Starting phenix.real_space_refine on Fri Aug 22 21:05:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zt2_60445/08_2025/8zt2_60445.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zt2_60445/08_2025/8zt2_60445.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8zt2_60445/08_2025/8zt2_60445.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zt2_60445/08_2025/8zt2_60445.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8zt2_60445/08_2025/8zt2_60445.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zt2_60445/08_2025/8zt2_60445.map" } resolution = 2.31 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= 0.052 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 1 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 1459 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7994 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: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {' CA': 1, ' MG': 1, 'ATP': 1, 'NAG': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} 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: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 74 Unusual residues: {' MG': 1, 'ATP': 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: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 74 Unusual residues: {' MG': 1, 'ATP': 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: "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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Time building chain proxies: 2.33, per 1000 atoms: 0.29 Number of scatterers: 7994 At special positions: 0 Unit cell: (88.168, 84.048, 120.304, 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 1 19.99 S 45 16.00 P 9 15.00 Mg 3 11.99 O 1459 8.00 N 1359 7.00 C 5118 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, 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 217 " - pdb=" SG CYS A 227 " distance=2.04 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 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 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 502 " - " ASN A 210 " " NAG A 503 " - " ASN A 153 " " NAG A 504 " - " ASN A 184 " " NAG B 503 " - " ASN B 210 " " NAG B 504 " - " ASN B 153 " " NAG B 505 " - " ASN B 184 " " NAG C 503 " - " ASN C 210 " " NAG C 504 " - " ASN C 153 " " NAG C 505 " - " ASN C 184 " Time building additional restraints: 0.63 Conformation dependent library (CDL) restraints added in 505.3 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 21 sheets defined 27.2% alpha, 46.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 26 through 47 removed outlier: 3.893A pdb=" N GLY A 30 " --> pdb=" O ASN A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 91 Processing helix chain 'A' and resid 179 through 184 removed outlier: 3.724A pdb=" N ASN A 184 " --> pdb=" O GLU A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 216 removed outlier: 3.585A pdb=" N LYS A 216 " --> pdb=" O THR A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 240 Processing helix chain 'A' and resid 242 through 250 removed outlier: 3.712A pdb=" N LYS A 249 " --> pdb=" O SER A 245 " (cutoff:3.500A) 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 47 Processing helix chain 'B' and resid 86 through 91 Processing helix chain 'B' and resid 128 through 132 Processing helix chain 'B' and resid 179 through 184 removed outlier: 3.717A pdb=" N ASN B 184 " --> pdb=" O GLU B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 216 removed outlier: 3.689A 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: 3.593A pdb=" N LEU B 246 " --> pdb=" O ASP B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 355 removed outlier: 3.552A pdb=" N THR B 331 " --> pdb=" O ASP B 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 46 Processing helix chain 'C' and resid 86 through 91 Processing helix chain 'C' and resid 179 through 184 removed outlier: 3.814A pdb=" N ASN C 184 " --> pdb=" O GLU C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 240 Processing helix chain 'C' and resid 242 through 250 removed outlier: 3.558A pdb=" N LEU C 246 " --> pdb=" O ASP C 242 " (cutoff:3.500A) removed outlier: 3.675A 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: 3.511A pdb=" N SER A 59 " --> pdb=" O ALA A 323 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA A 323 " --> pdb=" O SER A 59 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N CYS A 261 " --> pdb=" O GLY A 324 " (cutoff:3.500A) removed outlier: 9.166A pdb=" N PHE A 326 " --> pdb=" O CYS A 261 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 62 through 70 removed outlier: 3.985A pdb=" N THR A 186 " --> pdb=" O LYS A 70 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL A 200 " --> pdb=" O PHE A 195 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 62 through 70 removed outlier: 3.985A pdb=" N THR A 186 " --> pdb=" O LYS A 70 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 73 through 75 Processing sheet with id=AA5, first strand: chain 'A' and resid 99 through 112 removed outlier: 5.467A pdb=" N SER A 99 " --> pdb=" O ILE A 317 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N ILE A 317 " --> pdb=" O SER A 99 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N VAL A 101 " --> pdb=" O PHE A 315 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N PHE A 315 " --> pdb=" O VAL A 101 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N MET A 103 " --> pdb=" O ILE A 313 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ILE A 313 " --> pdb=" O MET A 103 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN A 111 " --> pdb=" O ARG A 305 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N ARG A 305 " --> pdb=" O GLN A 111 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N VAL A 252 " --> pdb=" O LEU A 279 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 99 through 112 removed outlier: 5.467A pdb=" N SER A 99 " --> pdb=" O ILE A 317 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N ILE A 317 " --> pdb=" O SER A 99 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N VAL A 101 " --> pdb=" O PHE A 315 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N PHE A 315 " --> pdb=" O VAL A 101 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N MET A 103 " --> pdb=" O ILE A 313 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ILE A 313 " --> pdb=" O MET A 103 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN A 111 " --> pdb=" O ARG A 305 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N ARG A 305 " --> pdb=" O GLN A 111 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 114 through 118 removed outlier: 5.181A pdb=" N ASN A 148 " --> pdb=" O GLU A 160 " (cutoff:3.500A) removed outlier: 8.801A pdb=" N PHE A 162 " --> pdb=" O THR A 146 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N THR A 146 " --> pdb=" O PHE A 162 " (cutoff:3.500A) removed outlier: 9.417A pdb=" N TRP A 164 " --> pdb=" O ILE A 144 " (cutoff:3.500A) removed outlier: 9.558A pdb=" N ILE A 144 " --> pdb=" O TRP A 164 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 56 through 59 removed outlier: 3.519A pdb=" N LYS B 325 " --> pdb=" O THR B 57 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER B 59 " --> pdb=" O ALA B 323 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA B 323 " --> pdb=" O SER B 59 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N CYS B 261 " --> pdb=" O GLY B 324 " (cutoff:3.500A) removed outlier: 9.522A pdb=" N PHE B 326 " --> pdb=" O CYS B 261 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 62 through 70 removed outlier: 3.541A 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: 3.541A 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 99 through 112 removed outlier: 5.497A pdb=" N SER B 99 " --> pdb=" O ILE B 317 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N ILE B 317 " --> pdb=" O SER B 99 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N VAL B 101 " --> pdb=" O PHE B 315 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N PHE B 315 " --> pdb=" O VAL B 101 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N MET B 103 " --> pdb=" O ILE B 313 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ILE B 313 " --> pdb=" O MET B 103 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLN B 111 " --> pdb=" O ARG B 305 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N ARG B 305 " --> pdb=" O GLN B 111 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY B 251 " --> pdb=" O GLY B 312 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL B 252 " --> pdb=" O LEU B 279 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 99 through 112 removed outlier: 5.497A pdb=" N SER B 99 " --> pdb=" O ILE B 317 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N ILE B 317 " --> pdb=" O SER B 99 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N VAL B 101 " --> pdb=" O PHE B 315 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N PHE B 315 " --> pdb=" O VAL B 101 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N MET B 103 " --> pdb=" O ILE B 313 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ILE B 313 " --> pdb=" O MET B 103 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLN B 111 " --> pdb=" O ARG B 305 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N ARG B 305 " --> pdb=" O GLN B 111 " (cutoff:3.500A) Processing sheet with id=AB5, 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: 8.530A pdb=" N PHE B 162 " --> pdb=" O THR B 146 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N THR B 146 " --> pdb=" O PHE B 162 " (cutoff:3.500A) removed outlier: 9.239A pdb=" N TRP B 164 " --> pdb=" O ILE B 144 " (cutoff:3.500A) removed outlier: 9.453A pdb=" N ILE B 144 " --> pdb=" O TRP B 164 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 56 through 59 removed outlier: 3.821A pdb=" N SER C 59 " --> pdb=" O ALA C 323 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA C 323 " --> pdb=" O SER C 59 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N CYS C 261 " --> pdb=" O GLY C 324 " (cutoff:3.500A) removed outlier: 9.300A pdb=" N PHE C 326 " --> pdb=" O CYS C 261 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 62 through 70 Processing sheet with id=AB8, first strand: chain 'C' and resid 62 through 70 Processing sheet with id=AB9, first strand: chain 'C' and resid 73 through 76 Processing sheet with id=AC1, first strand: chain 'C' and resid 99 through 112 removed outlier: 5.462A pdb=" N SER C 99 " --> pdb=" O ILE C 317 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N ILE C 317 " --> pdb=" O SER C 99 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N VAL C 101 " --> pdb=" O PHE C 315 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N PHE C 315 " --> pdb=" O VAL C 101 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N MET C 103 " --> pdb=" O ILE C 313 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N ILE C 313 " --> pdb=" O MET C 103 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N ARG C 305 " --> pdb=" O GLN C 111 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY C 251 " --> pdb=" O GLY C 312 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N VAL C 252 " --> pdb=" O LEU C 279 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 99 through 112 removed outlier: 5.462A pdb=" N SER C 99 " --> pdb=" O ILE C 317 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N ILE C 317 " --> pdb=" O SER C 99 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N VAL C 101 " --> pdb=" O PHE C 315 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N PHE C 315 " --> pdb=" O VAL C 101 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N MET C 103 " --> pdb=" O ILE C 313 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N ILE C 313 " --> pdb=" O MET C 103 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N ARG C 305 " --> pdb=" O GLN C 111 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 114 through 118 removed outlier: 5.143A pdb=" N ASN C 148 " --> pdb=" O GLU C 160 " (cutoff:3.500A) removed outlier: 8.561A pdb=" N PHE C 162 " --> pdb=" O THR C 146 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N THR C 146 " --> pdb=" O PHE C 162 " (cutoff:3.500A) removed outlier: 9.293A pdb=" N TRP C 164 " --> pdb=" O ILE C 144 " (cutoff:3.500A) removed outlier: 9.547A pdb=" N ILE C 144 " --> pdb=" O TRP C 164 " (cutoff:3.500A) 400 hydrogen bonds defined for protein. 1089 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: 1.31 Time building geometry restraints manager: 0.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2531 1.35 - 1.46: 2009 1.46 - 1.58: 3578 1.58 - 1.70: 15 1.70 - 1.82: 57 Bond restraints: 8190 Sorted by residual: bond pdb=" C4 ATP A 501 " pdb=" C5 ATP A 501 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.26e+01 bond pdb=" C4 ATP B 502 " pdb=" C5 ATP B 502 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.26e+01 bond pdb=" C4 ATP C 502 " pdb=" C5 ATP C 502 " ideal model delta sigma weight residual 1.388 1.466 -0.078 1.00e-02 1.00e+04 6.16e+01 bond pdb=" C5 ATP A 501 " pdb=" C6 ATP A 501 " ideal model delta sigma weight residual 1.409 1.480 -0.071 1.00e-02 1.00e+04 5.01e+01 bond pdb=" C5 ATP B 502 " pdb=" C6 ATP B 502 " ideal model delta sigma weight residual 1.409 1.479 -0.070 1.00e-02 1.00e+04 4.96e+01 ... (remaining 8185 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.37: 11042 3.37 - 6.73: 64 6.73 - 10.10: 9 10.10 - 13.46: 0 13.46 - 16.83: 6 Bond angle restraints: 11121 Sorted by residual: angle pdb=" PB ATP B 502 " pdb=" O3B ATP B 502 " pdb=" PG ATP B 502 " ideal model delta sigma weight residual 139.87 123.04 16.83 1.00e+00 1.00e+00 2.83e+02 angle pdb=" PB ATP C 502 " pdb=" O3B ATP C 502 " pdb=" PG ATP C 502 " ideal model delta sigma weight residual 139.87 123.24 16.63 1.00e+00 1.00e+00 2.77e+02 angle pdb=" PB ATP A 501 " pdb=" O3B ATP A 501 " pdb=" PG ATP A 501 " ideal model delta sigma weight residual 139.87 123.72 16.15 1.00e+00 1.00e+00 2.61e+02 angle pdb=" PA ATP C 502 " pdb=" O3A ATP C 502 " pdb=" PB ATP C 502 " ideal model delta sigma weight residual 136.83 122.45 14.38 1.00e+00 1.00e+00 2.07e+02 angle pdb=" PA ATP B 502 " pdb=" O3A ATP B 502 " pdb=" PB ATP B 502 " ideal model delta sigma weight residual 136.83 122.50 14.33 1.00e+00 1.00e+00 2.05e+02 ... (remaining 11116 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.59: 4678 14.59 - 29.18: 200 29.18 - 43.78: 32 43.78 - 58.37: 30 58.37 - 72.96: 7 Dihedral angle restraints: 4947 sinusoidal: 2157 harmonic: 2790 Sorted by residual: dihedral pdb=" CA CYS C 117 " pdb=" CB CYS C 117 " pdb=" SG CYS C 117 " pdb=" SG CYS C 165 " ideal model delta sinusoidal sigma weight residual -73.00 -124.73 51.73 1 2.00e+01 2.50e-03 9.13e+00 dihedral pdb=" N ASN C 120 " pdb=" CA ASN C 120 " pdb=" CB ASN C 120 " pdb=" CG ASN C 120 " ideal model delta sinusoidal sigma weight residual -180.00 -131.38 -48.62 3 1.50e+01 4.44e-03 8.66e+00 dihedral pdb=" CA LYS B 28 " pdb=" CB LYS B 28 " pdb=" CG LYS B 28 " pdb=" CD LYS B 28 " ideal model delta sinusoidal sigma weight residual -60.00 -107.43 47.43 3 1.50e+01 4.44e-03 8.49e+00 ... (remaining 4944 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1053 0.057 - 0.115: 170 0.115 - 0.172: 16 0.172 - 0.229: 0 0.229 - 0.287: 3 Chirality restraints: 1242 Sorted by residual: chirality pdb=" C1 NAG A 504 " pdb=" ND2 ASN A 184 " pdb=" C2 NAG A 504 " pdb=" O5 NAG A 504 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" C1 NAG C 505 " pdb=" ND2 ASN C 184 " pdb=" C2 NAG C 505 " pdb=" O5 NAG C 505 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" C1 NAG B 505 " pdb=" ND2 ASN B 184 " pdb=" C2 NAG B 505 " pdb=" O5 NAG B 505 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 1.97e+00 ... (remaining 1239 not shown) Planarity restraints: 1407 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS C 165 " 0.026 5.00e-02 4.00e+02 3.92e-02 2.46e+00 pdb=" N PRO C 166 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO C 166 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 166 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE C 92 " 0.022 5.00e-02 4.00e+02 3.39e-02 1.84e+00 pdb=" N PRO C 93 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO C 93 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 93 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 92 " -0.022 5.00e-02 4.00e+02 3.37e-02 1.82e+00 pdb=" N PRO B 93 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO B 93 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 93 " -0.019 5.00e-02 4.00e+02 ... (remaining 1404 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 34 2.52 - 3.12: 5866 3.12 - 3.71: 12121 3.71 - 4.31: 17735 4.31 - 4.90: 29443 Nonbonded interactions: 65199 Sorted by model distance: nonbonded pdb=" O3G ATP A 501 " pdb="MG MG B 501 " model vdw 1.928 2.170 nonbonded pdb="MG MG A 505 " pdb=" O3G ATP C 502 " model vdw 2.025 2.170 nonbonded pdb=" O3G ATP B 502 " pdb="MG MG C 501 " model vdw 2.048 2.170 nonbonded pdb=" O VAL C 298 " pdb=" O HOH C 601 " model vdw 2.253 3.040 nonbonded pdb=" O VAL B 298 " pdb=" O HOH C 601 " model vdw 2.283 3.040 ... (remaining 65194 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 503 through 504)) selection = (chain 'B' and (resid 26 through 355 or resid 503 through 504)) selection = (chain 'C' and (resid 26 through 355 or resid 503 through 504)) } 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: 1.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 9.460 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.010 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:7.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6646 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 0.079 8208 Z= 0.311 Angle : 0.744 16.831 11166 Z= 0.539 Chirality : 0.044 0.287 1242 Planarity : 0.003 0.039 1398 Dihedral : 9.506 72.962 3144 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 1.06 % Allowed : 2.60 % Favored : 96.34 % 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: -0.61 (0.25), residues: 984 helix: -0.63 (0.30), residues: 294 sheet: 1.65 (0.30), residues: 240 loop : -1.40 (0.25), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 244 TYR 0.008 0.001 TYR A 90 PHE 0.005 0.001 PHE C 342 TRP 0.005 0.000 TRP C 47 HIS 0.002 0.000 HIS A 306 Details of bonding type rmsd covalent geometry : bond 0.00398 ( 8190) covalent geometry : angle 0.72728 (11121) SS BOND : bond 0.00248 ( 9) SS BOND : angle 0.98478 ( 18) hydrogen bonds : bond 0.22036 ( 353) hydrogen bonds : angle 8.24364 ( 1089) link_NAG-ASN : bond 0.00759 ( 9) link_NAG-ASN : angle 3.21971 ( 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 202 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 193 time to evaluate : 0.340 Fit side-chains outliers start: 9 outliers final: 0 residues processed: 200 average time/residue: 0.7301 time to fit residues: 152.7761 Evaluate side-chains 95 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 10.0000 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 50.0000 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN A 112 GLN A 120 ASN A 180 HIS A 191 ASN A 220 HIS A 290 ASN B 112 GLN B 114 GLN B 180 HIS B 191 ASN B 220 HIS B 290 ASN C 112 GLN C 180 HIS C 191 ASN C 220 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.125294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.088298 restraints weight = 12222.477| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 2.52 r_work: 0.3158 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.3516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 8208 Z= 0.226 Angle : 0.753 11.914 11166 Z= 0.380 Chirality : 0.052 0.355 1242 Planarity : 0.005 0.041 1398 Dihedral : 9.615 88.456 1347 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.25 % Allowed : 10.87 % Favored : 86.88 % 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: 0.56 (0.27), residues: 984 helix: 0.79 (0.33), residues: 273 sheet: 1.24 (0.28), residues: 309 loop : -0.56 (0.31), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 197 TYR 0.029 0.002 TYR A 90 PHE 0.033 0.002 PHE A 92 TRP 0.007 0.001 TRP B 164 HIS 0.006 0.001 HIS A 306 Details of bonding type rmsd covalent geometry : bond 0.00502 ( 8190) covalent geometry : angle 0.71427 (11121) SS BOND : bond 0.00479 ( 9) SS BOND : angle 2.11217 ( 18) hydrogen bonds : bond 0.03831 ( 353) hydrogen bonds : angle 4.94095 ( 1089) link_NAG-ASN : bond 0.01016 ( 9) link_NAG-ASN : angle 4.62661 ( 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 121 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 102 time to evaluate : 0.306 Fit side-chains revert: symmetry clash REVERT: A 49 PHE cc_start: 0.8366 (m-80) cc_final: 0.7835 (m-10) REVERT: A 332 MET cc_start: 0.8379 (mmm) cc_final: 0.8064 (mtm) REVERT: B 51 TYR cc_start: 0.8689 (t80) cc_final: 0.8271 (t80) REVERT: B 159 CYS cc_start: 0.8542 (m) cc_final: 0.8270 (m) REVERT: B 197 ARG cc_start: 0.9065 (mtp-110) cc_final: 0.8845 (mtp-110) REVERT: C 76 GLN cc_start: 0.8655 (tp40) cc_final: 0.8400 (mm-40) REVERT: C 208 GLU cc_start: 0.8687 (mp0) cc_final: 0.8359 (mp0) outliers start: 19 outliers final: 6 residues processed: 118 average time/residue: 0.6413 time to fit residues: 79.8985 Evaluate side-chains 87 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 81 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain C residue 245 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 98 optimal weight: 6.9990 chunk 77 optimal weight: 0.3980 chunk 69 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 76 optimal weight: 6.9990 chunk 1 optimal weight: 7.9990 chunk 92 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.119463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.079650 restraints weight = 11320.194| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 2.60 r_work: 0.2930 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2811 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.3807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 8208 Z= 0.195 Angle : 0.704 10.678 11166 Z= 0.348 Chirality : 0.047 0.216 1242 Planarity : 0.005 0.041 1398 Dihedral : 9.849 85.137 1347 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.89 % Allowed : 14.07 % Favored : 84.04 % 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: 1.01 (0.27), residues: 984 helix: 1.52 (0.35), residues: 255 sheet: 1.27 (0.29), residues: 306 loop : -0.27 (0.31), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 197 TYR 0.020 0.002 TYR C 90 PHE 0.027 0.002 PHE C 92 TRP 0.006 0.001 TRP A 259 HIS 0.003 0.001 HIS C 306 Details of bonding type rmsd covalent geometry : bond 0.00433 ( 8190) covalent geometry : angle 0.66940 (11121) SS BOND : bond 0.00282 ( 9) SS BOND : angle 2.17172 ( 18) hydrogen bonds : bond 0.03589 ( 353) hydrogen bonds : angle 4.74764 ( 1089) link_NAG-ASN : bond 0.00607 ( 9) link_NAG-ASN : angle 4.18755 ( 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 103 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 87 time to evaluate : 0.283 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 PHE cc_start: 0.8352 (m-80) cc_final: 0.7624 (m-80) REVERT: A 332 MET cc_start: 0.8313 (mmm) cc_final: 0.8000 (mtm) REVERT: B 51 TYR cc_start: 0.8626 (t80) cc_final: 0.8184 (t80) REVERT: B 159 CYS cc_start: 0.8507 (m) cc_final: 0.8265 (m) REVERT: B 197 ARG cc_start: 0.9045 (mtp-110) cc_final: 0.8802 (mtp-110) REVERT: C 76 GLN cc_start: 0.8667 (tp40) cc_final: 0.8381 (mm-40) outliers start: 16 outliers final: 9 residues processed: 101 average time/residue: 0.6246 time to fit residues: 66.8688 Evaluate side-chains 87 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 78 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 275 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 92 optimal weight: 0.9980 chunk 33 optimal weight: 40.0000 chunk 59 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 67 optimal weight: 10.0000 chunk 85 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 chunk 22 optimal weight: 0.5980 chunk 18 optimal weight: 0.9990 chunk 87 optimal weight: 3.9990 chunk 68 optimal weight: 5.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 114 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.124813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.088241 restraints weight = 12454.280| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 2.50 r_work: 0.3142 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8794 moved from start: 0.3950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8208 Z= 0.152 Angle : 0.630 9.879 11166 Z= 0.314 Chirality : 0.046 0.308 1242 Planarity : 0.004 0.038 1398 Dihedral : 9.715 77.908 1347 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.65 % Allowed : 14.78 % Favored : 83.57 % 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: 1.02 (0.27), residues: 984 helix: 1.64 (0.35), residues: 255 sheet: 1.18 (0.28), residues: 306 loop : -0.26 (0.31), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 197 TYR 0.019 0.001 TYR C 90 PHE 0.024 0.002 PHE C 92 TRP 0.009 0.001 TRP A 164 HIS 0.003 0.000 HIS B 116 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 8190) covalent geometry : angle 0.60490 (11121) SS BOND : bond 0.00358 ( 9) SS BOND : angle 1.83367 ( 18) hydrogen bonds : bond 0.03092 ( 353) hydrogen bonds : angle 4.56301 ( 1089) link_NAG-ASN : bond 0.01090 ( 9) link_NAG-ASN : angle 3.34003 ( 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 102 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 88 time to evaluate : 0.326 Fit side-chains revert: symmetry clash REVERT: A 49 PHE cc_start: 0.8503 (m-80) cc_final: 0.7637 (m-80) REVERT: A 275 GLN cc_start: 0.8482 (mm110) cc_final: 0.8251 (mt0) REVERT: A 332 MET cc_start: 0.8330 (mmm) cc_final: 0.8046 (mtm) REVERT: B 51 TYR cc_start: 0.8683 (t80) cc_final: 0.8334 (t80) REVERT: B 159 CYS cc_start: 0.8636 (m) cc_final: 0.8379 (m) REVERT: B 208 GLU cc_start: 0.8593 (mp0) cc_final: 0.8228 (mp0) REVERT: C 76 GLN cc_start: 0.8674 (tp40) cc_final: 0.8472 (mm110) outliers start: 14 outliers final: 8 residues processed: 100 average time/residue: 0.6305 time to fit residues: 66.8154 Evaluate side-chains 93 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 85 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 258 ASP Chi-restraints excluded: chain C residue 314 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 98 optimal weight: 6.9990 chunk 26 optimal weight: 0.6980 chunk 84 optimal weight: 0.9990 chunk 78 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 31 optimal weight: 10.0000 chunk 22 optimal weight: 0.9980 chunk 82 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 44 optimal weight: 0.4980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.125460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.088607 restraints weight = 12311.733| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.48 r_work: 0.3177 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.4017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 8208 Z= 0.157 Angle : 0.708 13.620 11166 Z= 0.338 Chirality : 0.047 0.467 1242 Planarity : 0.005 0.044 1398 Dihedral : 9.492 74.795 1347 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.13 % Allowed : 15.01 % Favored : 82.86 % 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: 1.17 (0.28), residues: 984 helix: 2.14 (0.35), residues: 237 sheet: 1.12 (0.29), residues: 300 loop : -0.18 (0.30), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 197 TYR 0.018 0.001 TYR C 90 PHE 0.023 0.002 PHE B 326 TRP 0.006 0.001 TRP C 164 HIS 0.003 0.000 HIS B 116 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 8190) covalent geometry : angle 0.67296 (11121) SS BOND : bond 0.00272 ( 9) SS BOND : angle 1.72685 ( 18) hydrogen bonds : bond 0.02889 ( 353) hydrogen bonds : angle 4.46933 ( 1089) link_NAG-ASN : bond 0.02326 ( 9) link_NAG-ASN : angle 4.35278 ( 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 105 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 87 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 275 GLN cc_start: 0.8527 (mm110) cc_final: 0.8294 (mt0) REVERT: A 304 ARG cc_start: 0.8336 (OUTLIER) cc_final: 0.8102 (mtt180) REVERT: A 328 ILE cc_start: 0.8656 (mp) cc_final: 0.8163 (OUTLIER) REVERT: A 332 MET cc_start: 0.8327 (mmm) cc_final: 0.8022 (mtm) REVERT: B 51 TYR cc_start: 0.8673 (t80) cc_final: 0.8347 (t80) REVERT: B 159 CYS cc_start: 0.8625 (m) cc_final: 0.8369 (m) REVERT: B 172 LYS cc_start: 0.8147 (tppt) cc_final: 0.7907 (mmmt) REVERT: B 208 GLU cc_start: 0.8616 (mp0) cc_final: 0.8233 (mp0) REVERT: C 76 GLN cc_start: 0.8688 (tp40) cc_final: 0.8481 (mm110) REVERT: C 314 ARG cc_start: 0.8948 (OUTLIER) cc_final: 0.8709 (ptm160) REVERT: C 328 ILE cc_start: 0.8634 (mp) cc_final: 0.8041 (OUTLIER) outliers start: 18 outliers final: 12 residues processed: 102 average time/residue: 0.6388 time to fit residues: 69.0085 Evaluate side-chains 94 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 304 ARG Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 184 ASN Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 210 ASN Chi-restraints excluded: chain C residue 275 GLN Chi-restraints excluded: chain C residue 314 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 76 optimal weight: 7.9990 chunk 37 optimal weight: 3.9990 chunk 58 optimal weight: 0.0670 chunk 57 optimal weight: 0.8980 chunk 92 optimal weight: 0.7980 chunk 19 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 79 optimal weight: 5.9990 chunk 14 optimal weight: 6.9990 chunk 66 optimal weight: 50.0000 overall best weight: 1.9522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.122210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.085288 restraints weight = 12254.643| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 2.46 r_work: 0.3083 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8847 moved from start: 0.4325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 8208 Z= 0.214 Angle : 0.693 11.065 11166 Z= 0.347 Chirality : 0.047 0.339 1242 Planarity : 0.005 0.048 1398 Dihedral : 9.748 72.500 1347 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.60 % Allowed : 14.42 % Favored : 82.98 % 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: 1.17 (0.28), residues: 984 helix: 2.37 (0.36), residues: 231 sheet: 0.89 (0.28), residues: 315 loop : -0.13 (0.31), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 197 TYR 0.017 0.002 TYR C 90 PHE 0.033 0.002 PHE A 92 TRP 0.006 0.001 TRP C 259 HIS 0.003 0.001 HIS A 306 Details of bonding type rmsd covalent geometry : bond 0.00486 ( 8190) covalent geometry : angle 0.65754 (11121) SS BOND : bond 0.00410 ( 9) SS BOND : angle 2.71120 ( 18) hydrogen bonds : bond 0.03468 ( 353) hydrogen bonds : angle 4.63768 ( 1089) link_NAG-ASN : bond 0.00825 ( 9) link_NAG-ASN : angle 3.98787 ( 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 115 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 93 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 PHE cc_start: 0.8646 (OUTLIER) cc_final: 0.7676 (m-80) REVERT: A 208 GLU cc_start: 0.8366 (mp0) cc_final: 0.8080 (mp0) REVERT: A 275 GLN cc_start: 0.8500 (mm110) cc_final: 0.8261 (mt0) REVERT: A 304 ARG cc_start: 0.8476 (OUTLIER) cc_final: 0.8256 (mtt180) REVERT: A 328 ILE cc_start: 0.8718 (mp) cc_final: 0.8244 (OUTLIER) REVERT: A 332 MET cc_start: 0.8367 (mmm) cc_final: 0.8097 (mtm) REVERT: B 51 TYR cc_start: 0.8678 (t80) cc_final: 0.8432 (t80) REVERT: B 159 CYS cc_start: 0.8687 (m) cc_final: 0.8449 (m) REVERT: B 172 LYS cc_start: 0.8234 (tppt) cc_final: 0.7613 (tptt) REVERT: B 275 GLN cc_start: 0.8379 (mm110) cc_final: 0.8166 (mt0) REVERT: C 76 GLN cc_start: 0.8674 (tp40) cc_final: 0.8439 (mm-40) REVERT: C 216 LYS cc_start: 0.9165 (OUTLIER) cc_final: 0.8657 (pptt) REVERT: C 314 ARG cc_start: 0.8977 (OUTLIER) cc_final: 0.8562 (ttm170) outliers start: 22 outliers final: 10 residues processed: 109 average time/residue: 0.6252 time to fit residues: 72.1724 Evaluate side-chains 100 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 87 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 PHE Chi-restraints excluded: chain A residue 184 ASN Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 304 ARG Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain C residue 210 ASN Chi-restraints excluded: chain C residue 216 LYS Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 258 ASP Chi-restraints excluded: chain C residue 314 ARG Chi-restraints excluded: chain C residue 337 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 0 optimal weight: 50.0000 chunk 2 optimal weight: 0.0670 chunk 80 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 chunk 85 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 overall best weight: 2.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.120541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.082809 restraints weight = 12302.342| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 2.49 r_work: 0.3054 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8860 moved from start: 0.4504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 8208 Z= 0.232 Angle : 0.714 12.567 11166 Z= 0.359 Chirality : 0.049 0.335 1242 Planarity : 0.005 0.048 1398 Dihedral : 9.948 68.573 1347 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.25 % Allowed : 15.60 % Favored : 82.15 % 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: 1.04 (0.28), residues: 984 helix: 2.35 (0.36), residues: 231 sheet: 0.83 (0.28), residues: 315 loop : -0.28 (0.31), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 197 TYR 0.018 0.002 TYR C 90 PHE 0.036 0.002 PHE C 92 TRP 0.006 0.001 TRP A 259 HIS 0.004 0.001 HIS A 116 Details of bonding type rmsd covalent geometry : bond 0.00529 ( 8190) covalent geometry : angle 0.67816 (11121) SS BOND : bond 0.00582 ( 9) SS BOND : angle 2.65647 ( 18) hydrogen bonds : bond 0.03581 ( 353) hydrogen bonds : angle 4.66194 ( 1089) link_NAG-ASN : bond 0.00994 ( 9) link_NAG-ASN : angle 4.09046 ( 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 107 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 88 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 PHE cc_start: 0.8711 (OUTLIER) cc_final: 0.7685 (m-80) REVERT: A 208 GLU cc_start: 0.8372 (mp0) cc_final: 0.8147 (mp0) REVERT: A 275 GLN cc_start: 0.8514 (mm110) cc_final: 0.8281 (mt0) REVERT: A 304 ARG cc_start: 0.8494 (OUTLIER) cc_final: 0.8272 (mtt180) REVERT: A 328 ILE cc_start: 0.8727 (mp) cc_final: 0.8270 (OUTLIER) REVERT: A 332 MET cc_start: 0.8390 (mmm) cc_final: 0.8137 (mtm) REVERT: B 51 TYR cc_start: 0.8698 (t80) cc_final: 0.8454 (t80) REVERT: B 159 CYS cc_start: 0.8752 (m) cc_final: 0.8546 (m) REVERT: B 172 LYS cc_start: 0.8356 (tppt) cc_final: 0.8137 (mmmt) REVERT: B 275 GLN cc_start: 0.8352 (mm110) cc_final: 0.8116 (mt0) REVERT: B 328 ILE cc_start: 0.8767 (mp) cc_final: 0.8362 (mm) REVERT: C 76 GLN cc_start: 0.8695 (tp40) cc_final: 0.8485 (mm-40) REVERT: C 216 LYS cc_start: 0.9200 (OUTLIER) cc_final: 0.8763 (pptt) REVERT: C 314 ARG cc_start: 0.8989 (OUTLIER) cc_final: 0.8456 (ttm170) REVERT: C 328 ILE cc_start: 0.8611 (mp) cc_final: 0.8182 (OUTLIER) REVERT: C 332 MET cc_start: 0.8467 (mmm) cc_final: 0.8252 (mtm) outliers start: 19 outliers final: 11 residues processed: 104 average time/residue: 0.5702 time to fit residues: 62.5932 Evaluate side-chains 100 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 87 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 PHE Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 304 ARG Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 210 ASN Chi-restraints excluded: chain C residue 216 LYS Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 258 ASP Chi-restraints excluded: chain C residue 314 ARG Chi-restraints excluded: chain C residue 337 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 40 optimal weight: 0.9990 chunk 95 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 81 optimal weight: 0.9980 chunk 0 optimal weight: 50.0000 chunk 74 optimal weight: 0.9990 chunk 66 optimal weight: 50.0000 chunk 5 optimal weight: 0.3980 chunk 36 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 120 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.123571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.086467 restraints weight = 12207.139| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 2.44 r_work: 0.3130 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 moved from start: 0.4404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 8208 Z= 0.128 Angle : 0.615 11.056 11166 Z= 0.309 Chirality : 0.044 0.216 1242 Planarity : 0.005 0.055 1398 Dihedral : 9.187 86.566 1347 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.89 % Allowed : 16.19 % Favored : 81.91 % 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: 1.09 (0.27), residues: 984 helix: 2.37 (0.36), residues: 231 sheet: 0.90 (0.29), residues: 306 loop : -0.25 (0.30), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 197 TYR 0.019 0.001 TYR C 90 PHE 0.028 0.002 PHE A 326 TRP 0.006 0.001 TRP C 47 HIS 0.004 0.001 HIS A 116 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 8190) covalent geometry : angle 0.58047 (11121) SS BOND : bond 0.00361 ( 9) SS BOND : angle 2.19478 ( 18) hydrogen bonds : bond 0.02834 ( 353) hydrogen bonds : angle 4.44787 ( 1089) link_NAG-ASN : bond 0.00818 ( 9) link_NAG-ASN : angle 3.79475 ( 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 108 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 92 time to evaluate : 0.330 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 PHE cc_start: 0.8664 (OUTLIER) cc_final: 0.7628 (m-80) REVERT: A 208 GLU cc_start: 0.8263 (mp0) cc_final: 0.7958 (mp0) REVERT: A 275 GLN cc_start: 0.8503 (mm110) cc_final: 0.8257 (mt0) REVERT: A 304 ARG cc_start: 0.8338 (OUTLIER) cc_final: 0.8103 (mtt180) REVERT: A 328 ILE cc_start: 0.8751 (mp) cc_final: 0.8266 (OUTLIER) REVERT: A 332 MET cc_start: 0.8371 (mmm) cc_final: 0.8121 (mtm) REVERT: B 51 TYR cc_start: 0.8656 (t80) cc_final: 0.8430 (t80) REVERT: B 159 CYS cc_start: 0.8694 (m) cc_final: 0.8479 (m) REVERT: B 208 GLU cc_start: 0.8836 (mp0) cc_final: 0.8518 (mp0) REVERT: B 268 ARG cc_start: 0.8874 (ptt-90) cc_final: 0.8395 (ptt-90) REVERT: B 328 ILE cc_start: 0.8781 (mp) cc_final: 0.8543 (mm) REVERT: C 216 LYS cc_start: 0.9208 (OUTLIER) cc_final: 0.8806 (pptt) REVERT: C 328 ILE cc_start: 0.8630 (mp) cc_final: 0.8177 (OUTLIER) REVERT: C 332 MET cc_start: 0.8457 (mmm) cc_final: 0.8196 (mtm) outliers start: 16 outliers final: 9 residues processed: 103 average time/residue: 0.5922 time to fit residues: 64.5847 Evaluate side-chains 98 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 88 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 PHE Chi-restraints excluded: chain A residue 184 ASN Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 304 ARG Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain C residue 210 ASN Chi-restraints excluded: chain C residue 216 LYS Chi-restraints excluded: chain C residue 314 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 57 optimal weight: 4.9990 chunk 5 optimal weight: 0.8980 chunk 81 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 chunk 83 optimal weight: 0.7980 chunk 36 optimal weight: 4.9990 chunk 4 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 120 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.124061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.087194 restraints weight = 12172.705| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 2.47 r_work: 0.3130 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.4393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8208 Z= 0.132 Angle : 0.616 10.865 11166 Z= 0.313 Chirality : 0.044 0.200 1242 Planarity : 0.005 0.056 1398 Dihedral : 8.997 89.700 1347 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.01 % Allowed : 16.90 % Favored : 81.09 % 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: 1.08 (0.27), residues: 984 helix: 2.40 (0.36), residues: 231 sheet: 0.84 (0.29), residues: 309 loop : -0.24 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 197 TYR 0.017 0.001 TYR C 90 PHE 0.029 0.002 PHE B 326 TRP 0.006 0.001 TRP A 85 HIS 0.004 0.000 HIS A 116 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 8190) covalent geometry : angle 0.58706 (11121) SS BOND : bond 0.00280 ( 9) SS BOND : angle 2.07352 ( 18) hydrogen bonds : bond 0.02808 ( 353) hydrogen bonds : angle 4.36575 ( 1089) link_NAG-ASN : bond 0.00853 ( 9) link_NAG-ASN : angle 3.49586 ( 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: 17 poor density : 90 time to evaluate : 0.315 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 PHE cc_start: 0.8637 (OUTLIER) cc_final: 0.7567 (m-80) REVERT: A 208 GLU cc_start: 0.8303 (mp0) cc_final: 0.8051 (mp0) REVERT: A 275 GLN cc_start: 0.8487 (mm110) cc_final: 0.8255 (mt0) REVERT: A 304 ARG cc_start: 0.8337 (OUTLIER) cc_final: 0.8100 (mtt180) REVERT: A 328 ILE cc_start: 0.8777 (mp) cc_final: 0.8291 (OUTLIER) REVERT: A 332 MET cc_start: 0.8361 (mmm) cc_final: 0.8093 (mtm) REVERT: B 51 TYR cc_start: 0.8647 (t80) cc_final: 0.8412 (t80) REVERT: B 159 CYS cc_start: 0.8724 (m) cc_final: 0.8516 (m) REVERT: B 208 GLU cc_start: 0.8844 (mp0) cc_final: 0.8534 (mp0) REVERT: B 268 ARG cc_start: 0.8894 (ptt-90) cc_final: 0.8417 (ptt-90) REVERT: B 328 ILE cc_start: 0.8827 (mp) cc_final: 0.8600 (mm) REVERT: C 216 LYS cc_start: 0.9210 (OUTLIER) cc_final: 0.8834 (pptt) REVERT: C 328 ILE cc_start: 0.8630 (mp) cc_final: 0.8157 (OUTLIER) REVERT: C 332 MET cc_start: 0.8469 (mmm) cc_final: 0.8197 (mtm) outliers start: 17 outliers final: 11 residues processed: 104 average time/residue: 0.5631 time to fit residues: 62.1075 Evaluate side-chains 100 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 PHE Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 304 ARG Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain C residue 210 ASN Chi-restraints excluded: chain C residue 216 LYS Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 314 ARG Chi-restraints excluded: chain C residue 337 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 46 optimal weight: 6.9990 chunk 21 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 38 optimal weight: 0.9980 chunk 33 optimal weight: 30.0000 chunk 31 optimal weight: 5.9990 chunk 84 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.122919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.085917 restraints weight = 12260.883| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 2.48 r_work: 0.3107 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8830 moved from start: 0.4457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 8208 Z= 0.162 Angle : 0.640 10.572 11166 Z= 0.324 Chirality : 0.046 0.289 1242 Planarity : 0.005 0.061 1398 Dihedral : 9.147 89.542 1347 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.42 % Allowed : 17.02 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.06 (0.27), residues: 984 helix: 2.40 (0.36), residues: 231 sheet: 0.80 (0.28), residues: 309 loop : -0.23 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 197 TYR 0.017 0.001 TYR C 90 PHE 0.027 0.002 PHE A 326 TRP 0.005 0.001 TRP C 259 HIS 0.004 0.001 HIS A 116 Details of bonding type rmsd covalent geometry : bond 0.00370 ( 8190) covalent geometry : angle 0.60952 (11121) SS BOND : bond 0.00351 ( 9) SS BOND : angle 2.71830 ( 18) hydrogen bonds : bond 0.03020 ( 353) hydrogen bonds : angle 4.43413 ( 1089) link_NAG-ASN : bond 0.00809 ( 9) link_NAG-ASN : angle 3.41924 ( 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 98 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 86 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 PHE cc_start: 0.8670 (OUTLIER) cc_final: 0.7621 (m-80) REVERT: A 208 GLU cc_start: 0.8349 (mp0) cc_final: 0.8098 (mp0) REVERT: A 275 GLN cc_start: 0.8495 (mm110) cc_final: 0.8267 (mt0) REVERT: A 304 ARG cc_start: 0.8400 (OUTLIER) cc_final: 0.8157 (mtt180) REVERT: A 328 ILE cc_start: 0.8774 (mp) cc_final: 0.8292 (OUTLIER) REVERT: A 332 MET cc_start: 0.8373 (mmm) cc_final: 0.8100 (mtm) REVERT: B 51 TYR cc_start: 0.8657 (t80) cc_final: 0.8412 (t80) REVERT: B 159 CYS cc_start: 0.8762 (m) cc_final: 0.8543 (m) REVERT: B 208 GLU cc_start: 0.8862 (mp0) cc_final: 0.8538 (mp0) REVERT: B 268 ARG cc_start: 0.8902 (ptt-90) cc_final: 0.8427 (ptt-90) REVERT: B 328 ILE cc_start: 0.8807 (mp) cc_final: 0.8565 (mm) REVERT: C 216 LYS cc_start: 0.9200 (OUTLIER) cc_final: 0.8822 (pptt) REVERT: C 328 ILE cc_start: 0.8633 (mp) cc_final: 0.8173 (OUTLIER) REVERT: C 332 MET cc_start: 0.8478 (mmm) cc_final: 0.8233 (mtm) outliers start: 12 outliers final: 11 residues processed: 95 average time/residue: 0.5261 time to fit residues: 53.0886 Evaluate side-chains 98 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 86 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 PHE Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 304 ARG Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain C residue 210 ASN Chi-restraints excluded: chain C residue 216 LYS Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 314 ARG Chi-restraints excluded: chain C residue 337 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 97 optimal weight: 9.9990 chunk 72 optimal weight: 0.6980 chunk 41 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 84 optimal weight: 6.9990 chunk 51 optimal weight: 0.9990 chunk 86 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 chunk 96 optimal weight: 0.9990 chunk 54 optimal weight: 4.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.125163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.087373 restraints weight = 12019.027| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 2.51 r_work: 0.3128 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8812 moved from start: 0.4445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 8208 Z= 0.134 Angle : 0.623 10.590 11166 Z= 0.316 Chirality : 0.045 0.237 1242 Planarity : 0.005 0.063 1398 Dihedral : 8.867 84.532 1347 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.42 % Allowed : 17.26 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.79 (0.27), residues: 984 helix: 1.85 (0.36), residues: 249 sheet: 0.84 (0.29), residues: 309 loop : -0.50 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 197 TYR 0.017 0.001 TYR C 90 PHE 0.020 0.001 PHE C 92 TRP 0.006 0.001 TRP C 47 HIS 0.004 0.000 HIS A 116 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 8190) covalent geometry : angle 0.59559 (11121) SS BOND : bond 0.00318 ( 9) SS BOND : angle 2.41551 ( 18) hydrogen bonds : bond 0.02755 ( 353) hydrogen bonds : angle 4.35368 ( 1089) link_NAG-ASN : bond 0.00808 ( 9) link_NAG-ASN : angle 3.28129 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4157.43 seconds wall clock time: 71 minutes 23.96 seconds (4283.96 seconds total)