Starting phenix.real_space_refine on Wed Aug 5 02:08:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c2b_45153/08_2026/9c2b_45153.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c2b_45153/08_2026/9c2b_45153.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9c2b_45153/08_2026/9c2b_45153.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c2b_45153/08_2026/9c2b_45153.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9c2b_45153/08_2026/9c2b_45153.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c2b_45153/08_2026/9c2b_45153.map" } resolution = 2.42 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= 0.030 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: 6 Type Number sf(0) Gaussians P 9 5.49 5 Mg 3 5.21 5 S 42 5.16 5 C 5178 2.51 5 N 1350 2.21 5 O 1626 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8208 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2576 Classifications: {'peptide': 330} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 3, 'PTRANS': 12, 'TRANS': 314} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "B" Number of atoms: 2576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2576 Classifications: {'peptide': 330} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 3, 'PTRANS': 12, 'TRANS': 314} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "C" Number of atoms: 2576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2576 Classifications: {'peptide': 330} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 3, 'PTRANS': 12, 'TRANS': 314} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 46 Unusual residues: {' MG': 1, 'ATP': 1, 'NAG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 46 Unusual residues: {' MG': 1, 'ATP': 1, 'NAG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 46 Unusual residues: {' MG': 1, 'ATP': 1, 'NAG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 47 Classifications: {'water': 47} Link IDs: {None: 46} Chain: "B" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 47 Classifications: {'water': 47} Link IDs: {None: 46} Chain: "C" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 47 Classifications: {'water': 47} Link IDs: {None: 46} Time building chain proxies: 1.55, per 1000 atoms: 0.19 Number of scatterers: 8208 At special positions: 0 Unit cell: (90.832, 88.8856, 118.082, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 42 16.00 P 9 15.00 Mg 3 11.99 O 1626 8.00 N 1350 7.00 C 5178 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, 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=2.04 Simple disulfide: pdb=" SG CYS A 217 " - pdb=" SG CYS A 227 " distance=2.03 Simple disulfide: pdb=" SG CYS A 261 " - pdb=" SG CYS A 270 " distance=2.03 Simple disulfide: pdb=" SG CYS B 117 " - pdb=" SG CYS B 165 " distance=2.03 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 149 " distance=2.04 Simple disulfide: pdb=" SG CYS B 217 " - pdb=" SG CYS B 227 " distance=2.03 Simple disulfide: pdb=" SG CYS B 261 " - pdb=" SG CYS B 270 " 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 Simple disulfide: pdb=" SG CYS C 261 " - pdb=" SG CYS C 270 " 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 BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " NAG-ASN " NAG A 502 " - " ASN A 242 " " NAG B 502 " - " ASN B 242 " " NAG C 403 " - " ASN C 242 " " NAG D 1 " - " ASN A 153 " " NAG E 1 " - " ASN A 184 " " NAG F 1 " - " ASN B 153 " " NAG G 1 " - " ASN B 184 " " NAG H 1 " - " ASN C 153 " " NAG I 1 " - " ASN C 184 " Time building additional restraints: 0.45 Conformation dependent library (CDL) restraints added in 346.1 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: 1794 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 9 sheets defined 30.7% alpha, 25.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 27 through 47 Processing helix chain 'A' and resid 86 through 90 Processing helix chain 'A' and resid 120 through 124 Processing helix chain 'A' and resid 128 through 132 Processing helix chain 'A' and resid 179 through 184 Processing helix chain 'A' and resid 210 through 217 removed outlier: 3.565A pdb=" N THR A 216 " --> pdb=" O ALA A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 239 Processing helix chain 'A' and resid 242 through 250 removed outlier: 3.691A pdb=" N GLU A 248 " --> pdb=" O SER A 244 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LYS A 249 " --> pdb=" O THR A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 270 Processing helix chain 'A' and resid 327 through 356 Processing helix chain 'B' and resid 28 through 47 Processing helix chain 'B' and resid 86 through 90 Processing helix chain 'B' and resid 120 through 124 Processing helix chain 'B' and resid 128 through 132 Processing helix chain 'B' and resid 179 through 184 Processing helix chain 'B' and resid 210 through 217 removed outlier: 3.564A pdb=" N THR B 216 " --> pdb=" O ALA B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 239 Processing helix chain 'B' and resid 242 through 250 removed outlier: 3.691A pdb=" N GLU B 248 " --> pdb=" O SER B 244 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LYS B 249 " --> pdb=" O THR B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 270 Processing helix chain 'B' and resid 327 through 356 Processing helix chain 'C' and resid 28 through 47 Processing helix chain 'C' and resid 86 through 90 Processing helix chain 'C' and resid 120 through 124 Processing helix chain 'C' and resid 128 through 132 Processing helix chain 'C' and resid 179 through 184 Processing helix chain 'C' and resid 210 through 217 removed outlier: 3.565A pdb=" N THR C 216 " --> pdb=" O ALA C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 239 Processing helix chain 'C' and resid 242 through 250 removed outlier: 3.690A pdb=" N GLU C 248 " --> pdb=" O SER C 244 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LYS C 249 " --> pdb=" O THR C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 270 Processing helix chain 'C' and resid 327 through 356 Processing sheet with id=AA1, first strand: chain 'A' and resid 56 through 60 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 56 through 60 current: chain 'A' and resid 99 through 118 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 99 through 118 current: chain 'A' and resid 157 through 165 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 157 through 165 current: chain 'A' and resid 273 through 277 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 273 through 277 current: chain 'A' and resid 302 through 326 No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 62 through 70 Processing sheet with id=AA3, first strand: chain 'A' and resid 73 through 76 Processing sheet with id=AA4, first strand: chain 'B' and resid 56 through 60 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 56 through 60 current: chain 'B' and resid 99 through 118 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 99 through 118 current: chain 'B' and resid 157 through 165 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 157 through 165 current: chain 'B' and resid 273 through 277 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 273 through 277 current: chain 'B' and resid 302 through 326 No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 62 through 70 Processing sheet with id=AA6, first strand: chain 'B' and resid 73 through 76 Processing sheet with id=AA7, first strand: chain 'C' and resid 56 through 60 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 56 through 60 current: chain 'C' and resid 99 through 118 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 99 through 118 current: chain 'C' and resid 157 through 165 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 157 through 165 current: chain 'C' and resid 273 through 277 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 273 through 277 current: chain 'C' and resid 302 through 326 No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 62 through 70 Processing sheet with id=AA9, first strand: chain 'C' and resid 73 through 76 241 hydrogen bonds defined for protein. 606 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: 1.17 Time building geometry restraints manager: 0.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2523 1.34 - 1.46: 1934 1.46 - 1.58: 3754 1.58 - 1.70: 12 1.70 - 1.82: 51 Bond restraints: 8274 Sorted by residual: bond pdb=" C4 ATP C 401 " pdb=" C5 ATP C 401 " ideal model delta sigma weight residual 1.388 1.435 -0.047 1.00e-02 1.00e+04 2.17e+01 bond pdb=" C4 ATP A 500 " pdb=" C5 ATP A 500 " ideal model delta sigma weight residual 1.388 1.434 -0.046 1.00e-02 1.00e+04 2.13e+01 bond pdb=" C4 ATP B 500 " pdb=" C5 ATP B 500 " ideal model delta sigma weight residual 1.388 1.434 -0.046 1.00e-02 1.00e+04 2.09e+01 bond pdb=" C4 ATP A 500 " pdb=" N9 ATP A 500 " ideal model delta sigma weight residual 1.374 1.334 0.040 1.00e-02 1.00e+04 1.57e+01 bond pdb=" C8 ATP B 500 " pdb=" N7 ATP B 500 " ideal model delta sigma weight residual 1.310 1.349 -0.039 1.00e-02 1.00e+04 1.54e+01 ... (remaining 8269 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.69: 11195 3.69 - 7.39: 52 7.39 - 11.08: 3 11.08 - 14.78: 0 14.78 - 18.47: 6 Bond angle restraints: 11256 Sorted by residual: angle pdb=" PB ATP A 500 " pdb=" O3B ATP A 500 " pdb=" PG ATP A 500 " ideal model delta sigma weight residual 139.87 121.40 18.47 1.00e+00 1.00e+00 3.41e+02 angle pdb=" PB ATP C 401 " pdb=" O3B ATP C 401 " pdb=" PG ATP C 401 " ideal model delta sigma weight residual 139.87 121.41 18.46 1.00e+00 1.00e+00 3.41e+02 angle pdb=" PB ATP B 500 " pdb=" O3B ATP B 500 " pdb=" PG ATP B 500 " ideal model delta sigma weight residual 139.87 121.44 18.43 1.00e+00 1.00e+00 3.40e+02 angle pdb=" PA ATP C 401 " pdb=" O3A ATP C 401 " pdb=" PB ATP C 401 " ideal model delta sigma weight residual 136.83 121.74 15.09 1.00e+00 1.00e+00 2.28e+02 angle pdb=" PA ATP A 500 " pdb=" O3A ATP A 500 " pdb=" PB ATP A 500 " ideal model delta sigma weight residual 136.83 121.79 15.04 1.00e+00 1.00e+00 2.26e+02 ... (remaining 11251 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.12: 4551 21.12 - 42.24: 419 42.24 - 63.35: 94 63.35 - 84.47: 21 84.47 - 105.59: 21 Dihedral angle restraints: 5106 sinusoidal: 2298 harmonic: 2808 Sorted by residual: dihedral pdb=" CA PHE B 308 " pdb=" C PHE B 308 " pdb=" N LYS B 309 " pdb=" CA LYS B 309 " ideal model delta harmonic sigma weight residual 180.00 161.47 18.53 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA PHE C 308 " pdb=" C PHE C 308 " pdb=" N LYS C 309 " pdb=" CA LYS C 309 " ideal model delta harmonic sigma weight residual 180.00 161.47 18.53 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA PHE A 308 " pdb=" C PHE A 308 " pdb=" N LYS A 309 " pdb=" CA LYS A 309 " ideal model delta harmonic sigma weight residual 180.00 161.51 18.49 0 5.00e+00 4.00e-02 1.37e+01 ... (remaining 5103 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 866 0.052 - 0.103: 289 0.103 - 0.155: 120 0.155 - 0.206: 18 0.206 - 0.258: 9 Chirality restraints: 1302 Sorted by residual: chirality pdb=" C1 NAG H 2 " pdb=" O4 NAG H 1 " pdb=" C2 NAG H 2 " pdb=" O5 NAG H 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.28 -0.12 2.00e-02 2.50e+03 3.82e+01 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.28 -0.12 2.00e-02 2.50e+03 3.72e+01 chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.28 -0.12 2.00e-02 2.50e+03 3.68e+01 ... (remaining 1299 not shown) Planarity restraints: 1404 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 1 " -0.085 2.00e-02 2.50e+03 7.04e-02 6.20e+01 pdb=" C7 NAG D 1 " 0.028 2.00e-02 2.50e+03 pdb=" C8 NAG D 1 " -0.065 2.00e-02 2.50e+03 pdb=" N2 NAG D 1 " 0.111 2.00e-02 2.50e+03 pdb=" O7 NAG D 1 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 1 " 0.085 2.00e-02 2.50e+03 7.01e-02 6.14e+01 pdb=" C7 NAG F 1 " -0.027 2.00e-02 2.50e+03 pdb=" C8 NAG F 1 " 0.065 2.00e-02 2.50e+03 pdb=" N2 NAG F 1 " -0.111 2.00e-02 2.50e+03 pdb=" O7 NAG F 1 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG H 1 " -0.085 2.00e-02 2.50e+03 7.00e-02 6.13e+01 pdb=" C7 NAG H 1 " 0.027 2.00e-02 2.50e+03 pdb=" C8 NAG H 1 " -0.065 2.00e-02 2.50e+03 pdb=" N2 NAG H 1 " 0.111 2.00e-02 2.50e+03 pdb=" O7 NAG H 1 " 0.012 2.00e-02 2.50e+03 ... (remaining 1401 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 393 2.71 - 3.26: 7929 3.26 - 3.80: 14664 3.80 - 4.35: 18955 4.35 - 4.90: 29682 Nonbonded interactions: 71623 Sorted by model distance: nonbonded pdb=" O1G ATP B 500 " pdb="MG MG C 402 " model vdw 2.161 2.170 nonbonded pdb=" O1G ATP A 500 " pdb="MG MG B 501 " model vdw 2.161 2.170 nonbonded pdb="MG MG A 501 " pdb=" O1G ATP C 401 " model vdw 2.162 2.170 nonbonded pdb=" O HOH A 608 " pdb=" O HOH A 645 " model vdw 2.218 3.040 nonbonded pdb=" O HOH B 608 " pdb=" O HOH B 645 " model vdw 2.226 3.040 ... (remaining 71618 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: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and resid 27 through 356) selection = (chain 'B' and resid 27 through 356) selection = (chain 'C' and resid 27 through 356) } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'I' } 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: 4.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.160 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 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 : 0.007 0.053 8304 Z= 0.446 Angle : 0.991 18.470 11334 Z= 0.707 Chirality : 0.063 0.258 1302 Planarity : 0.007 0.070 1395 Dihedral : 18.261 105.589 3276 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 0.00 % Allowed : 16.67 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: 0.27 (0.27), residues: 984 helix: -0.27 (0.33), residues: 273 sheet: 0.47 (0.28), residues: 309 loop : 0.52 (0.33), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 180 TYR 0.019 0.002 TYR B 51 PHE 0.013 0.002 PHE A 276 TRP 0.010 0.002 TRP C 85 HIS 0.004 0.001 HIS A 355 Details of bonding type rmsd/Z covalent geometry : bond 0.00697 / 0.45 ( 8274) covalent geometry : angle 0.97577 / 0.71 (11256) SS BOND : bond 0.00273 / 0.19 ( 12) SS BOND : angle 1.10238 / 0.84 ( 24) hydrogen bonds : bond 0.16394 / 10.77 ( 241) hydrogen bonds : angle 6.24701 / 4.36 ( 606) link_BETA1-4 : bond 0.00290 / 0.17 ( 9) link_BETA1-4 : angle 1.38228 / 0.96 ( 27) link_NAG-ASN : bond 0.00904 / 0.60 ( 9) link_NAG-ASN : angle 3.45262 / 2.79 ( 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 128 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.185 Fit side-chains revert: symmetry clash REVERT: C 215 LYS cc_start: 0.8178 (tttp) cc_final: 0.7892 (ttmm) outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.5578 time to fit residues: 75.1436 Evaluate side-chains 115 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.273 ------------------------------------------------------------------------------- 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: 1.9990 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 4.9990 chunk 45 optimal weight: 6.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 237 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.158691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.110076 restraints weight = 7424.395| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 1.68 r_work: 0.3177 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8805 moved from start: 0.1116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 8304 Z= 0.313 Angle : 0.717 7.714 11334 Z= 0.366 Chirality : 0.051 0.184 1302 Planarity : 0.005 0.046 1395 Dihedral : 13.503 85.615 1530 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 3.14 % Allowed : 17.03 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: 0.96 (0.27), residues: 984 helix: 1.12 (0.33), residues: 273 sheet: 0.56 (0.27), residues: 324 loop : 0.56 (0.34), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 180 TYR 0.020 0.002 TYR C 90 PHE 0.020 0.003 PHE A 289 TRP 0.016 0.003 TRP A 85 HIS 0.005 0.001 HIS B 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00716 / 0.31 ( 8274) covalent geometry : angle 0.69275 / 0.36 (11256) SS BOND : bond 0.00493 / 0.34 ( 12) SS BOND : angle 1.63971 / 1.27 ( 24) hydrogen bonds : bond 0.04494 / 2.95 ( 241) hydrogen bonds : angle 4.99122 / 3.47 ( 606) link_BETA1-4 : bond 0.00494 / 0.31 ( 9) link_BETA1-4 : angle 1.95477 / 1.58 ( 27) link_NAG-ASN : bond 0.00393 / 0.26 ( 9) link_NAG-ASN : angle 3.08823 / 2.62 ( 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 144 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 118 time to evaluate : 0.300 Fit side-chains REVERT: A 138 LYS cc_start: 0.8705 (OUTLIER) cc_final: 0.8349 (tttt) REVERT: A 215 LYS cc_start: 0.8438 (tttt) cc_final: 0.8130 (ttmm) REVERT: A 275 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.7580 (mp0) REVERT: B 138 LYS cc_start: 0.8730 (OUTLIER) cc_final: 0.8270 (tttt) REVERT: B 215 LYS cc_start: 0.8500 (tttp) cc_final: 0.8100 (ttmm) REVERT: B 275 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.7375 (mp0) REVERT: C 138 LYS cc_start: 0.8754 (OUTLIER) cc_final: 0.8256 (tttt) REVERT: C 215 LYS cc_start: 0.8438 (tttp) cc_final: 0.8097 (ttmm) outliers start: 26 outliers final: 5 residues processed: 137 average time/residue: 0.5609 time to fit residues: 81.4094 Evaluate side-chains 123 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 113 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 138 LYS Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 138 LYS Chi-restraints excluded: chain B residue 275 GLU Chi-restraints excluded: chain C residue 138 LYS Chi-restraints excluded: chain C residue 275 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 30 optimal weight: 0.9990 chunk 86 optimal weight: 0.5980 chunk 91 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 45 optimal weight: 10.0000 chunk 15 optimal weight: 0.5980 chunk 26 optimal weight: 0.5980 chunk 28 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 66 optimal weight: 10.0000 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 237 GLN B 114 GLN C 114 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.162137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.114389 restraints weight = 7352.132| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 1.67 r_work: 0.3237 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.1246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8304 Z= 0.138 Angle : 0.569 6.282 11334 Z= 0.285 Chirality : 0.046 0.234 1302 Planarity : 0.004 0.044 1395 Dihedral : 11.162 89.500 1530 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.78 % Allowed : 18.00 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: 1.17 (0.28), residues: 984 helix: 1.50 (0.34), residues: 273 sheet: 0.52 (0.27), residues: 324 loop : 0.68 (0.35), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 180 TYR 0.016 0.002 TYR C 90 PHE 0.010 0.001 PHE B 289 TRP 0.008 0.001 TRP C 259 HIS 0.002 0.001 HIS C 306 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 ( 8274) covalent geometry : angle 0.54170 / 0.28 (11256) SS BOND : bond 0.00287 / 0.20 ( 12) SS BOND : angle 1.13331 / 0.88 ( 24) hydrogen bonds : bond 0.03169 / 2.07 ( 241) hydrogen bonds : angle 4.58910 / 3.22 ( 606) link_BETA1-4 : bond 0.00488 / 0.31 ( 9) link_BETA1-4 : angle 2.00688 / 1.64 ( 27) link_NAG-ASN : bond 0.00811 / 0.59 ( 9) link_NAG-ASN : angle 2.89530 / 2.36 ( 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 146 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 123 time to evaluate : 0.307 Fit side-chains REVERT: A 52 GLU cc_start: 0.7986 (tp30) cc_final: 0.7655 (mt-10) REVERT: A 275 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.7510 (mp0) REVERT: B 138 LYS cc_start: 0.8682 (OUTLIER) cc_final: 0.8207 (tttt) REVERT: B 215 LYS cc_start: 0.8409 (tttp) cc_final: 0.8030 (ttmm) REVERT: B 275 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7271 (mp0) REVERT: B 332 MET cc_start: 0.7679 (OUTLIER) cc_final: 0.6191 (mpm) REVERT: C 52 GLU cc_start: 0.8003 (tp30) cc_final: 0.7614 (mt-10) REVERT: C 148 LYS cc_start: 0.8374 (mppt) cc_final: 0.7742 (mmtt) REVERT: C 215 LYS cc_start: 0.8374 (tttp) cc_final: 0.8046 (ttmm) outliers start: 23 outliers final: 7 residues processed: 140 average time/residue: 0.5782 time to fit residues: 85.6175 Evaluate side-chains 132 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 121 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 138 LYS Chi-restraints excluded: chain B residue 237 GLN Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 275 GLU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain C residue 318 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 24 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 68.7715 > 50:) chunk 47 optimal weight: 0.7980 chunk 80 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 49 optimal weight: 4.9990 chunk 56 optimal weight: 5.9990 chunk 30 optimal weight: 7.9990 chunk 66 optimal weight: 10.0000 chunk 96 optimal weight: 8.9990 chunk 19 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 114 GLN A 237 GLN B 237 GLN C 114 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.159820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.111322 restraints weight = 7406.993| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 1.68 r_work: 0.3195 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8788 moved from start: 0.1279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 8304 Z= 0.236 Angle : 0.642 7.232 11334 Z= 0.327 Chirality : 0.048 0.182 1302 Planarity : 0.005 0.044 1395 Dihedral : 10.525 88.596 1530 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 4.11 % Allowed : 17.15 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: 1.13 (0.28), residues: 984 helix: 1.53 (0.35), residues: 273 sheet: 0.43 (0.27), residues: 324 loop : 0.67 (0.35), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 180 TYR 0.017 0.002 TYR C 90 PHE 0.016 0.002 PHE A 289 TRP 0.010 0.002 TRP A 259 HIS 0.003 0.001 HIS B 260 Details of bonding type rmsd/Z covalent geometry : bond 0.00535 / 0.24 ( 8274) covalent geometry : angle 0.62277 / 0.32 (11256) SS BOND : bond 0.00383 / 0.27 ( 12) SS BOND : angle 1.42975 / 1.11 ( 24) hydrogen bonds : bond 0.03508 / 2.31 ( 241) hydrogen bonds : angle 4.81130 / 3.37 ( 606) link_BETA1-4 : bond 0.00478 / 0.31 ( 9) link_BETA1-4 : angle 1.86784 / 1.51 ( 27) link_NAG-ASN : bond 0.00418 / 0.22 ( 9) link_NAG-ASN : angle 2.43956 / 2.06 ( 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 150 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 116 time to evaluate : 0.304 Fit side-chains REVERT: A 138 LYS cc_start: 0.8717 (OUTLIER) cc_final: 0.8354 (tttt) REVERT: A 275 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7521 (mp0) REVERT: A 332 MET cc_start: 0.7682 (OUTLIER) cc_final: 0.6145 (mpm) REVERT: B 138 LYS cc_start: 0.8726 (OUTLIER) cc_final: 0.8238 (tttt) REVERT: B 197 ARG cc_start: 0.8374 (ttm-80) cc_final: 0.7994 (ttm110) REVERT: B 215 LYS cc_start: 0.8464 (tttp) cc_final: 0.8073 (ttmm) REVERT: B 275 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7340 (mp0) REVERT: B 332 MET cc_start: 0.7762 (OUTLIER) cc_final: 0.6361 (mpm) REVERT: C 138 LYS cc_start: 0.8749 (OUTLIER) cc_final: 0.8297 (tttt) REVERT: C 215 LYS cc_start: 0.8389 (tttp) cc_final: 0.8051 (ttmm) REVERT: C 332 MET cc_start: 0.7680 (OUTLIER) cc_final: 0.6206 (mpm) outliers start: 34 outliers final: 11 residues processed: 141 average time/residue: 0.6136 time to fit residues: 91.5906 Evaluate side-chains 134 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 115 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 138 LYS Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 138 LYS Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 275 GLU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 138 LYS Chi-restraints excluded: chain C residue 275 GLU Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 332 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 41 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 60 optimal weight: 0.0050 chunk 87 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 48 optimal weight: 0.4980 chunk 91 optimal weight: 0.9980 chunk 51 optimal weight: 5.9990 chunk 10 optimal weight: 6.9990 chunk 62 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 114 GLN B 114 GLN C 114 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.161988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.114150 restraints weight = 7364.903| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 1.66 r_work: 0.3239 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.1377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8304 Z= 0.136 Angle : 0.556 7.128 11334 Z= 0.281 Chirality : 0.045 0.202 1302 Planarity : 0.004 0.043 1395 Dihedral : 9.754 88.263 1530 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 3.38 % Allowed : 17.51 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: 1.13 (0.28), residues: 984 helix: 1.58 (0.35), residues: 273 sheet: 0.39 (0.27), residues: 324 loop : 0.68 (0.35), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 180 TYR 0.016 0.001 TYR C 90 PHE 0.010 0.001 PHE B 276 TRP 0.008 0.001 TRP C 259 HIS 0.002 0.001 HIS A 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 ( 8274) covalent geometry : angle 0.53285 / 0.28 (11256) SS BOND : bond 0.00290 / 0.20 ( 12) SS BOND : angle 1.15316 / 0.90 ( 24) hydrogen bonds : bond 0.02921 / 1.92 ( 241) hydrogen bonds : angle 4.56085 / 3.20 ( 606) link_BETA1-4 : bond 0.00462 / 0.30 ( 9) link_BETA1-4 : angle 1.82290 / 1.47 ( 27) link_NAG-ASN : bond 0.00893 / 0.62 ( 9) link_NAG-ASN : angle 2.59175 / 2.03 ( 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 146 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 118 time to evaluate : 0.248 Fit side-chains REVERT: A 138 LYS cc_start: 0.8673 (OUTLIER) cc_final: 0.8317 (tttt) REVERT: A 275 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7500 (mp0) REVERT: A 332 MET cc_start: 0.7647 (OUTLIER) cc_final: 0.6085 (mpm) REVERT: B 138 LYS cc_start: 0.8670 (OUTLIER) cc_final: 0.8199 (tttt) REVERT: B 197 ARG cc_start: 0.8339 (ttm-80) cc_final: 0.7841 (ttm110) REVERT: B 215 LYS cc_start: 0.8407 (tttp) cc_final: 0.8021 (ttmm) REVERT: B 267 VAL cc_start: 0.7887 (m) cc_final: 0.7564 (p) REVERT: B 275 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7266 (mp0) REVERT: B 332 MET cc_start: 0.7699 (OUTLIER) cc_final: 0.6264 (mpm) REVERT: C 52 GLU cc_start: 0.7984 (tp30) cc_final: 0.7591 (mt-10) REVERT: C 138 LYS cc_start: 0.8706 (OUTLIER) cc_final: 0.8207 (tttt) REVERT: C 148 LYS cc_start: 0.8365 (mppt) cc_final: 0.7726 (mmtt) REVERT: C 332 MET cc_start: 0.7647 (OUTLIER) cc_final: 0.6115 (mpm) outliers start: 28 outliers final: 11 residues processed: 135 average time/residue: 0.6278 time to fit residues: 89.5438 Evaluate side-chains 138 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 119 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 138 LYS Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 138 LYS Chi-restraints excluded: chain B residue 237 GLN Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 275 GLU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain C residue 138 LYS Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 332 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 10 optimal weight: 5.9990 chunk 69 optimal weight: 9.9990 chunk 8 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 52 optimal weight: 0.5980 chunk 66 optimal weight: 10.0000 chunk 15 optimal weight: 0.7980 chunk 80 optimal weight: 4.9990 chunk 88 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 114 GLN A 237 GLN B 114 GLN C 114 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.161693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.113706 restraints weight = 7352.676| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 1.67 r_work: 0.3228 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8304 Z= 0.165 Angle : 0.581 7.593 11334 Z= 0.298 Chirality : 0.046 0.184 1302 Planarity : 0.004 0.042 1395 Dihedral : 9.660 88.302 1530 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 3.02 % Allowed : 18.12 % Favored : 78.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: 1.15 (0.28), residues: 984 helix: 1.60 (0.35), residues: 273 sheet: 0.39 (0.27), residues: 324 loop : 0.69 (0.35), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 180 TYR 0.016 0.001 TYR C 90 PHE 0.011 0.002 PHE B 289 TRP 0.008 0.001 TRP C 259 HIS 0.002 0.001 HIS C 260 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 ( 8274) covalent geometry : angle 0.56427 / 0.29 (11256) SS BOND : bond 0.00311 / 0.22 ( 12) SS BOND : angle 1.20236 / 0.93 ( 24) hydrogen bonds : bond 0.02938 / 1.93 ( 241) hydrogen bonds : angle 4.63325 / 3.26 ( 606) link_BETA1-4 : bond 0.00468 / 0.30 ( 9) link_BETA1-4 : angle 1.70503 / 1.37 ( 27) link_NAG-ASN : bond 0.00928 / 0.57 ( 9) link_NAG-ASN : angle 2.18502 / 1.81 ( 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 142 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 117 time to evaluate : 0.324 Fit side-chains REVERT: A 138 LYS cc_start: 0.8679 (OUTLIER) cc_final: 0.8320 (tttt) REVERT: A 275 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7522 (mp0) REVERT: A 332 MET cc_start: 0.7698 (OUTLIER) cc_final: 0.6153 (mpm) REVERT: B 138 LYS cc_start: 0.8683 (OUTLIER) cc_final: 0.8205 (tttt) REVERT: B 197 ARG cc_start: 0.8351 (ttm-80) cc_final: 0.7863 (ttm110) REVERT: B 215 LYS cc_start: 0.8421 (tttp) cc_final: 0.8038 (ttmm) REVERT: B 267 VAL cc_start: 0.7926 (m) cc_final: 0.7595 (p) REVERT: B 275 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7277 (mp0) REVERT: B 332 MET cc_start: 0.7747 (OUTLIER) cc_final: 0.6335 (mpm) REVERT: C 52 GLU cc_start: 0.8015 (tp30) cc_final: 0.7624 (mt-10) REVERT: C 138 LYS cc_start: 0.8713 (OUTLIER) cc_final: 0.8217 (tttt) REVERT: C 148 LYS cc_start: 0.8380 (mppt) cc_final: 0.7750 (mmtt) REVERT: C 332 MET cc_start: 0.7710 (OUTLIER) cc_final: 0.6205 (mpm) outliers start: 25 outliers final: 13 residues processed: 132 average time/residue: 0.6574 time to fit residues: 91.4922 Evaluate side-chains 135 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 114 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 138 LYS Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 138 LYS Chi-restraints excluded: chain B residue 237 GLN Chi-restraints excluded: chain B residue 275 GLU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 138 LYS Chi-restraints excluded: chain C residue 275 GLU Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 332 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 10 optimal weight: 5.9990 chunk 89 optimal weight: 0.5980 chunk 76 optimal weight: 4.9990 chunk 70 optimal weight: 0.9990 chunk 22 optimal weight: 0.2980 chunk 51 optimal weight: 0.7980 chunk 93 optimal weight: 0.5980 chunk 17 optimal weight: 0.6980 chunk 75 optimal weight: 0.4980 chunk 0 optimal weight: 10.0000 chunk 15 optimal weight: 0.8980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 114 GLN A 237 GLN B 114 GLN C 114 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.163114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.115450 restraints weight = 7474.289| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 1.68 r_work: 0.3257 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8304 Z= 0.120 Angle : 0.540 7.778 11334 Z= 0.273 Chirality : 0.044 0.142 1302 Planarity : 0.004 0.042 1395 Dihedral : 9.334 88.933 1530 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 3.02 % Allowed : 18.12 % Favored : 78.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: 1.17 (0.28), residues: 984 helix: 1.68 (0.35), residues: 273 sheet: 0.38 (0.27), residues: 324 loop : 0.67 (0.35), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 180 TYR 0.015 0.001 TYR C 90 PHE 0.008 0.001 PHE B 230 TRP 0.007 0.001 TRP C 259 HIS 0.002 0.001 HIS A 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 ( 8274) covalent geometry : angle 0.51846 / 0.27 (11256) SS BOND : bond 0.00273 / 0.19 ( 12) SS BOND : angle 1.07350 / 0.83 ( 24) hydrogen bonds : bond 0.02739 / 1.78 ( 241) hydrogen bonds : angle 4.48195 / 3.15 ( 606) link_BETA1-4 : bond 0.00461 / 0.30 ( 9) link_BETA1-4 : angle 1.60477 / 1.27 ( 27) link_NAG-ASN : bond 0.00831 / 0.62 ( 9) link_NAG-ASN : angle 2.58089 / 2.07 ( 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 140 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 115 time to evaluate : 0.304 Fit side-chains REVERT: A 138 LYS cc_start: 0.8655 (OUTLIER) cc_final: 0.8288 (tttt) REVERT: A 275 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7474 (mp0) REVERT: A 332 MET cc_start: 0.7649 (OUTLIER) cc_final: 0.6080 (mpm) REVERT: B 197 ARG cc_start: 0.8328 (ttm-80) cc_final: 0.7845 (ttm110) REVERT: B 215 LYS cc_start: 0.8369 (tttp) cc_final: 0.7980 (ttmm) REVERT: B 267 VAL cc_start: 0.7839 (m) cc_final: 0.7559 (p) REVERT: B 275 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7252 (mp0) REVERT: B 332 MET cc_start: 0.7682 (OUTLIER) cc_final: 0.6244 (mpm) REVERT: C 52 GLU cc_start: 0.7964 (tp30) cc_final: 0.7592 (mt-10) REVERT: C 138 LYS cc_start: 0.8693 (OUTLIER) cc_final: 0.8194 (tttt) REVERT: C 148 LYS cc_start: 0.8363 (mppt) cc_final: 0.7712 (mmtt) REVERT: C 332 MET cc_start: 0.7633 (OUTLIER) cc_final: 0.6108 (mpm) outliers start: 25 outliers final: 9 residues processed: 132 average time/residue: 0.6301 time to fit residues: 87.9409 Evaluate side-chains 131 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 115 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 138 LYS Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 237 GLN Chi-restraints excluded: chain B residue 275 GLU Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 138 LYS Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 332 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 52 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 chunk 40 optimal weight: 5.9990 chunk 33 optimal weight: 10.0000 chunk 87 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 90 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 114 GLN B 114 GLN C 114 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.160033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.111619 restraints weight = 7366.278| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 1.67 r_work: 0.3197 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 8304 Z= 0.252 Angle : 0.668 8.840 11334 Z= 0.342 Chirality : 0.049 0.257 1302 Planarity : 0.005 0.042 1395 Dihedral : 9.926 89.530 1530 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 3.74 % Allowed : 17.15 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: 1.14 (0.28), residues: 984 helix: 1.63 (0.35), residues: 273 sheet: 0.38 (0.27), residues: 324 loop : 0.67 (0.35), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 180 TYR 0.017 0.002 TYR C 90 PHE 0.016 0.002 PHE A 276 TRP 0.010 0.002 TRP A 259 HIS 0.003 0.001 HIS C 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00576 / 0.25 ( 8274) covalent geometry : angle 0.64476 / 0.34 (11256) SS BOND : bond 0.00397 / 0.28 ( 12) SS BOND : angle 1.41976 / 1.09 ( 24) hydrogen bonds : bond 0.03408 / 2.22 ( 241) hydrogen bonds : angle 4.77634 / 3.36 ( 606) link_BETA1-4 : bond 0.00433 / 0.28 ( 9) link_BETA1-4 : angle 1.54050 / 1.21 ( 27) link_NAG-ASN : bond 0.00644 / 0.45 ( 9) link_NAG-ASN : angle 3.16661 / 2.77 ( 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 141 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 110 time to evaluate : 0.321 Fit side-chains REVERT: A 138 LYS cc_start: 0.8681 (OUTLIER) cc_final: 0.8330 (tttt) REVERT: A 275 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.7532 (mp0) REVERT: A 332 MET cc_start: 0.7697 (OUTLIER) cc_final: 0.6185 (mpm) REVERT: B 138 LYS cc_start: 0.8709 (OUTLIER) cc_final: 0.8228 (tttt) REVERT: B 197 ARG cc_start: 0.8374 (ttm-80) cc_final: 0.7885 (ttm110) REVERT: B 215 LYS cc_start: 0.8450 (tttp) cc_final: 0.8070 (ttmm) REVERT: B 275 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7346 (mp0) REVERT: B 332 MET cc_start: 0.7763 (OUTLIER) cc_final: 0.6392 (mpm) REVERT: C 138 LYS cc_start: 0.8736 (OUTLIER) cc_final: 0.8272 (tttt) REVERT: C 215 LYS cc_start: 0.8402 (tttp) cc_final: 0.8062 (ttmm) REVERT: C 332 MET cc_start: 0.7729 (OUTLIER) cc_final: 0.6303 (mpm) outliers start: 31 outliers final: 12 residues processed: 128 average time/residue: 0.6167 time to fit residues: 83.5662 Evaluate side-chains 129 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 109 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 138 LYS Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 138 LYS Chi-restraints excluded: chain B residue 237 GLN Chi-restraints excluded: chain B residue 275 GLU Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 138 LYS Chi-restraints excluded: chain C residue 275 GLU Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 332 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 61 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 8 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 chunk 82 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 237 GLN B 114 GLN C 114 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.160449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.112221 restraints weight = 7352.074| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 1.66 r_work: 0.3210 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.1416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 8304 Z= 0.215 Angle : 0.659 15.391 11334 Z= 0.330 Chirality : 0.048 0.332 1302 Planarity : 0.005 0.042 1395 Dihedral : 9.848 89.575 1530 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 3.02 % Allowed : 18.12 % Favored : 78.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: 1.13 (0.28), residues: 984 helix: 1.64 (0.35), residues: 273 sheet: 0.37 (0.27), residues: 324 loop : 0.64 (0.35), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 180 TYR 0.017 0.002 TYR C 90 PHE 0.015 0.002 PHE B 289 TRP 0.008 0.002 TRP A 259 HIS 0.003 0.001 HIS B 260 Details of bonding type rmsd/Z covalent geometry : bond 0.00484 / 0.21 ( 8274) covalent geometry : angle 0.61234 / 0.32 (11256) SS BOND : bond 0.00352 / 0.25 ( 12) SS BOND : angle 1.34708 / 1.04 ( 24) hydrogen bonds : bond 0.03361 / 2.18 ( 241) hydrogen bonds : angle 4.71079 / 3.30 ( 606) link_BETA1-4 : bond 0.00467 / 0.32 ( 9) link_BETA1-4 : angle 1.51403 / 1.20 ( 27) link_NAG-ASN : bond 0.00444 / 0.35 ( 9) link_NAG-ASN : angle 4.69594 / 4.24 ( 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 132 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 107 time to evaluate : 0.313 Fit side-chains REVERT: A 138 LYS cc_start: 0.8696 (OUTLIER) cc_final: 0.8332 (tttt) REVERT: A 275 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7525 (mp0) REVERT: A 332 MET cc_start: 0.7673 (OUTLIER) cc_final: 0.6156 (mpm) REVERT: B 138 LYS cc_start: 0.8678 (OUTLIER) cc_final: 0.8195 (tttt) REVERT: B 197 ARG cc_start: 0.8356 (ttm-80) cc_final: 0.7854 (ttm110) REVERT: B 215 LYS cc_start: 0.8437 (tttp) cc_final: 0.8044 (ttmm) REVERT: B 275 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7307 (mp0) REVERT: B 332 MET cc_start: 0.7722 (OUTLIER) cc_final: 0.6333 (mpm) REVERT: C 52 GLU cc_start: 0.7994 (tp30) cc_final: 0.7579 (mt-10) REVERT: C 138 LYS cc_start: 0.8720 (OUTLIER) cc_final: 0.8235 (tttt) REVERT: C 215 LYS cc_start: 0.8396 (tttp) cc_final: 0.8047 (ttmm) REVERT: C 332 MET cc_start: 0.7696 (OUTLIER) cc_final: 0.6257 (mpm) outliers start: 25 outliers final: 10 residues processed: 122 average time/residue: 0.6374 time to fit residues: 82.2888 Evaluate side-chains 124 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 106 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 138 LYS Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 138 LYS Chi-restraints excluded: chain B residue 237 GLN Chi-restraints excluded: chain B residue 275 GLU Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 138 LYS Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 332 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 57 optimal weight: 0.3980 chunk 85 optimal weight: 4.9990 chunk 65 optimal weight: 7.9990 chunk 30 optimal weight: 0.7980 chunk 20 optimal weight: 4.9990 chunk 76 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 17 optimal weight: 0.8980 chunk 88 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 114 GLN A 237 GLN C 114 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.159945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.111809 restraints weight = 7370.488| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 1.66 r_work: 0.3199 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.1452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 8304 Z= 0.242 Angle : 0.676 12.219 11334 Z= 0.340 Chirality : 0.049 0.333 1302 Planarity : 0.005 0.042 1395 Dihedral : 9.871 88.138 1530 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.54 % Allowed : 18.84 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: 1.10 (0.28), residues: 984 helix: 1.61 (0.35), residues: 273 sheet: 0.36 (0.27), residues: 324 loop : 0.63 (0.35), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 180 TYR 0.017 0.002 TYR C 90 PHE 0.017 0.002 PHE A 243 TRP 0.010 0.002 TRP A 259 HIS 0.003 0.001 HIS B 260 Details of bonding type rmsd/Z covalent geometry : bond 0.00549 / 0.24 ( 8274) covalent geometry : angle 0.64075 / 0.33 (11256) SS BOND : bond 0.00382 / 0.27 ( 12) SS BOND : angle 1.41904 / 1.10 ( 24) hydrogen bonds : bond 0.03485 / 2.25 ( 241) hydrogen bonds : angle 4.79087 / 3.38 ( 606) link_BETA1-4 : bond 0.00418 / 0.27 ( 9) link_BETA1-4 : angle 1.49820 / 1.18 ( 27) link_NAG-ASN : bond 0.00165 / 0.13 ( 9) link_NAG-ASN : angle 4.11258 / 3.66 ( 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 130 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 109 time to evaluate : 0.322 Fit side-chains REVERT: A 138 LYS cc_start: 0.8670 (OUTLIER) cc_final: 0.8313 (tttt) REVERT: A 215 LYS cc_start: 0.8317 (tttt) cc_final: 0.8046 (ttmm) REVERT: A 275 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7534 (mp0) REVERT: A 332 MET cc_start: 0.7698 (OUTLIER) cc_final: 0.6192 (mpm) REVERT: B 138 LYS cc_start: 0.8678 (OUTLIER) cc_final: 0.8186 (tttt) REVERT: B 197 ARG cc_start: 0.8345 (ttm-80) cc_final: 0.7953 (ttm110) REVERT: B 215 LYS cc_start: 0.8440 (tttp) cc_final: 0.8044 (ttmm) REVERT: B 275 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7314 (mp0) REVERT: B 332 MET cc_start: 0.7744 (OUTLIER) cc_final: 0.6367 (mpm) REVERT: C 52 GLU cc_start: 0.8008 (tp30) cc_final: 0.7610 (mt-10) REVERT: C 138 LYS cc_start: 0.8722 (OUTLIER) cc_final: 0.8253 (tttt) REVERT: C 215 LYS cc_start: 0.8394 (tttp) cc_final: 0.8042 (ttmm) REVERT: C 332 MET cc_start: 0.7722 (OUTLIER) cc_final: 0.6287 (mpm) outliers start: 21 outliers final: 10 residues processed: 119 average time/residue: 0.6713 time to fit residues: 84.2569 Evaluate side-chains 125 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 107 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 138 LYS Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 138 LYS Chi-restraints excluded: chain B residue 237 GLN Chi-restraints excluded: chain B residue 275 GLU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 138 LYS Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 332 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 95 optimal weight: 4.9990 chunk 8 optimal weight: 0.9980 chunk 67 optimal weight: 5.9990 chunk 78 optimal weight: 0.0970 chunk 36 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 chunk 46 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 5 optimal weight: 0.0060 chunk 74 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 237 GLN B 114 GLN C 114 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.162879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.115242 restraints weight = 7435.045| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 1.67 r_work: 0.3255 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8304 Z= 0.125 Angle : 0.586 10.273 11334 Z= 0.292 Chirality : 0.046 0.281 1302 Planarity : 0.004 0.041 1395 Dihedral : 9.377 89.955 1530 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 2.42 % Allowed : 18.96 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: 1.24 (0.28), residues: 984 helix: 1.70 (0.36), residues: 273 sheet: 0.41 (0.27), residues: 318 loop : 0.75 (0.35), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 180 TYR 0.016 0.001 TYR B 90 PHE 0.009 0.001 PHE B 289 TRP 0.009 0.001 TRP C 259 HIS 0.002 0.001 HIS A 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 ( 8274) covalent geometry : angle 0.55457 / 0.29 (11256) SS BOND : bond 0.00278 / 0.20 ( 12) SS BOND : angle 1.11255 / 0.87 ( 24) hydrogen bonds : bond 0.02881 / 1.85 ( 241) hydrogen bonds : angle 4.53219 / 3.20 ( 606) link_BETA1-4 : bond 0.00461 / 0.30 ( 9) link_BETA1-4 : angle 1.46776 / 1.15 ( 27) link_NAG-ASN : bond 0.00670 / 0.48 ( 9) link_NAG-ASN : angle 3.57967 / 3.11 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3640.81 seconds wall clock time: 62 minutes 45.82 seconds (3765.82 seconds total)