Starting phenix.real_space_refine on Wed Sep 17 10:01:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zta_60457/09_2025/8zta_60457.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zta_60457/09_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_60457/09_2025/8zta_60457.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zta_60457/09_2025/8zta_60457.map" model { file = "/net/cci-nas-00/data/ceres_data/8zta_60457/09_2025/8zta_60457.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zta_60457/09_2025/8zta_60457.cif" } 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-2.0-5805/lib/python3.9/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, 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: 2.13, per 1000 atoms: 0.27 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: 0.57 Conformation dependent library (CDL) restraints added in 412.0 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 0.30 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: 1.29 Time building geometry restraints manager: 0.81 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: 2.110 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.680 Find NCS groups from input model: 0.150 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:8.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.780 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren 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 covalent geometry : bond 0.00424 ( 8190) covalent geometry : angle 0.75921 (11121) SS BOND : bond 0.00190 ( 13) SS BOND : angle 0.83866 ( 26) hydrogen bonds : bond 0.23580 ( 354) hydrogen bonds : angle 8.28198 ( 1050) link_NAG-ASN : bond 0.00755 ( 9) link_NAG-ASN : angle 3.44161 ( 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 : 0.327 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: 0.5387 time to fit residues: 142.7085 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 : 0.271 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 116 HIS A 180 HIS A 191 ASN A 220 HIS A 269 HIS 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 = 0.3649 r_free = 0.3649 target = 0.120634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.094482 restraints weight = 13031.357| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.96 r_work: 0.3140 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8212 Z= 0.177 Angle : 0.742 21.761 11174 Z= 0.365 Chirality : 0.050 0.333 1242 Planarity : 0.004 0.043 1398 Dihedral : 10.004 88.771 1355 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 5.20 % Allowed : 13.83 % Favored : 80.97 % 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 aren not related in a simple way. whole: 0.62 (0.27), residues: 984 helix: 1.00 (0.34), residues: 264 sheet: 1.42 (0.29), residues: 309 loop : -0.77 (0.29), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 244 TYR 0.032 0.002 TYR C 90 PHE 0.022 0.002 PHE C 92 TRP 0.007 0.001 TRP B 47 HIS 0.011 0.001 HIS B 180 Details of bonding type rmsd covalent geometry : bond 0.00397 ( 8190) covalent geometry : angle 0.67521 (11121) SS BOND : bond 0.00478 ( 13) SS BOND : angle 3.28446 ( 26) hydrogen bonds : bond 0.03488 ( 354) hydrogen bonds : angle 5.64457 ( 1050) link_NAG-ASN : bond 0.01058 ( 9) link_NAG-ASN : angle 5.44722 ( 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 163 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 119 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 56 GLN cc_start: 0.7860 (mt0) cc_final: 0.7452 (mt0) REVERT: A 138 GLU cc_start: 0.8549 (pm20) cc_final: 0.8331 (pt0) REVERT: A 327 ASP cc_start: 0.8091 (t0) cc_final: 0.7844 (t0) REVERT: B 44 VAL cc_start: 0.8472 (OUTLIER) cc_final: 0.8256 (m) REVERT: C 116 HIS cc_start: 0.7854 (m-70) cc_final: 0.7518 (m90) REVERT: C 181 GLU cc_start: 0.7916 (mm-30) cc_final: 0.7603 (mm-30) REVERT: C 208 GLU cc_start: 0.7693 (mp0) cc_final: 0.7488 (mp0) REVERT: C 320 ASP cc_start: 0.7915 (t0) cc_final: 0.7663 (t0) outliers start: 44 outliers final: 15 residues processed: 152 average time/residue: 0.4280 time to fit residues: 70.3455 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 : 0.343 ------------------------------------------------------------------------------- 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: 1.9990 chunk 27 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 19 optimal weight: 0.6980 chunk 76 optimal weight: 8.9990 chunk 1 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 32 optimal weight: 6.9990 chunk 31 optimal weight: 5.9990 chunk 2 optimal weight: 0.4980 overall best weight: 1.8386 ------------------------------------------------------------------------------- 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 114 GLN ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 180 HIS B 76 GLN B 114 GLN C 241 GLN C 269 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.111112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.083295 restraints weight = 12951.789| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 3.02 r_work: 0.2961 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.3561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 8212 Z= 0.206 Angle : 0.756 13.994 11174 Z= 0.372 Chirality : 0.050 0.299 1242 Planarity : 0.004 0.033 1398 Dihedral : 10.531 88.706 1353 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 5.32 % Allowed : 15.37 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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 aren not related in a simple way. whole: 0.56 (0.27), residues: 984 helix: 1.24 (0.34), residues: 264 sheet: 1.10 (0.29), residues: 297 loop : -0.70 (0.30), 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 0.030 0.002 PHE A 92 TRP 0.017 0.001 TRP C 164 HIS 0.004 0.001 HIS B 180 Details of bonding type rmsd covalent geometry : bond 0.00479 ( 8190) covalent geometry : angle 0.69751 (11121) SS BOND : bond 0.00701 ( 13) SS BOND : angle 4.15855 ( 26) hydrogen bonds : bond 0.03411 ( 354) hydrogen bonds : angle 5.35817 ( 1050) link_NAG-ASN : bond 0.00654 ( 9) link_NAG-ASN : angle 4.41703 ( 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 151 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 106 time to evaluate : 0.333 Fit side-chains revert: symmetry clash REVERT: A 56 GLN cc_start: 0.7797 (mt0) cc_final: 0.7448 (mt0) REVERT: A 108 MET cc_start: 0.9170 (OUTLIER) cc_final: 0.8142 (tpt) REVERT: A 210 ASN cc_start: 0.6345 (OUTLIER) cc_final: 0.6051 (p0) REVERT: A 327 ASP cc_start: 0.8011 (t0) cc_final: 0.7629 (t0) REVERT: B 44 VAL cc_start: 0.8392 (OUTLIER) cc_final: 0.8182 (m) REVERT: B 197 ARG cc_start: 0.8844 (mtp85) cc_final: 0.8462 (ttt90) REVERT: C 86 ASP cc_start: 0.7315 (p0) cc_final: 0.7071 (p0) REVERT: C 116 HIS cc_start: 0.7976 (m-70) cc_final: 0.7747 (m90) REVERT: C 122 GLU cc_start: 0.8966 (OUTLIER) cc_final: 0.8757 (pp20) outliers start: 45 outliers final: 14 residues processed: 137 average time/residue: 0.4286 time to fit residues: 63.5593 Evaluate side-chains 102 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 84 time to evaluate : 0.322 ------------------------------------------------------------------------------- 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 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: 0.7980 chunk 4 optimal weight: 0.9990 chunk 67 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 18 optimal weight: 0.3980 chunk 87 optimal weight: 0.0870 chunk 68 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 overall best weight: 0.6360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 GLN ** A 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.113153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.086005 restraints weight = 13119.898| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 2.95 r_work: 0.3053 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.3776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 8212 Z= 0.125 Angle : 0.675 10.980 11174 Z= 0.334 Chirality : 0.046 0.253 1242 Planarity : 0.004 0.038 1398 Dihedral : 9.514 89.017 1353 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.90 % Allowed : 17.61 % Favored : 78.49 % 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 aren not related in a simple way. whole: 0.48 (0.27), residues: 984 helix: 1.52 (0.35), residues: 255 sheet: 0.84 (0.30), residues: 273 loop : -0.69 (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 0.012 0.001 TRP C 164 HIS 0.004 0.000 HIS B 180 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 8190) covalent geometry : angle 0.62666 (11121) SS BOND : bond 0.00403 ( 13) SS BOND : angle 3.96278 ( 26) hydrogen bonds : bond 0.02787 ( 354) hydrogen bonds : angle 5.08198 ( 1050) link_NAG-ASN : bond 0.00768 ( 9) link_NAG-ASN : angle 3.44340 ( 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 130 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 97 time to evaluate : 0.343 Fit side-chains revert: symmetry clash REVERT: A 56 GLN cc_start: 0.7807 (mt0) cc_final: 0.7463 (mt0) REVERT: A 210 ASN cc_start: 0.6311 (OUTLIER) cc_final: 0.6023 (p0) REVERT: A 327 ASP cc_start: 0.8009 (t0) cc_final: 0.7607 (t0) REVERT: B 44 VAL cc_start: 0.8373 (OUTLIER) cc_final: 0.8171 (m) REVERT: B 197 ARG cc_start: 0.8859 (mtp85) cc_final: 0.8526 (ttt90) REVERT: B 258 ASP cc_start: 0.8700 (OUTLIER) cc_final: 0.7711 (t0) REVERT: C 316 ASP cc_start: 0.8556 (OUTLIER) cc_final: 0.8268 (t0) REVERT: C 320 ASP cc_start: 0.8122 (t0) cc_final: 0.7883 (t70) outliers start: 33 outliers final: 12 residues processed: 120 average time/residue: 0.4288 time to fit residues: 55.8989 Evaluate side-chains 99 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 83 time to evaluate : 0.256 ------------------------------------------------------------------------------- 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 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 44 VAL 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 126 CYS Chi-restraints excluded: chain C residue 316 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 53 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 82 optimal weight: 6.9990 chunk 19 optimal weight: 6.9990 chunk 44 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 chunk 87 optimal weight: 0.0470 chunk 20 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 overall best weight: 1.1282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 GLN ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 76 GLN B 266 HIS C 116 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.110947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.083449 restraints weight = 13081.556| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 2.93 r_work: 0.3005 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.3980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 8212 Z= 0.145 Angle : 0.662 10.427 11174 Z= 0.331 Chirality : 0.046 0.246 1242 Planarity : 0.004 0.038 1398 Dihedral : 9.212 85.170 1353 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 4.96 % Allowed : 18.20 % Favored : 76.83 % 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 aren not related in a simple way. whole: 0.50 (0.27), residues: 984 helix: 1.54 (0.35), residues: 261 sheet: 0.76 (0.30), residues: 273 loop : -0.64 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 244 TYR 0.027 0.002 TYR C 90 PHE 0.023 0.002 PHE C 326 TRP 0.012 0.001 TRP C 164 HIS 0.004 0.001 HIS B 180 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 8190) covalent geometry : angle 0.62027 (11121) SS BOND : bond 0.00463 ( 13) SS BOND : angle 3.76216 ( 26) hydrogen bonds : bond 0.02851 ( 354) hydrogen bonds : angle 5.01979 ( 1050) link_NAG-ASN : bond 0.00552 ( 9) link_NAG-ASN : angle 3.06066 ( 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 129 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 87 time to evaluate : 0.319 Fit side-chains revert: symmetry clash REVERT: A 56 GLN cc_start: 0.7797 (mt0) cc_final: 0.7442 (mt0) REVERT: A 108 MET cc_start: 0.9151 (OUTLIER) cc_final: 0.8140 (tpt) REVERT: A 210 ASN cc_start: 0.6409 (OUTLIER) cc_final: 0.6112 (p0) REVERT: A 327 ASP cc_start: 0.7995 (t0) cc_final: 0.7559 (t0) REVERT: B 197 ARG cc_start: 0.8883 (mtp85) cc_final: 0.8553 (ttt90) REVERT: B 258 ASP cc_start: 0.8717 (OUTLIER) cc_final: 0.7725 (t0) REVERT: C 116 HIS cc_start: 0.7734 (m-70) cc_final: 0.7431 (m90) REVERT: C 122 GLU cc_start: 0.8959 (OUTLIER) cc_final: 0.8688 (pp20) REVERT: C 316 ASP cc_start: 0.8564 (t70) cc_final: 0.8364 (t0) REVERT: C 320 ASP cc_start: 0.8130 (t0) cc_final: 0.7886 (t70) outliers start: 42 outliers final: 16 residues processed: 119 average time/residue: 0.4159 time to fit residues: 53.9357 Evaluate side-chains 99 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 79 time to evaluate : 0.279 ------------------------------------------------------------------------------- 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 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 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 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: 0.0000 chunk 79 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 66 optimal weight: 30.0000 chunk 59 optimal weight: 1.9990 chunk 40 optimal weight: 6.9990 chunk 95 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 overall best weight: 2.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 GLN ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3505 r_free = 0.3505 target = 0.109425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.082262 restraints weight = 13007.919| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 2.84 r_work: 0.2918 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.4444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.106 8212 Z= 0.238 Angle : 0.768 14.303 11174 Z= 0.391 Chirality : 0.051 0.346 1242 Planarity : 0.004 0.033 1398 Dihedral : 9.454 88.365 1353 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 4.73 % Allowed : 18.56 % Favored : 76.71 % 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 aren not related in a simple way. whole: 0.59 (0.27), residues: 984 helix: 1.73 (0.36), residues: 255 sheet: 0.69 (0.29), residues: 300 loop : -0.63 (0.29), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 295 TYR 0.025 0.002 TYR C 90 PHE 0.037 0.002 PHE A 92 TRP 0.020 0.001 TRP C 164 HIS 0.005 0.001 HIS B 180 Details of bonding type rmsd covalent geometry : bond 0.00561 ( 8190) covalent geometry : angle 0.71586 (11121) SS BOND : bond 0.00632 ( 13) SS BOND : angle 5.06172 ( 26) hydrogen bonds : bond 0.03396 ( 354) hydrogen bonds : angle 5.07536 ( 1050) link_NAG-ASN : bond 0.00512 ( 9) link_NAG-ASN : angle 2.88316 ( 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: 40 poor density : 84 time to evaluate : 0.336 Fit side-chains revert: symmetry clash REVERT: A 108 MET cc_start: 0.9198 (OUTLIER) cc_final: 0.8204 (tpt) REVERT: A 210 ASN cc_start: 0.6715 (OUTLIER) cc_final: 0.6406 (p0) REVERT: A 283 LYS cc_start: 0.8171 (OUTLIER) cc_final: 0.7954 (ptpp) REVERT: A 327 ASP cc_start: 0.8062 (t0) cc_final: 0.7648 (t0) REVERT: B 197 ARG cc_start: 0.8882 (mtp85) cc_final: 0.8600 (ttt90) REVERT: B 248 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.8305 (mm-30) REVERT: C 122 GLU cc_start: 0.8914 (OUTLIER) cc_final: 0.8657 (pp20) REVERT: C 316 ASP cc_start: 0.8608 (t70) cc_final: 0.8408 (t0) REVERT: C 320 ASP cc_start: 0.8234 (t0) cc_final: 0.7829 (t0) outliers start: 40 outliers final: 23 residues processed: 118 average time/residue: 0.4542 time to fit residues: 57.9788 Evaluate side-chains 105 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 77 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 133 THR 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 63 SER 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 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 122 GLU Chi-restraints excluded: chain C residue 126 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 2 optimal weight: 0.7980 chunk 69 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 43 optimal weight: 20.0000 chunk 85 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 86 optimal weight: 0.8980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 GLN ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 127 GLN A 303 ASN B 76 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 = 0.3533 r_free = 0.3533 target = 0.111809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.082651 restraints weight = 13206.373| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 3.10 r_work: 0.2955 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.4477 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= 0.137 Angle : 0.658 10.314 11174 Z= 0.336 Chirality : 0.046 0.242 1242 Planarity : 0.004 0.039 1398 Dihedral : 9.052 85.523 1353 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 4.14 % Allowed : 19.86 % Favored : 76.00 % 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 aren not related in a simple way. whole: 0.58 (0.27), residues: 984 helix: 1.79 (0.36), residues: 255 sheet: 0.72 (0.31), residues: 273 loop : -0.63 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 244 TYR 0.027 0.002 TYR C 90 PHE 0.023 0.002 PHE C 326 TRP 0.012 0.001 TRP C 164 HIS 0.004 0.000 HIS B 180 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 8190) covalent geometry : angle 0.62074 (11121) SS BOND : bond 0.00603 ( 13) SS BOND : angle 4.07275 ( 26) hydrogen bonds : bond 0.02889 ( 354) hydrogen bonds : angle 4.91241 ( 1050) link_NAG-ASN : bond 0.00479 ( 9) link_NAG-ASN : angle 2.09672 ( 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 117 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 82 time to evaluate : 0.277 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 108 MET cc_start: 0.9176 (OUTLIER) cc_final: 0.8196 (tpt) REVERT: A 210 ASN cc_start: 0.6538 (OUTLIER) cc_final: 0.6254 (p0) REVERT: A 327 ASP cc_start: 0.7991 (t0) cc_final: 0.7585 (t0) REVERT: B 197 ARG cc_start: 0.8896 (mtp85) cc_final: 0.8602 (ttt90) REVERT: C 122 GLU cc_start: 0.8866 (OUTLIER) cc_final: 0.8649 (pp20) REVERT: C 221 LYS cc_start: 0.8703 (OUTLIER) cc_final: 0.8237 (mtmp) REVERT: C 320 ASP cc_start: 0.8175 (t0) cc_final: 0.7751 (t0) REVERT: C 327 ASP cc_start: 0.5771 (t70) cc_final: 0.5517 (p0) outliers start: 35 outliers final: 19 residues processed: 110 average time/residue: 0.4243 time to fit residues: 50.6751 Evaluate side-chains 98 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 75 time to evaluate : 0.326 ------------------------------------------------------------------------------- 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 258 ASP Chi-restraints excluded: chain A residue 270 CYS Chi-restraints excluded: chain A residue 293 PHE 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 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 122 GLU Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 221 LYS 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: 4.9990 chunk 36 optimal weight: 5.9990 chunk 77 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 33 optimal weight: 7.9990 chunk 88 optimal weight: 6.9990 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 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3411 r_free = 0.3411 target = 0.102925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.074211 restraints weight = 13202.595| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 2.93 r_work: 0.2861 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2729 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.4886 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= 0.335 Angle : 0.817 13.231 11174 Z= 0.423 Chirality : 0.053 0.407 1242 Planarity : 0.005 0.047 1398 Dihedral : 9.604 87.414 1353 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 4.85 % Allowed : 19.27 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.49 (0.27), residues: 984 helix: 1.84 (0.35), residues: 249 sheet: 0.57 (0.29), residues: 300 loop : -0.72 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 244 TYR 0.031 0.002 TYR C 90 PHE 0.040 0.003 PHE A 92 TRP 0.020 0.002 TRP C 164 HIS 0.005 0.001 HIS B 180 Details of bonding type rmsd covalent geometry : bond 0.00794 ( 8190) covalent geometry : angle 0.77433 (11121) SS BOND : bond 0.00887 ( 13) SS BOND : angle 4.80412 ( 26) hydrogen bonds : bond 0.03825 ( 354) hydrogen bonds : angle 5.16612 ( 1050) link_NAG-ASN : bond 0.00444 ( 9) link_NAG-ASN : angle 2.64099 ( 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 119 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 78 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 108 MET cc_start: 0.9176 (OUTLIER) cc_final: 0.8262 (tpt) REVERT: A 327 ASP cc_start: 0.8090 (t0) cc_final: 0.7673 (t0) REVERT: B 197 ARG cc_start: 0.8867 (mtp85) cc_final: 0.8571 (ttt90) REVERT: B 248 GLU cc_start: 0.8672 (OUTLIER) cc_final: 0.8382 (mm-30) REVERT: C 122 GLU cc_start: 0.8920 (OUTLIER) cc_final: 0.8690 (pp20) REVERT: C 138 GLU cc_start: 0.8630 (pm20) cc_final: 0.8312 (mp0) REVERT: C 221 LYS cc_start: 0.8737 (OUTLIER) cc_final: 0.8262 (mtmp) REVERT: C 320 ASP cc_start: 0.8337 (t0) cc_final: 0.7971 (t0) outliers start: 41 outliers final: 22 residues processed: 108 average time/residue: 0.4736 time to fit residues: 55.1124 Evaluate side-chains 98 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 72 time to evaluate : 0.318 ------------------------------------------------------------------------------- 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 258 ASP Chi-restraints excluded: chain A residue 270 CYS Chi-restraints excluded: chain A residue 318 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 214 MET 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 335 ILE Chi-restraints excluded: chain B residue 339 ILE Chi-restraints excluded: chain B residue 342 PHE 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 9 optimal weight: 0.5980 chunk 36 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 66 optimal weight: 30.0000 chunk 22 optimal weight: 0.9990 chunk 79 optimal weight: 6.9990 chunk 88 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 GLN ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3473 r_free = 0.3473 target = 0.107363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.078672 restraints weight = 12944.487| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 2.98 r_work: 0.2920 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.4804 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= 0.139 Angle : 0.676 11.567 11174 Z= 0.344 Chirality : 0.046 0.270 1242 Planarity : 0.004 0.050 1398 Dihedral : 9.241 88.625 1353 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.43 % Allowed : 21.04 % Favored : 75.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.49 (0.27), residues: 984 helix: 1.90 (0.35), residues: 249 sheet: 0.68 (0.31), residues: 273 loop : -0.77 (0.27), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 244 TYR 0.034 0.001 TYR C 90 PHE 0.021 0.002 PHE C 326 TRP 0.010 0.001 TRP A 164 HIS 0.004 0.001 HIS B 180 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 8190) covalent geometry : angle 0.64860 (11121) SS BOND : bond 0.00643 ( 13) SS BOND : angle 3.56195 ( 26) hydrogen bonds : bond 0.02956 ( 354) hydrogen bonds : angle 4.96350 ( 1050) link_NAG-ASN : bond 0.00727 ( 9) link_NAG-ASN : angle 1.83792 ( 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 107 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 78 time to evaluate : 0.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 327 ASP cc_start: 0.7961 (t0) cc_final: 0.7559 (t0) REVERT: B 197 ARG cc_start: 0.8870 (mtp85) cc_final: 0.8575 (ttt90) REVERT: C 122 GLU cc_start: 0.8796 (OUTLIER) cc_final: 0.8592 (pp20) REVERT: C 221 LYS cc_start: 0.8730 (OUTLIER) cc_final: 0.8273 (mtmp) REVERT: C 320 ASP cc_start: 0.8149 (t0) cc_final: 0.7731 (t0) outliers start: 29 outliers final: 18 residues processed: 98 average time/residue: 0.4914 time to fit residues: 51.6006 Evaluate side-chains 91 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 71 time to evaluate : 0.316 ------------------------------------------------------------------------------- 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 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 148 ASN 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 B residue 342 PHE 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 221 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 31 optimal weight: 3.9990 chunk 84 optimal weight: 0.9980 chunk 34 optimal weight: 6.9990 chunk 96 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 89 optimal weight: 4.9990 chunk 67 optimal weight: 9.9990 chunk 81 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 GLN ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 76 GLN C 127 GLN C 284 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.104425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.075866 restraints weight = 13079.412| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 2.95 r_work: 0.2889 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.4913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.093 8212 Z= 0.253 Angle : 0.766 12.871 11174 Z= 0.393 Chirality : 0.049 0.338 1242 Planarity : 0.005 0.054 1398 Dihedral : 9.439 88.688 1353 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.31 % Allowed : 21.39 % 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 aren not related in a simple way. whole: 0.53 (0.27), residues: 984 helix: 1.86 (0.35), residues: 249 sheet: 0.67 (0.29), residues: 300 loop : -0.76 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 244 TYR 0.035 0.002 TYR C 90 PHE 0.034 0.002 PHE A 92 TRP 0.013 0.001 TRP C 164 HIS 0.005 0.001 HIS B 180 Details of bonding type rmsd covalent geometry : bond 0.00600 ( 8190) covalent geometry : angle 0.72799 (11121) SS BOND : bond 0.00347 ( 13) SS BOND : angle 4.54949 ( 26) hydrogen bonds : bond 0.03380 ( 354) hydrogen bonds : angle 5.04294 ( 1050) link_NAG-ASN : bond 0.00572 ( 9) link_NAG-ASN : angle 2.15669 ( 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 103 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 75 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 327 ASP cc_start: 0.8000 (t0) cc_final: 0.7607 (t0) REVERT: B 197 ARG cc_start: 0.8844 (mtp85) cc_final: 0.8566 (ttt90) REVERT: B 248 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.8255 (mm-30) REVERT: C 78 GLN cc_start: 0.8847 (mm-40) cc_final: 0.8119 (mp10) REVERT: C 122 GLU cc_start: 0.8781 (OUTLIER) cc_final: 0.8561 (pp20) REVERT: C 138 GLU cc_start: 0.8504 (pm20) cc_final: 0.8228 (mp0) REVERT: C 221 LYS cc_start: 0.8739 (OUTLIER) cc_final: 0.8223 (mtmp) REVERT: C 320 ASP cc_start: 0.8154 (t0) cc_final: 0.7770 (t0) outliers start: 28 outliers final: 23 residues processed: 95 average time/residue: 0.5105 time to fit residues: 52.0474 Evaluate side-chains 98 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 72 time to evaluate : 0.324 ------------------------------------------------------------------------------- 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 126 CYS Chi-restraints excluded: chain A residue 133 THR 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 116 HIS Chi-restraints excluded: chain B residue 126 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 248 GLU Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 339 ILE Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 80 LEU 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 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: 0.0060 chunk 54 optimal weight: 0.7980 chunk 77 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 75 optimal weight: 0.8980 chunk 97 optimal weight: 6.9990 chunk 80 optimal weight: 0.2980 chunk 89 optimal weight: 6.9990 chunk 92 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 78 optimal weight: 0.7980 overall best weight: 0.5596 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.109407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.080874 restraints weight = 12897.661| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 3.00 r_work: 0.2931 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.4842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 8212 Z= 0.125 Angle : 0.665 12.190 11174 Z= 0.339 Chirality : 0.045 0.247 1242 Planarity : 0.004 0.056 1398 Dihedral : 9.062 88.932 1353 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.60 % Allowed : 22.22 % Favored : 75.18 % 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 aren not related in a simple way. whole: 0.51 (0.27), residues: 984 helix: 1.86 (0.35), residues: 255 sheet: 0.71 (0.31), residues: 273 loop : -0.78 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 244 TYR 0.036 0.001 TYR C 90 PHE 0.020 0.002 PHE C 326 TRP 0.012 0.001 TRP A 164 HIS 0.004 0.001 HIS B 180 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 8190) covalent geometry : angle 0.63845 (11121) SS BOND : bond 0.00347 ( 13) SS BOND : angle 3.71372 ( 26) hydrogen bonds : bond 0.02654 ( 354) hydrogen bonds : angle 4.90061 ( 1050) link_NAG-ASN : bond 0.00517 ( 9) link_NAG-ASN : angle 1.44470 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2789.16 seconds wall clock time: 48 minutes 23.57 seconds (2903.57 seconds total)