Starting phenix.real_space_refine on Thu Jul 2 08:40:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zt2_60445/07_2026/8zt2_60445.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zt2_60445/07_2026/8zt2_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_60445/07_2026/8zt2_60445.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zt2_60445/07_2026/8zt2_60445.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8zt2_60445/07_2026/8zt2_60445.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zt2_60445/07_2026/8zt2_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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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, 74 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {' MG': 1, 'ATP': 1, 'NAG': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain breaks: 1 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: 1.50, per 1000 atoms: 0.19 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: 0.59 Conformation dependent library (CDL) restraints added in 303.4 milliseconds 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1776 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 21 sheets defined 27.2% alpha, 46.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 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: 0.99 Time building geometry restraints manager: 0.78 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: 0.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.460 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:6.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6962 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 are 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/Z covalent geometry : bond 0.00398 / 0.31 ( 8190) covalent geometry : angle 0.72728 / 0.54 (11121) SS BOND : bond 0.00248 / 0.13 ( 9) SS BOND : angle 0.98478 / 0.69 ( 18) hydrogen bonds : bond 0.22036 / 14.97 ( 353) hydrogen bonds : angle 8.24364 / 5.91 ( 1089) link_NAG-ASN : bond 0.00759 / 0.42 ( 9) link_NAG-ASN : angle 3.21971 / 2.17 ( 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 : 0.284 Fit side-chains outliers start: 9 outliers final: 0 residues processed: 200 average time/residue: 0.5711 time to fit residues: 119.8119 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 : 0.203 ------------------------------------------------------------------------------- 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: 1.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 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: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.128660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.091742 restraints weight = 12084.303| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.50 r_work: 0.3210 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8911 moved from start: 0.3087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 8208 Z= 0.204 Angle : 0.703 10.890 11166 Z= 0.352 Chirality : 0.051 0.390 1242 Planarity : 0.005 0.042 1398 Dihedral : 9.258 89.302 1347 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.01 % Allowed : 10.87 % Favored : 87.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.27), residues: 984 helix: 0.73 (0.33), residues: 273 sheet: 1.27 (0.28), residues: 309 loop : -0.60 (0.31), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 197 TYR 0.028 0.002 TYR B 90 PHE 0.027 0.002 PHE A 92 TRP 0.005 0.001 TRP B 164 HIS 0.005 0.001 HIS A 306 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.20 ( 8190) covalent geometry : angle 0.66426 / 0.34 (11121) SS BOND : bond 0.00796 / 0.42 ( 9) SS BOND : angle 2.07387 / 1.42 ( 18) hydrogen bonds : bond 0.03708 / 2.43 ( 353) hydrogen bonds : angle 5.03625 / 3.68 ( 1089) link_NAG-ASN : bond 0.01234 / 0.81 ( 9) link_NAG-ASN : angle 4.41796 / 2.97 ( 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 115 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 98 time to evaluate : 0.175 Fit side-chains REVERT: A 49 PHE cc_start: 0.8342 (m-80) cc_final: 0.7911 (m-10) REVERT: A 304 ARG cc_start: 0.8332 (OUTLIER) cc_final: 0.8129 (mtm-85) REVERT: A 332 MET cc_start: 0.8344 (mmm) cc_final: 0.8012 (mtm) REVERT: B 51 TYR cc_start: 0.8631 (t80) cc_final: 0.7810 (t80) REVERT: B 159 CYS cc_start: 0.8515 (m) cc_final: 0.8249 (m) outliers start: 17 outliers final: 6 residues processed: 113 average time/residue: 0.4527 time to fit residues: 54.0701 Evaluate side-chains 90 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 83 time to evaluate : 0.285 ------------------------------------------------------------------------------- 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 304 ARG Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 258 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 98 optimal weight: 5.9990 chunk 77 optimal weight: 7.9990 chunk 69 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 76 optimal weight: 9.9990 chunk 1 optimal weight: 5.9990 chunk 92 optimal weight: 0.5980 chunk 51 optimal weight: 0.6980 chunk 32 optimal weight: 9.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 114 GLN B 114 GLN C 76 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.123530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.087219 restraints weight = 12143.820| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 2.41 r_work: 0.3146 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8990 moved from start: 0.3686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 8208 Z= 0.226 Angle : 0.749 15.782 11166 Z= 0.367 Chirality : 0.054 0.445 1242 Planarity : 0.005 0.041 1398 Dihedral : 10.003 87.672 1347 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.25 % Allowed : 13.24 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.28), residues: 984 helix: 1.46 (0.35), residues: 255 sheet: 1.28 (0.29), residues: 309 loop : -0.29 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 197 TYR 0.021 0.002 TYR C 90 PHE 0.033 0.002 PHE A 92 TRP 0.006 0.001 TRP A 259 HIS 0.003 0.001 HIS C 306 Details of bonding type rmsd/Z covalent geometry : bond 0.00502 / 0.23 ( 8190) covalent geometry : angle 0.69359 / 0.35 (11121) SS BOND : bond 0.00341 / 0.18 ( 9) SS BOND : angle 2.04496 / 1.35 ( 18) hydrogen bonds : bond 0.03735 / 2.43 ( 353) hydrogen bonds : angle 4.81079 / 3.54 ( 1089) link_NAG-ASN : bond 0.00912 / 0.62 ( 9) link_NAG-ASN : angle 5.57653 / 3.39 ( 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 104 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 85 time to evaluate : 0.189 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 304 ARG cc_start: 0.8444 (OUTLIER) cc_final: 0.8157 (mtt180) REVERT: A 332 MET cc_start: 0.8373 (mmm) cc_final: 0.8076 (mtm) REVERT: B 51 TYR cc_start: 0.8658 (t80) cc_final: 0.8238 (t80) REVERT: B 159 CYS cc_start: 0.8602 (m) cc_final: 0.8374 (m) REVERT: B 216 LYS cc_start: 0.8354 (OUTLIER) cc_final: 0.8126 (pptt) REVERT: C 76 GLN cc_start: 0.8658 (OUTLIER) cc_final: 0.8365 (mm110) REVERT: C 314 ARG cc_start: 0.8961 (OUTLIER) cc_final: 0.8744 (ptm160) outliers start: 19 outliers final: 9 residues processed: 101 average time/residue: 0.4779 time to fit residues: 51.1115 Evaluate side-chains 90 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 77 time to evaluate : 0.202 ------------------------------------------------------------------------------- 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 304 ARG Chi-restraints excluded: chain B residue 216 LYS Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 76 GLN Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 210 ASN Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 275 GLN Chi-restraints excluded: chain C residue 314 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 92 optimal weight: 1.9990 chunk 33 optimal weight: 40.0000 chunk 59 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 67 optimal weight: 10.0000 chunk 85 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 22 optimal weight: 0.5980 chunk 18 optimal weight: 0.7980 chunk 87 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 114 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.125232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.088109 restraints weight = 12213.255| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 2.50 r_work: 0.3149 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8967 moved from start: 0.3823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 8208 Z= 0.157 Angle : 0.630 9.047 11166 Z= 0.319 Chirality : 0.048 0.427 1242 Planarity : 0.005 0.038 1398 Dihedral : 9.665 80.605 1347 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.89 % Allowed : 14.18 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.27), residues: 984 helix: 1.59 (0.35), residues: 255 sheet: 1.21 (0.29), residues: 306 loop : -0.25 (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 0.025 0.002 PHE C 92 TRP 0.005 0.001 TRP B 164 HIS 0.003 0.001 HIS B 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.16 ( 8190) covalent geometry : angle 0.60630 / 0.31 (11121) SS BOND : bond 0.00343 / 0.19 ( 9) SS BOND : angle 2.08028 / 1.40 ( 18) hydrogen bonds : bond 0.03160 / 2.06 ( 353) hydrogen bonds : angle 4.63059 / 3.42 ( 1089) link_NAG-ASN : bond 0.00581 / 0.34 ( 9) link_NAG-ASN : angle 3.17462 / 2.16 ( 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 101 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 85 time to evaluate : 0.302 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 PHE cc_start: 0.8513 (OUTLIER) cc_final: 0.7745 (m-80) REVERT: A 275 GLN cc_start: 0.8503 (mm110) cc_final: 0.8233 (mt0) REVERT: A 304 ARG cc_start: 0.8385 (OUTLIER) cc_final: 0.8095 (mtt180) REVERT: A 332 MET cc_start: 0.8354 (mmm) cc_final: 0.8045 (mtm) REVERT: B 51 TYR cc_start: 0.8658 (t80) cc_final: 0.8306 (t80) REVERT: B 159 CYS cc_start: 0.8611 (m) cc_final: 0.8378 (m) REVERT: C 332 MET cc_start: 0.8424 (mmm) cc_final: 0.8188 (mtm) outliers start: 16 outliers final: 10 residues processed: 97 average time/residue: 0.5492 time to fit residues: 56.4625 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 : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 PHE Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 304 ARG Chi-restraints excluded: chain B residue 184 ASN 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 210 ASN Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 258 ASP Chi-restraints excluded: chain C residue 275 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 98 optimal weight: 5.9990 chunk 26 optimal weight: 0.6980 chunk 84 optimal weight: 0.6980 chunk 78 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 31 optimal weight: 8.9990 chunk 22 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.126269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.088992 restraints weight = 12167.332| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 2.52 r_work: 0.3153 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8959 moved from start: 0.3961 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= 0.151 Angle : 0.643 11.071 11166 Z= 0.320 Chirality : 0.047 0.406 1242 Planarity : 0.005 0.045 1398 Dihedral : 9.532 76.042 1347 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.25 % Allowed : 14.54 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.27), residues: 984 helix: 1.63 (0.35), residues: 255 sheet: 1.09 (0.29), residues: 300 loop : -0.21 (0.31), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 197 TYR 0.018 0.001 TYR B 90 PHE 0.022 0.002 PHE B 92 TRP 0.009 0.001 TRP A 164 HIS 0.003 0.000 HIS B 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 ( 8190) covalent geometry : angle 0.61560 / 0.31 (11121) SS BOND : bond 0.00297 / 0.17 ( 9) SS BOND : angle 1.82974 / 1.23 ( 18) hydrogen bonds : bond 0.02933 / 1.91 ( 353) hydrogen bonds : angle 4.50062 / 3.33 ( 1089) link_NAG-ASN : bond 0.00824 / 0.45 ( 9) link_NAG-ASN : angle 3.56668 / 2.46 ( 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 108 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 89 time to evaluate : 0.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 PHE cc_start: 0.8472 (OUTLIER) cc_final: 0.7652 (m-80) REVERT: A 275 GLN cc_start: 0.8482 (mm110) cc_final: 0.8224 (mt0) REVERT: A 304 ARG cc_start: 0.8358 (OUTLIER) cc_final: 0.8067 (mtt180) REVERT: A 332 MET cc_start: 0.8360 (mmm) cc_final: 0.8071 (mtm) REVERT: B 51 TYR cc_start: 0.8652 (t80) cc_final: 0.8319 (t80) REVERT: B 159 CYS cc_start: 0.8612 (m) cc_final: 0.8376 (m) REVERT: B 328 ILE cc_start: 0.8729 (mp) cc_final: 0.8504 (mm) REVERT: C 314 ARG cc_start: 0.8965 (OUTLIER) cc_final: 0.8756 (ptm160) REVERT: C 328 ILE cc_start: 0.8641 (mp) cc_final: 0.8084 (OUTLIER) outliers start: 19 outliers final: 9 residues processed: 104 average time/residue: 0.5341 time to fit residues: 58.9549 Evaluate side-chains 93 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 82 time to evaluate : 0.305 ------------------------------------------------------------------------------- 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 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 184 ASN Chi-restraints excluded: chain C residue 210 ASN Chi-restraints excluded: chain C residue 245 SER 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: 6.9990 chunk 37 optimal weight: 0.6980 chunk 58 optimal weight: 0.0370 chunk 57 optimal weight: 0.8980 chunk 92 optimal weight: 0.0970 chunk 19 optimal weight: 0.7980 chunk 28 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 79 optimal weight: 6.9990 chunk 14 optimal weight: 0.7980 chunk 66 optimal weight: 50.0000 overall best weight: 0.4856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.128014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.090865 restraints weight = 11948.786| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 2.50 r_work: 0.3202 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8927 moved from start: 0.3936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8208 Z= 0.113 Angle : 0.597 9.648 11166 Z= 0.298 Chirality : 0.046 0.397 1242 Planarity : 0.004 0.048 1398 Dihedral : 8.936 73.030 1347 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.25 % Allowed : 15.13 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.27), residues: 984 helix: 1.21 (0.34), residues: 273 sheet: 1.03 (0.29), residues: 303 loop : -0.49 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 197 TYR 0.018 0.001 TYR C 90 PHE 0.023 0.001 PHE A 326 TRP 0.007 0.001 TRP C 164 HIS 0.004 0.000 HIS B 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 ( 8190) covalent geometry : angle 0.56851 / 0.29 (11121) SS BOND : bond 0.00261 / 0.15 ( 9) SS BOND : angle 2.18489 / 1.57 ( 18) hydrogen bonds : bond 0.02579 / 1.68 ( 353) hydrogen bonds : angle 4.40555 / 3.26 ( 1089) link_NAG-ASN : bond 0.00652 / 0.39 ( 9) link_NAG-ASN : angle 3.30054 / 2.36 ( 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 106 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 87 time to evaluate : 0.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 PHE cc_start: 0.8449 (OUTLIER) cc_final: 0.7501 (m-80) REVERT: A 275 GLN cc_start: 0.8433 (mm110) cc_final: 0.8173 (mt0) REVERT: A 304 ARG cc_start: 0.8216 (OUTLIER) cc_final: 0.7911 (mtt180) REVERT: A 328 ILE cc_start: 0.8641 (mp) cc_final: 0.8129 (OUTLIER) REVERT: A 332 MET cc_start: 0.8337 (mmm) cc_final: 0.8035 (mtm) REVERT: B 51 TYR cc_start: 0.8665 (t80) cc_final: 0.8318 (t80) REVERT: B 159 CYS cc_start: 0.8604 (m) cc_final: 0.8351 (m) REVERT: C 216 LYS cc_start: 0.9015 (OUTLIER) cc_final: 0.8491 (pptt) outliers start: 19 outliers final: 9 residues processed: 102 average time/residue: 0.5231 time to fit residues: 56.5489 Evaluate side-chains 96 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 85 time to evaluate : 0.260 ------------------------------------------------------------------------------- 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 184 ASN Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 184 ASN Chi-restraints excluded: chain C residue 210 ASN Chi-restraints excluded: chain C residue 216 LYS 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: 0.0370 chunk 80 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 16 optimal weight: 6.9990 chunk 97 optimal weight: 6.9990 chunk 85 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 overall best weight: 1.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.123202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.086164 restraints weight = 12293.324| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 2.50 r_work: 0.3106 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9016 moved from start: 0.4203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 8208 Z= 0.187 Angle : 0.666 12.591 11166 Z= 0.339 Chirality : 0.048 0.384 1242 Planarity : 0.005 0.049 1398 Dihedral : 9.545 73.501 1347 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.77 % Allowed : 15.96 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.27), residues: 984 helix: 1.40 (0.35), residues: 267 sheet: 0.88 (0.28), residues: 315 loop : -0.48 (0.31), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 197 TYR 0.017 0.002 TYR C 90 PHE 0.030 0.002 PHE C 92 TRP 0.006 0.001 TRP C 259 HIS 0.004 0.001 HIS C 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.19 ( 8190) covalent geometry : angle 0.63880 / 0.33 (11121) SS BOND : bond 0.00361 / 0.19 ( 9) SS BOND : angle 2.82761 / 2.07 ( 18) hydrogen bonds : bond 0.03184 / 2.09 ( 353) hydrogen bonds : angle 4.52003 / 3.35 ( 1089) link_NAG-ASN : bond 0.00687 / 0.38 ( 9) link_NAG-ASN : angle 3.14421 / 2.36 ( 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: 15 poor density : 92 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 PHE cc_start: 0.8569 (OUTLIER) cc_final: 0.7673 (m-80) REVERT: A 172 LYS cc_start: 0.8246 (tppt) cc_final: 0.8032 (mmmt) REVERT: A 208 GLU cc_start: 0.8385 (mp0) cc_final: 0.8104 (mp0) REVERT: A 275 GLN cc_start: 0.8497 (mm110) cc_final: 0.8259 (mt0) REVERT: A 304 ARG cc_start: 0.8458 (OUTLIER) cc_final: 0.8187 (mtt180) REVERT: A 328 ILE cc_start: 0.8704 (mp) cc_final: 0.8223 (OUTLIER) REVERT: A 332 MET cc_start: 0.8347 (mmm) cc_final: 0.8073 (mtm) REVERT: B 51 TYR cc_start: 0.8655 (t80) cc_final: 0.8388 (t80) REVERT: B 159 CYS cc_start: 0.8653 (m) cc_final: 0.8418 (m) REVERT: B 172 LYS cc_start: 0.8196 (tppt) cc_final: 0.7951 (mmmt) REVERT: B 275 GLN cc_start: 0.8383 (mm110) cc_final: 0.8174 (mt0) REVERT: C 216 LYS cc_start: 0.9119 (OUTLIER) cc_final: 0.8634 (pptt) REVERT: C 314 ARG cc_start: 0.8980 (OUTLIER) cc_final: 0.8769 (ptm160) REVERT: C 328 ILE cc_start: 0.8644 (mp) cc_final: 0.8216 (OUTLIER) REVERT: C 332 MET cc_start: 0.8435 (mmm) cc_final: 0.8171 (mtm) outliers start: 15 outliers final: 9 residues processed: 103 average time/residue: 0.5153 time to fit residues: 56.4048 Evaluate side-chains 100 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 89 time to evaluate : 0.293 ------------------------------------------------------------------------------- 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 184 ASN Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain C residue 184 ASN 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 40 optimal weight: 0.9980 chunk 95 optimal weight: 3.9990 chunk 18 optimal weight: 0.6980 chunk 81 optimal weight: 2.9990 chunk 0 optimal weight: 50.0000 chunk 74 optimal weight: 2.9990 chunk 66 optimal weight: 50.0000 chunk 5 optimal weight: 6.9990 chunk 36 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 chunk 28 optimal weight: 6.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 76 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.121202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.084036 restraints weight = 12249.202| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 2.46 r_work: 0.3064 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9050 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 : 0.006 0.078 8208 Z= 0.240 Angle : 0.705 11.498 11166 Z= 0.360 Chirality : 0.050 0.369 1242 Planarity : 0.005 0.053 1398 Dihedral : 10.161 69.718 1347 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.13 % Allowed : 15.96 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.28), residues: 984 helix: 1.87 (0.35), residues: 249 sheet: 0.87 (0.28), residues: 312 loop : -0.34 (0.31), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 197 TYR 0.017 0.002 TYR C 90 PHE 0.036 0.002 PHE A 92 TRP 0.006 0.001 TRP C 259 HIS 0.003 0.001 HIS B 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00550 / 0.24 ( 8190) covalent geometry : angle 0.67485 / 0.35 (11121) SS BOND : bond 0.00474 / 0.25 ( 9) SS BOND : angle 3.00287 / 2.15 ( 18) hydrogen bonds : bond 0.03606 / 2.36 ( 353) hydrogen bonds : angle 4.66984 / 3.46 ( 1089) link_NAG-ASN : bond 0.00528 / 0.31 ( 9) link_NAG-ASN : angle 3.44376 / 2.59 ( 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 105 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 87 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 PHE cc_start: 0.8637 (OUTLIER) cc_final: 0.7616 (m-80) REVERT: A 51 TYR cc_start: 0.8657 (t80) cc_final: 0.8335 (t80) REVERT: A 208 GLU cc_start: 0.8392 (mp0) cc_final: 0.8175 (mp0) REVERT: A 275 GLN cc_start: 0.8490 (mm110) cc_final: 0.8269 (mt0) REVERT: A 304 ARG cc_start: 0.8509 (OUTLIER) cc_final: 0.8248 (mtt180) REVERT: A 328 ILE cc_start: 0.8745 (mp) cc_final: 0.8278 (OUTLIER) REVERT: A 332 MET cc_start: 0.8401 (mmm) cc_final: 0.8132 (mtm) REVERT: B 51 TYR cc_start: 0.8657 (t80) cc_final: 0.8428 (t80) REVERT: B 159 CYS cc_start: 0.8770 (m) cc_final: 0.8544 (m) REVERT: B 172 LYS cc_start: 0.8342 (tppt) cc_final: 0.8117 (mmmt) REVERT: B 275 GLN cc_start: 0.8370 (mm110) cc_final: 0.8143 (mt0) REVERT: B 328 ILE cc_start: 0.8733 (mp) cc_final: 0.8344 (mm) REVERT: C 216 LYS cc_start: 0.9201 (OUTLIER) cc_final: 0.8805 (pptt) REVERT: C 328 ILE cc_start: 0.8648 (mp) cc_final: 0.8216 (OUTLIER) REVERT: C 332 MET cc_start: 0.8475 (mmm) cc_final: 0.8242 (mtm) outliers start: 18 outliers final: 13 residues processed: 100 average time/residue: 0.5339 time to fit residues: 56.6189 Evaluate side-chains 101 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 87 time to evaluate : 0.235 ------------------------------------------------------------------------------- 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 184 ASN 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 184 ASN 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 57 optimal weight: 0.5980 chunk 5 optimal weight: 0.3980 chunk 81 optimal weight: 0.5980 chunk 45 optimal weight: 4.9990 chunk 44 optimal weight: 7.9990 chunk 9 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 4 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.125713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.088216 restraints weight = 11980.314| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 2.51 r_work: 0.3142 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8994 moved from start: 0.4336 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= 0.124 Angle : 0.618 9.314 11166 Z= 0.314 Chirality : 0.046 0.365 1242 Planarity : 0.005 0.061 1398 Dihedral : 9.464 80.650 1347 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.89 % Allowed : 16.55 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.28), residues: 984 helix: 1.91 (0.35), residues: 249 sheet: 0.89 (0.29), residues: 306 loop : -0.30 (0.31), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 197 TYR 0.019 0.001 TYR C 90 PHE 0.018 0.001 PHE B 92 TRP 0.007 0.001 TRP C 47 HIS 0.004 0.000 HIS A 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 ( 8190) covalent geometry : angle 0.59490 / 0.31 (11121) SS BOND : bond 0.00326 / 0.18 ( 9) SS BOND : angle 2.39956 / 1.76 ( 18) hydrogen bonds : bond 0.02751 / 1.80 ( 353) hydrogen bonds : angle 4.43698 / 3.30 ( 1089) link_NAG-ASN : bond 0.00620 / 0.38 ( 9) link_NAG-ASN : angle 2.87815 / 2.21 ( 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 104 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 88 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 PHE cc_start: 0.8655 (OUTLIER) cc_final: 0.7688 (m-80) REVERT: A 208 GLU cc_start: 0.8283 (mp0) cc_final: 0.7975 (mp0) REVERT: A 275 GLN cc_start: 0.8470 (mm110) cc_final: 0.8233 (mt0) REVERT: A 304 ARG cc_start: 0.8365 (OUTLIER) cc_final: 0.8093 (mtt180) REVERT: A 328 ILE cc_start: 0.8751 (mp) cc_final: 0.8255 (OUTLIER) REVERT: A 332 MET cc_start: 0.8370 (mmm) cc_final: 0.8117 (mtm) REVERT: B 51 TYR cc_start: 0.8654 (t80) cc_final: 0.8396 (t80) REVERT: B 159 CYS cc_start: 0.8725 (m) cc_final: 0.8514 (m) REVERT: B 172 LYS cc_start: 0.8320 (tppt) cc_final: 0.8097 (mmmt) REVERT: B 328 ILE cc_start: 0.8767 (mp) cc_final: 0.8543 (mm) REVERT: C 216 LYS cc_start: 0.9187 (OUTLIER) cc_final: 0.8844 (pptt) REVERT: C 328 ILE cc_start: 0.8639 (mp) cc_final: 0.8186 (OUTLIER) REVERT: C 332 MET cc_start: 0.8467 (mmm) cc_final: 0.8220 (mtm) outliers start: 16 outliers final: 11 residues processed: 98 average time/residue: 0.5043 time to fit residues: 52.5407 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 : 0.290 ------------------------------------------------------------------------------- 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 184 ASN Chi-restraints excluded: chain B residue 216 LYS 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 184 ASN Chi-restraints excluded: chain C residue 210 ASN Chi-restraints excluded: chain C residue 216 LYS 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: 1.9990 chunk 21 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 80 optimal weight: 0.5980 chunk 44 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 38 optimal weight: 0.7980 chunk 33 optimal weight: 30.0000 chunk 31 optimal weight: 7.9990 chunk 84 optimal weight: 4.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.124078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.086399 restraints weight = 12076.799| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 2.53 r_work: 0.3093 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9025 moved from start: 0.4373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 8208 Z= 0.161 Angle : 0.644 8.919 11166 Z= 0.328 Chirality : 0.047 0.349 1242 Planarity : 0.005 0.061 1398 Dihedral : 9.537 88.124 1347 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.65 % Allowed : 16.90 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.28), residues: 984 helix: 1.92 (0.35), residues: 249 sheet: 0.80 (0.29), residues: 309 loop : -0.22 (0.31), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 197 TYR 0.017 0.002 TYR C 90 PHE 0.027 0.002 PHE B 92 TRP 0.007 0.001 TRP A 47 HIS 0.004 0.001 HIS B 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.16 ( 8190) covalent geometry : angle 0.62140 / 0.32 (11121) SS BOND : bond 0.00322 / 0.17 ( 9) SS BOND : angle 2.48249 / 1.79 ( 18) hydrogen bonds : bond 0.03032 / 1.98 ( 353) hydrogen bonds : angle 4.45421 / 3.31 ( 1089) link_NAG-ASN : bond 0.00534 / 0.32 ( 9) link_NAG-ASN : angle 2.86671 / 2.24 ( 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 101 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 87 time to evaluate : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 PHE cc_start: 0.8618 (OUTLIER) cc_final: 0.7679 (m-80) REVERT: A 51 TYR cc_start: 0.8670 (t80) cc_final: 0.8078 (t80) REVERT: A 208 GLU cc_start: 0.8364 (mp0) cc_final: 0.8147 (mp0) REVERT: A 275 GLN cc_start: 0.8493 (mm110) cc_final: 0.8253 (mt0) REVERT: A 304 ARG cc_start: 0.8451 (OUTLIER) cc_final: 0.8176 (mtt180) REVERT: A 328 ILE cc_start: 0.8776 (mp) cc_final: 0.8284 (OUTLIER) REVERT: A 332 MET cc_start: 0.8381 (mmm) cc_final: 0.8124 (mtm) REVERT: B 51 TYR cc_start: 0.8637 (t80) cc_final: 0.8373 (t80) REVERT: B 159 CYS cc_start: 0.8749 (m) cc_final: 0.8538 (m) REVERT: B 328 ILE cc_start: 0.8773 (mp) cc_final: 0.8392 (mm) REVERT: C 216 LYS cc_start: 0.9207 (OUTLIER) cc_final: 0.8906 (pptt) REVERT: C 328 ILE cc_start: 0.8636 (mp) cc_final: 0.8178 (OUTLIER) REVERT: C 332 MET cc_start: 0.8483 (mmm) cc_final: 0.8240 (mtm) outliers start: 14 outliers final: 11 residues processed: 96 average time/residue: 0.5161 time to fit residues: 52.6800 Evaluate side-chains 97 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 85 time to evaluate : 0.222 ------------------------------------------------------------------------------- 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 184 ASN 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 184 ASN Chi-restraints excluded: chain C residue 210 ASN Chi-restraints excluded: chain C residue 216 LYS 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: 7.9990 chunk 72 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 84 optimal weight: 4.9990 chunk 51 optimal weight: 0.5980 chunk 86 optimal weight: 0.6980 chunk 6 optimal weight: 0.7980 chunk 96 optimal weight: 0.9990 chunk 54 optimal weight: 0.4980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.124852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.088218 restraints weight = 12209.080| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 2.49 r_work: 0.3146 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8991 moved from start: 0.4342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8208 Z= 0.124 Angle : 0.606 8.961 11166 Z= 0.308 Chirality : 0.046 0.344 1242 Planarity : 0.005 0.063 1398 Dihedral : 9.250 86.632 1347 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % 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 are not related in a simple way. whole: 0.65 (0.27), residues: 984 helix: 1.29 (0.34), residues: 273 sheet: 0.85 (0.29), residues: 309 loop : -0.43 (0.31), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 197 TYR 0.018 0.001 TYR C 90 PHE 0.019 0.001 PHE B 92 TRP 0.006 0.001 TRP C 47 HIS 0.004 0.000 HIS A 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 ( 8190) covalent geometry : angle 0.58675 / 0.30 (11121) SS BOND : bond 0.00282 / 0.16 ( 9) SS BOND : angle 2.22440 / 1.62 ( 18) hydrogen bonds : bond 0.02693 / 1.76 ( 353) hydrogen bonds : angle 4.35760 / 3.24 ( 1089) link_NAG-ASN : bond 0.00565 / 0.34 ( 9) link_NAG-ASN : angle 2.64099 / 2.07 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3524.61 seconds wall clock time: 60 minutes 37.99 seconds (3637.99 seconds total)