Starting phenix.real_space_refine on Fri Jul 25 18:06:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zta_60457/07_2025/8zta_60457.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zta_60457/07_2025/8zta_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8zta_60457/07_2025/8zta_60457.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zta_60457/07_2025/8zta_60457.map" model { file = "/net/cci-nas-00/data/ceres_data/8zta_60457/07_2025/8zta_60457.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zta_60457/07_2025/8zta_60457.cif" } resolution = 2.58 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= 0.048 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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, 76 Unusual residues: {' CA': 2, ' MG': 1, 'ATP': 1, 'NAG': 3} Classifications: {'undetermined': 7} Link IDs: {None: 6} 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, 44 Unusual residues: {' CA': 1, ' MG': 1, 'NAG': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} 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, 106 Unusual residues: {' CA': 1, ' MG': 1, 'ATP': 2, 'NAG': 3} Classifications: {'undetermined': 7} Link IDs: {None: 6} 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: 5.85, per 1000 atoms: 0.73 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: 2.32 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 1.08 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: 2.33 Time building geometry restraints manager: 2.71 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: 1.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 23.550 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.030 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:12.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6789 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.27), residues: 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 TRP 0.004 0.001 TRP C 47 HIS 0.002 0.000 HIS A 355 PHE 0.012 0.001 PHE C 342 TYR 0.009 0.001 TYR B 90 ARG 0.002 0.000 ARG B 244 Details of bonding type rmsd link_NAG-ASN : bond 0.00755 ( 9) link_NAG-ASN : angle 3.44161 ( 27) hydrogen bonds : bond 0.23580 ( 354) hydrogen bonds : angle 8.28198 ( 1050) SS BOND : bond 0.00190 ( 13) SS BOND : angle 0.83866 ( 26) covalent geometry : bond 0.00424 ( 8190) covalent geometry : angle 0.75921 (11121) *********************** 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 : 0.939 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: 1.0886 time to fit residues: 289.2332 Evaluate side-chains 118 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 115 time to evaluate : 0.833 ------------------------------------------------------------------------------- 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 83 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 50 optimal weight: 0.3980 chunk 40 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 chunk 57 optimal weight: 0.0570 chunk 89 optimal weight: 5.9990 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 HIS A 180 HIS A 191 ASN A 241 GLN A 269 HIS B 56 GLN B 76 GLN B 180 HIS B 191 ASN B 220 HIS B 300 ASN C 56 GLN ** 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: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.125724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.100311 restraints weight = 12904.929| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 2.98 r_work: 0.3232 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 8212 Z= 0.145 Angle : 0.710 20.350 11174 Z= 0.349 Chirality : 0.049 0.340 1242 Planarity : 0.004 0.042 1398 Dihedral : 9.482 89.581 1355 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 4.37 % Allowed : 14.18 % Favored : 81.44 % 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: 0.63 (0.27), residues: 984 helix: 1.00 (0.34), residues: 264 sheet: 1.50 (0.29), residues: 309 loop : -0.82 (0.29), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 47 HIS 0.010 0.001 HIS B 180 PHE 0.018 0.001 PHE A 308 TYR 0.030 0.002 TYR C 90 ARG 0.007 0.001 ARG C 244 Details of bonding type rmsd link_NAG-ASN : bond 0.01297 ( 9) link_NAG-ASN : angle 5.62950 ( 27) hydrogen bonds : bond 0.03732 ( 354) hydrogen bonds : angle 5.81074 ( 1050) SS BOND : bond 0.00515 ( 13) SS BOND : angle 3.13532 ( 26) covalent geometry : bond 0.00325 ( 8190) covalent geometry : angle 0.63807 (11121) *********************** 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 165 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 128 time to evaluate : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 GLN cc_start: 0.7786 (mt0) cc_final: 0.7398 (mt0) REVERT: A 138 GLU cc_start: 0.8576 (pm20) cc_final: 0.8304 (pt0) REVERT: A 197 ARG cc_start: 0.8360 (OUTLIER) cc_final: 0.7649 (ttp80) REVERT: A 327 ASP cc_start: 0.8118 (t0) cc_final: 0.7875 (t0) REVERT: B 44 VAL cc_start: 0.8465 (OUTLIER) cc_final: 0.8259 (m) REVERT: B 322 LYS cc_start: 0.8637 (pttm) cc_final: 0.8384 (pttm) REVERT: C 86 ASP cc_start: 0.7009 (p0) cc_final: 0.6698 (p0) REVERT: C 89 ASP cc_start: 0.7838 (m-30) cc_final: 0.7592 (m-30) REVERT: C 116 HIS cc_start: 0.7681 (m-70) cc_final: 0.7309 (m90) outliers start: 37 outliers final: 12 residues processed: 153 average time/residue: 0.8497 time to fit residues: 141.1998 Evaluate side-chains 116 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 102 time to evaluate : 0.971 ------------------------------------------------------------------------------- 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 63 SER Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 197 ARG Chi-restraints excluded: chain A residue 210 ASN Chi-restraints excluded: chain A residue 275 GLN Chi-restraints excluded: chain B residue 44 VAL 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 335 ILE 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 89 optimal weight: 0.9990 chunk 68 optimal weight: 0.4980 chunk 28 optimal weight: 5.9990 chunk 83 optimal weight: 3.9990 chunk 91 optimal weight: 0.1980 chunk 63 optimal weight: 6.9990 chunk 57 optimal weight: 1.9990 chunk 74 optimal weight: 6.9990 chunk 27 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 GLN A 83 GLN A 116 HIS A 120 ASN A 180 HIS A 220 HIS B 76 GLN C 191 ASN 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 = 0.3632 r_free = 0.3632 target = 0.118940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.091804 restraints weight = 13109.887| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 3.07 r_work: 0.3108 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.3046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 8212 Z= 0.142 Angle : 0.685 13.048 11174 Z= 0.341 Chirality : 0.049 0.370 1242 Planarity : 0.004 0.034 1398 Dihedral : 9.646 89.807 1353 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 5.20 % Allowed : 15.01 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: 0.66 (0.27), residues: 984 helix: 1.32 (0.35), residues: 261 sheet: 1.24 (0.29), residues: 312 loop : -0.78 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 164 HIS 0.004 0.001 HIS B 180 PHE 0.018 0.002 PHE C 92 TYR 0.025 0.002 TYR C 90 ARG 0.006 0.001 ARG B 268 Details of bonding type rmsd link_NAG-ASN : bond 0.00754 ( 9) link_NAG-ASN : angle 4.17998 ( 27) hydrogen bonds : bond 0.03182 ( 354) hydrogen bonds : angle 5.45517 ( 1050) SS BOND : bond 0.00741 ( 13) SS BOND : angle 4.01267 ( 26) covalent geometry : bond 0.00329 ( 8190) covalent geometry : angle 0.62530 (11121) *********************** 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 151 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 107 time to evaluate : 0.940 Fit side-chains revert: symmetry clash REVERT: A 56 GLN cc_start: 0.7733 (mt0) cc_final: 0.7331 (mt0) REVERT: A 108 MET cc_start: 0.9085 (OUTLIER) cc_final: 0.8122 (tpt) REVERT: A 210 ASN cc_start: 0.6195 (OUTLIER) cc_final: 0.5891 (p0) REVERT: A 327 ASP cc_start: 0.8040 (t0) cc_final: 0.7633 (t0) REVERT: C 116 HIS cc_start: 0.7679 (m-70) cc_final: 0.7359 (m90) outliers start: 44 outliers final: 12 residues processed: 139 average time/residue: 0.7634 time to fit residues: 115.9696 Evaluate side-chains 105 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 91 time to evaluate : 0.907 ------------------------------------------------------------------------------- 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 72 LEU 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 126 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 41 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 32 optimal weight: 8.9990 chunk 31 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 GLN A 114 GLN A 116 HIS A 180 HIS A 241 GLN B 76 GLN B 180 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.104834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.076271 restraints weight = 13034.531| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 2.93 r_work: 0.2904 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.4241 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= 0.350 Angle : 0.897 14.541 11174 Z= 0.448 Chirality : 0.055 0.423 1242 Planarity : 0.005 0.037 1398 Dihedral : 10.609 89.755 1353 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 6.03 % Allowed : 15.72 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: 0.56 (0.27), residues: 984 helix: 1.30 (0.35), residues: 264 sheet: 0.96 (0.28), residues: 297 loop : -0.63 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 164 HIS 0.009 0.001 HIS B 180 PHE 0.048 0.003 PHE A 92 TYR 0.030 0.002 TYR C 90 ARG 0.006 0.001 ARG C 295 Details of bonding type rmsd link_NAG-ASN : bond 0.00801 ( 9) link_NAG-ASN : angle 4.51352 ( 27) hydrogen bonds : bond 0.03878 ( 354) hydrogen bonds : angle 5.37509 ( 1050) SS BOND : bond 0.00452 ( 13) SS BOND : angle 4.72203 ( 26) covalent geometry : bond 0.00824 ( 8190) covalent geometry : angle 0.84123 (11121) *********************** 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 133 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 82 time to evaluate : 0.860 Fit side-chains revert: symmetry clash REVERT: A 108 MET cc_start: 0.9191 (OUTLIER) cc_final: 0.8243 (tpt) REVERT: A 210 ASN cc_start: 0.6541 (OUTLIER) cc_final: 0.6272 (p0) REVERT: A 283 LYS cc_start: 0.8299 (OUTLIER) cc_final: 0.7708 (ptmt) REVERT: A 327 ASP cc_start: 0.8031 (t0) cc_final: 0.7602 (t0) REVERT: B 197 ARG cc_start: 0.8862 (mtp85) cc_final: 0.8545 (ttt90) REVERT: B 322 LYS cc_start: 0.8604 (pttm) cc_final: 0.8300 (pttm) REVERT: C 78 GLN cc_start: 0.8923 (tp40) cc_final: 0.8703 (mp10) REVERT: C 122 GLU cc_start: 0.8925 (OUTLIER) cc_final: 0.8693 (pp20) outliers start: 51 outliers final: 21 residues processed: 124 average time/residue: 0.8232 time to fit residues: 111.3025 Evaluate side-chains 98 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 73 time to evaluate : 0.950 ------------------------------------------------------------------------------- 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 258 ASP Chi-restraints excluded: chain A residue 270 CYS Chi-restraints excluded: chain A residue 283 LYS Chi-restraints excluded: chain B residue 117 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 8 optimal weight: 0.8980 chunk 75 optimal weight: 0.7980 chunk 94 optimal weight: 0.8980 chunk 38 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 89 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 92 optimal weight: 0.3980 chunk 79 optimal weight: 4.9990 chunk 34 optimal weight: 7.9990 chunk 97 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 GLN B 266 HIS C 116 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.110298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.081882 restraints weight = 12740.396| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 2.97 r_work: 0.2971 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.4239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 8212 Z= 0.141 Angle : 0.700 12.791 11174 Z= 0.350 Chirality : 0.047 0.276 1242 Planarity : 0.004 0.046 1398 Dihedral : 9.581 87.040 1353 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 4.02 % Allowed : 18.44 % Favored : 77.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.22 % Twisted General : 0.11 % 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: 0.58 (0.27), residues: 984 helix: 1.59 (0.35), residues: 255 sheet: 0.81 (0.29), residues: 300 loop : -0.64 (0.28), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 164 HIS 0.002 0.000 HIS B 277 PHE 0.017 0.002 PHE A 92 TYR 0.030 0.002 TYR C 90 ARG 0.004 0.000 ARG C 244 Details of bonding type rmsd link_NAG-ASN : bond 0.00292 ( 9) link_NAG-ASN : angle 3.17783 ( 27) hydrogen bonds : bond 0.02867 ( 354) hydrogen bonds : angle 5.14118 ( 1050) SS BOND : bond 0.00526 ( 13) SS BOND : angle 3.99484 ( 26) covalent geometry : bond 0.00338 ( 8190) covalent geometry : angle 0.65648 (11121) *********************** 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 126 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 92 time to evaluate : 0.832 Fit side-chains revert: symmetry clash REVERT: A 56 GLN cc_start: 0.7809 (mt0) cc_final: 0.7520 (mt0) REVERT: A 108 MET cc_start: 0.9109 (OUTLIER) cc_final: 0.8157 (tpt) REVERT: A 148 ASN cc_start: 0.8385 (m-40) cc_final: 0.8176 (m-40) REVERT: A 210 ASN cc_start: 0.6431 (OUTLIER) cc_final: 0.6121 (p0) REVERT: A 327 ASP cc_start: 0.7973 (t0) cc_final: 0.7561 (t0) REVERT: B 197 ARG cc_start: 0.8886 (mtp85) cc_final: 0.8575 (ttt90) REVERT: B 258 ASP cc_start: 0.8662 (OUTLIER) cc_final: 0.7938 (t0) REVERT: B 322 LYS cc_start: 0.8619 (pttm) cc_final: 0.8345 (pttm) REVERT: C 78 GLN cc_start: 0.8868 (tp40) cc_final: 0.8667 (mp10) REVERT: C 122 GLU cc_start: 0.8917 (OUTLIER) cc_final: 0.8643 (pp20) outliers start: 34 outliers final: 14 residues processed: 114 average time/residue: 0.7742 time to fit residues: 96.6965 Evaluate side-chains 100 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 82 time to evaluate : 0.969 ------------------------------------------------------------------------------- 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 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 270 CYS Chi-restraints excluded: chain B residue 117 CYS Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 132 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 B residue 339 ILE Chi-restraints excluded: chain C residue 122 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 56 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 22 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 73 optimal weight: 0.7980 chunk 63 optimal weight: 0.9990 chunk 87 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3509 r_free = 0.3509 target = 0.109867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.081558 restraints weight = 12894.803| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 2.98 r_work: 0.2948 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.4343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.101 8212 Z= 0.143 Angle : 0.674 11.525 11174 Z= 0.339 Chirality : 0.046 0.292 1242 Planarity : 0.004 0.038 1398 Dihedral : 9.283 86.862 1353 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 4.61 % Allowed : 18.56 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 0.58 (0.27), residues: 984 helix: 1.70 (0.35), residues: 255 sheet: 0.80 (0.31), residues: 273 loop : -0.62 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 164 HIS 0.003 0.001 HIS B 277 PHE 0.023 0.002 PHE C 92 TYR 0.028 0.002 TYR C 90 ARG 0.004 0.000 ARG C 244 Details of bonding type rmsd link_NAG-ASN : bond 0.00639 ( 9) link_NAG-ASN : angle 2.60968 ( 27) hydrogen bonds : bond 0.02864 ( 354) hydrogen bonds : angle 5.02062 ( 1050) SS BOND : bond 0.00474 ( 13) SS BOND : angle 3.86442 ( 26) covalent geometry : bond 0.00344 ( 8190) covalent geometry : angle 0.63673 (11121) *********************** 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 125 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 86 time to evaluate : 0.985 Fit side-chains revert: symmetry clash REVERT: A 56 GLN cc_start: 0.7813 (mt0) cc_final: 0.7501 (mt0) REVERT: A 108 MET cc_start: 0.9141 (OUTLIER) cc_final: 0.8173 (tpt) REVERT: A 210 ASN cc_start: 0.6341 (OUTLIER) cc_final: 0.6071 (p0) REVERT: A 327 ASP cc_start: 0.7969 (t0) cc_final: 0.7545 (t0) REVERT: B 127 GLN cc_start: 0.8740 (mp10) cc_final: 0.8510 (mp10) REVERT: B 197 ARG cc_start: 0.8877 (mtp85) cc_final: 0.8549 (ttt90) REVERT: B 258 ASP cc_start: 0.8666 (OUTLIER) cc_final: 0.7942 (t0) REVERT: B 322 LYS cc_start: 0.8616 (pttm) cc_final: 0.8339 (pttm) REVERT: C 78 GLN cc_start: 0.8865 (tp40) cc_final: 0.8663 (mp10) REVERT: C 97 ASP cc_start: 0.7654 (t0) cc_final: 0.7419 (t0) REVERT: C 122 GLU cc_start: 0.8868 (OUTLIER) cc_final: 0.8655 (pp20) outliers start: 39 outliers final: 20 residues processed: 114 average time/residue: 0.7636 time to fit residues: 95.6822 Evaluate side-chains 106 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 82 time to evaluate : 0.902 ------------------------------------------------------------------------------- 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 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 270 CYS Chi-restraints excluded: chain B residue 117 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 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 Chi-restraints excluded: chain C residue 214 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 11 optimal weight: 0.3980 chunk 83 optimal weight: 3.9990 chunk 89 optimal weight: 0.9980 chunk 71 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 44 optimal weight: 0.0970 chunk 45 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 14 optimal weight: 7.9990 chunk 97 optimal weight: 0.9980 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3525 r_free = 0.3525 target = 0.111226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.082798 restraints weight = 13025.058| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 3.05 r_work: 0.2964 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.4401 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= 0.124 Angle : 0.629 10.298 11174 Z= 0.319 Chirality : 0.045 0.223 1242 Planarity : 0.004 0.043 1398 Dihedral : 8.930 87.533 1353 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.90 % Allowed : 20.21 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.63 (0.27), residues: 984 helix: 1.68 (0.35), residues: 261 sheet: 0.80 (0.31), residues: 273 loop : -0.55 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 164 HIS 0.003 0.000 HIS B 277 PHE 0.024 0.002 PHE C 326 TYR 0.028 0.002 TYR C 90 ARG 0.003 0.000 ARG C 244 Details of bonding type rmsd link_NAG-ASN : bond 0.00470 ( 9) link_NAG-ASN : angle 2.13850 ( 27) hydrogen bonds : bond 0.02674 ( 354) hydrogen bonds : angle 4.94169 ( 1050) SS BOND : bond 0.00525 ( 13) SS BOND : angle 3.14235 ( 26) covalent geometry : bond 0.00296 ( 8190) covalent geometry : angle 0.60323 (11121) *********************** 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 129 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 96 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 56 GLN cc_start: 0.7785 (mt0) cc_final: 0.7484 (mt0) REVERT: A 108 MET cc_start: 0.9144 (OUTLIER) cc_final: 0.8209 (tpt) REVERT: A 327 ASP cc_start: 0.7934 (t0) cc_final: 0.7539 (t0) REVERT: B 127 GLN cc_start: 0.8726 (mp10) cc_final: 0.8477 (mp10) REVERT: B 197 ARG cc_start: 0.8889 (mtp85) cc_final: 0.8564 (ttt90) REVERT: B 258 ASP cc_start: 0.8653 (OUTLIER) cc_final: 0.7949 (t0) REVERT: C 78 GLN cc_start: 0.8867 (tp40) cc_final: 0.8660 (mp10) outliers start: 33 outliers final: 19 residues processed: 121 average time/residue: 0.7536 time to fit residues: 100.2017 Evaluate side-chains 105 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 84 time to evaluate : 0.847 ------------------------------------------------------------------------------- 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 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 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 214 MET 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 126 CYS Chi-restraints excluded: chain C residue 214 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 91 optimal weight: 5.9990 chunk 19 optimal weight: 6.9990 chunk 61 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 32 optimal weight: 6.9990 chunk 82 optimal weight: 4.9990 chunk 47 optimal weight: 0.9990 chunk 90 optimal weight: 0.4980 chunk 44 optimal weight: 1.9990 overall best weight: 1.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3494 r_free = 0.3494 target = 0.108885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.080560 restraints weight = 13149.130| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 3.00 r_work: 0.2954 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.4524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 8212 Z= 0.156 Angle : 0.644 11.099 11174 Z= 0.328 Chirality : 0.046 0.240 1242 Planarity : 0.004 0.044 1398 Dihedral : 8.926 89.508 1353 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.90 % Allowed : 20.92 % Favored : 75.18 % 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: 0.63 (0.27), residues: 984 helix: 1.70 (0.35), residues: 261 sheet: 0.81 (0.31), residues: 273 loop : -0.57 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 164 HIS 0.003 0.001 HIS B 277 PHE 0.026 0.002 PHE C 92 TYR 0.029 0.002 TYR C 90 ARG 0.003 0.000 ARG B 197 Details of bonding type rmsd link_NAG-ASN : bond 0.00420 ( 9) link_NAG-ASN : angle 2.09019 ( 27) hydrogen bonds : bond 0.02969 ( 354) hydrogen bonds : angle 4.92300 ( 1050) SS BOND : bond 0.00736 ( 13) SS BOND : angle 3.42736 ( 26) covalent geometry : bond 0.00366 ( 8190) covalent geometry : angle 0.61552 (11121) *********************** 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 115 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 82 time to evaluate : 0.844 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 56 GLN cc_start: 0.7847 (mt0) cc_final: 0.7538 (mt0) REVERT: A 108 MET cc_start: 0.9154 (OUTLIER) cc_final: 0.8189 (tpt) REVERT: A 148 ASN cc_start: 0.8269 (m-40) cc_final: 0.8046 (m-40) REVERT: A 327 ASP cc_start: 0.7999 (t0) cc_final: 0.7588 (t0) REVERT: B 127 GLN cc_start: 0.8727 (mp10) cc_final: 0.8477 (mp10) REVERT: B 167 VAL cc_start: 0.5651 (OUTLIER) cc_final: 0.5369 (m) REVERT: B 197 ARG cc_start: 0.8890 (mtp85) cc_final: 0.8573 (ttt90) REVERT: B 258 ASP cc_start: 0.8664 (OUTLIER) cc_final: 0.7939 (t0) outliers start: 33 outliers final: 22 residues processed: 108 average time/residue: 0.7399 time to fit residues: 87.8308 Evaluate side-chains 106 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 81 time to evaluate : 0.849 ------------------------------------------------------------------------------- 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 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 270 CYS Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain B residue 45 ILE 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 167 VAL Chi-restraints excluded: chain B residue 214 MET 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 80 LEU Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 214 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 36 optimal weight: 4.9990 chunk 75 optimal weight: 0.9980 chunk 27 optimal weight: 0.0980 chunk 84 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 12 optimal weight: 6.9990 chunk 93 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 GLN A 127 GLN B 76 GLN C 127 GLN C 241 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.108660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.080024 restraints weight = 13119.589| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 3.01 r_work: 0.2927 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.4623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 8212 Z= 0.166 Angle : 0.668 10.490 11174 Z= 0.342 Chirality : 0.047 0.270 1242 Planarity : 0.004 0.045 1398 Dihedral : 8.981 86.078 1353 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 4.02 % Allowed : 20.57 % 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 (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: 0.70 (0.27), residues: 984 helix: 1.84 (0.35), residues: 255 sheet: 0.84 (0.29), residues: 300 loop : -0.64 (0.29), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 164 HIS 0.003 0.001 HIS B 266 PHE 0.027 0.002 PHE C 92 TYR 0.031 0.002 TYR C 90 ARG 0.002 0.000 ARG C 244 Details of bonding type rmsd link_NAG-ASN : bond 0.00580 ( 9) link_NAG-ASN : angle 2.04695 ( 27) hydrogen bonds : bond 0.02948 ( 354) hydrogen bonds : angle 4.91062 ( 1050) SS BOND : bond 0.00522 ( 13) SS BOND : angle 3.57768 ( 26) covalent geometry : bond 0.00392 ( 8190) covalent geometry : angle 0.63945 (11121) *********************** 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 114 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 80 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 GLN cc_start: 0.7846 (mt0) cc_final: 0.7582 (mt0) REVERT: A 108 MET cc_start: 0.9161 (OUTLIER) cc_final: 0.8214 (tpt) REVERT: A 148 ASN cc_start: 0.8276 (m-40) cc_final: 0.8068 (m-40) REVERT: A 327 ASP cc_start: 0.7980 (t0) cc_final: 0.7556 (t0) REVERT: B 127 GLN cc_start: 0.8717 (mp10) cc_final: 0.8464 (mp10) REVERT: B 197 ARG cc_start: 0.8882 (mtp85) cc_final: 0.8564 (ttt90) REVERT: B 258 ASP cc_start: 0.8673 (OUTLIER) cc_final: 0.7944 (t0) REVERT: C 221 LYS cc_start: 0.8665 (OUTLIER) cc_final: 0.8192 (mtmp) outliers start: 34 outliers final: 24 residues processed: 105 average time/residue: 0.8139 time to fit residues: 93.5537 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 : 0.937 ------------------------------------------------------------------------------- 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 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 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 214 MET 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 80 LEU Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 214 MET 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 28 optimal weight: 4.9990 chunk 65 optimal weight: 8.9990 chunk 30 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 chunk 14 optimal weight: 0.0030 chunk 23 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 50 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 10 optimal weight: 20.0000 overall best weight: 1.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3483 r_free = 0.3483 target = 0.108252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.079640 restraints weight = 12958.562| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 3.00 r_work: 0.2936 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.4706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 8212 Z= 0.163 Angle : 0.668 12.233 11174 Z= 0.341 Chirality : 0.047 0.251 1242 Planarity : 0.004 0.049 1398 Dihedral : 8.923 82.243 1353 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 4.02 % Allowed : 20.69 % 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 (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: 0.68 (0.27), residues: 984 helix: 1.87 (0.35), residues: 255 sheet: 0.82 (0.29), residues: 300 loop : -0.68 (0.29), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 164 HIS 0.003 0.001 HIS B 266 PHE 0.027 0.002 PHE C 92 TYR 0.030 0.002 TYR C 90 ARG 0.003 0.000 ARG C 244 Details of bonding type rmsd link_NAG-ASN : bond 0.00588 ( 9) link_NAG-ASN : angle 1.91855 ( 27) hydrogen bonds : bond 0.02903 ( 354) hydrogen bonds : angle 4.89216 ( 1050) SS BOND : bond 0.00536 ( 13) SS BOND : angle 3.60949 ( 26) covalent geometry : bond 0.00385 ( 8190) covalent geometry : angle 0.63950 (11121) ********************** 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 113 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 79 time to evaluate : 0.919 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 56 GLN cc_start: 0.7829 (mt0) cc_final: 0.7566 (mt0) REVERT: A 108 MET cc_start: 0.9155 (OUTLIER) cc_final: 0.8193 (tpt) REVERT: A 148 ASN cc_start: 0.8351 (m-40) cc_final: 0.8149 (m-40) REVERT: A 327 ASP cc_start: 0.7986 (t0) cc_final: 0.7604 (t0) REVERT: B 127 GLN cc_start: 0.8690 (mp10) cc_final: 0.8441 (mp10) REVERT: B 197 ARG cc_start: 0.8886 (mtp85) cc_final: 0.8563 (ttt90) REVERT: B 258 ASP cc_start: 0.8684 (OUTLIER) cc_final: 0.7946 (t70) REVERT: C 221 LYS cc_start: 0.8664 (OUTLIER) cc_final: 0.8178 (mtmp) outliers start: 34 outliers final: 25 residues processed: 103 average time/residue: 0.8017 time to fit residues: 90.5242 Evaluate side-chains 103 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 75 time to evaluate : 0.902 ------------------------------------------------------------------------------- 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 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 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 214 MET 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 80 LEU Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 214 MET 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 34 optimal weight: 5.9990 chunk 26 optimal weight: 0.9980 chunk 89 optimal weight: 0.1980 chunk 4 optimal weight: 3.9990 chunk 67 optimal weight: 10.0000 chunk 84 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 73 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 70 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 GLN A 127 GLN B 76 GLN C 114 GLN C 127 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.109448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.080898 restraints weight = 12927.484| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 3.01 r_work: 0.2956 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.4716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 8212 Z= 0.142 Angle : 0.653 12.271 11174 Z= 0.333 Chirality : 0.046 0.238 1242 Planarity : 0.004 0.053 1398 Dihedral : 8.804 80.884 1353 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.66 % Allowed : 20.92 % 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 (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: 0.68 (0.27), residues: 984 helix: 1.71 (0.35), residues: 261 sheet: 0.82 (0.29), residues: 300 loop : -0.60 (0.30), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 164 HIS 0.002 0.001 HIS B 277 PHE 0.024 0.002 PHE C 326 TYR 0.035 0.002 TYR C 90 ARG 0.003 0.000 ARG C 244 Details of bonding type rmsd link_NAG-ASN : bond 0.00512 ( 9) link_NAG-ASN : angle 1.65418 ( 27) hydrogen bonds : bond 0.02769 ( 354) hydrogen bonds : angle 4.89288 ( 1050) SS BOND : bond 0.00302 ( 13) SS BOND : angle 3.39849 ( 26) covalent geometry : bond 0.00335 ( 8190) covalent geometry : angle 0.62863 (11121) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5142.11 seconds wall clock time: 88 minutes 45.80 seconds (5325.80 seconds total)