Starting phenix.real_space_refine on Sun Apr 5 03:42:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9uwy_64568/04_2026/9uwy_64568.cif Found real_map, /net/cci-nas-00/data/ceres_data/9uwy_64568/04_2026/9uwy_64568.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9uwy_64568/04_2026/9uwy_64568.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9uwy_64568/04_2026/9uwy_64568.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9uwy_64568/04_2026/9uwy_64568.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9uwy_64568/04_2026/9uwy_64568.map" } resolution = 2.48 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= -0.000 sd= 0.026 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: 5 Type Number sf(0) Gaussians P 9 5.49 5 S 39 5.16 5 C 4941 2.51 5 N 1275 2.21 5 O 1461 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7725 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2516 Classifications: {'peptide': 322} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 306} Chain: "C" Number of atoms: 2516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2516 Classifications: {'peptide': 322} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 306} Chain: "A" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {'ATP': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {'ATP': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Restraints were copied for chains: B Time building chain proxies: 2.46, per 1000 atoms: 0.32 Number of scatterers: 7725 At special positions: 0 Unit cell: (84.55, 90.25, 121.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 39 16.00 P 9 15.00 O 1461 8.00 N 1275 7.00 C 4941 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 125 " - pdb=" SG CYS A 176 " distance=2.03 Simple disulfide: pdb=" SG CYS A 136 " - pdb=" SG CYS A 159 " distance=2.03 Simple disulfide: pdb=" SG CYS A 142 " - pdb=" SG CYS A 170 " distance=2.03 Simple disulfide: pdb=" SG CYS A 226 " - pdb=" SG CYS A 236 " distance=2.03 Simple disulfide: pdb=" SG CYS A 270 " - pdb=" SG CYS A 279 " distance=2.03 Simple disulfide: pdb=" SG CYS B 125 " - pdb=" SG CYS B 176 " distance=2.03 Simple disulfide: pdb=" SG CYS B 125 " - pdb=" SG CYS B 125 " distance=0.00 Simple disulfide: pdb=" SG CYS B 125 " - pdb=" SG CYS B 176 " distance=2.03 Simple disulfide: pdb=" SG CYS B 136 " - pdb=" SG CYS B 159 " distance=2.03 Simple disulfide: pdb=" SG CYS B 136 " - pdb=" SG CYS B 136 " distance=0.00 Simple disulfide: pdb=" SG CYS B 136 " - pdb=" SG CYS B 159 " distance=2.03 Simple disulfide: pdb=" SG CYS B 142 " - pdb=" SG CYS B 170 " distance=2.03 Simple disulfide: pdb=" SG CYS B 142 " - pdb=" SG CYS B 142 " distance=0.00 Simple disulfide: pdb=" SG CYS B 142 " - pdb=" SG CYS B 170 " distance=2.03 Simple disulfide: pdb=" SG CYS B 159 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 159 " - pdb=" SG CYS B 159 " distance=0.00 Simple disulfide: pdb=" SG CYS B 170 " - pdb=" SG CYS B 142 " distance=2.03 Simple disulfide: pdb=" SG CYS B 170 " - pdb=" SG CYS B 170 " distance=0.00 Simple disulfide: pdb=" SG CYS B 176 " - pdb=" SG CYS B 125 " distance=2.03 Simple disulfide: pdb=" SG CYS B 176 " - pdb=" SG CYS B 176 " distance=0.00 Simple disulfide: pdb=" SG CYS B 226 " - pdb=" SG CYS B 236 " distance=2.04 Simple disulfide: pdb=" SG CYS B 226 " - pdb=" SG CYS B 226 " distance=0.00 Simple disulfide: pdb=" SG CYS B 226 " - pdb=" SG CYS B 236 " distance=2.04 Simple disulfide: pdb=" SG CYS B 236 " - pdb=" SG CYS B 226 " distance=2.04 Simple disulfide: pdb=" SG CYS B 236 " - pdb=" SG CYS B 236 " distance=0.00 Simple disulfide: pdb=" SG CYS B 270 " - pdb=" SG CYS B 279 " distance=2.03 Simple disulfide: pdb=" SG CYS B 270 " - pdb=" SG CYS B 270 " distance=0.00 Simple disulfide: pdb=" SG CYS B 270 " - pdb=" SG CYS B 279 " distance=2.03 Simple disulfide: pdb=" SG CYS B 279 " - pdb=" SG CYS B 270 " distance=2.03 Simple disulfide: pdb=" SG CYS B 279 " - pdb=" SG CYS B 279 " distance=0.00 Simple disulfide: pdb=" SG CYS B 359 " - pdb=" SG CYS B 359 " distance=0.00 Simple disulfide: pdb=" SG CYS B 125 " - pdb=" SG CYS B 176 " distance=2.03 Simple disulfide: pdb=" SG CYS B 136 " - pdb=" SG CYS B 159 " distance=2.03 Simple disulfide: pdb=" SG CYS B 142 " - pdb=" SG CYS B 170 " distance=2.03 Simple disulfide: pdb=" SG CYS B 226 " - pdb=" SG CYS B 236 " distance=2.04 Simple disulfide: pdb=" SG CYS B 270 " - pdb=" SG CYS B 279 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 501 " - " ASN A 133 " " NAG A 502 " - " ASN A 194 " " NAG B 501 " - " ASN B 133 " " NAG B 502 " - " ASN B 194 " " NAG C 502 " - " ASN C 133 " " NAG C 503 " - " ASN C 194 " Time building additional restraints: 0.83 Conformation dependent library (CDL) restraints added in 304.0 milliseconds 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1764 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 9 sheets defined 26.8% alpha, 26.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 41 through 60 Processing helix chain 'A' and resid 94 through 98 removed outlier: 3.722A pdb=" N TYR A 98 " --> pdb=" O ASP A 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 94 through 98' Processing helix chain 'A' and resid 138 through 142 removed outlier: 3.529A pdb=" N CYS A 142 " --> pdb=" O ASP A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 194 Processing helix chain 'A' and resid 221 through 225 removed outlier: 3.770A pdb=" N LYS A 224 " --> pdb=" O GLY A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 248 Processing helix chain 'A' and resid 251 through 259 Processing helix chain 'A' and resid 275 through 279 removed outlier: 3.588A pdb=" N CYS A 279 " --> pdb=" O ALA A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 362 removed outlier: 3.578A pdb=" N THR A 341 " --> pdb=" O SER A 337 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N VAL A 352 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLY A 353 " --> pdb=" O LEU A 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 60 Processing helix chain 'B' and resid 94 through 98 removed outlier: 3.722A pdb=" N TYR B 98 " --> pdb=" O ASP B 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 94 through 98' Processing helix chain 'B' and resid 138 through 142 removed outlier: 3.529A pdb=" N CYS B 142 " --> pdb=" O ASP B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 194 Processing helix chain 'B' and resid 221 through 225 removed outlier: 3.770A pdb=" N LYS B 224 " --> pdb=" O GLY B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 248 Processing helix chain 'B' and resid 251 through 259 Processing helix chain 'B' and resid 275 through 279 removed outlier: 3.588A pdb=" N CYS B 279 " --> pdb=" O ALA B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 362 removed outlier: 3.578A pdb=" N THR B 341 " --> pdb=" O SER B 337 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N VAL B 352 " --> pdb=" O ALA B 348 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLY B 353 " --> pdb=" O LEU B 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 60 Processing helix chain 'C' and resid 94 through 98 removed outlier: 3.722A pdb=" N TYR C 98 " --> pdb=" O ASP C 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 94 through 98' Processing helix chain 'C' and resid 138 through 142 removed outlier: 3.529A pdb=" N CYS C 142 " --> pdb=" O ASP C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 194 Processing helix chain 'C' and resid 221 through 225 removed outlier: 3.770A pdb=" N LYS C 224 " --> pdb=" O GLY C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 248 Processing helix chain 'C' and resid 251 through 259 Processing helix chain 'C' and resid 275 through 279 removed outlier: 3.588A pdb=" N CYS C 279 " --> pdb=" O ALA C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 362 removed outlier: 3.578A pdb=" N THR C 341 " --> pdb=" O SER C 337 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N VAL C 352 " --> pdb=" O ALA C 348 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLY C 353 " --> pdb=" O LEU C 349 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 68 through 71 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 68 through 71 current: chain 'A' and resid 107 through 126 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 107 through 126 current: chain 'A' and resid 168 through 176 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 168 through 176 current: chain 'A' and resid 281 through 287 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 281 through 287 current: chain 'A' and resid 312 through 336 No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 75 through 83 Processing sheet with id=AA3, first strand: chain 'A' and resid 86 through 88 Processing sheet with id=AA4, first strand: chain 'B' and resid 68 through 71 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 68 through 71 current: chain 'B' and resid 107 through 126 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 107 through 126 current: chain 'B' and resid 168 through 176 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 168 through 176 current: chain 'B' and resid 281 through 287 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 281 through 287 current: chain 'B' and resid 312 through 336 No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 75 through 83 Processing sheet with id=AA6, first strand: chain 'B' and resid 86 through 88 Processing sheet with id=AA7, first strand: chain 'C' and resid 68 through 71 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 68 through 71 current: chain 'C' and resid 107 through 126 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 107 through 126 current: chain 'C' and resid 168 through 176 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 168 through 176 current: chain 'C' and resid 281 through 287 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 281 through 287 current: chain 'C' and resid 312 through 336 No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 75 through 83 Processing sheet with id=AA9, first strand: chain 'C' and resid 86 through 88 196 hydrogen bonds defined for protein. 507 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: 1.09 Time building geometry restraints manager: 1.08 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: 2409 1.34 - 1.46: 2004 1.46 - 1.58: 3453 1.58 - 1.70: 15 1.70 - 1.82: 45 Bond restraints: 7926 Sorted by residual: bond pdb=" C4 ATP A 503 " pdb=" C5 ATP A 503 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.34e+01 bond pdb=" C4 ATP C 501 " pdb=" C5 ATP C 501 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.33e+01 bond pdb=" C4 ATP B 503 " pdb=" C5 ATP B 503 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.27e+01 bond pdb=" C5 ATP C 501 " pdb=" C6 ATP C 501 " ideal model delta sigma weight residual 1.409 1.479 -0.070 1.00e-02 1.00e+04 4.84e+01 bond pdb=" C5 ATP B 503 " pdb=" C6 ATP B 503 " ideal model delta sigma weight residual 1.409 1.478 -0.069 1.00e-02 1.00e+04 4.82e+01 ... (remaining 7921 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.36: 10712 3.36 - 6.73: 61 6.73 - 10.09: 9 10.09 - 13.46: 0 13.46 - 16.82: 6 Bond angle restraints: 10788 Sorted by residual: angle pdb=" PB ATP A 503 " pdb=" O3B ATP A 503 " pdb=" PG ATP A 503 " ideal model delta sigma weight residual 139.87 123.05 16.82 1.00e+00 1.00e+00 2.83e+02 angle pdb=" PB ATP C 501 " pdb=" O3B ATP C 501 " pdb=" PG ATP C 501 " ideal model delta sigma weight residual 139.87 123.07 16.80 1.00e+00 1.00e+00 2.82e+02 angle pdb=" PB ATP B 503 " pdb=" O3B ATP B 503 " pdb=" PG ATP B 503 " ideal model delta sigma weight residual 139.87 123.09 16.78 1.00e+00 1.00e+00 2.82e+02 angle pdb=" PA ATP B 503 " pdb=" O3A ATP B 503 " pdb=" PB ATP B 503 " ideal model delta sigma weight residual 136.83 121.92 14.91 1.00e+00 1.00e+00 2.22e+02 angle pdb=" PA ATP A 503 " pdb=" O3A ATP A 503 " pdb=" PB ATP A 503 " ideal model delta sigma weight residual 136.83 121.94 14.89 1.00e+00 1.00e+00 2.22e+02 ... (remaining 10783 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 4365 17.89 - 35.79: 370 35.79 - 53.68: 45 53.68 - 71.58: 21 71.58 - 89.47: 6 Dihedral angle restraints: 4807 sinusoidal: 2035 harmonic: 2772 Sorted by residual: dihedral pdb=" CA THR C 117 " pdb=" C THR C 117 " pdb=" N HIS C 118 " pdb=" CA HIS C 118 " ideal model delta harmonic sigma weight residual -180.00 -158.95 -21.05 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" CA THR B 117 " pdb=" C THR B 117 " pdb=" N HIS B 118 " pdb=" CA HIS B 118 " ideal model delta harmonic sigma weight residual -180.00 -158.97 -21.03 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" CA THR A 117 " pdb=" C THR A 117 " pdb=" N HIS A 118 " pdb=" CA HIS A 118 " ideal model delta harmonic sigma weight residual -180.00 -158.97 -21.03 0 5.00e+00 4.00e-02 1.77e+01 ... (remaining 4804 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 741 0.037 - 0.074: 309 0.074 - 0.111: 126 0.111 - 0.148: 39 0.148 - 0.185: 3 Chirality restraints: 1218 Sorted by residual: chirality pdb=" C1 NAG C 502 " pdb=" ND2 ASN C 133 " pdb=" C2 NAG C 502 " pdb=" O5 NAG C 502 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-01 2.50e+01 8.53e-01 chirality pdb=" C1 NAG A 501 " pdb=" ND2 ASN A 133 " pdb=" C2 NAG A 501 " pdb=" O5 NAG A 501 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-01 2.50e+01 8.29e-01 chirality pdb=" C1 NAG B 501 " pdb=" ND2 ASN B 133 " pdb=" C2 NAG B 501 " pdb=" O5 NAG B 501 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-01 2.50e+01 7.99e-01 ... (remaining 1215 not shown) Planarity restraints: 1344 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 285 " -0.011 2.00e-02 2.50e+03 1.17e-02 2.38e+00 pdb=" CG PHE A 285 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 PHE A 285 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE A 285 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE A 285 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 285 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A 285 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 285 " -0.011 2.00e-02 2.50e+03 1.16e-02 2.35e+00 pdb=" CG PHE B 285 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 PHE B 285 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE B 285 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE B 285 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE B 285 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE B 285 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 285 " -0.011 2.00e-02 2.50e+03 1.16e-02 2.34e+00 pdb=" CG PHE C 285 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 PHE C 285 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE C 285 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE C 285 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE C 285 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE C 285 " -0.001 2.00e-02 2.50e+03 ... (remaining 1341 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 62 2.60 - 3.18: 6418 3.18 - 3.75: 10978 3.75 - 4.33: 15980 4.33 - 4.90: 26875 Nonbonded interactions: 60313 Sorted by model distance: nonbonded pdb=" SG CYS C 125 " pdb=" SG CYS C 176 " model vdw 2.027 3.760 nonbonded pdb=" SG CYS C 136 " pdb=" SG CYS C 159 " model vdw 2.030 3.760 nonbonded pdb=" SG CYS C 270 " pdb=" SG CYS C 279 " model vdw 2.031 3.760 nonbonded pdb=" SG CYS C 142 " pdb=" SG CYS C 170 " model vdw 2.034 3.760 nonbonded pdb=" SG CYS C 226 " pdb=" SG CYS C 236 " model vdw 2.035 3.760 ... (remaining 60308 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 41 through 362 or resid 502)) selection = (chain 'B' and (resid 41 through 362 or resid 502)) selection = (chain 'C' and (resid 41 through 362 or resid 502)) } 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: 4.240 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 9.150 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 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 : 0.005 0.080 7942 Z= 0.334 Angle : 0.797 16.819 10837 Z= 0.579 Chirality : 0.049 0.185 1218 Planarity : 0.004 0.029 1338 Dihedral : 13.739 89.471 2991 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: -1.62 (0.25), residues: 960 helix: -1.57 (0.30), residues: 213 sheet: 0.04 (0.25), residues: 354 loop : -1.76 (0.28), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 286 TYR 0.008 0.001 TYR A 98 PHE 0.027 0.002 PHE A 285 TRP 0.007 0.001 TRP A 268 HIS 0.004 0.001 HIS C 118 Details of bonding type rmsd covalent geometry : bond 0.00504 ( 7926) covalent geometry : angle 0.79627 (10788) SS BOND : bond 0.00291 ( 10) SS BOND : angle 0.76976 ( 31) hydrogen bonds : bond 0.14051 ( 196) hydrogen bonds : angle 5.32776 ( 507) link_NAG-ASN : bond 0.00197 ( 6) link_NAG-ASN : angle 1.32826 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 GLN cc_start: 0.9241 (mm110) cc_final: 0.9038 (mm110) REVERT: B 64 GLN cc_start: 0.9289 (mm110) cc_final: 0.9072 (mm110) REVERT: B 69 GLU cc_start: 0.7852 (mt-10) cc_final: 0.7637 (pm20) REVERT: B 164 GLN cc_start: 0.8942 (pm20) cc_final: 0.8210 (pm20) REVERT: C 64 GLN cc_start: 0.9247 (mm110) cc_final: 0.9041 (mm110) REVERT: C 69 GLU cc_start: 0.7819 (mt-10) cc_final: 0.7530 (pt0) REVERT: C 164 GLN cc_start: 0.8935 (pm20) cc_final: 0.8390 (pm20) outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.5442 time to fit residues: 60.1776 Evaluate side-chains 79 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.0870 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 45 optimal weight: 0.0570 chunk 74 optimal weight: 5.9990 overall best weight: 1.0080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 344 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.103398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.067564 restraints weight = 14758.181| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 3.25 r_work: 0.2802 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.1330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 7942 Z= 0.164 Angle : 0.601 8.060 10837 Z= 0.319 Chirality : 0.049 0.197 1218 Planarity : 0.004 0.034 1338 Dihedral : 9.971 76.511 1272 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.72 % Allowed : 8.57 % Favored : 90.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: -0.78 (0.25), residues: 960 helix: -0.43 (0.34), residues: 198 sheet: 0.32 (0.26), residues: 354 loop : -1.25 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 218 TYR 0.013 0.001 TYR C 222 PHE 0.022 0.002 PHE C 285 TRP 0.008 0.001 TRP C 268 HIS 0.007 0.001 HIS A 204 Details of bonding type rmsd covalent geometry : bond 0.00396 ( 7926) covalent geometry : angle 0.59802 (10788) SS BOND : bond 0.00267 ( 10) SS BOND : angle 0.69064 ( 31) hydrogen bonds : bond 0.04491 ( 196) hydrogen bonds : angle 4.61156 ( 507) link_NAG-ASN : bond 0.00169 ( 6) link_NAG-ASN : angle 1.52220 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 87 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 69 GLU cc_start: 0.8294 (mt-10) cc_final: 0.7868 (pm20) REVERT: B 152 ASN cc_start: 0.9227 (m-40) cc_final: 0.8867 (m110) REVERT: B 164 GLN cc_start: 0.9001 (pm20) cc_final: 0.8252 (pm20) REVERT: C 59 TYR cc_start: 0.8116 (t80) cc_final: 0.7892 (t80) REVERT: C 64 GLN cc_start: 0.9180 (mm110) cc_final: 0.8943 (mm110) REVERT: C 69 GLU cc_start: 0.8273 (mt-10) cc_final: 0.7951 (pt0) REVERT: C 152 ASN cc_start: 0.9280 (m-40) cc_final: 0.8883 (m110) REVERT: C 164 GLN cc_start: 0.8981 (pm20) cc_final: 0.8425 (pm20) outliers start: 6 outliers final: 1 residues processed: 91 average time/residue: 0.5811 time to fit residues: 56.1032 Evaluate side-chains 81 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 80 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 338 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 37 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 81 optimal weight: 0.1980 chunk 63 optimal weight: 7.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.102653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.066901 restraints weight = 14678.854| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 3.23 r_work: 0.2802 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 7942 Z= 0.189 Angle : 0.591 7.055 10837 Z= 0.311 Chirality : 0.049 0.201 1218 Planarity : 0.004 0.038 1338 Dihedral : 9.708 89.086 1272 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.21 % Allowed : 9.78 % Favored : 89.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: -0.39 (0.26), residues: 960 helix: 0.05 (0.35), residues: 198 sheet: 0.57 (0.26), residues: 348 loop : -1.09 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 315 TYR 0.013 0.001 TYR A 59 PHE 0.018 0.002 PHE B 285 TRP 0.008 0.001 TRP C 268 HIS 0.007 0.001 HIS A 204 Details of bonding type rmsd covalent geometry : bond 0.00461 ( 7926) covalent geometry : angle 0.58783 (10788) SS BOND : bond 0.00291 ( 10) SS BOND : angle 0.70951 ( 31) hydrogen bonds : bond 0.04329 ( 196) hydrogen bonds : angle 4.47176 ( 507) link_NAG-ASN : bond 0.00264 ( 6) link_NAG-ASN : angle 1.56226 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 84 time to evaluate : 0.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 LYS cc_start: 0.9166 (mttm) cc_final: 0.8792 (mtpp) REVERT: B 69 GLU cc_start: 0.8266 (mt-10) cc_final: 0.7847 (pm20) REVERT: B 152 ASN cc_start: 0.9244 (m-40) cc_final: 0.8849 (m110) REVERT: B 164 GLN cc_start: 0.8994 (pm20) cc_final: 0.8760 (pm20) REVERT: B 258 LYS cc_start: 0.8880 (OUTLIER) cc_final: 0.8586 (mppt) REVERT: C 59 TYR cc_start: 0.8172 (t80) cc_final: 0.7948 (t80) REVERT: C 64 GLN cc_start: 0.9185 (mm110) cc_final: 0.8942 (mm110) REVERT: C 69 GLU cc_start: 0.8316 (mt-10) cc_final: 0.7950 (pt0) REVERT: C 152 ASN cc_start: 0.9315 (m-40) cc_final: 0.8859 (m110) REVERT: C 164 GLN cc_start: 0.9002 (pm20) cc_final: 0.8427 (pm20) outliers start: 10 outliers final: 1 residues processed: 87 average time/residue: 0.6123 time to fit residues: 56.2946 Evaluate side-chains 81 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 79 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain C residue 258 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 10 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 52 optimal weight: 0.6980 chunk 69 optimal weight: 0.5980 chunk 63 optimal weight: 0.0980 chunk 47 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 89 optimal weight: 0.0570 chunk 13 optimal weight: 0.6980 overall best weight: 0.4298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.104674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.069015 restraints weight = 14780.860| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 3.28 r_work: 0.2837 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 7942 Z= 0.102 Angle : 0.533 7.843 10837 Z= 0.278 Chirality : 0.047 0.197 1218 Planarity : 0.004 0.039 1338 Dihedral : 9.125 86.404 1272 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.85 % Allowed : 11.11 % Favored : 88.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: -0.04 (0.26), residues: 960 helix: 0.45 (0.36), residues: 198 sheet: 0.73 (0.26), residues: 354 loop : -0.90 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 218 TYR 0.016 0.001 TYR B 59 PHE 0.014 0.001 PHE A 252 TRP 0.005 0.001 TRP B 93 HIS 0.006 0.001 HIS B 204 Details of bonding type rmsd covalent geometry : bond 0.00235 ( 7926) covalent geometry : angle 0.53042 (10788) SS BOND : bond 0.00200 ( 10) SS BOND : angle 0.51379 ( 31) hydrogen bonds : bond 0.03725 ( 196) hydrogen bonds : angle 4.35909 ( 507) link_NAG-ASN : bond 0.00331 ( 6) link_NAG-ASN : angle 1.38323 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 83 time to evaluate : 0.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 LYS cc_start: 0.9145 (mttm) cc_final: 0.8842 (mtpp) REVERT: B 69 GLU cc_start: 0.8286 (mt-10) cc_final: 0.7841 (pm20) REVERT: B 89 GLU cc_start: 0.8281 (tp30) cc_final: 0.7716 (tp30) REVERT: B 152 ASN cc_start: 0.9214 (m-40) cc_final: 0.8827 (m110) REVERT: B 164 GLN cc_start: 0.8988 (pm20) cc_final: 0.8294 (pm20) REVERT: B 258 LYS cc_start: 0.8816 (OUTLIER) cc_final: 0.8556 (mppt) REVERT: C 59 TYR cc_start: 0.8201 (t80) cc_final: 0.7986 (t80) REVERT: C 64 GLN cc_start: 0.9250 (mm110) cc_final: 0.9005 (mm110) REVERT: C 69 GLU cc_start: 0.8334 (mt-10) cc_final: 0.7989 (pt0) REVERT: C 152 ASN cc_start: 0.9239 (m-40) cc_final: 0.8761 (m110) REVERT: C 164 GLN cc_start: 0.8976 (pm20) cc_final: 0.8430 (pm20) outliers start: 7 outliers final: 2 residues processed: 88 average time/residue: 0.6159 time to fit residues: 57.3172 Evaluate side-chains 84 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 81 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 258 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 64 optimal weight: 20.0000 chunk 50 optimal weight: 0.5980 chunk 28 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 1 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 85 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.103505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.067960 restraints weight = 14841.861| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 3.25 r_work: 0.2807 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7942 Z= 0.138 Angle : 0.551 7.639 10837 Z= 0.286 Chirality : 0.048 0.196 1218 Planarity : 0.004 0.040 1338 Dihedral : 8.842 80.896 1272 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.85 % Allowed : 12.20 % Favored : 86.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: 0.21 (0.27), residues: 960 helix: 0.55 (0.36), residues: 198 sheet: 0.90 (0.27), residues: 354 loop : -0.71 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 302 TYR 0.015 0.001 TYR B 59 PHE 0.015 0.001 PHE A 252 TRP 0.006 0.001 TRP C 268 HIS 0.005 0.001 HIS A 204 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 7926) covalent geometry : angle 0.54871 (10788) SS BOND : bond 0.00246 ( 10) SS BOND : angle 0.58465 ( 31) hydrogen bonds : bond 0.03721 ( 196) hydrogen bonds : angle 4.29634 ( 507) link_NAG-ASN : bond 0.00263 ( 6) link_NAG-ASN : angle 1.43079 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 82 time to evaluate : 0.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 LYS cc_start: 0.9068 (mttm) cc_final: 0.8761 (mtpp) REVERT: B 69 GLU cc_start: 0.8286 (mt-10) cc_final: 0.7934 (pt0) REVERT: B 152 ASN cc_start: 0.9218 (m-40) cc_final: 0.8815 (m110) REVERT: B 164 GLN cc_start: 0.8978 (pm20) cc_final: 0.8315 (pm20) REVERT: B 230 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7864 (mp0) REVERT: B 258 LYS cc_start: 0.8849 (OUTLIER) cc_final: 0.8554 (mppt) REVERT: C 59 TYR cc_start: 0.8228 (t80) cc_final: 0.8000 (t80) REVERT: C 64 GLN cc_start: 0.9234 (mm110) cc_final: 0.8998 (mm110) REVERT: C 69 GLU cc_start: 0.8314 (mt-10) cc_final: 0.7951 (pt0) REVERT: C 152 ASN cc_start: 0.9267 (m-40) cc_final: 0.8784 (m110) REVERT: C 164 GLN cc_start: 0.8970 (pm20) cc_final: 0.8440 (pm20) outliers start: 7 outliers final: 3 residues processed: 85 average time/residue: 0.6441 time to fit residues: 57.8856 Evaluate side-chains 85 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 80 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 230 GLU Chi-restraints excluded: chain C residue 258 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 50 optimal weight: 0.9990 chunk 42 optimal weight: 4.9990 chunk 52 optimal weight: 0.0040 chunk 87 optimal weight: 1.9990 chunk 46 optimal weight: 0.0770 chunk 31 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 34 optimal weight: 0.0370 chunk 54 optimal weight: 0.9980 overall best weight: 0.4230 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.105042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.069630 restraints weight = 14901.952| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 3.26 r_work: 0.2846 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 7942 Z= 0.099 Angle : 0.538 8.059 10837 Z= 0.276 Chirality : 0.046 0.194 1218 Planarity : 0.003 0.041 1338 Dihedral : 8.481 74.472 1272 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 2.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.97 % Allowed : 12.56 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: 0.45 (0.27), residues: 960 helix: 0.78 (0.36), residues: 198 sheet: 1.08 (0.27), residues: 351 loop : -0.59 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 218 TYR 0.013 0.001 TYR A 59 PHE 0.014 0.001 PHE A 252 TRP 0.004 0.001 TRP C 268 HIS 0.005 0.001 HIS A 204 Details of bonding type rmsd covalent geometry : bond 0.00233 ( 7926) covalent geometry : angle 0.53585 (10788) SS BOND : bond 0.00189 ( 10) SS BOND : angle 0.49598 ( 31) hydrogen bonds : bond 0.03297 ( 196) hydrogen bonds : angle 4.22166 ( 507) link_NAG-ASN : bond 0.00338 ( 6) link_NAG-ASN : angle 1.32520 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 85 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 291 LYS cc_start: 0.8461 (mptt) cc_final: 0.8253 (mptt) REVERT: B 69 GLU cc_start: 0.8304 (mt-10) cc_final: 0.7944 (pt0) REVERT: B 152 ASN cc_start: 0.9168 (m-40) cc_final: 0.8757 (m110) REVERT: B 164 GLN cc_start: 0.8963 (pm20) cc_final: 0.8282 (pm20) REVERT: B 230 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7792 (mp0) REVERT: B 258 LYS cc_start: 0.8807 (OUTLIER) cc_final: 0.8543 (mppt) REVERT: C 59 TYR cc_start: 0.8214 (t80) cc_final: 0.7934 (t80) REVERT: C 64 GLN cc_start: 0.9242 (mm110) cc_final: 0.8987 (mm110) REVERT: C 69 GLU cc_start: 0.8299 (mt-10) cc_final: 0.7933 (pt0) REVERT: C 152 ASN cc_start: 0.9212 (m-40) cc_final: 0.8708 (m110) REVERT: C 164 GLN cc_start: 0.8955 (pm20) cc_final: 0.8433 (pm20) outliers start: 8 outliers final: 2 residues processed: 90 average time/residue: 0.6106 time to fit residues: 58.1895 Evaluate side-chains 90 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 86 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 258 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 44 optimal weight: 0.7980 chunk 32 optimal weight: 20.0000 chunk 40 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 17 optimal weight: 0.4980 chunk 64 optimal weight: 20.0000 chunk 38 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.103832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.068328 restraints weight = 14810.702| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 3.24 r_work: 0.2808 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 7942 Z= 0.142 Angle : 0.561 7.793 10837 Z= 0.290 Chirality : 0.047 0.194 1218 Planarity : 0.004 0.040 1338 Dihedral : 8.481 71.480 1272 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.45 % Allowed : 12.56 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: 0.57 (0.27), residues: 960 helix: 0.78 (0.36), residues: 198 sheet: 1.15 (0.27), residues: 348 loop : -0.45 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 302 TYR 0.015 0.001 TYR B 59 PHE 0.014 0.001 PHE A 252 TRP 0.006 0.001 TRP C 268 HIS 0.005 0.001 HIS A 204 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 7926) covalent geometry : angle 0.55885 (10788) SS BOND : bond 0.00240 ( 10) SS BOND : angle 0.56453 ( 31) hydrogen bonds : bond 0.03584 ( 196) hydrogen bonds : angle 4.23622 ( 507) link_NAG-ASN : bond 0.00256 ( 6) link_NAG-ASN : angle 1.40801 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 83 time to evaluate : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7482 (mp0) REVERT: B 41 LEU cc_start: 0.3856 (OUTLIER) cc_final: 0.3644 (pp) REVERT: B 69 GLU cc_start: 0.8272 (mt-10) cc_final: 0.7902 (pt0) REVERT: B 152 ASN cc_start: 0.9196 (m-40) cc_final: 0.8797 (m110) REVERT: B 164 GLN cc_start: 0.8935 (pm20) cc_final: 0.8307 (pm20) REVERT: B 230 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7850 (mp0) REVERT: B 258 LYS cc_start: 0.8885 (OUTLIER) cc_final: 0.8579 (mppt) REVERT: C 59 TYR cc_start: 0.8292 (t80) cc_final: 0.8015 (t80) REVERT: C 64 GLN cc_start: 0.9232 (mm110) cc_final: 0.8981 (mm110) REVERT: C 69 GLU cc_start: 0.8343 (mt-10) cc_final: 0.7969 (pt0) REVERT: C 152 ASN cc_start: 0.9258 (m-40) cc_final: 0.8758 (m110) REVERT: C 164 GLN cc_start: 0.8938 (pm20) cc_final: 0.8403 (pm20) outliers start: 12 outliers final: 2 residues processed: 91 average time/residue: 0.6435 time to fit residues: 61.7924 Evaluate side-chains 89 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 83 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 258 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 78 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 64 optimal weight: 20.0000 chunk 67 optimal weight: 0.1980 chunk 51 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 81 optimal weight: 0.0070 chunk 69 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 overall best weight: 0.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.104269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.068779 restraints weight = 14865.604| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 3.26 r_work: 0.2827 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7942 Z= 0.119 Angle : 0.598 18.760 10837 Z= 0.299 Chirality : 0.047 0.248 1218 Planarity : 0.004 0.040 1338 Dihedral : 8.380 68.572 1272 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.97 % Allowed : 13.16 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: 0.64 (0.27), residues: 960 helix: 0.76 (0.36), residues: 198 sheet: 1.15 (0.27), residues: 351 loop : -0.32 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 218 TYR 0.015 0.001 TYR A 59 PHE 0.014 0.001 PHE A 252 TRP 0.005 0.001 TRP C 268 HIS 0.005 0.001 HIS A 204 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 7926) covalent geometry : angle 0.59497 (10788) SS BOND : bond 0.00208 ( 10) SS BOND : angle 0.52097 ( 31) hydrogen bonds : bond 0.03467 ( 196) hydrogen bonds : angle 4.22738 ( 507) link_NAG-ASN : bond 0.00443 ( 6) link_NAG-ASN : angle 1.71745 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 84 time to evaluate : 0.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 69 GLU cc_start: 0.8304 (mt-10) cc_final: 0.7933 (pt0) REVERT: B 152 ASN cc_start: 0.9186 (m-40) cc_final: 0.8778 (m110) REVERT: B 164 GLN cc_start: 0.8946 (pm20) cc_final: 0.8383 (pm20) REVERT: B 230 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7850 (mp0) REVERT: C 59 TYR cc_start: 0.8315 (t80) cc_final: 0.8025 (t80) REVERT: C 64 GLN cc_start: 0.9244 (mm110) cc_final: 0.8988 (mm110) REVERT: C 69 GLU cc_start: 0.8344 (mt-10) cc_final: 0.7971 (pt0) REVERT: C 152 ASN cc_start: 0.9244 (m-40) cc_final: 0.8725 (m110) REVERT: C 164 GLN cc_start: 0.8937 (pm20) cc_final: 0.8407 (pm20) outliers start: 8 outliers final: 3 residues processed: 88 average time/residue: 0.6667 time to fit residues: 61.8250 Evaluate side-chains 87 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 83 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 191 MET Chi-restraints excluded: chain C residue 258 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 44 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 78 optimal weight: 0.1980 chunk 66 optimal weight: 0.6980 chunk 64 optimal weight: 20.0000 chunk 81 optimal weight: 0.0070 chunk 37 optimal weight: 0.9990 chunk 54 optimal weight: 0.8980 chunk 12 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.104668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.069245 restraints weight = 14847.345| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 3.26 r_work: 0.2835 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7942 Z= 0.115 Angle : 0.629 18.893 10837 Z= 0.306 Chirality : 0.048 0.314 1218 Planarity : 0.004 0.039 1338 Dihedral : 8.296 65.684 1272 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.72 % Allowed : 13.89 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.26), residues: 960 helix: 0.39 (0.35), residues: 216 sheet: 1.24 (0.27), residues: 348 loop : -0.26 (0.30), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 46 TYR 0.016 0.001 TYR A 59 PHE 0.013 0.001 PHE A 252 TRP 0.005 0.001 TRP C 268 HIS 0.004 0.001 HIS A 204 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 7926) covalent geometry : angle 0.62509 (10788) SS BOND : bond 0.00201 ( 10) SS BOND : angle 0.50795 ( 31) hydrogen bonds : bond 0.03400 ( 196) hydrogen bonds : angle 4.30066 ( 507) link_NAG-ASN : bond 0.00620 ( 6) link_NAG-ASN : angle 1.85654 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 82 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 GLN cc_start: 0.9185 (mm110) cc_final: 0.8701 (mp10) REVERT: A 164 GLN cc_start: 0.8725 (mp10) cc_final: 0.8524 (pm20) REVERT: B 69 GLU cc_start: 0.8297 (mt-10) cc_final: 0.7935 (pt0) REVERT: B 152 ASN cc_start: 0.9183 (m-40) cc_final: 0.8785 (m110) REVERT: B 164 GLN cc_start: 0.8927 (pm20) cc_final: 0.8381 (pm20) REVERT: B 230 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7852 (mp0) REVERT: C 59 TYR cc_start: 0.8321 (t80) cc_final: 0.8022 (t80) REVERT: C 64 GLN cc_start: 0.9257 (mm110) cc_final: 0.8997 (mm110) REVERT: C 69 GLU cc_start: 0.8358 (mt-10) cc_final: 0.7983 (pt0) REVERT: C 152 ASN cc_start: 0.9270 (m-40) cc_final: 0.8719 (m110) REVERT: C 164 GLN cc_start: 0.8939 (pm20) cc_final: 0.8410 (pm20) outliers start: 6 outliers final: 4 residues processed: 85 average time/residue: 0.5958 time to fit residues: 53.4535 Evaluate side-chains 87 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 82 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain C residue 49 GLN Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 191 MET Chi-restraints excluded: chain C residue 258 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 80 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 85 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 88 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 38 optimal weight: 0.1980 chunk 14 optimal weight: 0.1980 chunk 70 optimal weight: 1.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.104788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.069546 restraints weight = 14720.748| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 3.24 r_work: 0.2839 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7942 Z= 0.114 Angle : 0.653 17.341 10837 Z= 0.312 Chirality : 0.048 0.199 1218 Planarity : 0.004 0.039 1338 Dihedral : 8.228 63.010 1272 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.72 % Allowed : 13.89 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: 0.62 (0.26), residues: 960 helix: 0.32 (0.34), residues: 216 sheet: 1.26 (0.27), residues: 348 loop : -0.22 (0.30), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 46 TYR 0.017 0.001 TYR B 59 PHE 0.014 0.001 PHE A 252 TRP 0.005 0.001 TRP C 268 HIS 0.004 0.001 HIS A 204 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 7926) covalent geometry : angle 0.65070 (10788) SS BOND : bond 0.00199 ( 10) SS BOND : angle 0.49170 ( 31) hydrogen bonds : bond 0.03387 ( 196) hydrogen bonds : angle 4.33323 ( 507) link_NAG-ASN : bond 0.00414 ( 6) link_NAG-ASN : angle 1.56406 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 81 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 GLN cc_start: 0.9199 (mm110) cc_final: 0.8629 (mp10) REVERT: B 69 GLU cc_start: 0.8294 (mt-10) cc_final: 0.7957 (pt0) REVERT: B 152 ASN cc_start: 0.9188 (m-40) cc_final: 0.8787 (m110) REVERT: B 164 GLN cc_start: 0.8901 (pm20) cc_final: 0.8368 (pm20) REVERT: B 230 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7833 (mp0) REVERT: C 59 TYR cc_start: 0.8324 (t80) cc_final: 0.8021 (t80) REVERT: C 64 GLN cc_start: 0.9263 (mm110) cc_final: 0.9022 (mm110) REVERT: C 65 LYS cc_start: 0.9121 (mttm) cc_final: 0.8917 (mtpp) REVERT: C 69 GLU cc_start: 0.8362 (mt-10) cc_final: 0.7998 (pt0) REVERT: C 152 ASN cc_start: 0.9269 (m-40) cc_final: 0.8720 (m110) REVERT: C 164 GLN cc_start: 0.8935 (pm20) cc_final: 0.8408 (pm20) outliers start: 6 outliers final: 1 residues processed: 84 average time/residue: 0.6254 time to fit residues: 55.5941 Evaluate side-chains 82 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 80 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain C residue 258 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 15 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 52 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 chunk 49 optimal weight: 0.5980 chunk 11 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.104098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.068663 restraints weight = 14685.197| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 3.24 r_work: 0.2815 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7942 Z= 0.136 Angle : 0.680 18.092 10837 Z= 0.327 Chirality : 0.048 0.195 1218 Planarity : 0.004 0.039 1338 Dihedral : 8.271 60.709 1272 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.48 % Allowed : 13.89 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: 0.56 (0.26), residues: 960 helix: 0.21 (0.35), residues: 216 sheet: 1.24 (0.27), residues: 348 loop : -0.23 (0.30), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 130 TYR 0.017 0.001 TYR B 59 PHE 0.014 0.001 PHE A 252 TRP 0.006 0.001 TRP C 268 HIS 0.005 0.001 HIS A 132 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 7926) covalent geometry : angle 0.67644 (10788) SS BOND : bond 0.00224 ( 10) SS BOND : angle 0.54419 ( 31) hydrogen bonds : bond 0.03576 ( 196) hydrogen bonds : angle 4.39515 ( 507) link_NAG-ASN : bond 0.00268 ( 6) link_NAG-ASN : angle 1.91962 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3123.67 seconds wall clock time: 53 minutes 56.59 seconds (3236.59 seconds total)