Starting phenix.real_space_refine on Fri Oct 23 02:31:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9uwy_64568/10_2026/9uwy_64568.cif Found real_map, /net/cci-nas-00/data/ceres_data/9uwy_64568/10_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9uwy_64568/10_2026/9uwy_64568.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9uwy_64568/10_2026/9uwy_64568.map" model { file = "/net/cci-nas-00/data/ceres_data/9uwy_64568/10_2026/9uwy_64568.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9uwy_64568/10_2026/9uwy_64568.cif" } 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-2.3rc1-6221/lib/python3.11/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: 2.45, 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=15, 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 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 Simple disulfide: pdb=" SG CYS C 125 " - pdb=" SG CYS C 176 " distance=2.03 Simple disulfide: pdb=" SG CYS C 136 " - pdb=" SG CYS C 159 " distance=2.03 Simple disulfide: pdb=" SG CYS C 142 " - pdb=" SG CYS C 170 " distance=2.03 Simple disulfide: pdb=" SG CYS C 226 " - pdb=" SG CYS C 236 " distance=2.04 Simple disulfide: pdb=" SG CYS C 270 " - pdb=" SG CYS C 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: 0.59 Conformation dependent library (CDL) restraints added in 357.8 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: 0.21 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: 0.93 Time building geometry restraints manager: 0.82 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: 4371 17.89 - 35.79: 357 35.79 - 53.68: 45 53.68 - 71.58: 21 71.58 - 89.47: 6 Dihedral angle restraints: 4800 sinusoidal: 2028 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 4797 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: 2.22 - 2.76: 1044 2.76 - 3.29: 6988 3.29 - 3.83: 12148 3.83 - 4.36: 14607 4.36 - 4.90: 25511 Nonbonded interactions: 60298 Sorted by model distance: nonbonded pdb=" O GLU C 89 " pdb=" ND1 HIS C 90 " model vdw 2.221 3.120 nonbonded pdb=" O GLU A 89 " pdb=" ND1 HIS A 90 " model vdw 2.221 3.120 nonbonded pdb=" O GLY A 84 " pdb=" OH TYR A 98 " model vdw 2.222 3.040 nonbonded pdb=" O GLU B 89 " pdb=" ND1 HIS B 90 " model vdw 2.222 3.120 nonbonded pdb=" O GLY C 84 " pdb=" OH TYR C 98 " model vdw 2.222 3.040 ... (remaining 60293 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: 2.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.420 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 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 7947 Z= 0.334 Angle : 0.798 16.819 10836 Z= 0.579 Chirality : 0.049 0.185 1218 Planarity : 0.004 0.029 1338 Dihedral : 13.739 89.471 2991 Min Nonbonded Distance : 2.221 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/Z covalent geometry : bond 0.00504 / 0.33 ( 7926) covalent geometry : angle 0.79627 / 0.58 (10788) SS BOND : bond 0.00293 / 0.19 ( 15) SS BOND : angle 0.95533 / 0.66 ( 30) hydrogen bonds : bond 0.14051 / 8.55 ( 196) hydrogen bonds : angle 5.32776 / 3.73 ( 507) link_NAG-ASN : bond 0.00197 / 0.12 ( 6) link_NAG-ASN : angle 1.32826 / 0.89 ( 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 : 0.183 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: 0.4803 time to fit residues: 53.2849 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 : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: [49, 53, 5, 33, 65, 62, 51, 38, 61, 45, 74] 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: 4.9990 overall best weight: 1.0080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 344 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.103547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.067785 restraints weight = 14683.801| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 3.24 r_work: 0.2814 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.1252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 7947 Z= 0.165 Angle : 0.598 7.949 10836 Z= 0.318 Chirality : 0.049 0.196 1218 Planarity : 0.004 0.035 1338 Dihedral : 9.972 78.966 1272 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 2.62 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: -0.79 (0.26), residues: 960 helix: -0.45 (0.34), residues: 198 sheet: 0.32 (0.26), residues: 354 loop : -1.26 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 218 TYR 0.012 0.001 TYR C 222 PHE 0.021 0.002 PHE A 285 TRP 0.007 0.001 TRP C 268 HIS 0.008 0.001 HIS A 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.17 ( 7926) covalent geometry : angle 0.59461 / 0.32 (10788) SS BOND : bond 0.00266 / 0.18 ( 15) SS BOND : angle 0.82641 / 0.56 ( 30) hydrogen bonds : bond 0.04473 / 2.94 ( 196) hydrogen bonds : angle 4.61167 / 3.17 ( 507) link_NAG-ASN : bond 0.00166 / 0.10 ( 6) link_NAG-ASN : angle 1.50236 / 0.99 ( 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 95 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 89 time to evaluate : 0.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 69 GLU cc_start: 0.8295 (mt-10) cc_final: 0.7875 (pm20) REVERT: B 152 ASN cc_start: 0.9224 (m-40) cc_final: 0.8847 (m110) REVERT: B 164 GLN cc_start: 0.9001 (pm20) cc_final: 0.8253 (pm20) REVERT: C 59 TYR cc_start: 0.8167 (t80) cc_final: 0.7940 (t80) REVERT: C 64 GLN cc_start: 0.9197 (mm110) cc_final: 0.8962 (mm110) REVERT: C 69 GLU cc_start: 0.8264 (mt-10) cc_final: 0.7943 (pt0) REVERT: C 152 ASN cc_start: 0.9274 (m-40) cc_final: 0.8860 (m110) REVERT: C 164 GLN cc_start: 0.8978 (pm20) cc_final: 0.8418 (pm20) outliers start: 6 outliers final: 1 residues processed: 92 average time/residue: 0.4905 time to fit residues: 48.1008 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 : 0.233 ------------------------------------------------------------------------------- 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: [37, 73, 72, 78, 28, 41, 35, 16, 93, 81, 63] chunk 37 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 72 optimal weight: 0.7980 chunk 78 optimal weight: 3.9990 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: 0.9990 chunk 81 optimal weight: 0.4980 chunk 63 optimal weight: 4.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.103858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.068045 restraints weight = 14638.852| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 3.25 r_work: 0.2819 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 7947 Z= 0.139 Angle : 0.559 7.442 10836 Z= 0.293 Chirality : 0.048 0.237 1218 Planarity : 0.004 0.039 1338 Dihedral : 9.615 88.983 1272 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.97 % Allowed : 10.39 % Favored : 88.65 % 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: -0.30 (0.26), residues: 960 helix: 0.14 (0.35), residues: 198 sheet: 0.58 (0.26), residues: 354 loop : -1.03 (0.30), residues: 408 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 0.015 0.001 PHE C 252 TRP 0.006 0.001 TRP C 268 HIS 0.007 0.001 HIS A 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 ( 7926) covalent geometry : angle 0.55548 / 0.29 (10788) SS BOND : bond 0.00236 / 0.16 ( 15) SS BOND : angle 0.72932 / 0.50 ( 30) hydrogen bonds : bond 0.04020 / 2.64 ( 196) hydrogen bonds : angle 4.43381 / 3.05 ( 507) link_NAG-ASN : bond 0.00260 / 0.16 ( 6) link_NAG-ASN : angle 1.44221 / 0.96 ( 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 89 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 81 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 LYS cc_start: 0.9170 (mttm) cc_final: 0.8811 (mtpp) REVERT: A 164 GLN cc_start: 0.8895 (pm20) cc_final: 0.8694 (pm20) REVERT: B 69 GLU cc_start: 0.8285 (mt-10) cc_final: 0.7854 (pm20) REVERT: B 152 ASN cc_start: 0.9233 (m-40) cc_final: 0.8842 (m110) REVERT: B 164 GLN cc_start: 0.8987 (pm20) cc_final: 0.8747 (pm20) REVERT: C 59 TYR cc_start: 0.8148 (t80) cc_final: 0.7906 (t80) REVERT: C 64 GLN cc_start: 0.9198 (mm110) cc_final: 0.8922 (mm110) REVERT: C 69 GLU cc_start: 0.8304 (mt-10) cc_final: 0.7964 (pt0) REVERT: C 152 ASN cc_start: 0.9312 (m-40) cc_final: 0.8850 (m110) REVERT: C 164 GLN cc_start: 0.8988 (pm20) cc_final: 0.8441 (pm20) outliers start: 8 outliers final: 1 residues processed: 86 average time/residue: 0.5169 time to fit residues: 47.2983 Evaluate side-chains 76 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 75 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: [10, 48, 52, 69, 63, 47, 75, 92, 35, 89, 13] chunk 10 optimal weight: 5.9990 chunk 48 optimal weight: 0.4980 chunk 52 optimal weight: 0.6980 chunk 69 optimal weight: 0.9990 chunk 63 optimal weight: 4.9990 chunk 47 optimal weight: 0.7980 chunk 75 optimal weight: 0.0270 chunk 92 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 89 optimal weight: 0.4980 chunk 13 optimal weight: 0.9980 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.104835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.069318 restraints weight = 14791.803| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 3.25 r_work: 0.2836 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 7947 Z= 0.104 Angle : 0.520 7.407 10836 Z= 0.271 Chirality : 0.047 0.196 1218 Planarity : 0.004 0.041 1338 Dihedral : 9.014 84.973 1272 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.85 % Allowed : 11.23 % Favored : 87.92 % 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: 0.49 (0.36), residues: 198 sheet: 0.80 (0.27), residues: 354 loop : -0.86 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 218 TYR 0.016 0.001 TYR B 59 PHE 0.013 0.001 PHE A 252 TRP 0.005 0.001 TRP B 93 HIS 0.006 0.001 HIS A 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.10 ( 7926) covalent geometry : angle 0.51728 / 0.27 (10788) SS BOND : bond 0.00198 / 0.13 ( 15) SS BOND : angle 0.64120 / 0.44 ( 30) hydrogen bonds : bond 0.03554 / 2.35 ( 196) hydrogen bonds : angle 4.33023 / 3.02 ( 507) link_NAG-ASN : bond 0.00310 / 0.19 ( 6) link_NAG-ASN : angle 1.36548 / 0.92 ( 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 : 0.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 LYS cc_start: 0.9132 (mttm) cc_final: 0.8773 (mtpp) REVERT: A 164 GLN cc_start: 0.8926 (pm20) cc_final: 0.8722 (pm20) REVERT: B 69 GLU cc_start: 0.8278 (mt-10) cc_final: 0.7877 (pm20) REVERT: B 152 ASN cc_start: 0.9214 (m-40) cc_final: 0.8838 (m110) REVERT: B 164 GLN cc_start: 0.8973 (pm20) cc_final: 0.8715 (pm20) REVERT: C 59 TYR cc_start: 0.8161 (t80) cc_final: 0.7940 (t80) REVERT: C 64 GLN cc_start: 0.9227 (mm110) cc_final: 0.8998 (mm110) REVERT: C 69 GLU cc_start: 0.8306 (mt-10) cc_final: 0.7949 (pt0) REVERT: C 152 ASN cc_start: 0.9297 (m-40) cc_final: 0.8834 (m110) REVERT: C 164 GLN cc_start: 0.8979 (pm20) cc_final: 0.8446 (pm20) REVERT: C 291 LYS cc_start: 0.8361 (mptt) cc_final: 0.8107 (mptt) outliers start: 7 outliers final: 3 residues processed: 87 average time/residue: 0.5345 time to fit residues: 49.3461 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 : 0.299 ------------------------------------------------------------------------------- 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: [64, 50, 28, 39, 90, 42, 20, 1, 48, 85, 21] chunk 64 optimal weight: 20.0000 chunk 50 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 48 optimal weight: 0.0370 chunk 85 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 overall best weight: 0.7660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 152 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.104267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.068680 restraints weight = 14762.956| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 3.26 r_work: 0.2824 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7947 Z= 0.133 Angle : 0.545 7.549 10836 Z= 0.284 Chirality : 0.047 0.195 1218 Planarity : 0.004 0.040 1338 Dihedral : 8.726 78.872 1272 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 2.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.85 % Allowed : 11.96 % Favored : 87.20 % 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: 0.24 (0.26), residues: 960 helix: 0.62 (0.36), residues: 198 sheet: 0.91 (0.27), residues: 354 loop : -0.70 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 218 TYR 0.015 0.001 TYR B 59 PHE 0.013 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/Z covalent geometry : bond 0.00322 / 0.13 ( 7926) covalent geometry : angle 0.54173 / 0.28 (10788) SS BOND : bond 0.00227 / 0.15 ( 15) SS BOND : angle 0.68536 / 0.46 ( 30) hydrogen bonds : bond 0.03700 / 2.48 ( 196) hydrogen bonds : angle 4.26428 / 2.97 ( 507) link_NAG-ASN : bond 0.00265 / 0.17 ( 6) link_NAG-ASN : angle 1.40732 / 0.93 ( 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 90 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 83 time to evaluate : 0.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 LYS cc_start: 0.9093 (mttm) cc_final: 0.8796 (mtpp) REVERT: A 164 GLN cc_start: 0.8891 (pm20) cc_final: 0.8685 (pm20) REVERT: A 230 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7559 (mp0) REVERT: B 69 GLU cc_start: 0.8297 (mt-10) cc_final: 0.7839 (pm20) REVERT: B 152 ASN cc_start: 0.9203 (m-40) cc_final: 0.8823 (m110) REVERT: B 164 GLN cc_start: 0.8996 (pm20) cc_final: 0.8330 (pm20) REVERT: B 230 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7696 (mp0) REVERT: B 258 LYS cc_start: 0.8862 (mppt) cc_final: 0.8570 (mppt) REVERT: C 59 TYR cc_start: 0.8204 (t80) cc_final: 0.7975 (t80) REVERT: C 64 GLN cc_start: 0.9235 (mm110) cc_final: 0.8999 (mm110) REVERT: C 69 GLU cc_start: 0.8297 (mt-10) cc_final: 0.7935 (pt0) REVERT: C 152 ASN cc_start: 0.9299 (m-40) cc_final: 0.8858 (m110) REVERT: C 164 GLN cc_start: 0.8953 (pm20) cc_final: 0.8444 (pm20) outliers start: 7 outliers final: 1 residues processed: 89 average time/residue: 0.5758 time to fit residues: 54.1445 Evaluate side-chains 85 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 82 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain B 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: [50, 42, 52, 87, 46, 31, 20, 63, 9, 34, 54] chunk 50 optimal weight: 0.0870 chunk 42 optimal weight: 2.9990 chunk 52 optimal weight: 0.4980 chunk 87 optimal weight: 0.9990 chunk 46 optimal weight: 0.0270 chunk 31 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 overall best weight: 0.5216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.105027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.069594 restraints weight = 14819.859| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 3.26 r_work: 0.2844 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7947 Z= 0.107 Angle : 0.536 7.779 10836 Z= 0.278 Chirality : 0.047 0.194 1218 Planarity : 0.004 0.040 1338 Dihedral : 8.418 72.477 1272 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.97 % Allowed : 12.44 % Favored : 86.59 % 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: 0.46 (0.27), residues: 960 helix: 0.77 (0.36), residues: 198 sheet: 1.07 (0.27), residues: 351 loop : -0.57 (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 B 59 PHE 0.013 0.001 PHE C 252 TRP 0.005 0.001 TRP C 268 HIS 0.005 0.001 HIS A 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 ( 7926) covalent geometry : angle 0.53312 / 0.28 (10788) SS BOND : bond 0.00198 / 0.13 ( 15) SS BOND : angle 0.61864 / 0.42 ( 30) hydrogen bonds : bond 0.03333 / 2.23 ( 196) hydrogen bonds : angle 4.20924 / 2.96 ( 507) link_NAG-ASN : bond 0.00318 / 0.20 ( 6) link_NAG-ASN : angle 1.34852 / 0.92 ( 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 230 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7594 (mp0) REVERT: B 69 GLU cc_start: 0.8303 (mt-10) cc_final: 0.7942 (pt0) REVERT: B 152 ASN cc_start: 0.9220 (m-40) cc_final: 0.8834 (m110) REVERT: B 164 GLN cc_start: 0.8926 (pm20) cc_final: 0.8335 (pm20) REVERT: B 230 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7850 (mp0) REVERT: C 59 TYR cc_start: 0.8256 (t80) cc_final: 0.7968 (t80) REVERT: C 64 GLN cc_start: 0.9250 (mm110) cc_final: 0.9002 (mm110) REVERT: C 69 GLU cc_start: 0.8314 (mt-10) cc_final: 0.7977 (pt0) REVERT: C 152 ASN cc_start: 0.9280 (m-40) cc_final: 0.8792 (m110) REVERT: C 164 GLN cc_start: 0.8944 (pm20) cc_final: 0.8441 (pm20) REVERT: C 230 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7829 (mp0) outliers start: 8 outliers final: 2 residues processed: 90 average time/residue: 0.6009 time to fit residues: 57.2052 Evaluate side-chains 89 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 84 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain B residue 230 GLU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: [44, 32, 40, 83, 45, 20, 54, 17, 64, 38, 84] chunk 44 optimal weight: 0.5980 chunk 32 optimal weight: 20.0000 chunk 40 optimal weight: 0.3980 chunk 83 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 54 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 64 optimal weight: 20.0000 chunk 38 optimal weight: 0.9980 chunk 84 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 152 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.104712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.069340 restraints weight = 14719.857| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 3.24 r_work: 0.2836 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7947 Z= 0.121 Angle : 0.589 17.849 10836 Z= 0.295 Chirality : 0.047 0.193 1218 Planarity : 0.004 0.040 1338 Dihedral : 8.360 69.673 1272 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.33 % Allowed : 12.92 % Favored : 85.75 % 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: 0.53 (0.26), residues: 960 helix: 0.73 (0.36), residues: 198 sheet: 1.10 (0.27), residues: 351 loop : -0.44 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 218 TYR 0.014 0.001 TYR B 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/Z covalent geometry : bond 0.00296 / 0.12 ( 7926) covalent geometry : angle 0.58683 / 0.29 (10788) SS BOND : bond 0.00205 / 0.14 ( 15) SS BOND : angle 0.62973 / 0.43 ( 30) hydrogen bonds : bond 0.03430 / 2.29 ( 196) hydrogen bonds : angle 4.24837 / 3.00 ( 507) link_NAG-ASN : bond 0.00281 / 0.18 ( 6) link_NAG-ASN : angle 1.33784 / 0.90 ( 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 94 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 83 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7598 (mp0) REVERT: B 69 GLU cc_start: 0.8305 (mt-10) cc_final: 0.7948 (pt0) REVERT: B 152 ASN cc_start: 0.9201 (m-40) cc_final: 0.8789 (m110) REVERT: B 164 GLN cc_start: 0.8911 (pm20) cc_final: 0.8365 (pm20) REVERT: B 230 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7853 (mp0) REVERT: C 59 TYR cc_start: 0.8283 (t80) cc_final: 0.8003 (t80) REVERT: C 64 GLN cc_start: 0.9247 (mm110) cc_final: 0.8992 (mm110) REVERT: C 69 GLU cc_start: 0.8315 (mt-10) cc_final: 0.7972 (pt0) REVERT: C 152 ASN cc_start: 0.9264 (m-40) cc_final: 0.8774 (m110) REVERT: C 164 GLN cc_start: 0.8943 (pm20) cc_final: 0.8437 (pm20) REVERT: C 230 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7787 (mp0) outliers start: 11 outliers final: 2 residues processed: 90 average time/residue: 0.5619 time to fit residues: 53.5353 Evaluate side-chains 88 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 83 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain B residue 230 GLU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: [78, 11, 33, 29, 64, 67, 51, 3, 81, 69, 5] chunk 78 optimal weight: 0.9990 chunk 11 optimal weight: 0.0670 chunk 33 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 64 optimal weight: 20.0000 chunk 67 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 overall best weight: 1.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 152 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.103624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.067777 restraints weight = 14837.897| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 3.28 r_work: 0.2799 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 7947 Z= 0.164 Angle : 0.622 15.503 10836 Z= 0.314 Chirality : 0.049 0.249 1218 Planarity : 0.004 0.040 1338 Dihedral : 8.467 67.432 1272 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.85 % Allowed : 13.65 % Favored : 85.51 % 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: 0.41 (0.26), residues: 960 helix: 0.36 (0.35), residues: 216 sheet: 1.07 (0.27), residues: 351 loop : -0.45 (0.30), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 302 TYR 0.017 0.001 TYR A 59 PHE 0.014 0.001 PHE A 252 TRP 0.007 0.001 TRP C 268 HIS 0.005 0.001 HIS A 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.16 ( 7926) covalent geometry : angle 0.61754 / 0.31 (10788) SS BOND : bond 0.00251 / 0.17 ( 15) SS BOND : angle 0.75012 / 0.50 ( 30) hydrogen bonds : bond 0.03687 / 2.45 ( 196) hydrogen bonds : angle 4.27391 / 3.01 ( 507) link_NAG-ASN : bond 0.00336 / 0.19 ( 6) link_NAG-ASN : angle 1.80264 / 1.11 ( 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 91 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 84 time to evaluate : 0.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 69 GLU cc_start: 0.8288 (mt-10) cc_final: 0.7922 (pt0) REVERT: B 152 ASN cc_start: 0.9230 (m-40) cc_final: 0.8827 (m110) REVERT: B 164 GLN cc_start: 0.8918 (pm20) cc_final: 0.8389 (pm20) REVERT: B 258 LYS cc_start: 0.8893 (OUTLIER) cc_final: 0.8605 (mppt) REVERT: C 59 TYR cc_start: 0.8298 (t80) cc_final: 0.7996 (t80) REVERT: C 64 GLN cc_start: 0.9220 (mm110) cc_final: 0.8978 (mm110) REVERT: C 69 GLU cc_start: 0.8321 (mt-10) cc_final: 0.7953 (pt0) REVERT: C 152 ASN cc_start: 0.9281 (m-40) cc_final: 0.8807 (m110) REVERT: C 164 GLN cc_start: 0.8935 (pm20) cc_final: 0.8432 (pm20) REVERT: C 230 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7826 (mp0) outliers start: 7 outliers final: 2 residues processed: 88 average time/residue: 0.5782 time to fit residues: 53.6632 Evaluate side-chains 88 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 84 time to evaluate : 0.277 ------------------------------------------------------------------------------- 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 230 GLU 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: [44, 2, 78, 66, 64, 81, 37, 54, 12, 58, 90] chunk 44 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 78 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 64 optimal weight: 20.0000 chunk 81 optimal weight: 0.9980 chunk 37 optimal weight: 0.0270 chunk 54 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 overall best weight: 0.9640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 152 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.103581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.067989 restraints weight = 14745.699| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 3.25 r_work: 0.2799 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 7947 Z= 0.161 Angle : 0.670 17.787 10836 Z= 0.330 Chirality : 0.050 0.322 1218 Planarity : 0.004 0.040 1338 Dihedral : 8.498 65.151 1272 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.97 % Allowed : 13.89 % Favored : 85.14 % 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: 0.41 (0.26), residues: 960 helix: 0.27 (0.35), residues: 216 sheet: 1.09 (0.27), residues: 351 loop : -0.40 (0.30), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 302 TYR 0.017 0.001 TYR B 59 PHE 0.014 0.001 PHE A 252 TRP 0.007 0.001 TRP C 268 HIS 0.005 0.001 HIS A 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.16 ( 7926) covalent geometry : angle 0.66525 / 0.33 (10788) SS BOND : bond 0.00248 / 0.17 ( 15) SS BOND : angle 0.75100 / 0.50 ( 30) hydrogen bonds : bond 0.03732 / 2.46 ( 196) hydrogen bonds : angle 4.30220 / 3.03 ( 507) link_NAG-ASN : bond 0.00382 / 0.22 ( 6) link_NAG-ASN : angle 1.96067 / 1.26 ( 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 90 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 82 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 69 GLU cc_start: 0.8288 (mt-10) cc_final: 0.7924 (pt0) REVERT: B 152 ASN cc_start: 0.9219 (m-40) cc_final: 0.8825 (m110) REVERT: B 164 GLN cc_start: 0.8915 (pm20) cc_final: 0.8387 (pm20) REVERT: B 258 LYS cc_start: 0.8885 (OUTLIER) cc_final: 0.8610 (mppt) REVERT: C 59 TYR cc_start: 0.8308 (t80) cc_final: 0.7992 (t80) REVERT: C 64 GLN cc_start: 0.9235 (mm110) cc_final: 0.8988 (mm110) REVERT: C 69 GLU cc_start: 0.8315 (mt-10) cc_final: 0.7944 (pt0) REVERT: C 152 ASN cc_start: 0.9276 (m-40) cc_final: 0.8800 (m110) REVERT: C 164 GLN cc_start: 0.8933 (pm20) cc_final: 0.8432 (pm20) outliers start: 8 outliers final: 3 residues processed: 86 average time/residue: 0.5697 time to fit residues: 51.7839 Evaluate side-chains 85 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 81 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain C residue 49 GLN Chi-restraints excluded: chain C residue 60 VAL 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: [80, 45, 85, 19, 21, 88, 35, 76, 38, 14, 70] chunk 80 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 chunk 85 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 88 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 76 optimal weight: 0.5980 chunk 38 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.104051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.068595 restraints weight = 14639.949| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 3.24 r_work: 0.2811 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7947 Z= 0.141 Angle : 0.688 17.354 10836 Z= 0.332 Chirality : 0.049 0.202 1218 Planarity : 0.004 0.040 1338 Dihedral : 8.432 63.287 1272 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 2.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % 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: 0.42 (0.26), residues: 960 helix: 0.23 (0.34), residues: 216 sheet: 1.11 (0.27), residues: 351 loop : -0.37 (0.30), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 46 TYR 0.023 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/Z covalent geometry : bond 0.00348 / 0.14 ( 7926) covalent geometry : angle 0.68508 / 0.33 (10788) SS BOND : bond 0.00221 / 0.15 ( 15) SS BOND : angle 0.69408 / 0.46 ( 30) hydrogen bonds : bond 0.03614 / 2.39 ( 196) hydrogen bonds : angle 4.31957 / 3.04 ( 507) link_NAG-ASN : bond 0.00379 / 0.22 ( 6) link_NAG-ASN : angle 1.64045 / 1.17 ( 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 : 0.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 GLN cc_start: 0.9217 (mm110) cc_final: 0.8801 (mp10) REVERT: B 69 GLU cc_start: 0.8289 (mt-10) cc_final: 0.7959 (pt0) REVERT: B 152 ASN cc_start: 0.9209 (m-40) cc_final: 0.8815 (m110) REVERT: B 164 GLN cc_start: 0.8906 (pm20) cc_final: 0.8380 (pm20) REVERT: C 59 TYR cc_start: 0.8316 (t80) cc_final: 0.8028 (t80) REVERT: C 64 GLN cc_start: 0.9258 (mm110) cc_final: 0.8998 (mm110) REVERT: C 69 GLU cc_start: 0.8340 (mt-10) cc_final: 0.7984 (pt0) REVERT: C 152 ASN cc_start: 0.9263 (m-40) cc_final: 0.8773 (m110) REVERT: C 164 GLN cc_start: 0.8930 (pm20) cc_final: 0.8611 (pm20) outliers start: 6 outliers final: 2 residues processed: 84 average time/residue: 0.6020 time to fit residues: 53.3424 Evaluate side-chains 83 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 81 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 49 GLN 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: [15, 76, 58, 60, 42, 52, 5, 49, 11, 73, 23] chunk 15 optimal weight: 0.7980 chunk 76 optimal weight: 0.7980 chunk 58 optimal weight: 0.6980 chunk 60 optimal weight: 2.9990 chunk 42 optimal weight: 0.0970 chunk 52 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 73 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 152 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.104503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.068971 restraints weight = 14587.011| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 3.25 r_work: 0.2827 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 7947 Z= 0.129 Angle : 0.689 18.039 10836 Z= 0.332 Chirality : 0.048 0.192 1218 Planarity : 0.004 0.040 1338 Dihedral : 8.332 60.843 1272 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.24 % Allowed : 14.37 % 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: 0.45 (0.26), residues: 960 helix: 0.21 (0.34), residues: 216 sheet: 1.15 (0.27), residues: 351 loop : -0.34 (0.30), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 130 TYR 0.026 0.001 TYR B 59 PHE 0.015 0.001 PHE A 252 TRP 0.005 0.001 TRP C 268 HIS 0.005 0.001 HIS A 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.13 ( 7926) covalent geometry : angle 0.68603 / 0.33 (10788) SS BOND : bond 0.00209 / 0.14 ( 15) SS BOND : angle 0.64517 / 0.43 ( 30) hydrogen bonds : bond 0.03485 / 2.30 ( 196) hydrogen bonds : angle 4.36958 / 3.08 ( 507) link_NAG-ASN : bond 0.00324 / 0.19 ( 6) link_NAG-ASN : angle 1.84394 / 1.38 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2913.31 seconds wall clock time: 50 minutes 31.83 seconds (3031.83 seconds total)