue 324 GLN Chi-restraints excluded: chain b residue 341 VAL Chi-restraints excluded: chain b residue 381 SER Chi-restraints excluded: chain c residue 332 MET Chi-restraints excluded: chain c residue 358 ILE Chi-restraints excluded: chain c residue 380 THR Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 179 HIS Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 179 HIS Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 251 ASP Chi-restraints excluded: chain C residue 258 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 88 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 38 optimal weight: 0.7980 chunk 6 optimal weight: 0.5980 chunk 3 optimal weight: 0.1980 chunk 28 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 335 GLN c 390 ASN B 170 HIS C 127 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.150427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.128324 restraints weight = 13611.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.131450 restraints weight = 9012.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.133696 restraints weight = 6815.936| |-----------------------------------------------------------------------------| r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7020 moved from start: 0.4694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9079 Z= 0.191 Angle : 0.649 10.218 12275 Z= 0.321 Chirality : 0.044 0.223 1471 Planarity : 0.003 0.034 1497 Dihedral : 9.409 118.947 1967 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 3.32 % Allowed : 17.58 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.01 (0.27), residues: 1011 helix: 1.35 (0.30), residues: 321 sheet: -0.53 (0.40), residues: 174 loop : -0.65 (0.27), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 227 HIS 0.010 0.001 HIS B 93 PHE 0.007 0.001 PHE A 191 TYR 0.017 0.001 TYR A 94 ARG 0.006 0.000 ARG a 379 *********************** 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 196 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 165 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 312 MET cc_start: 0.8229 (mmm) cc_final: 0.8014 (mmm) REVERT: b 361 ILE cc_start: 0.8526 (OUTLIER) cc_final: 0.8310 (mt) REVERT: c 357 ASP cc_start: 0.8052 (t0) cc_final: 0.7656 (t0) REVERT: A 158 ASN cc_start: 0.8408 (m-40) cc_final: 0.8206 (m-40) REVERT: A 191 PHE cc_start: 0.7150 (t80) cc_final: 0.6932 (t80) REVERT: A 255 SER cc_start: 0.7906 (m) cc_final: 0.7688 (t) REVERT: C 125 LYS cc_start: 0.8479 (tppt) cc_final: 0.7579 (ttmm) REVERT: C 143 SER cc_start: 0.8368 (m) cc_final: 0.8111 (t) outliers start: 31 outliers final: 18 residues processed: 182 average time/residue: 0.2122 time to fit residues: 53.4946 Evaluate side-chains 173 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 154 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 265 THR Chi-restraints excluded: chain a residue 290 LEU Chi-restraints excluded: chain a residue 324 GLN Chi-restraints excluded: chain a residue 381 SER Chi-restraints excluded: chain b residue 341 VAL Chi-restraints excluded: chain b residue 361 ILE Chi-restraints excluded: chain b residue 381 SER Chi-restraints excluded: chain c residue 332 MET 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 170 HIS Chi-restraints excluded: chain B residue 179 HIS Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 179 HIS Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 258 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 29 optimal weight: 0.9990 chunk 98 optimal weight: 0.8980 chunk 50 optimal weight: 4.9990 chunk 48 optimal weight: 8.9990 chunk 55 optimal weight: 0.9990 chunk 47 optimal weight: 5.9990 chunk 95 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 chunk 75 optimal weight: 0.8980 chunk 68 optimal weight: 0.7980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 335 GLN c 390 ASN B 170 HIS C 127 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.148757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.126315 restraints weight = 13772.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.129499 restraints weight = 9157.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.131599 restraints weight = 6957.894| |-----------------------------------------------------------------------------| r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7069 moved from start: 0.4941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9079 Z= 0.217 Angle : 0.653 9.377 12275 Z= 0.322 Chirality : 0.044 0.220 1471 Planarity : 0.003 0.033 1497 Dihedral : 9.220 118.678 1967 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 3.64 % Allowed : 17.79 % Favored : 78.56 % 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: 0.02 (0.27), residues: 1011 helix: 1.43 (0.30), residues: 321 sheet: -0.52 (0.41), residues: 174 loop : -0.67 (0.27), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 210 HIS 0.011 0.001 HIS B 93 PHE 0.008 0.001 PHE A 191 TYR 0.013 0.001 TYR A 94 ARG 0.003 0.000 ARG a 379 *********************** 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 197 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 163 time to evaluate : 0.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 361 ILE cc_start: 0.8559 (OUTLIER) cc_final: 0.8341 (mt) REVERT: c 357 ASP cc_start: 0.8090 (t0) cc_final: 0.7669 (t0) REVERT: A 63 LYS cc_start: 0.6925 (OUTLIER) cc_final: 0.6693 (tptp) REVERT: A 255 SER cc_start: 0.7874 (m) cc_final: 0.7630 (t) REVERT: C 125 LYS cc_start: 0.8378 (tppt) cc_final: 0.7556 (ttmm) REVERT: C 143 SER cc_start: 0.8402 (m) cc_final: 0.8112 (t) REVERT: C 194 MET cc_start: 0.7656 (OUTLIER) cc_final: 0.7452 (ttt) outliers start: 34 outliers final: 18 residues processed: 182 average time/residue: 0.2194 time to fit residues: 54.4245 Evaluate side-chains 175 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 154 time to evaluate : 0.961 ------------------------------------------------------------------------------- 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 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 380 THR Chi-restraints excluded: chain A residue 63 LYS Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 179 HIS Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 179 HIS Chi-restraints excluded: chain C residue 194 MET Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 258 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 9 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 35 optimal weight: 0.3980 chunk 67 optimal weight: 0.8980 chunk 57 optimal weight: 4.9990 chunk 77 optimal weight: 8.9990 chunk 56 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 335 GLN c 390 ASN C 127 ASN C 146 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.146868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.124034 restraints weight = 13992.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.127148 restraints weight = 9300.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.129299 restraints weight = 7093.740| |-----------------------------------------------------------------------------| r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7121 moved from start: 0.5342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9079 Z= 0.235 Angle : 0.684 12.220 12275 Z= 0.338 Chirality : 0.045 0.216 1471 Planarity : 0.003 0.029 1497 Dihedral : 9.055 117.803 1967 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 3.86 % Allowed : 18.86 % Favored : 77.28 % 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: -0.05 (0.27), residues: 1011 helix: 1.36 (0.30), residues: 324 sheet: -0.52 (0.41), residues: 174 loop : -0.73 (0.28), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 210 HIS 0.010 0.001 HIS B 93 PHE 0.008 0.001 PHE c 399 TYR 0.013 0.001 TYR B 253 ARG 0.004 0.000 ARG a 379 *********************** 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 197 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 161 time to evaluate : 1.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 287 GLU cc_start: 0.7860 (mp0) cc_final: 0.7556 (mp0) REVERT: a 312 MET cc_start: 0.8116 (mmt) cc_final: 0.7830 (mmt) REVERT: a 357 ASP cc_start: 0.7392 (t0) cc_final: 0.7106 (t0) REVERT: b 361 ILE cc_start: 0.8585 (OUTLIER) cc_final: 0.8345 (mt) REVERT: c 357 ASP cc_start: 0.8092 (t0) cc_final: 0.7643 (t0) REVERT: A 63 LYS cc_start: 0.6924 (OUTLIER) cc_final: 0.6480 (tptp) REVERT: A 70 THR cc_start: 0.8143 (OUTLIER) cc_final: 0.7849 (p) REVERT: A 255 SER cc_start: 0.7984 (m) cc_final: 0.7759 (t) REVERT: C 125 LYS cc_start: 0.8381 (tppt) cc_final: 0.7598 (ttmm) REVERT: C 194 MET cc_start: 0.7700 (OUTLIER) cc_final: 0.7347 (ttt) outliers start: 36 outliers final: 18 residues processed: 182 average time/residue: 0.3254 time to fit residues: 84.2777 Evaluate side-chains 174 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 152 time to evaluate : 1.232 ------------------------------------------------------------------------------- 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 341 VAL Chi-restraints excluded: chain b residue 361 ILE Chi-restraints excluded: chain b residue 381 SER Chi-restraints excluded: chain c residue 284 MET Chi-restraints excluded: chain c residue 310 CYS Chi-restraints excluded: chain c residue 380 THR Chi-restraints excluded: chain c residue 390 ASN Chi-restraints excluded: chain A residue 63 LYS Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 179 HIS Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 179 HIS Chi-restraints excluded: chain C residue 194 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: 0.9990 chunk 11 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 24 optimal weight: 0.0060 chunk 47 optimal weight: 3.9990 chunk 22 optimal weight: 0.6980 chunk 28 optimal weight: 0.9990 chunk 75 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 chunk 71 optimal weight: 0.5980 overall best weight: 0.6600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 335 GLN c 390 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.148048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.125314 restraints weight = 13741.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.128447 restraints weight = 9198.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.130599 restraints weight = 7017.104| |-----------------------------------------------------------------------------| r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 moved from start: 0.5459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9079 Z= 0.201 Angle : 0.677 11.438 12275 Z= 0.331 Chirality : 0.044 0.216 1471 Planarity : 0.003 0.032 1497 Dihedral : 8.903 116.902 1967 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.57 % Allowed : 20.04 % Favored : 77.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.04 (0.27), residues: 1011 helix: 1.41 (0.30), residues: 324 sheet: -0.51 (0.41), residues: 174 loop : -0.77 (0.28), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 210 HIS 0.011 0.001 HIS B 93 PHE 0.008 0.001 PHE A 191 TYR 0.013 0.001 TYR B 129 ARG 0.004 0.000 ARG C 193 *********************** 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 187 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 163 time to evaluate : 0.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 312 MET cc_start: 0.7901 (mmt) cc_final: 0.7664 (mmt) REVERT: a 357 ASP cc_start: 0.7443 (t0) cc_final: 0.6877 (t0) REVERT: b 312 MET cc_start: 0.8320 (mmm) cc_final: 0.7998 (mmm) REVERT: b 361 ILE cc_start: 0.8609 (OUTLIER) cc_final: 0.8372 (mt) REVERT: c 357 ASP cc_start: 0.8022 (t0) cc_final: 0.7663 (t0) REVERT: A 63 LYS cc_start: 0.6943 (OUTLIER) cc_final: 0.6525 (tptp) REVERT: A 255 SER cc_start: 0.7930 (m) cc_final: 0.7718 (t) REVERT: B 67 GLU cc_start: 0.4362 (tm-30) cc_final: 0.3856 (tm-30) REVERT: B 244 LEU cc_start: 0.8098 (tt) cc_final: 0.7842 (tt) REVERT: C 227 TRP cc_start: 0.6195 (t60) cc_final: 0.5865 (t60) outliers start: 24 outliers final: 17 residues processed: 178 average time/residue: 0.2069 time to fit residues: 50.5696 Evaluate side-chains 170 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 151 time to evaluate : 0.991 ------------------------------------------------------------------------------- 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 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 358 ILE Chi-restraints excluded: chain c residue 366 TYR Chi-restraints excluded: chain A residue 63 LYS Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 179 HIS Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 179 HIS 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: 5.9990 chunk 55 optimal weight: 0.7980 chunk 79 optimal weight: 0.4980 chunk 37 optimal weight: 0.9990 chunk 45 optimal weight: 5.9990 chunk 61 optimal weight: 4.9990 chunk 46 optimal weight: 0.8980 chunk 90 optimal weight: 4.9990 chunk 63 optimal weight: 7.9990 chunk 86 optimal weight: 0.7980 chunk 81 optimal weight: 0.2980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 335 GLN c 390 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.148238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.125370 restraints weight = 13700.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.128511 restraints weight = 9158.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.130733 restraints weight = 6985.710| |-----------------------------------------------------------------------------| r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7094 moved from start: 0.5679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9079 Z= 0.199 Angle : 0.680 11.998 12275 Z= 0.332 Chirality : 0.044 0.212 1471 Planarity : 0.003 0.043 1497 Dihedral : 8.683 116.055 1967 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.25 % Allowed : 20.36 % Favored : 77.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.02 (0.27), residues: 1011 helix: 1.51 (0.30), residues: 321 sheet: -0.52 (0.41), residues: 174 loop : -0.79 (0.27), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 210 HIS 0.012 0.001 HIS B 93 PHE 0.012 0.001 PHE A 157 TYR 0.014 0.001 TYR C 253 ARG 0.007 0.000 ARG C 193 ********************** 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 183 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 162 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 312 MET cc_start: 0.7946 (mmt) cc_final: 0.7694 (mmt) REVERT: a 357 ASP cc_start: 0.7526 (t0) cc_final: 0.6953 (t0) REVERT: b 361 ILE cc_start: 0.8615 (OUTLIER) cc_final: 0.8383 (mt) REVERT: c 357 ASP cc_start: 0.8083 (t0) cc_final: 0.7737 (t0) REVERT: A 63 LYS cc_start: 0.6727 (OUTLIER) cc_final: 0.6335 (tptp) REVERT: A 255 SER cc_start: 0.7982 (m) cc_final: 0.7747 (t) REVERT: B 67 GLU cc_start: 0.4332 (tm-30) cc_final: 0.3829 (tm-30) REVERT: C 67 GLU cc_start: 0.6249 (tm-30) cc_final: 0.5526 (tm-30) REVERT: C 86 CYS cc_start: 0.2930 (p) cc_final: 0.2197 (p) REVERT: C 134 MET cc_start: 0.8199 (mmm) cc_final: 0.7893 (tpt) outliers start: 21 outliers final: 16 residues processed: 176 average time/residue: 0.2118 time to fit residues: 52.2554 Evaluate side-chains 170 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 152 time to evaluate : 1.003 ------------------------------------------------------------------------------- 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 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 358 ILE Chi-restraints excluded: chain c residue 380 THR Chi-restraints excluded: chain A residue 63 LYS Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 179 HIS Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 179 HIS 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 96 optimal weight: 0.0470 chunk 68 optimal weight: 0.0970 chunk 94 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 60 optimal weight: 0.8980 chunk 53 optimal weight: 4.9990 chunk 92 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 43 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 6 optimal weight: 0.0000 overall best weight: 0.3280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 390 ASN ** 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 = 0.3891 r_free = 0.3891 target = 0.150523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.127866 restraints weight = 13654.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.131018 restraints weight = 9146.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.132989 restraints weight = 6939.553| |-----------------------------------------------------------------------------| r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7055 moved from start: 0.5774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9079 Z= 0.180 Angle : 0.670 12.126 12275 Z= 0.329 Chirality : 0.043 0.221 1471 Planarity : 0.004 0.051 1497 Dihedral : 8.388 114.460 1967 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.93 % Allowed : 20.90 % 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: -0.04 (0.27), residues: 1011 helix: 1.45 (0.30), residues: 324 sheet: -0.54 (0.41), residues: 174 loop : -0.78 (0.28), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 210 HIS 0.010 0.001 HIS B 93 PHE 0.011 0.001 PHE A 157 TYR 0.014 0.001 TYR C 253 ARG 0.008 0.000 ARG C 193 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2978.79 seconds wall clock time: 54 minutes 2.19 seconds (3242.19 seconds total)