Starting phenix.real_space_refine on Thu Jul 2 08:37:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zta_60457/07_2026/8zta_60457.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zta_60457/07_2026/8zta_60457.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8zta_60457/07_2026/8zta_60457.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zta_60457/07_2026/8zta_60457.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8zta_60457/07_2026/8zta_60457.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zta_60457/07_2026/8zta_60457.map" } resolution = 2.58 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.048 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: 7 Type Number sf(0) Gaussians Ca 4 9.91 5 P 9 5.49 5 Mg 3 5.21 5 S 45 5.16 5 C 5118 2.51 5 N 1359 2.21 5 O 1457 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7995 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2588 Classifications: {'peptide': 330} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 314} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 2588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2588 Classifications: {'peptide': 330} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 314} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 2588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2588 Classifications: {'peptide': 330} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 314} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 74 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {' MG': 1, 'ATP': 1, 'NAG': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 43 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {' MG': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 105 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {' MG': 1, 'ATP': 2, 'NAG': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 1.90, per 1000 atoms: 0.24 Number of scatterers: 7995 At special positions: 0 Unit cell: (84.68, 87.6, 119.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 4 19.99 S 45 16.00 P 9 15.00 Mg 3 11.99 O 1457 8.00 N 1359 7.00 C 5118 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=13, symmetry=0 Simple disulfide: pdb=" SG CYS A 117 " - pdb=" SG CYS A 165 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 149 " distance=2.03 Simple disulfide: pdb=" SG CYS A 132 " - pdb=" SG CYS A 159 " distance=2.03 Simple disulfide: pdb=" SG CYS A 217 " - pdb=" SG CYS A 227 " distance=2.03 Simple disulfide: pdb=" SG CYS A 261 " - pdb=" SG CYS A 270 " distance=2.03 Simple disulfide: pdb=" SG CYS B 117 " - pdb=" SG CYS B 165 " distance=2.03 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 149 " distance=2.03 Simple disulfide: pdb=" SG CYS B 132 " - pdb=" SG CYS B 159 " distance=2.03 Simple disulfide: pdb=" SG CYS B 217 " - pdb=" SG CYS B 227 " distance=2.03 Simple disulfide: pdb=" SG CYS C 117 " - pdb=" SG CYS C 165 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 149 " distance=2.03 Simple disulfide: pdb=" SG CYS C 132 " - pdb=" SG CYS C 159 " distance=2.03 Simple disulfide: pdb=" SG CYS C 217 " - pdb=" SG CYS C 227 " 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 NAG-ASN " NAG A 402 " - " ASN A 210 " " NAG A 403 " - " ASN A 153 " " NAG A 404 " - " ASN A 184 " " NAG B 502 " - " ASN B 210 " " NAG B 503 " - " ASN B 153 " " NAG B 504 " - " ASN B 184 " " NAG C 404 " - " ASN C 210 " " NAG C 405 " - " ASN C 153 " " NAG C 406 " - " ASN C 184 " Time building additional restraints: 0.65 Conformation dependent library (CDL) restraints added in 391.6 milliseconds 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1776 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 19 sheets defined 27.7% alpha, 45.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 26 through 51 removed outlier: 4.686A pdb=" N VAL A 48 " --> pdb=" O VAL A 44 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N PHE A 49 " --> pdb=" O ILE A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 91 Processing helix chain 'A' and resid 179 through 183 Processing helix chain 'A' and resid 210 through 216 removed outlier: 3.667A pdb=" N LYS A 216 " --> pdb=" O THR A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 239 Processing helix chain 'A' and resid 242 through 250 Processing helix chain 'A' and resid 266 through 270 Processing helix chain 'A' and resid 327 through 355 Processing helix chain 'B' and resid 27 through 49 removed outlier: 3.859A pdb=" N ILE B 45 " --> pdb=" O LEU B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 91 Processing helix chain 'B' and resid 179 through 184 removed outlier: 3.756A pdb=" N ASN B 184 " --> pdb=" O GLU B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 217 removed outlier: 3.686A pdb=" N LYS B 215 " --> pdb=" O GLY B 211 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N LYS B 216 " --> pdb=" O THR B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 240 Processing helix chain 'B' and resid 242 through 250 removed outlier: 3.700A pdb=" N GLU B 248 " --> pdb=" O ARG B 244 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N LYS B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 354 Processing helix chain 'C' and resid 27 through 47 Processing helix chain 'C' and resid 86 through 91 Processing helix chain 'C' and resid 180 through 184 removed outlier: 3.704A pdb=" N ASN C 184 " --> pdb=" O GLU C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 216 removed outlier: 3.821A pdb=" N LYS C 215 " --> pdb=" O GLY C 211 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LYS C 216 " --> pdb=" O THR C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 239 Processing helix chain 'C' and resid 242 through 250 removed outlier: 3.512A pdb=" N LYS C 249 " --> pdb=" O SER C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 270 Processing helix chain 'C' and resid 327 through 355 Processing sheet with id=AA1, first strand: chain 'A' and resid 56 through 59 removed outlier: 3.634A pdb=" N LYS A 325 " --> pdb=" O THR A 57 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER A 59 " --> pdb=" O ALA A 323 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA A 323 " --> pdb=" O SER A 59 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY A 251 " --> pdb=" O GLY A 312 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL A 252 " --> pdb=" O LEU A 279 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 99 through 112 removed outlier: 5.574A pdb=" N SER A 99 " --> pdb=" O ILE A 317 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N ILE A 317 " --> pdb=" O SER A 99 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N VAL A 101 " --> pdb=" O PHE A 315 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N PHE A 315 " --> pdb=" O VAL A 101 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N MET A 103 " --> pdb=" O ILE A 313 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ILE A 313 " --> pdb=" O MET A 103 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN A 111 " --> pdb=" O ARG A 305 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N ARG A 305 " --> pdb=" O GLN A 111 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 62 through 70 removed outlier: 4.004A pdb=" N THR A 186 " --> pdb=" O LYS A 70 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 62 through 70 removed outlier: 4.004A pdb=" N THR A 186 " --> pdb=" O LYS A 70 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 73 through 76 Processing sheet with id=AA6, first strand: chain 'A' and resid 114 through 118 removed outlier: 5.037A pdb=" N ASN A 148 " --> pdb=" O GLU A 160 " (cutoff:3.500A) removed outlier: 8.765A pdb=" N PHE A 162 " --> pdb=" O THR A 146 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N THR A 146 " --> pdb=" O PHE A 162 " (cutoff:3.500A) removed outlier: 9.376A pdb=" N TRP A 164 " --> pdb=" O ILE A 144 " (cutoff:3.500A) removed outlier: 9.358A pdb=" N ILE A 144 " --> pdb=" O TRP A 164 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 56 through 60 removed outlier: 3.672A pdb=" N LYS B 325 " --> pdb=" O THR B 57 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N SER B 59 " --> pdb=" O ALA B 323 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ALA B 323 " --> pdb=" O SER B 59 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLY B 251 " --> pdb=" O GLY B 312 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N CYS B 261 " --> pdb=" O LYS B 322 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY B 324 " --> pdb=" O CYS B 261 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL B 252 " --> pdb=" O LEU B 279 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 100 through 112 removed outlier: 5.373A pdb=" N VAL B 101 " --> pdb=" O PHE B 315 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N PHE B 315 " --> pdb=" O VAL B 101 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N MET B 103 " --> pdb=" O ILE B 313 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ILE B 313 " --> pdb=" O MET B 103 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN B 111 " --> pdb=" O ARG B 305 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N ARG B 305 " --> pdb=" O GLN B 111 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 62 through 70 removed outlier: 3.958A pdb=" N THR B 186 " --> pdb=" O LYS B 70 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 62 through 70 removed outlier: 3.958A pdb=" N THR B 186 " --> pdb=" O LYS B 70 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 73 through 75 Processing sheet with id=AB3, first strand: chain 'B' and resid 114 through 118 removed outlier: 5.174A pdb=" N ASN B 148 " --> pdb=" O GLU B 160 " (cutoff:3.500A) removed outlier: 8.562A pdb=" N PHE B 162 " --> pdb=" O THR B 146 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N THR B 146 " --> pdb=" O PHE B 162 " (cutoff:3.500A) removed outlier: 9.383A pdb=" N TRP B 164 " --> pdb=" O ILE B 144 " (cutoff:3.500A) removed outlier: 9.656A pdb=" N ILE B 144 " --> pdb=" O TRP B 164 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 56 through 60 removed outlier: 3.540A pdb=" N LYS C 325 " --> pdb=" O THR C 57 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER C 59 " --> pdb=" O ALA C 323 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ALA C 323 " --> pdb=" O SER C 59 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLY C 251 " --> pdb=" O GLY C 312 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TRP C 259 " --> pdb=" O ASP C 320 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N CYS C 261 " --> pdb=" O LYS C 322 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY C 324 " --> pdb=" O CYS C 261 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 99 through 112 removed outlier: 5.443A pdb=" N SER C 99 " --> pdb=" O ILE C 317 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N ILE C 317 " --> pdb=" O SER C 99 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N VAL C 101 " --> pdb=" O PHE C 315 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N PHE C 315 " --> pdb=" O VAL C 101 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N MET C 103 " --> pdb=" O ILE C 313 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ILE C 313 " --> pdb=" O MET C 103 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N ARG C 305 " --> pdb=" O GLN C 111 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 62 through 70 removed outlier: 3.989A pdb=" N THR C 186 " --> pdb=" O LYS C 70 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL C 200 " --> pdb=" O PHE C 195 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 62 through 70 removed outlier: 3.989A pdb=" N THR C 186 " --> pdb=" O LYS C 70 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 73 through 75 Processing sheet with id=AB9, first strand: chain 'C' and resid 114 through 118 Processing sheet with id=AC1, first strand: chain 'C' and resid 135 through 136 381 hydrogen bonds defined for protein. 1050 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.19 Time building geometry restraints manager: 0.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2519 1.34 - 1.46: 1960 1.46 - 1.58: 3639 1.58 - 1.70: 15 1.70 - 1.82: 57 Bond restraints: 8190 Sorted by residual: bond pdb=" C4 ATP A 401 " pdb=" C5 ATP A 401 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.47e+01 bond pdb=" C4 ATP C 403 " pdb=" C5 ATP C 403 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.31e+01 bond pdb=" C4 ATP C 401 " pdb=" C5 ATP C 401 " ideal model delta sigma weight residual 1.388 1.466 -0.078 1.00e-02 1.00e+04 6.15e+01 bond pdb=" C5 ATP C 403 " pdb=" C6 ATP C 403 " ideal model delta sigma weight residual 1.409 1.479 -0.070 1.00e-02 1.00e+04 4.88e+01 bond pdb=" C5 ATP A 401 " pdb=" C6 ATP A 401 " ideal model delta sigma weight residual 1.409 1.479 -0.070 1.00e-02 1.00e+04 4.85e+01 ... (remaining 8185 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.41: 11046 3.41 - 6.81: 60 6.81 - 10.22: 9 10.22 - 13.62: 1 13.62 - 17.03: 5 Bond angle restraints: 11121 Sorted by residual: angle pdb=" PB ATP A 401 " pdb=" O3B ATP A 401 " pdb=" PG ATP A 401 " ideal model delta sigma weight residual 139.87 122.84 17.03 1.00e+00 1.00e+00 2.90e+02 angle pdb=" PB ATP C 403 " pdb=" O3B ATP C 403 " pdb=" PG ATP C 403 " ideal model delta sigma weight residual 139.87 122.97 16.90 1.00e+00 1.00e+00 2.85e+02 angle pdb=" PB ATP C 401 " pdb=" O3B ATP C 401 " pdb=" PG ATP C 401 " ideal model delta sigma weight residual 139.87 123.06 16.81 1.00e+00 1.00e+00 2.83e+02 angle pdb=" PA ATP C 401 " pdb=" O3A ATP C 401 " pdb=" PB ATP C 401 " ideal model delta sigma weight residual 136.83 121.94 14.89 1.00e+00 1.00e+00 2.22e+02 angle pdb=" PA ATP C 403 " pdb=" O3A ATP C 403 " pdb=" PB ATP C 403 " ideal model delta sigma weight residual 136.83 122.55 14.28 1.00e+00 1.00e+00 2.04e+02 ... (remaining 11116 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 4722 17.69 - 35.37: 172 35.37 - 53.06: 43 53.06 - 70.74: 13 70.74 - 88.43: 9 Dihedral angle restraints: 4959 sinusoidal: 2169 harmonic: 2790 Sorted by residual: dihedral pdb=" CB GLU B 168 " pdb=" CG GLU B 168 " pdb=" CD GLU B 168 " pdb=" OE1 GLU B 168 " ideal model delta sinusoidal sigma weight residual 0.00 88.43 -88.43 1 3.00e+01 1.11e-03 1.04e+01 dihedral pdb=" CB GLU A 260 " pdb=" CG GLU A 260 " pdb=" CD GLU A 260 " pdb=" OE1 GLU A 260 " ideal model delta sinusoidal sigma weight residual 0.00 -83.57 83.57 1 3.00e+01 1.11e-03 9.47e+00 dihedral pdb=" CA LEU A 72 " pdb=" CB LEU A 72 " pdb=" CG LEU A 72 " pdb=" CD1 LEU A 72 " ideal model delta sinusoidal sigma weight residual 60.00 118.84 -58.84 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 4956 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1063 0.069 - 0.138: 166 0.138 - 0.206: 10 0.206 - 0.275: 0 0.275 - 0.344: 3 Chirality restraints: 1242 Sorted by residual: chirality pdb=" C1 NAG B 504 " pdb=" ND2 ASN B 184 " pdb=" C2 NAG B 504 " pdb=" O5 NAG B 504 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.96e+00 chirality pdb=" C1 NAG C 406 " pdb=" ND2 ASN C 184 " pdb=" C2 NAG C 406 " pdb=" O5 NAG C 406 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.94e+00 chirality pdb=" C1 NAG A 404 " pdb=" ND2 ASN A 184 " pdb=" C2 NAG A 404 " pdb=" O5 NAG A 404 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.84e+00 ... (remaining 1239 not shown) Planarity restraints: 1407 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 329 " -0.040 5.00e-02 4.00e+02 6.09e-02 5.93e+00 pdb=" N PRO B 330 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO B 330 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 330 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 329 " 0.028 5.00e-02 4.00e+02 4.25e-02 2.89e+00 pdb=" N PRO C 330 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO C 330 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 330 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 329 " -0.025 5.00e-02 4.00e+02 3.85e-02 2.37e+00 pdb=" N PRO A 330 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 330 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 330 " -0.022 5.00e-02 4.00e+02 ... (remaining 1404 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.38: 13 2.38 - 3.01: 4401 3.01 - 3.64: 11607 3.64 - 4.27: 18428 4.27 - 4.90: 30761 Nonbonded interactions: 65210 Sorted by model distance: nonbonded pdb=" O3G ATP C 401 " pdb="MG MG C 402 " model vdw 1.749 2.170 nonbonded pdb="MG MG A 405 " pdb=" O3G ATP C 403 " model vdw 2.043 2.170 nonbonded pdb=" O3G ATP A 401 " pdb="MG MG B 501 " model vdw 2.280 2.170 nonbonded pdb=" O GLU C 183 " pdb=" N GLY C 233 " model vdw 2.313 3.120 nonbonded pdb=" O ILE B 189 " pdb=" ND2 ASN B 204 " model vdw 2.334 3.120 ... (remaining 65205 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' and (resid 26 through 355 or resid 404)) selection = (chain 'B' and (resid 26 through 355 or resid 504)) selection = (chain 'C' and (resid 26 through 355 or resid 404)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.130 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.560 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7102 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 8212 Z= 0.333 Angle : 0.777 17.027 11174 Z= 0.570 Chirality : 0.049 0.344 1242 Planarity : 0.004 0.061 1398 Dihedral : 10.699 88.425 3144 Min Nonbonded Distance : 1.749 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.84 % Allowed : 4.73 % Favored : 92.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.27), residues: 984 helix: 0.33 (0.34), residues: 279 sheet: 1.39 (0.28), residues: 303 loop : -1.21 (0.29), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 244 TYR 0.009 0.001 TYR B 90 PHE 0.012 0.001 PHE C 342 TRP 0.004 0.001 TRP C 47 HIS 0.002 0.000 HIS A 355 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.33 ( 8190) covalent geometry : angle 0.75921 / 0.57 (11121) SS BOND : bond 0.00190 / 0.13 ( 13) SS BOND : angle 0.83866 / 0.57 ( 26) hydrogen bonds : bond 0.23580 / 15.80 ( 354) hydrogen bonds : angle 8.28198 / 5.80 ( 1050) link_NAG-ASN : bond 0.00755 / 0.44 ( 9) link_NAG-ASN : angle 3.44161 / 2.35 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 236 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 3 residues processed: 250 average time/residue: 0.5255 time to fit residues: 139.7803 Evaluate side-chains 117 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 114 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ARG Chi-restraints excluded: chain A residue 210 ASN Chi-restraints excluded: chain B residue 284 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 30.0000 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 7.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 116 HIS A 180 HIS A 191 ASN A 220 HIS A 241 GLN B 56 GLN B 76 GLN B 180 HIS B 191 ASN B 220 HIS B 300 ASN ** C 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 220 HIS C 241 GLN C 269 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.120790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.094680 restraints weight = 13021.414| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 2.98 r_work: 0.3144 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8212 Z= 0.180 Angle : 0.741 20.892 11174 Z= 0.366 Chirality : 0.051 0.335 1242 Planarity : 0.004 0.043 1398 Dihedral : 9.927 88.403 1355 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 5.08 % Allowed : 13.59 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.27), residues: 984 helix: 1.02 (0.34), residues: 264 sheet: 1.44 (0.29), residues: 309 loop : -0.77 (0.29), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 244 TYR 0.030 0.002 TYR C 90 PHE 0.021 0.002 PHE C 92 TRP 0.006 0.001 TRP B 47 HIS 0.011 0.001 HIS B 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.18 ( 8190) covalent geometry : angle 0.67459 / 0.35 (11121) SS BOND : bond 0.00473 / 0.28 ( 13) SS BOND : angle 3.08039 / 2.20 ( 26) hydrogen bonds : bond 0.03800 / 2.48 ( 354) hydrogen bonds : angle 5.68090 / 3.93 ( 1050) link_NAG-ASN : bond 0.01444 / 1.00 ( 9) link_NAG-ASN : angle 5.52186 / 3.49 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 118 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 56 GLN cc_start: 0.7866 (mt0) cc_final: 0.7463 (mt0) REVERT: A 138 GLU cc_start: 0.8566 (pm20) cc_final: 0.8332 (pt0) REVERT: A 327 ASP cc_start: 0.8094 (t0) cc_final: 0.7851 (t0) REVERT: B 44 VAL cc_start: 0.8481 (OUTLIER) cc_final: 0.8266 (m) REVERT: C 116 HIS cc_start: 0.7828 (m-70) cc_final: 0.7487 (m90) REVERT: C 181 GLU cc_start: 0.7918 (mm-30) cc_final: 0.7603 (mm-30) REVERT: C 208 GLU cc_start: 0.7704 (mp0) cc_final: 0.7501 (mp0) REVERT: C 320 ASP cc_start: 0.7918 (t0) cc_final: 0.7648 (t0) outliers start: 43 outliers final: 15 residues processed: 149 average time/residue: 0.4262 time to fit residues: 68.8361 Evaluate side-chains 114 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 98 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ARG Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 210 ASN Chi-restraints excluded: chain A residue 270 CYS Chi-restraints excluded: chain A residue 275 GLN Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 339 ILE Chi-restraints excluded: chain C residue 44 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 69 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 76 optimal weight: 9.9990 chunk 1 optimal weight: 7.9990 chunk 92 optimal weight: 0.4980 chunk 51 optimal weight: 0.4980 chunk 32 optimal weight: 6.9990 chunk 31 optimal weight: 5.9990 chunk 2 optimal weight: 0.9980 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 37 GLN A 83 GLN A 116 HIS ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 180 HIS A 241 GLN B 76 GLN B 114 GLN B 180 HIS C 241 GLN C 269 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.112009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.084373 restraints weight = 12946.452| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 2.99 r_work: 0.2983 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.3507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 8212 Z= 0.191 Angle : 0.759 13.112 11174 Z= 0.373 Chirality : 0.049 0.272 1242 Planarity : 0.004 0.033 1398 Dihedral : 10.480 88.554 1353 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 5.44 % Allowed : 14.89 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.27), residues: 984 helix: 1.29 (0.35), residues: 261 sheet: 1.06 (0.29), residues: 300 loop : -0.74 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 244 TYR 0.026 0.002 TYR C 90 PHE 0.027 0.002 PHE A 92 TRP 0.012 0.001 TRP C 164 HIS 0.007 0.001 HIS B 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.19 ( 8190) covalent geometry : angle 0.70704 / 0.36 (11121) SS BOND : bond 0.00582 / 0.34 ( 13) SS BOND : angle 4.15761 / 2.97 ( 26) hydrogen bonds : bond 0.03410 / 2.20 ( 354) hydrogen bonds : angle 5.36719 / 3.69 ( 1050) link_NAG-ASN : bond 0.00725 / 0.45 ( 9) link_NAG-ASN : angle 3.94478 / 2.63 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 101 time to evaluate : 0.342 Fit side-chains revert: symmetry clash REVERT: A 56 GLN cc_start: 0.7780 (mt0) cc_final: 0.7439 (mt0) REVERT: A 108 MET cc_start: 0.9137 (OUTLIER) cc_final: 0.8113 (tpt) REVERT: A 210 ASN cc_start: 0.6320 (OUTLIER) cc_final: 0.6040 (p0) REVERT: A 327 ASP cc_start: 0.8018 (t0) cc_final: 0.7637 (t0) REVERT: B 44 VAL cc_start: 0.8393 (OUTLIER) cc_final: 0.8184 (m) REVERT: B 197 ARG cc_start: 0.8859 (mtp85) cc_final: 0.8479 (ttt90) REVERT: C 116 HIS cc_start: 0.7934 (m-70) cc_final: 0.7663 (m90) REVERT: C 122 GLU cc_start: 0.8982 (OUTLIER) cc_final: 0.8754 (pp20) outliers start: 46 outliers final: 16 residues processed: 135 average time/residue: 0.3441 time to fit residues: 50.6566 Evaluate side-chains 106 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 86 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ARG Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain A residue 149 CYS Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 210 ASN Chi-restraints excluded: chain A residue 270 CYS Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 339 ILE Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain C residue 126 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 92 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 chunk 41 optimal weight: 4.9990 chunk 22 optimal weight: 0.7980 chunk 18 optimal weight: 0.5980 chunk 87 optimal weight: 0.0170 chunk 68 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 overall best weight: 0.6620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 37 GLN ** A 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS C 191 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.113588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.085920 restraints weight = 13129.111| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 3.03 r_work: 0.2995 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.3782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 8212 Z= 0.125 Angle : 0.680 12.043 11174 Z= 0.337 Chirality : 0.046 0.244 1242 Planarity : 0.004 0.041 1398 Dihedral : 9.501 89.242 1353 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.66 % Allowed : 18.20 % Favored : 78.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.27), residues: 984 helix: 1.55 (0.35), residues: 255 sheet: 0.87 (0.30), residues: 273 loop : -0.74 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 244 TYR 0.027 0.001 TYR C 90 PHE 0.017 0.001 PHE C 92 TRP 0.010 0.001 TRP C 164 HIS 0.003 0.000 HIS B 266 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.12 ( 8190) covalent geometry : angle 0.62959 / 0.32 (11121) SS BOND : bond 0.00428 / 0.27 ( 13) SS BOND : angle 4.02768 / 2.95 ( 26) hydrogen bonds : bond 0.02828 / 1.79 ( 354) hydrogen bonds : angle 5.12385 / 3.53 ( 1050) link_NAG-ASN : bond 0.00414 / 0.21 ( 9) link_NAG-ASN : angle 3.52853 / 2.44 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 98 time to evaluate : 0.418 Fit side-chains revert: symmetry clash REVERT: A 56 GLN cc_start: 0.7799 (mt0) cc_final: 0.7477 (mt0) REVERT: A 108 MET cc_start: 0.9126 (OUTLIER) cc_final: 0.8175 (tpt) REVERT: A 210 ASN cc_start: 0.6277 (OUTLIER) cc_final: 0.5995 (p0) REVERT: A 327 ASP cc_start: 0.8026 (t0) cc_final: 0.7619 (t0) REVERT: B 197 ARG cc_start: 0.8850 (mtp85) cc_final: 0.8516 (ttt90) REVERT: B 258 ASP cc_start: 0.8716 (OUTLIER) cc_final: 0.7978 (t0) REVERT: B 322 LYS cc_start: 0.8654 (pttm) cc_final: 0.8389 (pttm) REVERT: C 320 ASP cc_start: 0.8113 (t0) cc_final: 0.7879 (t70) outliers start: 31 outliers final: 11 residues processed: 122 average time/residue: 0.3849 time to fit residues: 51.0122 Evaluate side-chains 96 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 82 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ARG Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain A residue 149 CYS Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 210 ASN Chi-restraints excluded: chain A residue 270 CYS Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain C residue 126 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 53 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 31 optimal weight: 6.9990 chunk 22 optimal weight: 0.7980 chunk 82 optimal weight: 6.9990 chunk 19 optimal weight: 0.3980 chunk 44 optimal weight: 5.9990 chunk 84 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 20 optimal weight: 0.0870 chunk 14 optimal weight: 4.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 37 GLN ** A 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 114 GLN C 116 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.113975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.086402 restraints weight = 13111.797| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 3.07 r_work: 0.3017 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.3907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 8212 Z= 0.119 Angle : 0.648 10.129 11174 Z= 0.324 Chirality : 0.045 0.216 1242 Planarity : 0.004 0.040 1398 Dihedral : 9.096 83.294 1353 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 4.26 % Allowed : 18.20 % Favored : 77.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.27), residues: 984 helix: 1.59 (0.35), residues: 261 sheet: 0.82 (0.30), residues: 273 loop : -0.70 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 244 TYR 0.026 0.002 TYR C 90 PHE 0.016 0.002 PHE C 92 TRP 0.010 0.001 TRP C 164 HIS 0.002 0.000 HIS A 277 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 ( 8190) covalent geometry : angle 0.60432 / 0.31 (11121) SS BOND : bond 0.00411 / 0.29 ( 13) SS BOND : angle 3.89097 / 2.76 ( 26) hydrogen bonds : bond 0.02712 / 1.72 ( 354) hydrogen bonds : angle 5.02941 / 3.46 ( 1050) link_NAG-ASN : bond 0.00531 / 0.23 ( 9) link_NAG-ASN : angle 2.92667 / 2.07 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 88 time to evaluate : 0.302 Fit side-chains revert: symmetry clash REVERT: A 56 GLN cc_start: 0.7808 (mt0) cc_final: 0.7464 (mt0) REVERT: A 108 MET cc_start: 0.9148 (OUTLIER) cc_final: 0.8184 (tpt) REVERT: A 210 ASN cc_start: 0.6346 (OUTLIER) cc_final: 0.6004 (p0) REVERT: A 327 ASP cc_start: 0.8017 (t0) cc_final: 0.7566 (t0) REVERT: B 197 ARG cc_start: 0.8866 (mtp85) cc_final: 0.8423 (ttt90) REVERT: B 258 ASP cc_start: 0.8708 (OUTLIER) cc_final: 0.7990 (t0) REVERT: C 320 ASP cc_start: 0.8111 (t0) cc_final: 0.7859 (t70) outliers start: 36 outliers final: 13 residues processed: 115 average time/residue: 0.3376 time to fit residues: 42.7008 Evaluate side-chains 98 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 82 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ARG Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 149 CYS Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 210 ASN Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain C residue 64 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 19 optimal weight: 6.9990 chunk 28 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 79 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 66 optimal weight: 30.0000 chunk 59 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 95 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 37 GLN ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 127 GLN B 76 GLN ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 114 GLN C 116 HIS C 127 GLN C 191 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.103851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.075063 restraints weight = 13081.930| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 2.97 r_work: 0.2877 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.4570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.106 8212 Z= 0.348 Angle : 0.853 13.056 11174 Z= 0.438 Chirality : 0.055 0.391 1242 Planarity : 0.005 0.041 1398 Dihedral : 9.856 89.670 1353 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 4.96 % Allowed : 18.68 % Favored : 76.36 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.27), residues: 984 helix: 1.57 (0.35), residues: 258 sheet: 0.76 (0.29), residues: 297 loop : -0.67 (0.29), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 295 TYR 0.026 0.002 TYR C 90 PHE 0.046 0.003 PHE C 92 TRP 0.020 0.002 TRP C 164 HIS 0.014 0.001 HIS A 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00825 / 0.35 ( 8190) covalent geometry : angle 0.80235 / 0.42 (11121) SS BOND : bond 0.00907 / 0.68 ( 13) SS BOND : angle 5.15500 / 3.50 ( 26) hydrogen bonds : bond 0.03847 / 2.53 ( 354) hydrogen bonds : angle 5.25369 / 3.63 ( 1050) link_NAG-ASN : bond 0.00599 / 0.25 ( 9) link_NAG-ASN : angle 3.26015 / 2.17 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 82 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 MET cc_start: 0.9191 (OUTLIER) cc_final: 0.8175 (tpt) REVERT: A 283 LYS cc_start: 0.8395 (OUTLIER) cc_final: 0.7810 (ptmt) REVERT: A 327 ASP cc_start: 0.8043 (t0) cc_final: 0.7617 (t0) REVERT: B 197 ARG cc_start: 0.8844 (mtp85) cc_final: 0.8555 (ttt90) REVERT: B 248 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.8233 (mm-30) REVERT: C 78 GLN cc_start: 0.8917 (tp40) cc_final: 0.8699 (mp10) REVERT: C 122 GLU cc_start: 0.8912 (OUTLIER) cc_final: 0.8634 (pp20) REVERT: C 221 LYS cc_start: 0.8724 (OUTLIER) cc_final: 0.8238 (mtmp) outliers start: 42 outliers final: 22 residues processed: 116 average time/residue: 0.3986 time to fit residues: 50.3812 Evaluate side-chains 106 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 79 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ARG Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 149 CYS Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 210 ASN Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 270 CYS Chi-restraints excluded: chain A residue 283 LYS Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 132 CYS Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 248 GLU Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 339 ILE Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 117 CYS Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 221 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 2 optimal weight: 0.3980 chunk 69 optimal weight: 4.9990 chunk 16 optimal weight: 0.6980 chunk 97 optimal weight: 0.9990 chunk 43 optimal weight: 9.9990 chunk 85 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 27 optimal weight: 0.3980 chunk 3 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 37 GLN B 76 GLN C 127 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.108656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.079954 restraints weight = 13017.039| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 2.99 r_work: 0.2924 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.4525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 8212 Z= 0.138 Angle : 0.666 11.132 11174 Z= 0.340 Chirality : 0.046 0.266 1242 Planarity : 0.004 0.040 1398 Dihedral : 9.259 87.989 1353 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 4.37 % Allowed : 19.39 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.27), residues: 984 helix: 1.72 (0.36), residues: 255 sheet: 0.74 (0.31), residues: 273 loop : -0.69 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 244 TYR 0.030 0.002 TYR C 90 PHE 0.022 0.002 PHE C 326 TRP 0.008 0.001 TRP A 259 HIS 0.004 0.000 HIS B 277 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 ( 8190) covalent geometry : angle 0.63348 / 0.33 (11121) SS BOND : bond 0.00588 / 0.43 ( 13) SS BOND : angle 3.77631 / 2.54 ( 26) hydrogen bonds : bond 0.02860 / 1.82 ( 354) hydrogen bonds : angle 5.03344 / 3.46 ( 1050) link_NAG-ASN : bond 0.00510 / 0.24 ( 9) link_NAG-ASN : angle 2.12196 / 1.44 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 93 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 GLN cc_start: 0.7828 (mt0) cc_final: 0.7536 (mt0) REVERT: A 108 MET cc_start: 0.9174 (OUTLIER) cc_final: 0.8188 (tpt) REVERT: A 327 ASP cc_start: 0.7962 (t0) cc_final: 0.7570 (t0) REVERT: B 197 ARG cc_start: 0.8873 (mtp85) cc_final: 0.8568 (ttt90) REVERT: B 258 ASP cc_start: 0.8666 (OUTLIER) cc_final: 0.7906 (t0) REVERT: C 78 GLN cc_start: 0.8904 (tp40) cc_final: 0.8688 (mp10) REVERT: C 122 GLU cc_start: 0.8890 (OUTLIER) cc_final: 0.8647 (pp20) REVERT: C 264 ASP cc_start: 0.8844 (m-30) cc_final: 0.8599 (m-30) outliers start: 37 outliers final: 19 residues processed: 122 average time/residue: 0.3679 time to fit residues: 49.1727 Evaluate side-chains 101 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 79 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ARG Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 149 CYS Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 210 ASN Chi-restraints excluded: chain A residue 270 CYS Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 132 CYS Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 117 CYS Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 193 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 66 optimal weight: 30.0000 chunk 5 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 33 optimal weight: 20.0000 chunk 88 optimal weight: 0.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 37 GLN A 116 HIS ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 127 GLN B 76 GLN C 127 GLN C 284 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.105267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.076629 restraints weight = 13027.721| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 2.95 r_work: 0.2898 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.4702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.097 8212 Z= 0.260 Angle : 0.770 16.989 11174 Z= 0.397 Chirality : 0.050 0.360 1242 Planarity : 0.005 0.043 1398 Dihedral : 9.483 89.482 1353 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 5.08 % Allowed : 19.03 % Favored : 75.89 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.22 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.27), residues: 984 helix: 1.84 (0.35), residues: 249 sheet: 0.67 (0.29), residues: 300 loop : -0.70 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 295 TYR 0.031 0.002 TYR C 90 PHE 0.038 0.002 PHE C 92 TRP 0.012 0.001 TRP C 164 HIS 0.004 0.001 HIS C 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00613 / 0.26 ( 8190) covalent geometry : angle 0.72744 / 0.38 (11121) SS BOND : bond 0.00936 / 0.58 ( 13) SS BOND : angle 4.74999 / 3.19 ( 26) hydrogen bonds : bond 0.03547 / 2.36 ( 354) hydrogen bonds : angle 5.14148 / 3.54 ( 1050) link_NAG-ASN : bond 0.00431 / 0.18 ( 9) link_NAG-ASN : angle 2.36250 / 1.57 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 78 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 MET cc_start: 0.9204 (OUTLIER) cc_final: 0.8187 (tpt) REVERT: A 327 ASP cc_start: 0.8017 (t0) cc_final: 0.7608 (t0) REVERT: B 197 ARG cc_start: 0.8849 (mtp85) cc_final: 0.8571 (ttt90) REVERT: B 248 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.8202 (mm-30) REVERT: C 78 GLN cc_start: 0.8939 (tp40) cc_final: 0.8726 (mp10) REVERT: C 122 GLU cc_start: 0.8866 (OUTLIER) cc_final: 0.8622 (pp20) REVERT: C 138 GLU cc_start: 0.8510 (pm20) cc_final: 0.8195 (mp0) outliers start: 43 outliers final: 25 residues processed: 113 average time/residue: 0.3940 time to fit residues: 48.5391 Evaluate side-chains 102 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 74 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ARG Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 149 CYS Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 210 ASN Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 270 CYS Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 132 CYS Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain B residue 159 CYS Chi-restraints excluded: chain B residue 165 CYS Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 248 GLU Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 339 ILE Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 117 CYS Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 280 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 9 optimal weight: 6.9990 chunk 36 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 66 optimal weight: 30.0000 chunk 22 optimal weight: 0.6980 chunk 79 optimal weight: 4.9990 chunk 88 optimal weight: 0.8980 chunk 51 optimal weight: 0.5980 chunk 46 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 37 GLN A 116 HIS B 76 GLN C 127 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.109149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.080438 restraints weight = 12931.143| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 3.05 r_work: 0.2904 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.4697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 8212 Z= 0.139 Angle : 0.693 12.783 11174 Z= 0.352 Chirality : 0.046 0.211 1242 Planarity : 0.004 0.044 1398 Dihedral : 9.154 87.205 1353 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.55 % Allowed : 21.04 % Favored : 75.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.27), residues: 984 helix: 1.85 (0.35), residues: 249 sheet: 0.71 (0.31), residues: 273 loop : -0.78 (0.27), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 244 TYR 0.033 0.002 TYR C 90 PHE 0.021 0.002 PHE C 326 TRP 0.024 0.001 TRP B 164 HIS 0.002 0.000 HIS B 277 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 ( 8190) covalent geometry : angle 0.66876 / 0.34 (11121) SS BOND : bond 0.00611 / 0.45 ( 13) SS BOND : angle 3.39183 / 2.32 ( 26) hydrogen bonds : bond 0.02880 / 1.86 ( 354) hydrogen bonds : angle 5.03963 / 3.46 ( 1050) link_NAG-ASN : bond 0.00860 / 0.37 ( 9) link_NAG-ASN : angle 1.81110 / 1.25 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 80 time to evaluate : 0.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 GLN cc_start: 0.7841 (mt0) cc_final: 0.7490 (mt0) REVERT: A 108 MET cc_start: 0.9166 (OUTLIER) cc_final: 0.8237 (tpt) REVERT: A 327 ASP cc_start: 0.7953 (t0) cc_final: 0.7572 (t0) REVERT: B 197 ARG cc_start: 0.8868 (mtp85) cc_final: 0.8566 (ttt90) REVERT: B 258 ASP cc_start: 0.8686 (OUTLIER) cc_final: 0.7927 (t0) REVERT: C 78 GLN cc_start: 0.8919 (tp40) cc_final: 0.8710 (mp10) REVERT: C 122 GLU cc_start: 0.8863 (OUTLIER) cc_final: 0.8660 (pp20) REVERT: C 221 LYS cc_start: 0.8726 (OUTLIER) cc_final: 0.8259 (mtmp) REVERT: C 316 ASP cc_start: 0.8578 (t70) cc_final: 0.8270 (t0) outliers start: 30 outliers final: 19 residues processed: 102 average time/residue: 0.4081 time to fit residues: 45.1291 Evaluate side-chains 99 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 76 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ARG Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 149 CYS Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 210 ASN Chi-restraints excluded: chain A residue 270 CYS Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 132 CYS Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain B residue 159 CYS Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 339 ILE Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 221 LYS Chi-restraints excluded: chain C residue 280 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 31 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 chunk 34 optimal weight: 4.9990 chunk 96 optimal weight: 3.9990 chunk 27 optimal weight: 0.3980 chunk 89 optimal weight: 4.9990 chunk 67 optimal weight: 10.0000 chunk 81 optimal weight: 10.0000 chunk 14 optimal weight: 0.0670 chunk 24 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 overall best weight: 1.0922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 37 GLN A 127 GLN B 76 GLN C 127 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.109039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.080239 restraints weight = 12981.877| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 3.07 r_work: 0.2923 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.4774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 8212 Z= 0.152 Angle : 0.699 12.084 11174 Z= 0.356 Chirality : 0.046 0.201 1242 Planarity : 0.004 0.045 1398 Dihedral : 9.019 86.297 1353 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.07 % Allowed : 21.51 % Favored : 75.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.27), residues: 984 helix: 1.76 (0.35), residues: 255 sheet: 0.72 (0.31), residues: 273 loop : -0.76 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 244 TYR 0.033 0.002 TYR C 90 PHE 0.024 0.002 PHE C 92 TRP 0.012 0.001 TRP B 164 HIS 0.006 0.001 HIS C 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.15 ( 8190) covalent geometry : angle 0.66925 / 0.34 (11121) SS BOND : bond 0.00350 / 0.22 ( 13) SS BOND : angle 3.85648 / 2.62 ( 26) hydrogen bonds : bond 0.02858 / 1.85 ( 354) hydrogen bonds : angle 4.97364 / 3.42 ( 1050) link_NAG-ASN : bond 0.00575 / 0.25 ( 9) link_NAG-ASN : angle 1.80292 / 1.28 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 78 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 56 GLN cc_start: 0.7844 (mt0) cc_final: 0.7539 (mt0) REVERT: A 108 MET cc_start: 0.9197 (OUTLIER) cc_final: 0.8249 (tpt) REVERT: A 327 ASP cc_start: 0.7978 (t0) cc_final: 0.7588 (t0) REVERT: B 197 ARG cc_start: 0.8874 (mtp85) cc_final: 0.8553 (ttt90) REVERT: B 258 ASP cc_start: 0.8664 (OUTLIER) cc_final: 0.7946 (t0) REVERT: C 78 GLN cc_start: 0.8905 (tp40) cc_final: 0.8701 (mp10) REVERT: C 221 LYS cc_start: 0.8691 (OUTLIER) cc_final: 0.8224 (mtmp) outliers start: 26 outliers final: 17 residues processed: 97 average time/residue: 0.4185 time to fit residues: 44.0141 Evaluate side-chains 98 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 78 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ARG Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 149 CYS Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 210 ASN Chi-restraints excluded: chain A residue 270 CYS Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 132 CYS Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 339 ILE Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 117 CYS Chi-restraints excluded: chain C residue 221 LYS Chi-restraints excluded: chain C residue 280 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 96 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 77 optimal weight: 0.4980 chunk 68 optimal weight: 3.9990 chunk 75 optimal weight: 0.0870 chunk 97 optimal weight: 3.9990 chunk 80 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 7 optimal weight: 5.9990 chunk 78 optimal weight: 2.9990 overall best weight: 0.8962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 37 GLN B 76 GLN C 127 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.110436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.082467 restraints weight = 12930.307| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 2.97 r_work: 0.2993 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.4796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 8212 Z= 0.144 Angle : 0.689 12.248 11174 Z= 0.353 Chirality : 0.046 0.235 1242 Planarity : 0.004 0.042 1398 Dihedral : 8.824 84.090 1353 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.96 % Allowed : 21.75 % Favored : 75.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.27), residues: 984 helix: 1.82 (0.35), residues: 255 sheet: 0.69 (0.30), residues: 273 loop : -0.79 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 244 TYR 0.034 0.002 TYR C 90 PHE 0.023 0.002 PHE C 326 TRP 0.011 0.001 TRP B 164 HIS 0.005 0.001 HIS A 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.14 ( 8190) covalent geometry : angle 0.65902 / 0.34 (11121) SS BOND : bond 0.00355 / 0.25 ( 13) SS BOND : angle 3.99014 / 2.66 ( 26) hydrogen bonds : bond 0.02731 / 1.76 ( 354) hydrogen bonds : angle 4.92527 / 3.39 ( 1050) link_NAG-ASN : bond 0.00510 / 0.23 ( 9) link_NAG-ASN : angle 1.57517 / 1.15 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2517.69 seconds wall clock time: 43 minutes 52.35 seconds (2632.35 seconds total)