Starting phenix.real_space_refine on Sun Apr 5 04:05:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9uwx_64567/04_2026/9uwx_64567.cif Found real_map, /net/cci-nas-00/data/ceres_data/9uwx_64567/04_2026/9uwx_64567.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9uwx_64567/04_2026/9uwx_64567.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9uwx_64567/04_2026/9uwx_64567.map" model { file = "/net/cci-nas-00/data/ceres_data/9uwx_64567/04_2026/9uwx_64567.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9uwx_64567/04_2026/9uwx_64567.cif" } resolution = 2.41 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= 0.025 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 5034 2.51 5 N 1299 2.21 5 O 1479 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 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: 7860 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2561 Classifications: {'peptide': 327} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 311} Chain: "C" Number of atoms: 2561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2561 Classifications: {'peptide': 327} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 311} 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: 2.27, per 1000 atoms: 0.29 Number of scatterers: 7860 At special positions: 0 Unit cell: (92.15, 87.4, 123.5, 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 1479 8.00 N 1299 7.00 C 5034 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B 236 " - pdb=" SG CYS B 226 " distance=2.03 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=2.03 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: 0.60 Conformation dependent library (CDL) restraints added in 242.0 milliseconds 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1794 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 9 sheets defined 28.2% alpha, 25.1% 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 40 through 60 Processing helix chain 'A' and resid 94 through 98 removed outlier: 3.670A 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 Processing helix chain 'A' and resid 191 through 194 Processing helix chain 'A' and resid 221 through 225 removed outlier: 3.622A pdb=" N LYS A 224 " --> pdb=" O GLY A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 249 Processing helix chain 'A' and resid 251 through 259 Processing helix chain 'A' and resid 275 through 279 removed outlier: 3.816A pdb=" N CYS A 279 " --> pdb=" O ALA A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 357 removed outlier: 3.545A pdb=" N THR A 341 " --> pdb=" O SER A 337 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLY A 355 " --> pdb=" O SER A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 366 Processing helix chain 'B' and resid 41 through 60 Processing helix chain 'B' and resid 94 through 98 removed outlier: 3.670A 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 Processing helix chain 'B' and resid 191 through 194 Processing helix chain 'B' and resid 221 through 225 removed outlier: 3.621A pdb=" N LYS B 224 " --> pdb=" O GLY B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 249 Processing helix chain 'B' and resid 251 through 259 Processing helix chain 'B' and resid 275 through 279 removed outlier: 3.816A pdb=" N CYS B 279 " --> pdb=" O ALA B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 357 removed outlier: 3.546A pdb=" N THR B 341 " --> pdb=" O SER B 337 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLY B 355 " --> pdb=" O SER B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 366 Processing helix chain 'C' and resid 41 through 60 Processing helix chain 'C' and resid 94 through 98 removed outlier: 3.670A 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 Processing helix chain 'C' and resid 191 through 194 Processing helix chain 'C' and resid 221 through 225 removed outlier: 3.622A pdb=" N LYS C 224 " --> pdb=" O GLY C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 249 Processing helix chain 'C' and resid 251 through 259 Processing helix chain 'C' and resid 275 through 279 removed outlier: 3.816A pdb=" N CYS C 279 " --> pdb=" O ALA C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 357 removed outlier: 3.546A pdb=" N THR C 341 " --> pdb=" O SER C 337 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLY C 355 " --> pdb=" O SER C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 366 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 87 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 87 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 87 202 hydrogen bonds defined for protein. 525 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: 1.04 Time building geometry restraints manager: 0.77 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: 2442 1.34 - 1.46: 2029 1.46 - 1.58: 3533 1.58 - 1.70: 15 1.70 - 1.82: 45 Bond restraints: 8064 Sorted by residual: bond pdb=" C4 ATP B 503 " pdb=" C5 ATP B 503 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 5.86e+01 bond pdb=" C4 ATP A 503 " pdb=" C5 ATP A 503 " ideal model delta sigma weight residual 1.388 1.464 -0.076 1.00e-02 1.00e+04 5.82e+01 bond pdb=" C4 ATP C 501 " pdb=" C5 ATP C 501 " ideal model delta sigma weight residual 1.388 1.464 -0.076 1.00e-02 1.00e+04 5.79e+01 bond pdb=" C5 ATP A 503 " pdb=" C6 ATP A 503 " ideal model delta sigma weight residual 1.409 1.477 -0.068 1.00e-02 1.00e+04 4.59e+01 bond pdb=" C5 ATP C 501 " pdb=" C6 ATP C 501 " ideal model delta sigma weight residual 1.409 1.476 -0.067 1.00e-02 1.00e+04 4.50e+01 ... (remaining 8059 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.42: 10896 3.42 - 6.83: 60 6.83 - 10.25: 12 10.25 - 13.66: 0 13.66 - 17.08: 6 Bond angle restraints: 10974 Sorted by residual: angle pdb=" PB ATP C 501 " pdb=" O3B ATP C 501 " pdb=" PG ATP C 501 " ideal model delta sigma weight residual 139.87 122.79 17.08 1.00e+00 1.00e+00 2.92e+02 angle pdb=" PB ATP B 503 " pdb=" O3B ATP B 503 " pdb=" PG ATP B 503 " ideal model delta sigma weight residual 139.87 122.80 17.07 1.00e+00 1.00e+00 2.91e+02 angle pdb=" PB ATP A 503 " pdb=" O3B ATP A 503 " pdb=" PG ATP A 503 " ideal model delta sigma weight residual 139.87 122.81 17.06 1.00e+00 1.00e+00 2.91e+02 angle pdb=" PA ATP C 501 " pdb=" O3A ATP C 501 " pdb=" PB ATP C 501 " ideal model delta sigma weight residual 136.83 122.56 14.27 1.00e+00 1.00e+00 2.04e+02 angle pdb=" PA ATP B 503 " pdb=" O3A ATP B 503 " pdb=" PB ATP B 503 " ideal model delta sigma weight residual 136.83 122.58 14.25 1.00e+00 1.00e+00 2.03e+02 ... (remaining 10969 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 4449 17.65 - 35.30: 360 35.30 - 52.95: 65 52.95 - 70.60: 6 70.60 - 88.25: 8 Dihedral angle restraints: 4888 sinusoidal: 2071 harmonic: 2817 Sorted by residual: dihedral pdb=" CB CYS B 136 " pdb=" SG CYS B 136 " pdb=" SG CYS B 159 " pdb=" CB CYS B 159 " ideal model delta sinusoidal sigma weight residual -86.00 -170.94 84.94 1 1.00e+01 1.00e-02 8.75e+01 dihedral pdb=" CB CYS A 136 " pdb=" SG CYS A 136 " pdb=" SG CYS A 159 " pdb=" CB CYS A 159 " ideal model delta sinusoidal sigma weight residual -86.00 -170.91 84.91 1 1.00e+01 1.00e-02 8.75e+01 dihedral pdb=" CB CYS B 226 " pdb=" SG CYS B 226 " pdb=" SG CYS B 226 " pdb=" CB CYS B 226 " ideal model delta sinusoidal sigma weight residual 0.00 0.00 0.00 1 1.00e+01 1.00e-02 0.00e+00 ... (remaining 4885 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 811 0.043 - 0.086: 306 0.086 - 0.129: 118 0.129 - 0.172: 4 0.172 - 0.215: 3 Chirality restraints: 1242 Sorted by residual: chirality pdb=" C1 NAG C 503 " pdb=" ND2 ASN C 194 " pdb=" C2 NAG C 503 " pdb=" O5 NAG C 503 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" C1 NAG B 502 " pdb=" ND2 ASN B 194 " pdb=" C2 NAG B 502 " pdb=" O5 NAG B 502 " both_signs ideal model delta sigma weight residual False -2.40 -2.19 -0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" C1 NAG A 502 " pdb=" ND2 ASN A 194 " pdb=" C2 NAG A 502 " pdb=" O5 NAG A 502 " both_signs ideal model delta sigma weight residual False -2.40 -2.19 -0.21 2.00e-01 2.50e+01 1.14e+00 ... (remaining 1239 not shown) Planarity restraints: 1365 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS B 125 " -0.021 5.00e-02 4.00e+02 3.18e-02 1.62e+00 pdb=" N PRO B 126 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO B 126 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 126 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS A 125 " -0.021 5.00e-02 4.00e+02 3.16e-02 1.60e+00 pdb=" N PRO A 126 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO A 126 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 126 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS C 125 " 0.021 5.00e-02 4.00e+02 3.16e-02 1.60e+00 pdb=" N PRO C 126 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO C 126 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 126 " 0.018 5.00e-02 4.00e+02 ... (remaining 1362 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 59 2.60 - 3.18: 6466 3.18 - 3.75: 11025 3.75 - 4.33: 16221 4.33 - 4.90: 27049 Nonbonded interactions: 60820 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 226 " pdb=" SG CYS C 236 " model vdw 2.030 3.760 nonbonded pdb=" SG CYS C 270 " pdb=" SG CYS C 279 " model vdw 2.030 3.760 nonbonded pdb=" SG CYS C 136 " pdb=" SG CYS C 159 " model vdw 2.031 3.760 nonbonded pdb=" SG CYS C 142 " pdb=" SG CYS C 170 " model vdw 2.033 3.760 ... (remaining 60815 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 40 through 366 or resid 502)) selection = (chain 'B' and (resid 40 through 366 or resid 502)) selection = (chain 'C' and (resid 40 through 366 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: 3.110 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: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 8.600 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:6.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 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 : 0.006 0.077 8080 Z= 0.352 Angle : 0.814 17.077 11023 Z= 0.581 Chirality : 0.050 0.215 1242 Planarity : 0.004 0.032 1359 Dihedral : 13.312 88.248 3042 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % 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: -1.37 (0.24), residues: 975 helix: -1.62 (0.29), residues: 207 sheet: 0.53 (0.27), residues: 342 loop : -1.72 (0.26), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 286 TYR 0.009 0.001 TYR C 321 PHE 0.011 0.001 PHE B 303 TRP 0.013 0.001 TRP A 268 HIS 0.005 0.001 HIS A 118 Details of bonding type rmsd covalent geometry : bond 0.00570 ( 8064) covalent geometry : angle 0.81060 (10974) SS BOND : bond 0.00233 ( 10) SS BOND : angle 0.74386 ( 31) hydrogen bonds : bond 0.17502 ( 202) hydrogen bonds : angle 7.85664 ( 525) link_NAG-ASN : bond 0.00417 ( 6) link_NAG-ASN : angle 2.11092 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.288 Fit side-chains REVERT: A 64 GLN cc_start: 0.8489 (mp10) cc_final: 0.8278 (mp10) REVERT: A 332 GLN cc_start: 0.8590 (tt0) cc_final: 0.8373 (tt0) REVERT: C 64 GLN cc_start: 0.8503 (mp10) cc_final: 0.8252 (mp10) outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.5381 time to fit residues: 54.3267 Evaluate side-chains 70 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.284 ------------------------------------------------------------------------------- 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: 1.9990 chunk 53 optimal weight: 0.0020 chunk 5 optimal weight: 0.1980 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 0.2980 overall best weight: 0.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 ASN A 344 ASN B 201 ASN B 344 ASN C 201 ASN C 310 ASN C 344 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.100013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.069130 restraints weight = 14803.188| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 2.88 r_work: 0.2895 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 moved from start: 0.1348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8080 Z= 0.116 Angle : 0.560 7.390 11023 Z= 0.292 Chirality : 0.048 0.206 1242 Planarity : 0.004 0.030 1359 Dihedral : 10.042 82.159 1290 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.07 % Allowed : 7.47 % Favored : 91.46 % 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: -0.18 (0.26), residues: 975 helix: 0.33 (0.35), residues: 210 sheet: 0.83 (0.27), residues: 354 loop : -1.21 (0.28), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 130 TYR 0.011 0.001 TYR C 222 PHE 0.009 0.001 PHE A 243 TRP 0.007 0.001 TRP A 268 HIS 0.003 0.001 HIS A 90 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 8064) covalent geometry : angle 0.55393 (10974) SS BOND : bond 0.00211 ( 10) SS BOND : angle 0.55160 ( 31) hydrogen bonds : bond 0.04770 ( 202) hydrogen bonds : angle 5.66790 ( 525) link_NAG-ASN : bond 0.00579 ( 6) link_NAG-ASN : angle 2.06840 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 70 time to evaluate : 0.296 Fit side-chains REVERT: A 64 GLN cc_start: 0.8924 (mp10) cc_final: 0.8619 (mp10) REVERT: C 64 GLN cc_start: 0.9002 (mp10) cc_final: 0.8663 (mp10) outliers start: 9 outliers final: 3 residues processed: 73 average time/residue: 0.4316 time to fit residues: 34.0537 Evaluate side-chains 69 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 66 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 CYS Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain B residue 270 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 63 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 64 optimal weight: 20.0000 chunk 31 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.097494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.066662 restraints weight = 14736.778| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 2.81 r_work: 0.2861 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2753 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8786 moved from start: 0.1431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 8080 Z= 0.199 Angle : 0.605 7.328 11023 Z= 0.319 Chirality : 0.051 0.241 1242 Planarity : 0.004 0.033 1359 Dihedral : 9.905 80.267 1290 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 1.90 % Allowed : 8.54 % Favored : 89.56 % 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: 0.05 (0.26), residues: 975 helix: 0.60 (0.35), residues: 210 sheet: 0.90 (0.27), residues: 345 loop : -0.99 (0.28), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 130 TYR 0.012 0.002 TYR A 222 PHE 0.010 0.001 PHE A 243 TRP 0.010 0.001 TRP A 268 HIS 0.005 0.001 HIS A 118 Details of bonding type rmsd covalent geometry : bond 0.00475 ( 8064) covalent geometry : angle 0.59840 (10974) SS BOND : bond 0.00385 ( 10) SS BOND : angle 0.63693 ( 31) hydrogen bonds : bond 0.04807 ( 202) hydrogen bonds : angle 5.49002 ( 525) link_NAG-ASN : bond 0.00515 ( 6) link_NAG-ASN : angle 2.26528 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 69 time to evaluate : 0.292 Fit side-chains revert: symmetry clash REVERT: A 64 GLN cc_start: 0.8862 (OUTLIER) cc_final: 0.8558 (mp10) REVERT: C 64 GLN cc_start: 0.8973 (OUTLIER) cc_final: 0.8614 (mp10) outliers start: 16 outliers final: 7 residues processed: 76 average time/residue: 0.4771 time to fit residues: 38.9682 Evaluate side-chains 73 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 64 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 GLN Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 270 CYS Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 270 CYS Chi-restraints excluded: chain C residue 64 GLN Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 352 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 59 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 76 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.098112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.067436 restraints weight = 14955.232| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 2.81 r_work: 0.2875 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2766 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8080 Z= 0.158 Angle : 0.564 7.927 11023 Z= 0.298 Chirality : 0.049 0.224 1242 Planarity : 0.004 0.032 1359 Dihedral : 9.562 77.813 1290 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.02 % Allowed : 9.73 % Favored : 88.26 % 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: 0.17 (0.26), residues: 975 helix: 0.60 (0.34), residues: 210 sheet: 1.01 (0.26), residues: 354 loop : -0.92 (0.29), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 130 TYR 0.010 0.001 TYR C 222 PHE 0.009 0.001 PHE A 243 TRP 0.009 0.001 TRP A 268 HIS 0.004 0.001 HIS B 118 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 8064) covalent geometry : angle 0.55801 (10974) SS BOND : bond 0.00312 ( 10) SS BOND : angle 0.52227 ( 31) hydrogen bonds : bond 0.04389 ( 202) hydrogen bonds : angle 5.25932 ( 525) link_NAG-ASN : bond 0.00520 ( 6) link_NAG-ASN : angle 2.05171 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 67 time to evaluate : 0.238 Fit side-chains revert: symmetry clash REVERT: A 64 GLN cc_start: 0.8876 (OUTLIER) cc_final: 0.8535 (mp10) REVERT: A 89 GLU cc_start: 0.8089 (mt-10) cc_final: 0.7770 (pp20) REVERT: C 64 GLN cc_start: 0.9010 (OUTLIER) cc_final: 0.8587 (mp10) outliers start: 17 outliers final: 4 residues processed: 71 average time/residue: 0.4888 time to fit residues: 37.2799 Evaluate side-chains 71 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 65 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 GLN Chi-restraints excluded: chain A residue 270 CYS Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain B residue 270 CYS Chi-restraints excluded: chain C residue 64 GLN Chi-restraints excluded: chain C residue 196 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 15 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 85 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 32 optimal weight: 20.0000 chunk 86 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 chunk 95 optimal weight: 5.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.096998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.066293 restraints weight = 14981.254| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 2.81 r_work: 0.2852 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2746 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8817 moved from start: 0.1635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 8080 Z= 0.209 Angle : 0.591 7.254 11023 Z= 0.316 Chirality : 0.051 0.245 1242 Planarity : 0.004 0.032 1359 Dihedral : 9.861 79.968 1290 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.14 % Allowed : 10.44 % Favored : 87.43 % 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: 0.16 (0.25), residues: 975 helix: 0.48 (0.34), residues: 210 sheet: 0.96 (0.26), residues: 345 loop : -0.78 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 130 TYR 0.012 0.002 TYR A 222 PHE 0.009 0.001 PHE A 243 TRP 0.011 0.001 TRP A 268 HIS 0.005 0.001 HIS A 118 Details of bonding type rmsd covalent geometry : bond 0.00501 ( 8064) covalent geometry : angle 0.58442 (10974) SS BOND : bond 0.00391 ( 10) SS BOND : angle 0.63823 ( 31) hydrogen bonds : bond 0.04606 ( 202) hydrogen bonds : angle 5.35053 ( 525) link_NAG-ASN : bond 0.00471 ( 6) link_NAG-ASN : angle 2.21227 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 66 time to evaluate : 0.301 Fit side-chains REVERT: A 89 GLU cc_start: 0.8089 (mt-10) cc_final: 0.7776 (pp20) REVERT: A 246 GLU cc_start: 0.9008 (tm-30) cc_final: 0.8718 (tp30) REVERT: B 64 GLN cc_start: 0.9014 (mp10) cc_final: 0.8525 (mp10) REVERT: B 89 GLU cc_start: 0.7344 (pm20) cc_final: 0.7120 (pm20) REVERT: C 64 GLN cc_start: 0.8973 (OUTLIER) cc_final: 0.8535 (mp10) outliers start: 18 outliers final: 11 residues processed: 75 average time/residue: 0.4650 time to fit residues: 37.6883 Evaluate side-chains 74 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 270 CYS Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 270 CYS Chi-restraints excluded: chain B residue 339 ILE Chi-restraints excluded: chain C residue 64 GLN Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 339 ILE Chi-restraints excluded: chain C residue 352 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 36 optimal weight: 2.9990 chunk 18 optimal weight: 0.0770 chunk 83 optimal weight: 0.9980 chunk 85 optimal weight: 0.6980 chunk 25 optimal weight: 7.9990 chunk 10 optimal weight: 0.0970 chunk 70 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 94 optimal weight: 0.9990 chunk 6 optimal weight: 0.1980 chunk 91 optimal weight: 0.7980 overall best weight: 0.3736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 186 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.099700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.069109 restraints weight = 14743.223| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 2.83 r_work: 0.2912 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8080 Z= 0.101 Angle : 0.534 8.095 11023 Z= 0.282 Chirality : 0.047 0.198 1242 Planarity : 0.004 0.028 1359 Dihedral : 8.911 78.646 1290 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.66 % Allowed : 11.86 % Favored : 86.48 % 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: 0.36 (0.26), residues: 975 helix: 0.56 (0.35), residues: 210 sheet: 1.21 (0.26), residues: 354 loop : -0.78 (0.29), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 130 TYR 0.008 0.001 TYR C 222 PHE 0.007 0.001 PHE A 243 TRP 0.006 0.001 TRP B 268 HIS 0.002 0.000 HIS B 118 Details of bonding type rmsd covalent geometry : bond 0.00215 ( 8064) covalent geometry : angle 0.53079 (10974) SS BOND : bond 0.00217 ( 10) SS BOND : angle 0.41277 ( 31) hydrogen bonds : bond 0.03703 ( 202) hydrogen bonds : angle 5.03600 ( 525) link_NAG-ASN : bond 0.00536 ( 6) link_NAG-ASN : angle 1.69538 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 68 time to evaluate : 0.293 Fit side-chains REVERT: A 89 GLU cc_start: 0.8061 (mt-10) cc_final: 0.7766 (pp20) REVERT: A 246 GLU cc_start: 0.9032 (tm-30) cc_final: 0.8772 (tp30) REVERT: B 64 GLN cc_start: 0.9117 (mp10) cc_final: 0.8647 (mp10) REVERT: C 64 GLN cc_start: 0.9041 (OUTLIER) cc_final: 0.8607 (mp10) outliers start: 14 outliers final: 6 residues processed: 76 average time/residue: 0.4697 time to fit residues: 38.4569 Evaluate side-chains 71 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 64 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 270 CYS Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 270 CYS Chi-restraints excluded: chain C residue 64 GLN Chi-restraints excluded: chain C residue 352 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 17 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 53 optimal weight: 0.5980 chunk 91 optimal weight: 1.9990 chunk 87 optimal weight: 0.5980 chunk 61 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 1 optimal weight: 4.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.097845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.067124 restraints weight = 14866.182| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 2.87 r_work: 0.2867 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2759 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8080 Z= 0.165 Angle : 0.584 8.028 11023 Z= 0.311 Chirality : 0.050 0.226 1242 Planarity : 0.004 0.029 1359 Dihedral : 9.414 77.158 1290 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.25 % Allowed : 11.63 % Favored : 86.12 % 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: 0.35 (0.26), residues: 975 helix: 0.54 (0.35), residues: 210 sheet: 1.16 (0.26), residues: 354 loop : -0.74 (0.29), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 130 TYR 0.010 0.001 TYR A 222 PHE 0.009 0.001 PHE A 243 TRP 0.009 0.001 TRP A 268 HIS 0.004 0.001 HIS A 118 Details of bonding type rmsd covalent geometry : bond 0.00391 ( 8064) covalent geometry : angle 0.57999 (10974) SS BOND : bond 0.00316 ( 10) SS BOND : angle 0.55337 ( 31) hydrogen bonds : bond 0.04103 ( 202) hydrogen bonds : angle 5.12913 ( 525) link_NAG-ASN : bond 0.00478 ( 6) link_NAG-ASN : angle 1.83971 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 66 time to evaluate : 0.370 Fit side-chains REVERT: A 89 GLU cc_start: 0.8082 (mt-10) cc_final: 0.7767 (pp20) REVERT: A 246 GLU cc_start: 0.9050 (tm-30) cc_final: 0.8716 (tp30) REVERT: B 64 GLN cc_start: 0.9117 (OUTLIER) cc_final: 0.8632 (mp10) REVERT: B 129 ILE cc_start: 0.9232 (OUTLIER) cc_final: 0.9005 (mm) REVERT: C 64 GLN cc_start: 0.8996 (OUTLIER) cc_final: 0.8557 (mp10) outliers start: 19 outliers final: 10 residues processed: 76 average time/residue: 0.4745 time to fit residues: 38.9342 Evaluate side-chains 77 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 270 CYS Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain B residue 64 GLN Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 270 CYS Chi-restraints excluded: chain B residue 339 ILE Chi-restraints excluded: chain C residue 64 GLN Chi-restraints excluded: chain C residue 90 HIS Chi-restraints excluded: chain C residue 352 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 66 optimal weight: 2.9990 chunk 38 optimal weight: 0.0980 chunk 63 optimal weight: 6.9990 chunk 80 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 53 optimal weight: 0.5980 chunk 6 optimal weight: 0.5980 chunk 21 optimal weight: 0.8980 chunk 0 optimal weight: 20.0000 chunk 34 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.098149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.067451 restraints weight = 14979.200| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 2.85 r_work: 0.2882 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2776 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8080 Z= 0.145 Angle : 0.603 9.454 11023 Z= 0.320 Chirality : 0.050 0.218 1242 Planarity : 0.004 0.029 1359 Dihedral : 9.335 76.561 1290 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.25 % Allowed : 11.39 % Favored : 86.36 % 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: 975 helix: 1.13 (0.36), residues: 186 sheet: 1.14 (0.26), residues: 354 loop : -0.89 (0.28), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 130 TYR 0.009 0.001 TYR A 45 PHE 0.008 0.001 PHE A 243 TRP 0.007 0.001 TRP A 268 HIS 0.003 0.001 HIS A 118 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 8064) covalent geometry : angle 0.59925 (10974) SS BOND : bond 0.00281 ( 10) SS BOND : angle 0.49546 ( 31) hydrogen bonds : bond 0.03980 ( 202) hydrogen bonds : angle 5.13709 ( 525) link_NAG-ASN : bond 0.00506 ( 6) link_NAG-ASN : angle 1.79484 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 62 time to evaluate : 0.315 Fit side-chains REVERT: A 89 GLU cc_start: 0.8082 (mt-10) cc_final: 0.7760 (pp20) REVERT: A 246 GLU cc_start: 0.9045 (tm-30) cc_final: 0.8712 (tp30) REVERT: B 64 GLN cc_start: 0.9111 (OUTLIER) cc_final: 0.8632 (mp10) REVERT: B 89 GLU cc_start: 0.7786 (pm20) cc_final: 0.7390 (pm20) REVERT: B 129 ILE cc_start: 0.9212 (OUTLIER) cc_final: 0.8987 (mm) REVERT: C 64 GLN cc_start: 0.8979 (OUTLIER) cc_final: 0.8529 (mp10) outliers start: 19 outliers final: 12 residues processed: 74 average time/residue: 0.4334 time to fit residues: 34.7488 Evaluate side-chains 75 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 60 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 270 CYS Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain B residue 64 GLN Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 270 CYS Chi-restraints excluded: chain B residue 339 ILE Chi-restraints excluded: chain C residue 64 GLN Chi-restraints excluded: chain C residue 90 HIS Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 352 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 59 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 chunk 89 optimal weight: 0.1980 chunk 17 optimal weight: 2.9990 chunk 95 optimal weight: 5.9990 chunk 69 optimal weight: 0.0170 chunk 19 optimal weight: 0.0970 chunk 16 optimal weight: 0.9990 chunk 84 optimal weight: 0.2980 chunk 56 optimal weight: 0.0570 chunk 13 optimal weight: 1.9990 overall best weight: 0.1334 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.101902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.071527 restraints weight = 14845.625| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 2.83 r_work: 0.2956 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 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 : 0.002 0.038 8080 Z= 0.101 Angle : 0.582 9.185 11023 Z= 0.302 Chirality : 0.047 0.187 1242 Planarity : 0.003 0.029 1359 Dihedral : 8.370 82.862 1290 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.42 % Allowed : 12.69 % Favored : 85.88 % 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: 0.54 (0.26), residues: 975 helix: 1.18 (0.37), residues: 186 sheet: 1.29 (0.26), residues: 354 loop : -0.81 (0.28), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 130 TYR 0.010 0.001 TYR A 45 PHE 0.007 0.001 PHE B 243 TRP 0.004 0.001 TRP B 268 HIS 0.001 0.000 HIS B 90 Details of bonding type rmsd covalent geometry : bond 0.00206 ( 8064) covalent geometry : angle 0.57936 (10974) SS BOND : bond 0.00182 ( 10) SS BOND : angle 0.36761 ( 31) hydrogen bonds : bond 0.03263 ( 202) hydrogen bonds : angle 4.91746 ( 525) link_NAG-ASN : bond 0.00561 ( 6) link_NAG-ASN : angle 1.50495 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 71 time to evaluate : 0.336 Fit side-chains REVERT: A 89 GLU cc_start: 0.8019 (mt-10) cc_final: 0.7737 (pp20) REVERT: A 246 GLU cc_start: 0.9034 (tm-30) cc_final: 0.8771 (tp30) REVERT: B 64 GLN cc_start: 0.9172 (OUTLIER) cc_final: 0.8643 (mp10) REVERT: C 64 GLN cc_start: 0.9092 (OUTLIER) cc_final: 0.8658 (mp10) outliers start: 12 outliers final: 5 residues processed: 75 average time/residue: 0.4944 time to fit residues: 39.7983 Evaluate side-chains 76 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 69 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 270 CYS Chi-restraints excluded: chain B residue 64 GLN Chi-restraints excluded: chain B residue 270 CYS Chi-restraints excluded: chain C residue 64 GLN Chi-restraints excluded: chain C residue 90 HIS Chi-restraints excluded: chain C residue 196 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 37 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 95 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 12 optimal weight: 0.0010 overall best weight: 0.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.098686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.068103 restraints weight = 14870.766| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 2.82 r_work: 0.2886 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2778 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8080 Z= 0.155 Angle : 0.629 9.436 11023 Z= 0.328 Chirality : 0.050 0.214 1242 Planarity : 0.004 0.046 1359 Dihedral : 9.048 74.825 1290 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.19 % Allowed : 13.52 % Favored : 85.29 % 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: 0.58 (0.26), residues: 975 helix: 1.25 (0.36), residues: 186 sheet: 1.24 (0.26), residues: 354 loop : -0.73 (0.28), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 130 TYR 0.010 0.001 TYR A 45 PHE 0.008 0.001 PHE A 243 TRP 0.008 0.001 TRP A 268 HIS 0.004 0.001 HIS A 118 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 8064) covalent geometry : angle 0.62617 (10974) SS BOND : bond 0.00284 ( 10) SS BOND : angle 0.49536 ( 31) hydrogen bonds : bond 0.03734 ( 202) hydrogen bonds : angle 4.97400 ( 525) link_NAG-ASN : bond 0.00460 ( 6) link_NAG-ASN : angle 1.57501 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 69 time to evaluate : 0.335 Fit side-chains REVERT: A 89 GLU cc_start: 0.8082 (mt-10) cc_final: 0.7760 (pp20) REVERT: A 246 GLU cc_start: 0.9054 (tm-30) cc_final: 0.8746 (tp30) REVERT: B 64 GLN cc_start: 0.9145 (OUTLIER) cc_final: 0.8662 (mp10) outliers start: 10 outliers final: 5 residues processed: 73 average time/residue: 0.5043 time to fit residues: 39.4851 Evaluate side-chains 72 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 66 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 270 CYS Chi-restraints excluded: chain B residue 64 GLN Chi-restraints excluded: chain B residue 270 CYS Chi-restraints excluded: chain C residue 90 HIS Chi-restraints excluded: chain C residue 196 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 66 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 44 optimal weight: 0.0870 chunk 29 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 57 optimal weight: 0.3980 chunk 15 optimal weight: 0.4980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 186 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.099642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.069161 restraints weight = 14762.888| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 2.81 r_work: 0.2905 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8080 Z= 0.117 Angle : 0.614 9.325 11023 Z= 0.318 Chirality : 0.049 0.204 1242 Planarity : 0.004 0.039 1359 Dihedral : 8.840 76.521 1290 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.95 % Allowed : 13.76 % Favored : 85.29 % 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: 0.72 (0.26), residues: 975 helix: 1.86 (0.37), residues: 168 sheet: 1.26 (0.26), residues: 354 loop : -0.71 (0.27), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 130 TYR 0.010 0.001 TYR A 45 PHE 0.007 0.001 PHE A 243 TRP 0.005 0.001 TRP A 268 HIS 0.002 0.000 HIS A 118 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 8064) covalent geometry : angle 0.61225 (10974) SS BOND : bond 0.00216 ( 10) SS BOND : angle 0.42586 ( 31) hydrogen bonds : bond 0.03551 ( 202) hydrogen bonds : angle 4.91228 ( 525) link_NAG-ASN : bond 0.00523 ( 6) link_NAG-ASN : angle 1.54758 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3990.63 seconds wall clock time: 68 minutes 27.36 seconds (4107.36 seconds total)