Starting phenix.real_space_refine on Mon Apr 28 23:28:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c2b_45153/04_2025/9c2b_45153.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c2b_45153/04_2025/9c2b_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9c2b_45153/04_2025/9c2b_45153.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c2b_45153/04_2025/9c2b_45153.map" model { file = "/net/cci-nas-00/data/ceres_data/9c2b_45153/04_2025/9c2b_45153.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c2b_45153/04_2025/9c2b_45153.cif" } resolution = 2.42 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.030 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: 6.88, per 1000 atoms: 0.84 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: 2.66 Conformation dependent library (CDL) restraints added in 890.3 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: 0.82 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: 2.03 Time building geometry restraints manager: 3.07 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: 5.310 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: 0.400 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 24.150 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (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 TRP 0.010 0.002 TRP C 85 HIS 0.004 0.001 HIS A 355 PHE 0.013 0.002 PHE A 276 TYR 0.019 0.002 TYR B 51 ARG 0.007 0.001 ARG A 180 Details of bonding type rmsd link_NAG-ASN : bond 0.00904 ( 9) link_NAG-ASN : angle 3.45262 ( 27) link_BETA1-4 : bond 0.00290 ( 9) link_BETA1-4 : angle 1.38228 ( 27) hydrogen bonds : bond 0.16394 ( 241) hydrogen bonds : angle 6.24701 ( 606) SS BOND : bond 0.00273 ( 12) SS BOND : angle 1.10238 ( 24) covalent geometry : bond 0.00697 ( 8274) covalent geometry : angle 0.97577 (11256) *********************** 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 : 0.887 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: 1.4723 time to fit residues: 198.4538 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 : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 83 optimal weight: 0.2980 chunk 75 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 57 optimal weight: 0.0370 chunk 89 optimal weight: 0.5980 overall best weight: 0.7460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 237 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.162667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.114847 restraints weight = 7337.541| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 1.67 r_work: 0.3242 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.1099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8304 Z= 0.146 Angle : 0.592 7.450 11334 Z= 0.300 Chirality : 0.046 0.172 1302 Planarity : 0.004 0.045 1395 Dihedral : 12.727 89.330 1530 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 2.54 % Allowed : 17.15 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.28), residues: 984 helix: 1.21 (0.34), residues: 273 sheet: 0.52 (0.28), residues: 309 loop : 0.69 (0.34), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 85 HIS 0.003 0.001 HIS B 220 PHE 0.014 0.002 PHE A 326 TYR 0.017 0.002 TYR C 90 ARG 0.007 0.001 ARG B 180 Details of bonding type rmsd link_NAG-ASN : bond 0.00332 ( 9) link_NAG-ASN : angle 2.37668 ( 27) link_BETA1-4 : bond 0.00596 ( 9) link_BETA1-4 : angle 1.97882 ( 27) hydrogen bonds : bond 0.03662 ( 241) hydrogen bonds : angle 4.72284 ( 606) SS BOND : bond 0.00304 ( 12) SS BOND : angle 1.12994 ( 24) covalent geometry : bond 0.00325 ( 8274) covalent geometry : angle 0.57237 (11256) *********************** 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 138 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 117 time to evaluate : 0.923 Fit side-chains REVERT: A 52 GLU cc_start: 0.7947 (tp30) cc_final: 0.7632 (mt-10) REVERT: A 275 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.7540 (mp0) REVERT: B 138 LYS cc_start: 0.8671 (OUTLIER) cc_final: 0.8191 (tttt) REVERT: B 197 ARG cc_start: 0.8290 (ttm-80) cc_final: 0.7881 (ttm110) REVERT: B 215 LYS cc_start: 0.8374 (tttp) cc_final: 0.7992 (ttmm) REVERT: B 275 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.7335 (mp0) REVERT: C 52 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7554 (mt-10) REVERT: C 138 LYS cc_start: 0.8705 (OUTLIER) cc_final: 0.8104 (tttt) REVERT: C 148 LYS cc_start: 0.8379 (mppt) cc_final: 0.7828 (mmtt) outliers start: 21 outliers final: 4 residues processed: 133 average time/residue: 1.6097 time to fit residues: 226.2760 Evaluate side-chains 123 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 114 time to evaluate : 0.862 ------------------------------------------------------------------------------- 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 275 GLU Chi-restraints excluded: chain C residue 52 GLU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 138 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 91 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 76 optimal weight: 0.2980 chunk 71 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 47 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 237 GLN C 114 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.162975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.115089 restraints weight = 7402.823| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 1.68 r_work: 0.3247 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.1216 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= 0.134 Angle : 0.566 6.593 11334 Z= 0.284 Chirality : 0.045 0.186 1302 Planarity : 0.004 0.044 1395 Dihedral : 11.149 89.998 1530 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 2.78 % Allowed : 18.24 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.28), residues: 984 helix: 1.51 (0.34), residues: 273 sheet: 0.45 (0.28), residues: 309 loop : 0.76 (0.35), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 259 HIS 0.002 0.001 HIS B 355 PHE 0.009 0.002 PHE B 243 TYR 0.016 0.001 TYR C 90 ARG 0.007 0.000 ARG B 180 Details of bonding type rmsd link_NAG-ASN : bond 0.00637 ( 9) link_NAG-ASN : angle 2.54851 ( 27) link_BETA1-4 : bond 0.00530 ( 9) link_BETA1-4 : angle 1.94799 ( 27) hydrogen bonds : bond 0.03182 ( 241) hydrogen bonds : angle 4.56069 ( 606) SS BOND : bond 0.00287 ( 12) SS BOND : angle 1.08276 ( 24) covalent geometry : bond 0.00297 ( 8274) covalent geometry : angle 0.54319 (11256) *********************** 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 143 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 120 time to evaluate : 0.933 Fit side-chains REVERT: A 138 LYS cc_start: 0.8677 (OUTLIER) cc_final: 0.8290 (tttt) REVERT: A 275 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7481 (mp0) REVERT: A 332 MET cc_start: 0.7582 (OUTLIER) cc_final: 0.6043 (mpm) REVERT: B 138 LYS cc_start: 0.8673 (OUTLIER) cc_final: 0.8184 (tttt) REVERT: B 197 ARG cc_start: 0.8276 (ttm-80) cc_final: 0.7874 (ttm110) REVERT: B 215 LYS cc_start: 0.8380 (tttp) cc_final: 0.7994 (ttmm) REVERT: B 275 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7307 (mp0) REVERT: B 332 MET cc_start: 0.7698 (OUTLIER) cc_final: 0.6228 (mpm) REVERT: C 138 LYS cc_start: 0.8717 (OUTLIER) cc_final: 0.8183 (tttt) REVERT: C 148 LYS cc_start: 0.8359 (mppt) cc_final: 0.7815 (mmtt) outliers start: 23 outliers final: 7 residues processed: 133 average time/residue: 1.3955 time to fit residues: 196.1841 Evaluate side-chains 126 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 112 time to evaluate : 0.912 ------------------------------------------------------------------------------- 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 332 MET 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 138 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 0 optimal weight: 10.0000 chunk 69 optimal weight: 6.9990 chunk 65 optimal weight: 3.9990 chunk 48 optimal weight: 0.5980 chunk 34 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 18 optimal weight: 7.9990 chunk 67 optimal weight: 0.9980 chunk 78 optimal weight: 5.9990 chunk 31 optimal weight: 7.9990 chunk 83 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN A 237 GLN B 114 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.161703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.113658 restraints weight = 7349.506| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 1.67 r_work: 0.3232 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.1240 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= 0.169 Angle : 0.583 7.074 11334 Z= 0.294 Chirality : 0.046 0.209 1302 Planarity : 0.004 0.044 1395 Dihedral : 10.133 89.545 1530 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.28), residues: 984 helix: 1.65 (0.35), residues: 273 sheet: 0.49 (0.27), residues: 324 loop : 0.74 (0.35), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 259 HIS 0.003 0.001 HIS C 260 PHE 0.012 0.002 PHE A 243 TYR 0.016 0.002 TYR C 90 ARG 0.007 0.000 ARG B 180 Details of bonding type rmsd link_NAG-ASN : bond 0.00756 ( 9) link_NAG-ASN : angle 2.32494 ( 27) link_BETA1-4 : bond 0.00497 ( 9) link_BETA1-4 : angle 1.86114 ( 27) hydrogen bonds : bond 0.03148 ( 241) hydrogen bonds : angle 4.61327 ( 606) SS BOND : bond 0.00319 ( 12) SS BOND : angle 1.20541 ( 24) covalent geometry : bond 0.00379 ( 8274) covalent geometry : angle 0.56334 (11256) *********************** 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 146 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 115 time to evaluate : 0.930 Fit side-chains REVERT: A 138 LYS cc_start: 0.8667 (OUTLIER) cc_final: 0.8305 (tttt) REVERT: A 275 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.7474 (mp0) REVERT: A 332 MET cc_start: 0.7606 (OUTLIER) cc_final: 0.6015 (mpm) REVERT: B 138 LYS cc_start: 0.8700 (OUTLIER) cc_final: 0.8221 (tttt) REVERT: B 197 ARG cc_start: 0.8315 (ttm-80) cc_final: 0.7917 (ttm110) REVERT: B 215 LYS cc_start: 0.8377 (tttp) cc_final: 0.7992 (ttmm) REVERT: B 275 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.7259 (mp0) REVERT: B 332 MET cc_start: 0.7695 (OUTLIER) cc_final: 0.6247 (mpm) REVERT: C 52 GLU cc_start: 0.7989 (tp30) cc_final: 0.7561 (mt-10) REVERT: C 138 LYS cc_start: 0.8708 (OUTLIER) cc_final: 0.8198 (tttt) REVERT: C 148 LYS cc_start: 0.8335 (mppt) cc_final: 0.7768 (mmtt) REVERT: C 332 MET cc_start: 0.7636 (OUTLIER) cc_final: 0.6099 (mpm) outliers start: 31 outliers final: 10 residues processed: 136 average time/residue: 1.4152 time to fit residues: 202.9229 Evaluate side-chains 132 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 114 time to evaluate : 0.835 ------------------------------------------------------------------------------- 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 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 332 MET 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 33 optimal weight: 10.0000 chunk 63 optimal weight: 0.0980 chunk 85 optimal weight: 2.9990 chunk 64 optimal weight: 8.9990 chunk 73 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 56 optimal weight: 0.4980 chunk 92 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 66 optimal weight: 10.0000 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN C 114 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.161012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.112959 restraints weight = 7316.540| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 1.66 r_work: 0.3222 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.1285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8304 Z= 0.189 Angle : 0.584 7.438 11334 Z= 0.297 Chirality : 0.046 0.150 1302 Planarity : 0.004 0.044 1395 Dihedral : 9.793 89.579 1530 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 3.62 % Allowed : 17.27 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.28), residues: 984 helix: 1.63 (0.35), residues: 273 sheet: 0.47 (0.27), residues: 324 loop : 0.76 (0.35), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 85 HIS 0.003 0.001 HIS C 260 PHE 0.013 0.002 PHE A 276 TYR 0.016 0.002 TYR C 90 ARG 0.008 0.001 ARG B 180 Details of bonding type rmsd link_NAG-ASN : bond 0.00598 ( 9) link_NAG-ASN : angle 2.56290 ( 27) link_BETA1-4 : bond 0.00454 ( 9) link_BETA1-4 : angle 1.72731 ( 27) hydrogen bonds : bond 0.03222 ( 241) hydrogen bonds : angle 4.63572 ( 606) SS BOND : bond 0.00335 ( 12) SS BOND : angle 1.28110 ( 24) covalent geometry : bond 0.00427 ( 8274) covalent geometry : angle 0.56251 (11256) *********************** 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 147 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 117 time to evaluate : 0.921 Fit side-chains REVERT: A 138 LYS cc_start: 0.8681 (OUTLIER) cc_final: 0.8317 (tttt) REVERT: A 275 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7514 (mp0) REVERT: A 332 MET cc_start: 0.7647 (OUTLIER) cc_final: 0.6103 (mpm) REVERT: B 138 LYS cc_start: 0.8691 (OUTLIER) cc_final: 0.8208 (tttt) REVERT: B 215 LYS cc_start: 0.8410 (tttp) cc_final: 0.8025 (ttmm) REVERT: B 275 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7274 (mp0) REVERT: B 332 MET cc_start: 0.7728 (OUTLIER) cc_final: 0.6308 (mpm) REVERT: C 138 LYS cc_start: 0.8717 (OUTLIER) cc_final: 0.8226 (tttt) REVERT: C 148 LYS cc_start: 0.8316 (mppt) cc_final: 0.7681 (mmtt) REVERT: C 215 LYS cc_start: 0.8367 (tttp) cc_final: 0.8027 (ttmm) REVERT: C 332 MET cc_start: 0.7647 (OUTLIER) cc_final: 0.6120 (mpm) outliers start: 30 outliers final: 11 residues processed: 136 average time/residue: 1.3992 time to fit residues: 200.8900 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 : 0.934 ------------------------------------------------------------------------------- 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 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 332 MET 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 15 optimal weight: 0.6980 chunk 78 optimal weight: 3.9990 chunk 95 optimal weight: 0.4980 chunk 80 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 98 optimal weight: 8.9990 chunk 93 optimal weight: 0.2980 chunk 90 optimal weight: 0.2980 chunk 1 optimal weight: 7.9990 chunk 36 optimal weight: 0.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3865 r_free = 0.3865 target = 0.163364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.115913 restraints weight = 7338.062| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 1.66 r_work: 0.3260 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8304 Z= 0.117 Angle : 0.543 7.423 11334 Z= 0.275 Chirality : 0.044 0.144 1302 Planarity : 0.004 0.043 1395 Dihedral : 9.350 89.958 1530 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 3.14 % Allowed : 17.87 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.29), residues: 984 helix: 1.67 (0.35), residues: 273 sheet: 0.49 (0.27), residues: 324 loop : 0.78 (0.36), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 259 HIS 0.002 0.001 HIS A 296 PHE 0.012 0.001 PHE A 243 TYR 0.015 0.001 TYR B 90 ARG 0.008 0.000 ARG B 180 Details of bonding type rmsd link_NAG-ASN : bond 0.00460 ( 9) link_NAG-ASN : angle 2.24292 ( 27) link_BETA1-4 : bond 0.00463 ( 9) link_BETA1-4 : angle 1.62297 ( 27) hydrogen bonds : bond 0.02747 ( 241) hydrogen bonds : angle 4.50546 ( 606) SS BOND : bond 0.00274 ( 12) SS BOND : angle 1.07417 ( 24) covalent geometry : bond 0.00262 ( 8274) covalent geometry : angle 0.52560 (11256) *********************** 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 145 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 119 time to evaluate : 0.890 Fit side-chains REVERT: A 52 GLU cc_start: 0.7960 (tp30) cc_final: 0.7615 (mt-10) REVERT: A 138 LYS cc_start: 0.8654 (OUTLIER) cc_final: 0.8284 (tttt) REVERT: A 275 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7485 (mp0) REVERT: A 332 MET cc_start: 0.7610 (OUTLIER) cc_final: 0.6050 (mpm) REVERT: B 215 LYS cc_start: 0.8366 (tttp) cc_final: 0.7982 (ttmm) REVERT: B 267 VAL cc_start: 0.7848 (m) cc_final: 0.7572 (p) REVERT: B 275 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7226 (mp0) REVERT: B 332 MET cc_start: 0.7700 (OUTLIER) cc_final: 0.6269 (mpm) REVERT: C 52 GLU cc_start: 0.7973 (tp30) cc_final: 0.7594 (mt-10) REVERT: C 148 LYS cc_start: 0.8303 (mppt) cc_final: 0.7731 (mmtt) REVERT: C 332 MET cc_start: 0.7604 (OUTLIER) cc_final: 0.6059 (mpm) outliers start: 26 outliers final: 9 residues processed: 136 average time/residue: 1.7922 time to fit residues: 258.1253 Evaluate side-chains 135 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 120 time to evaluate : 1.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ILE 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 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 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 83 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 94 optimal weight: 4.9990 chunk 75 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 33 optimal weight: 10.0000 chunk 58 optimal weight: 5.9990 chunk 62 optimal weight: 7.9990 chunk 31 optimal weight: 8.9990 chunk 72 optimal weight: 0.0870 overall best weight: 1.5162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3838 r_free = 0.3838 target = 0.160832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.112774 restraints weight = 7355.591| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 1.66 r_work: 0.3217 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.1376 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= 0.211 Angle : 0.628 9.550 11334 Z= 0.322 Chirality : 0.048 0.319 1302 Planarity : 0.005 0.043 1395 Dihedral : 9.763 88.867 1530 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 3.86 % Allowed : 17.39 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.28), residues: 984 helix: 1.69 (0.35), residues: 273 sheet: 0.46 (0.27), residues: 324 loop : 0.76 (0.36), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 259 HIS 0.003 0.001 HIS C 260 PHE 0.014 0.002 PHE A 289 TYR 0.016 0.002 TYR C 90 ARG 0.008 0.001 ARG B 180 Details of bonding type rmsd link_NAG-ASN : bond 0.00682 ( 9) link_NAG-ASN : angle 3.46854 ( 27) link_BETA1-4 : bond 0.00452 ( 9) link_BETA1-4 : angle 1.52539 ( 27) hydrogen bonds : bond 0.03292 ( 241) hydrogen bonds : angle 4.65594 ( 606) SS BOND : bond 0.00362 ( 12) SS BOND : angle 1.31749 ( 24) covalent geometry : bond 0.00478 ( 8274) covalent geometry : angle 0.59907 (11256) *********************** 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 144 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 112 time to evaluate : 0.851 Fit side-chains REVERT: A 138 LYS cc_start: 0.8692 (OUTLIER) cc_final: 0.8325 (tttt) REVERT: A 275 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7511 (mp0) REVERT: A 332 MET cc_start: 0.7666 (OUTLIER) cc_final: 0.6128 (mpm) REVERT: B 138 LYS cc_start: 0.8689 (OUTLIER) cc_final: 0.8203 (tttt) REVERT: B 215 LYS cc_start: 0.8419 (tttp) cc_final: 0.8028 (ttmm) REVERT: B 267 VAL cc_start: 0.7882 (m) cc_final: 0.7536 (p) REVERT: B 275 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7301 (mp0) REVERT: B 332 MET cc_start: 0.7729 (OUTLIER) cc_final: 0.6302 (mpm) REVERT: C 52 GLU cc_start: 0.8022 (tp30) cc_final: 0.7606 (mt-10) REVERT: C 148 LYS cc_start: 0.8295 (mppt) cc_final: 0.7653 (mmtt) REVERT: C 215 LYS cc_start: 0.8367 (tttp) cc_final: 0.8012 (ttmm) REVERT: C 332 MET cc_start: 0.7680 (OUTLIER) cc_final: 0.6185 (mpm) outliers start: 32 outliers final: 11 residues processed: 131 average time/residue: 1.3464 time to fit residues: 186.4465 Evaluate side-chains 132 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 114 time to evaluate : 0.844 ------------------------------------------------------------------------------- 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 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 332 MET Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 237 GLN Chi-restraints excluded: chain C residue 275 GLU 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 29 optimal weight: 5.9990 chunk 94 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 89 optimal weight: 0.1980 chunk 45 optimal weight: 9.9990 chunk 92 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 85 optimal weight: 4.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN C 114 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.162408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.114479 restraints weight = 7450.879| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 1.67 r_work: 0.3241 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.1498 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= 0.156 Angle : 0.623 9.733 11334 Z= 0.318 Chirality : 0.047 0.278 1302 Planarity : 0.004 0.042 1395 Dihedral : 9.789 89.342 1530 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 2.90 % Allowed : 18.60 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.28), residues: 984 helix: 1.72 (0.35), residues: 273 sheet: 0.44 (0.27), residues: 324 loop : 0.75 (0.36), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 85 HIS 0.002 0.001 HIS C 260 PHE 0.012 0.002 PHE B 243 TYR 0.015 0.001 TYR C 90 ARG 0.008 0.000 ARG B 180 Details of bonding type rmsd link_NAG-ASN : bond 0.00820 ( 9) link_NAG-ASN : angle 3.82159 ( 27) link_BETA1-4 : bond 0.00448 ( 9) link_BETA1-4 : angle 1.48519 ( 27) hydrogen bonds : bond 0.03042 ( 241) hydrogen bonds : angle 4.60233 ( 606) SS BOND : bond 0.00300 ( 12) SS BOND : angle 1.16092 ( 24) covalent geometry : bond 0.00351 ( 8274) covalent geometry : angle 0.58996 (11256) *********************** 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 139 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 115 time to evaluate : 0.871 Fit side-chains REVERT: A 138 LYS cc_start: 0.8693 (OUTLIER) cc_final: 0.8328 (tttt) REVERT: A 275 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7520 (mp0) REVERT: A 332 MET cc_start: 0.7669 (OUTLIER) cc_final: 0.6129 (mpm) REVERT: B 138 LYS cc_start: 0.8672 (OUTLIER) cc_final: 0.8208 (tttt) REVERT: B 215 LYS cc_start: 0.8405 (tttp) cc_final: 0.8029 (ttmm) REVERT: B 267 VAL cc_start: 0.7917 (m) cc_final: 0.7619 (p) REVERT: B 275 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7273 (mp0) REVERT: B 332 MET cc_start: 0.7756 (OUTLIER) cc_final: 0.6344 (mpm) REVERT: C 52 GLU cc_start: 0.7998 (tp30) cc_final: 0.7606 (mt-10) REVERT: C 148 LYS cc_start: 0.8314 (mppt) cc_final: 0.7677 (mmtt) REVERT: C 332 MET cc_start: 0.7699 (OUTLIER) cc_final: 0.6221 (mpm) outliers start: 24 outliers final: 10 residues processed: 127 average time/residue: 1.6170 time to fit residues: 216.7980 Evaluate side-chains 133 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 116 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ILE 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 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 332 MET Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 237 GLN 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 20 optimal weight: 4.9990 chunk 77 optimal weight: 0.5980 chunk 64 optimal weight: 10.0000 chunk 59 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 36 optimal weight: 0.3980 chunk 94 optimal weight: 4.9990 chunk 33 optimal weight: 10.0000 chunk 62 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3854 r_free = 0.3854 target = 0.162260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.114406 restraints weight = 7500.546| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 1.67 r_work: 0.3239 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.1540 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= 0.160 Angle : 0.596 8.199 11334 Z= 0.303 Chirality : 0.046 0.171 1302 Planarity : 0.004 0.042 1395 Dihedral : 9.537 89.757 1530 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 2.78 % Allowed : 18.48 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.29), residues: 984 helix: 1.72 (0.36), residues: 273 sheet: 0.43 (0.27), residues: 324 loop : 0.76 (0.36), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 259 HIS 0.002 0.001 HIS A 296 PHE 0.011 0.002 PHE C 276 TYR 0.015 0.001 TYR C 90 ARG 0.008 0.000 ARG B 180 Details of bonding type rmsd link_NAG-ASN : bond 0.00841 ( 9) link_NAG-ASN : angle 3.29876 ( 27) link_BETA1-4 : bond 0.00450 ( 9) link_BETA1-4 : angle 1.43557 ( 27) hydrogen bonds : bond 0.03122 ( 241) hydrogen bonds : angle 4.60243 ( 606) SS BOND : bond 0.00304 ( 12) SS BOND : angle 1.19112 ( 24) covalent geometry : bond 0.00359 ( 8274) covalent geometry : angle 0.56876 (11256) *********************** 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 144 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 121 time to evaluate : 0.876 Fit side-chains REVERT: A 52 GLU cc_start: 0.7992 (tp30) cc_final: 0.7660 (mt-10) REVERT: A 138 LYS cc_start: 0.8688 (OUTLIER) cc_final: 0.8333 (tttt) REVERT: A 267 VAL cc_start: 0.7943 (m) cc_final: 0.7662 (p) REVERT: A 275 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7512 (mp0) REVERT: A 332 MET cc_start: 0.7683 (OUTLIER) cc_final: 0.6148 (mpm) REVERT: B 138 LYS cc_start: 0.8677 (OUTLIER) cc_final: 0.8202 (tttt) REVERT: B 215 LYS cc_start: 0.8420 (tttp) cc_final: 0.8042 (ttmm) REVERT: B 242 ASN cc_start: 0.6875 (OUTLIER) cc_final: 0.6160 (m-40) REVERT: B 267 VAL cc_start: 0.7914 (m) cc_final: 0.7617 (p) REVERT: B 275 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7919 (tp30) REVERT: B 332 MET cc_start: 0.7743 (OUTLIER) cc_final: 0.6326 (mpm) REVERT: C 52 GLU cc_start: 0.7999 (tp30) cc_final: 0.7599 (mt-10) REVERT: C 148 LYS cc_start: 0.8291 (mppt) cc_final: 0.7723 (mtpt) REVERT: C 215 LYS cc_start: 0.8381 (tttp) cc_final: 0.8050 (ttmm) REVERT: C 332 MET cc_start: 0.7704 (OUTLIER) cc_final: 0.6275 (mpm) outliers start: 23 outliers final: 11 residues processed: 133 average time/residue: 1.4676 time to fit residues: 206.1724 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 : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ILE 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 242 ASN 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 237 GLN 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 11 optimal weight: 1.9990 chunk 48 optimal weight: 0.0170 chunk 64 optimal weight: 10.0000 chunk 20 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 85 optimal weight: 0.0670 chunk 43 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 96 optimal weight: 0.0970 chunk 91 optimal weight: 0.0980 chunk 81 optimal weight: 3.9990 overall best weight: 0.4556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3871 r_free = 0.3871 target = 0.163927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.116391 restraints weight = 7382.882| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 1.67 r_work: 0.3269 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8304 Z= 0.114 Angle : 0.558 8.249 11334 Z= 0.282 Chirality : 0.045 0.154 1302 Planarity : 0.004 0.042 1395 Dihedral : 9.174 87.712 1530 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.29), residues: 984 helix: 1.78 (0.36), residues: 273 sheet: 0.60 (0.29), residues: 297 loop : 0.62 (0.34), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 259 HIS 0.002 0.000 HIS A 296 PHE 0.008 0.001 PHE B 230 TYR 0.015 0.001 TYR B 90 ARG 0.008 0.000 ARG B 180 Details of bonding type rmsd link_NAG-ASN : bond 0.00706 ( 9) link_NAG-ASN : angle 2.89784 ( 27) link_BETA1-4 : bond 0.00494 ( 9) link_BETA1-4 : angle 1.41962 ( 27) hydrogen bonds : bond 0.02812 ( 241) hydrogen bonds : angle 4.48692 ( 606) SS BOND : bond 0.00270 ( 12) SS BOND : angle 1.05895 ( 24) covalent geometry : bond 0.00255 ( 8274) covalent geometry : angle 0.53458 (11256) ********************** 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 141 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 121 time to evaluate : 0.859 Fit side-chains REVERT: A 52 GLU cc_start: 0.7993 (tp30) cc_final: 0.7649 (mt-10) REVERT: A 267 VAL cc_start: 0.7968 (m) cc_final: 0.7716 (p) REVERT: A 275 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7492 (mp0) REVERT: A 332 MET cc_start: 0.7665 (OUTLIER) cc_final: 0.6132 (mpm) REVERT: B 197 ARG cc_start: 0.8322 (ttm-80) cc_final: 0.7823 (ttm110) REVERT: B 215 LYS cc_start: 0.8386 (tttp) cc_final: 0.8007 (ttmm) REVERT: B 242 ASN cc_start: 0.6680 (OUTLIER) cc_final: 0.6049 (m-40) REVERT: B 267 VAL cc_start: 0.7860 (m) cc_final: 0.7636 (p) REVERT: B 275 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7911 (tp30) REVERT: B 332 MET cc_start: 0.7703 (OUTLIER) cc_final: 0.6260 (mpm) REVERT: C 52 GLU cc_start: 0.7966 (tp30) cc_final: 0.7580 (mt-10) REVERT: C 138 LYS cc_start: 0.8688 (OUTLIER) cc_final: 0.8207 (tttt) REVERT: C 148 LYS cc_start: 0.8289 (mppt) cc_final: 0.7737 (mmtt) REVERT: C 215 LYS cc_start: 0.8363 (tttp) cc_final: 0.7993 (ttmm) REVERT: C 267 VAL cc_start: 0.7826 (m) cc_final: 0.7585 (p) REVERT: C 332 MET cc_start: 0.7713 (OUTLIER) cc_final: 0.6245 (mpm) outliers start: 20 outliers final: 9 residues processed: 132 average time/residue: 1.3360 time to fit residues: 186.1525 Evaluate side-chains 134 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 118 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ILE 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 242 ASN 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 237 GLN 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 48 optimal weight: 0.6980 chunk 41 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 63 optimal weight: 0.6980 chunk 7 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3853 r_free = 0.3853 target = 0.162059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.114064 restraints weight = 7457.531| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 1.69 r_work: 0.3232 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8304 Z= 0.178 Angle : 0.606 8.376 11334 Z= 0.307 Chirality : 0.046 0.165 1302 Planarity : 0.004 0.042 1395 Dihedral : 9.466 89.328 1530 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 2.17 % Allowed : 19.32 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.29), residues: 984 helix: 1.75 (0.36), residues: 273 sheet: 0.49 (0.27), residues: 318 loop : 0.86 (0.36), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 259 HIS 0.002 0.001 HIS C 260 PHE 0.012 0.002 PHE A 276 TYR 0.015 0.001 TYR C 90 ARG 0.007 0.001 ARG B 180 Details of bonding type rmsd link_NAG-ASN : bond 0.00536 ( 9) link_NAG-ASN : angle 2.95901 ( 27) link_BETA1-4 : bond 0.00441 ( 9) link_BETA1-4 : angle 1.40988 ( 27) hydrogen bonds : bond 0.03121 ( 241) hydrogen bonds : angle 4.62388 ( 606) SS BOND : bond 0.00326 ( 12) SS BOND : angle 1.22596 ( 24) covalent geometry : bond 0.00403 ( 8274) covalent geometry : angle 0.58328 (11256) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7872.52 seconds wall clock time: 138 minutes 7.49 seconds (8287.49 seconds total)