Starting phenix.real_space_refine on Thu Jul 2 08:26:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ztd_60458/07_2026/8ztd_60458.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ztd_60458/07_2026/8ztd_60458.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ztd_60458/07_2026/8ztd_60458.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ztd_60458/07_2026/8ztd_60458.map" model { file = "/net/cci-nas-00/data/ceres_data/8ztd_60458/07_2026/8ztd_60458.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ztd_60458/07_2026/8ztd_60458.cif" } resolution = 2.63 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.044 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: 7 Type Number sf(0) Gaussians Ca 2 9.91 5 P 9 5.49 5 Mg 3 5.21 5 S 45 5.16 5 C 5118 2.51 5 N 1359 2.21 5 O 1455 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7991 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2588 Classifications: {'peptide': 330} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 314} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 2588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2588 Classifications: {'peptide': 330} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 314} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 2588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2588 Classifications: {'peptide': 330} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 314} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 105 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {' MG': 1, 'ATP': 2, 'NAG': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 43 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {' MG': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 74 Unusual residues: {' MG': 1, 'ATP': 1, 'NAG': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 1.49, per 1000 atoms: 0.19 Number of scatterers: 7991 At special positions: 0 Unit cell: (86.14, 87.6, 118.26, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 2 19.99 S 45 16.00 P 9 15.00 Mg 3 11.99 O 1455 8.00 N 1359 7.00 C 5118 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=13, symmetry=0 Simple disulfide: pdb=" SG CYS A 117 " - pdb=" SG CYS A 165 " distance=2.02 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 149 " distance=2.03 Simple disulfide: pdb=" SG CYS A 132 " - pdb=" SG CYS A 159 " distance=2.03 Simple disulfide: pdb=" SG CYS A 217 " - pdb=" SG CYS A 227 " distance=2.03 Simple disulfide: pdb=" SG CYS A 261 " - pdb=" SG CYS A 270 " distance=2.03 Simple disulfide: pdb=" SG CYS B 117 " - pdb=" SG CYS B 165 " distance=2.03 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 149 " distance=2.03 Simple disulfide: pdb=" SG CYS B 132 " - pdb=" SG CYS B 159 " distance=2.03 Simple disulfide: pdb=" SG CYS B 217 " - pdb=" SG CYS B 227 " distance=2.03 Simple disulfide: pdb=" SG CYS C 117 " - pdb=" SG CYS C 165 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 149 " distance=2.03 Simple disulfide: pdb=" SG CYS C 132 " - pdb=" SG CYS C 159 " distance=2.03 Simple disulfide: pdb=" SG CYS C 217 " - pdb=" SG CYS C 227 " 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 402 " - " ASN A 210 " " NAG A 403 " - " ASN A 153 " " NAG A 404 " - " ASN A 184 " " NAG B 502 " - " ASN B 210 " " NAG B 503 " - " ASN B 153 " " NAG B 504 " - " ASN B 184 " " NAG C 403 " - " ASN C 210 " " NAG C 404 " - " ASN C 153 " " NAG C 405 " - " ASN C 184 " Time building additional restraints: 0.48 Conformation dependent library (CDL) restraints added in 337.4 milliseconds 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1776 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 12 sheets defined 27.4% alpha, 21.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 26 through 47 Processing helix chain 'A' and resid 86 through 91 Processing helix chain 'A' and resid 179 through 184 removed outlier: 3.924A pdb=" N ASN A 184 " --> pdb=" O GLU A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 240 Processing helix chain 'A' and resid 242 through 250 removed outlier: 3.641A pdb=" N LYS A 249 " --> pdb=" O SER A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 355 Processing helix chain 'B' and resid 27 through 51 removed outlier: 4.728A pdb=" N VAL B 48 " --> pdb=" O VAL B 44 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N PHE B 49 " --> pdb=" O ILE B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 91 Processing helix chain 'B' and resid 179 through 184 removed outlier: 3.903A pdb=" N ASN B 184 " --> pdb=" O GLU B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 216 removed outlier: 3.736A pdb=" N LYS B 215 " --> pdb=" O GLY B 211 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LYS B 216 " --> pdb=" O THR B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 240 removed outlier: 3.531A pdb=" N GLY B 240 " --> pdb=" O VAL B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 250 removed outlier: 3.908A pdb=" N LYS B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 270 Processing helix chain 'B' and resid 327 through 355 Processing helix chain 'C' and resid 27 through 51 removed outlier: 4.822A pdb=" N VAL C 48 " --> pdb=" O VAL C 44 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N PHE C 49 " --> pdb=" O ILE C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 91 Processing helix chain 'C' and resid 179 through 184 removed outlier: 3.922A pdb=" N ASN C 184 " --> pdb=" O GLU C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 217 removed outlier: 4.170A pdb=" N LYS C 216 " --> pdb=" O THR C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 240 removed outlier: 3.641A pdb=" N GLY C 240 " --> pdb=" O VAL C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 249 Processing helix chain 'C' and resid 266 through 270 Processing helix chain 'C' and resid 327 through 348 removed outlier: 3.512A pdb=" N THR C 331 " --> pdb=" O ASP C 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 355 Processing sheet with id=AA1, first strand: chain 'A' and resid 56 through 59 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 56 through 59 current: chain 'A' and resid 157 through 165 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 157 through 165 current: chain 'A' and resid 273 through 279 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 273 through 279 current: chain 'A' and resid 302 through 326 No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 62 through 70 removed outlier: 3.521A pdb=" N SER A 194 " --> pdb=" O ILE A 62 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER A 64 " --> pdb=" O SER A 192 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER A 192 " --> pdb=" O SER A 64 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N THR A 186 " --> pdb=" O LYS A 70 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 73 through 76 Processing sheet with id=AA4, first strand: chain 'A' and resid 135 through 136 Processing sheet with id=AA5, first strand: chain 'B' and resid 62 through 70 removed outlier: 3.551A pdb=" N SER B 64 " --> pdb=" O SER B 192 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER B 192 " --> pdb=" O SER B 64 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N THR B 186 " --> pdb=" O LYS B 70 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL B 200 " --> pdb=" O PHE B 195 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 73 through 75 Processing sheet with id=AA7, first strand: chain 'B' and resid 100 through 118 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 100 through 118 current: chain 'B' and resid 157 through 165 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 157 through 165 current: chain 'B' and resid 273 through 279 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 273 through 279 current: chain 'B' and resid 302 through 320 No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 261 through 262 removed outlier: 7.609A pdb=" N CYS B 261 " --> pdb=" O GLY B 324 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 56 through 57 removed outlier: 3.663A pdb=" N LYS C 325 " --> pdb=" O THR C 57 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N CYS C 261 " --> pdb=" O GLY C 324 " (cutoff:3.500A) removed outlier: 9.528A pdb=" N PHE C 326 " --> pdb=" O CYS C 261 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 62 through 70 removed outlier: 3.585A pdb=" N SER C 64 " --> pdb=" O SER C 192 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER C 192 " --> pdb=" O SER C 64 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N THR C 186 " --> pdb=" O LYS C 70 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL C 200 " --> pdb=" O PHE C 195 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 73 through 76 Processing sheet with id=AB3, first strand: chain 'C' and resid 99 through 105 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 99 through 105 current: chain 'C' and resid 157 through 165 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 157 through 165 current: chain 'C' and resid 273 through 279 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 273 through 279 current: chain 'C' and resid 302 through 320 No H-bonds generated for sheet with id=AB3 214 hydrogen bonds defined for protein. 585 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: 0.97 Time building geometry restraints manager: 0.71 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: 2512 1.34 - 1.46: 1924 1.46 - 1.58: 3681 1.58 - 1.70: 16 1.70 - 1.82: 57 Bond restraints: 8190 Sorted by residual: bond pdb=" C4 ATP A 401 " pdb=" C5 ATP A 401 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.93e+01 bond pdb=" C4 ATP A 405 " pdb=" C5 ATP A 405 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.90e+01 bond pdb=" C4 ATP C 401 " pdb=" C5 ATP C 401 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.89e+01 bond pdb=" C5 ATP A 401 " pdb=" C6 ATP A 401 " ideal model delta sigma weight residual 1.409 1.482 -0.073 1.00e-02 1.00e+04 5.34e+01 bond pdb=" C5 ATP C 401 " pdb=" C6 ATP C 401 " ideal model delta sigma weight residual 1.409 1.482 -0.073 1.00e-02 1.00e+04 5.27e+01 ... (remaining 8185 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.93: 11047 3.93 - 7.86: 59 7.86 - 11.79: 9 11.79 - 15.72: 2 15.72 - 19.65: 4 Bond angle restraints: 11121 Sorted by residual: angle pdb=" PB ATP C 401 " pdb=" O3B ATP C 401 " pdb=" PG ATP C 401 " ideal model delta sigma weight residual 139.87 120.22 19.65 1.00e+00 1.00e+00 3.86e+02 angle pdb=" PB ATP A 405 " pdb=" O3B ATP A 405 " pdb=" PG ATP A 405 " ideal model delta sigma weight residual 139.87 120.86 19.01 1.00e+00 1.00e+00 3.61e+02 angle pdb=" PB ATP A 401 " pdb=" O3B ATP A 401 " pdb=" PG ATP A 401 " ideal model delta sigma weight residual 139.87 121.30 18.57 1.00e+00 1.00e+00 3.45e+02 angle pdb=" PA ATP C 401 " pdb=" O3A ATP C 401 " pdb=" PB ATP C 401 " ideal model delta sigma weight residual 136.83 121.01 15.82 1.00e+00 1.00e+00 2.50e+02 angle pdb=" PA ATP A 405 " pdb=" O3A ATP A 405 " pdb=" PB ATP A 405 " ideal model delta sigma weight residual 136.83 121.19 15.64 1.00e+00 1.00e+00 2.45e+02 ... (remaining 11116 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.74: 4725 15.74 - 31.49: 183 31.49 - 47.23: 35 47.23 - 62.97: 15 62.97 - 78.72: 1 Dihedral angle restraints: 4959 sinusoidal: 2169 harmonic: 2790 Sorted by residual: dihedral pdb=" C THR C 346 " pdb=" N THR C 346 " pdb=" CA THR C 346 " pdb=" CB THR C 346 " ideal model delta harmonic sigma weight residual -122.00 -135.06 13.06 0 2.50e+00 1.60e-01 2.73e+01 dihedral pdb=" N THR C 346 " pdb=" C THR C 346 " pdb=" CA THR C 346 " pdb=" CB THR C 346 " ideal model delta harmonic sigma weight residual 123.40 135.18 -11.78 0 2.50e+00 1.60e-01 2.22e+01 dihedral pdb=" CA CYS A 165 " pdb=" C CYS A 165 " pdb=" N PRO A 166 " pdb=" CA PRO A 166 " ideal model delta harmonic sigma weight residual 0.00 22.60 -22.60 0 5.00e+00 4.00e-02 2.04e+01 ... (remaining 4956 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 1149 0.097 - 0.194: 83 0.194 - 0.290: 8 0.290 - 0.387: 1 0.387 - 0.484: 1 Chirality restraints: 1242 Sorted by residual: chirality pdb=" CA THR C 346 " pdb=" N THR C 346 " pdb=" C THR C 346 " pdb=" CB THR C 346 " both_signs ideal model delta sigma weight residual False 2.53 2.04 0.48 2.00e-01 2.50e+01 5.86e+00 chirality pdb=" CA CYS C 349 " pdb=" N CYS C 349 " pdb=" C CYS C 349 " pdb=" CB CYS C 349 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.31 2.00e-01 2.50e+01 2.33e+00 chirality pdb=" C1 NAG B 504 " pdb=" ND2 ASN B 184 " pdb=" C2 NAG B 504 " pdb=" O5 NAG B 504 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 1.95e+00 ... (remaining 1239 not shown) Planarity restraints: 1407 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 271 " -0.024 5.00e-02 4.00e+02 3.73e-02 2.23e+00 pdb=" N PRO A 272 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO A 272 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 272 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE C 92 " -0.023 5.00e-02 4.00e+02 3.51e-02 1.97e+00 pdb=" N PRO C 93 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO C 93 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO C 93 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY C 343 " -0.007 2.00e-02 2.50e+03 1.32e-02 1.73e+00 pdb=" C GLY C 343 " 0.023 2.00e-02 2.50e+03 pdb=" O GLY C 343 " -0.009 2.00e-02 2.50e+03 pdb=" N VAL C 344 " -0.008 2.00e-02 2.50e+03 ... (remaining 1404 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 103 2.65 - 3.21: 7050 3.21 - 3.77: 12447 3.77 - 4.34: 17338 4.34 - 4.90: 28229 Nonbonded interactions: 65167 Sorted by model distance: nonbonded pdb=" OD1 ASP A 170 " pdb="MG MG A 406 " model vdw 2.082 2.170 nonbonded pdb=" O PHE C 33 " pdb=" NE2 GLN C 37 " model vdw 2.259 3.120 nonbonded pdb=" NZ LYS B 309 " pdb=" O3G ATP A 401 " model vdw 2.301 3.120 nonbonded pdb=" OD2 ASP B 128 " pdb=" OG SER B 130 " model vdw 2.303 3.040 nonbonded pdb=" NZ LYS C 309 " pdb=" O3G ATP C 401 " model vdw 2.331 3.120 ... (remaining 65162 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 26 through 355 or resid 403 through 404)) selection = (chain 'B' and (resid 26 through 355 or resid 503 through 504)) selection = (chain 'C' and (resid 26 through 355 or resid 403 through 404)) } 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: 2.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 7.200 Find NCS groups from input model: 0.110 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:7.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6595 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 : 0.004 0.083 8212 Z= 0.340 Angle : 0.813 19.654 11174 Z= 0.599 Chirality : 0.051 0.484 1242 Planarity : 0.003 0.037 1398 Dihedral : 8.925 78.716 3144 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.42 % Allowed : 3.19 % Favored : 95.39 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 6.67 % 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: -0.63 (0.26), residues: 984 helix: -0.31 (0.34), residues: 255 sheet: 0.71 (0.30), residues: 264 loop : -1.12 (0.26), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 244 TYR 0.010 0.001 TYR B 90 PHE 0.006 0.001 PHE B 342 TRP 0.007 0.001 TRP A 164 HIS 0.005 0.000 HIS A 355 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.34 ( 8190) covalent geometry : angle 0.79943 / 0.60 (11121) SS BOND : bond 0.00321 / 0.18 ( 13) SS BOND : angle 0.69076 / 0.43 ( 26) hydrogen bonds : bond 0.20908 / 13.48 ( 214) hydrogen bonds : angle 7.55817 / 5.03 ( 585) link_NAG-ASN : bond 0.00826 / 0.46 ( 9) link_NAG-ASN : angle 3.17332 / 2.16 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 234 time to evaluate : 0.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 242 ASP cc_start: 0.6724 (t70) cc_final: 0.6513 (t0) outliers start: 12 outliers final: 1 residues processed: 246 average time/residue: 0.4118 time to fit residues: 107.8819 Evaluate side-chains 116 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 115 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 210 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 0.0570 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 30.0000 chunk 65 optimal weight: 20.0000 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 38 optimal weight: 0.0060 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 9.9990 overall best weight: 0.7316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 56 GLN A 191 ASN A 220 HIS A 241 GLN B 76 GLN B 112 GLN B 180 HIS B 191 ASN B 220 HIS C 56 GLN C 76 GLN C 191 ASN C 220 HIS C 290 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.133802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.106435 restraints weight = 13626.644| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 3.21 r_work: 0.3438 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8212 Z= 0.133 Angle : 0.612 9.007 11174 Z= 0.304 Chirality : 0.046 0.319 1242 Planarity : 0.004 0.039 1398 Dihedral : 9.101 92.004 1349 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.31 % Allowed : 13.95 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 0.38 (0.27), residues: 984 helix: 0.89 (0.35), residues: 240 sheet: 1.08 (0.30), residues: 279 loop : -0.57 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 244 TYR 0.035 0.002 TYR C 90 PHE 0.019 0.002 PHE A 326 TRP 0.008 0.001 TRP A 47 HIS 0.007 0.001 HIS B 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 ( 8190) covalent geometry : angle 0.58727 / 0.30 (11121) SS BOND : bond 0.00817 / 0.57 ( 13) SS BOND : angle 1.32267 / 0.86 ( 26) hydrogen bonds : bond 0.02989 / 1.99 ( 214) hydrogen bonds : angle 5.14315 / 3.42 ( 585) link_NAG-ASN : bond 0.00844 / 0.42 ( 9) link_NAG-ASN : angle 3.32232 / 2.40 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 124 time to evaluate : 0.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 GLU cc_start: 0.8306 (mp0) cc_final: 0.7905 (mp0) REVERT: B 80 LEU cc_start: 0.8364 (mp) cc_final: 0.8109 (pp) REVERT: B 83 GLN cc_start: 0.7806 (tt0) cc_final: 0.7570 (tt0) REVERT: B 181 GLU cc_start: 0.7791 (mt-10) cc_final: 0.7530 (mt-10) REVERT: B 185 PHE cc_start: 0.5625 (m-10) cc_final: 0.5199 (m-10) REVERT: B 341 ILE cc_start: 0.8095 (mt) cc_final: 0.7874 (tt) REVERT: C 129 ASP cc_start: 0.8559 (OUTLIER) cc_final: 0.8238 (m-30) REVERT: C 185 PHE cc_start: 0.5192 (m-10) cc_final: 0.4853 (m-10) REVERT: C 270 CYS cc_start: 0.6662 (OUTLIER) cc_final: 0.6262 (m) outliers start: 28 outliers final: 6 residues processed: 143 average time/residue: 0.3728 time to fit residues: 57.3349 Evaluate side-chains 97 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 89 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain C residue 129 ASP Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 210 ASN Chi-restraints excluded: chain C residue 270 CYS Chi-restraints excluded: chain C residue 328 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 6 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 98 optimal weight: 10.0000 chunk 77 optimal weight: 0.0050 chunk 69 optimal weight: 6.9990 chunk 27 optimal weight: 4.9990 chunk 38 optimal weight: 0.0370 chunk 19 optimal weight: 6.9990 chunk 76 optimal weight: 20.0000 chunk 1 optimal weight: 5.9990 overall best weight: 1.8078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 76 GLN B 116 HIS B 180 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.120215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.091608 restraints weight = 13755.243| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 3.17 r_work: 0.3142 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.4190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8212 Z= 0.191 Angle : 0.651 11.042 11174 Z= 0.324 Chirality : 0.048 0.354 1242 Planarity : 0.004 0.052 1398 Dihedral : 8.954 87.591 1349 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 4.02 % Allowed : 14.54 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 0.67 (0.27), residues: 984 helix: 1.17 (0.36), residues: 240 sheet: 1.09 (0.31), residues: 261 loop : -0.25 (0.28), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 244 TYR 0.030 0.002 TYR B 90 PHE 0.030 0.002 PHE C 92 TRP 0.013 0.001 TRP C 47 HIS 0.010 0.001 HIS B 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.19 ( 8190) covalent geometry : angle 0.61479 / 0.32 (11121) SS BOND : bond 0.00396 / 0.21 ( 13) SS BOND : angle 1.52629 / 0.97 ( 26) hydrogen bonds : bond 0.03201 / 2.15 ( 214) hydrogen bonds : angle 4.78094 / 3.23 ( 585) link_NAG-ASN : bond 0.00668 / 0.45 ( 9) link_NAG-ASN : angle 4.16240 / 2.95 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 79 time to evaluate : 0.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 ARG cc_start: 0.8488 (mtp-110) cc_final: 0.8281 (mtp85) REVERT: B 80 LEU cc_start: 0.8317 (mp) cc_final: 0.8037 (pp) REVERT: B 181 GLU cc_start: 0.8344 (mt-10) cc_final: 0.8093 (mt-10) REVERT: C 129 ASP cc_start: 0.8501 (OUTLIER) cc_final: 0.8298 (m-30) REVERT: C 170 ASP cc_start: 0.7492 (OUTLIER) cc_final: 0.7056 (m-30) REVERT: C 260 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7845 (tm-30) outliers start: 34 outliers final: 14 residues processed: 105 average time/residue: 0.3010 time to fit residues: 34.4084 Evaluate side-chains 86 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 69 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain B residue 132 CYS Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 99 SER Chi-restraints excluded: chain C residue 129 ASP Chi-restraints excluded: chain C residue 132 CYS Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 170 ASP Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 210 ASN Chi-restraints excluded: chain C residue 260 GLU Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 328 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 32 optimal weight: 20.0000 chunk 48 optimal weight: 0.2980 chunk 24 optimal weight: 2.9990 chunk 66 optimal weight: 30.0000 chunk 11 optimal weight: 4.9990 chunk 94 optimal weight: 5.9990 chunk 92 optimal weight: 3.9990 chunk 33 optimal weight: 30.0000 chunk 59 optimal weight: 0.7980 chunk 4 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 26 ASN ** B 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 114 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.114714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.084459 restraints weight = 13827.521| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 3.15 r_work: 0.3072 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.4786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 8212 Z= 0.230 Angle : 0.649 12.478 11174 Z= 0.327 Chirality : 0.050 0.421 1242 Planarity : 0.004 0.035 1398 Dihedral : 9.120 89.618 1349 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 4.49 % Allowed : 15.13 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 0.71 (0.27), residues: 984 helix: 1.33 (0.36), residues: 240 sheet: 1.00 (0.31), residues: 261 loop : -0.21 (0.28), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 244 TYR 0.029 0.002 TYR C 90 PHE 0.034 0.002 PHE C 92 TRP 0.007 0.001 TRP A 164 HIS 0.003 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00528 / 0.23 ( 8190) covalent geometry : angle 0.61334 / 0.32 (11121) SS BOND : bond 0.00321 / 0.20 ( 13) SS BOND : angle 1.54763 / 1.01 ( 26) hydrogen bonds : bond 0.03092 / 2.10 ( 214) hydrogen bonds : angle 4.69156 / 3.20 ( 585) link_NAG-ASN : bond 0.00373 / 0.25 ( 9) link_NAG-ASN : angle 4.15048 / 3.04 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 71 time to evaluate : 0.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 304 ARG cc_start: 0.8012 (OUTLIER) cc_final: 0.7568 (mtt-85) REVERT: B 181 GLU cc_start: 0.8503 (mt-10) cc_final: 0.8276 (mt-10) REVERT: C 170 ASP cc_start: 0.7479 (OUTLIER) cc_final: 0.7040 (m-30) REVERT: C 260 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7799 (tm-30) REVERT: C 283 LYS cc_start: 0.7549 (mmtt) cc_final: 0.7262 (ttpp) outliers start: 38 outliers final: 14 residues processed: 101 average time/residue: 0.3390 time to fit residues: 37.0218 Evaluate side-chains 77 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 60 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 304 ARG Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain B residue 132 CYS Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 99 SER Chi-restraints excluded: chain C residue 132 CYS Chi-restraints excluded: chain C residue 170 ASP Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 210 ASN Chi-restraints excluded: chain C residue 260 GLU Chi-restraints excluded: chain C residue 284 ASN Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 328 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 19 optimal weight: 6.9990 chunk 56 optimal weight: 0.9980 chunk 14 optimal weight: 5.9990 chunk 12 optimal weight: 0.5980 chunk 31 optimal weight: 9.9990 chunk 57 optimal weight: 5.9990 chunk 83 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 84 optimal weight: 6.9990 chunk 98 optimal weight: 20.0000 chunk 26 optimal weight: 0.8980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 114 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.116601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.086563 restraints weight = 13716.687| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 3.23 r_work: 0.3115 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.4920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8212 Z= 0.133 Angle : 0.589 11.415 11174 Z= 0.291 Chirality : 0.046 0.424 1242 Planarity : 0.004 0.048 1398 Dihedral : 8.982 88.098 1349 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.96 % Allowed : 16.67 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 0.76 (0.27), residues: 984 helix: 1.44 (0.37), residues: 240 sheet: 1.05 (0.31), residues: 261 loop : -0.24 (0.28), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 244 TYR 0.025 0.001 TYR C 90 PHE 0.022 0.002 PHE B 92 TRP 0.010 0.001 TRP A 47 HIS 0.002 0.001 HIS A 355 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 ( 8190) covalent geometry : angle 0.55847 / 0.28 (11121) SS BOND : bond 0.00253 / 0.16 ( 13) SS BOND : angle 1.18470 / 0.78 ( 26) hydrogen bonds : bond 0.02607 / 1.78 ( 214) hydrogen bonds : angle 4.65847 / 3.18 ( 585) link_NAG-ASN : bond 0.00598 / 0.32 ( 9) link_NAG-ASN : angle 3.68936 / 2.72 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 69 time to evaluate : 0.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 ARG cc_start: 0.8478 (mtp-110) cc_final: 0.8276 (mtp85) REVERT: C 283 LYS cc_start: 0.7605 (mmtt) cc_final: 0.7200 (ttpp) outliers start: 25 outliers final: 9 residues processed: 85 average time/residue: 0.3096 time to fit residues: 28.7178 Evaluate side-chains 72 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 132 CYS Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 132 CYS Chi-restraints excluded: chain C residue 210 ASN Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 328 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 68 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 40 optimal weight: 7.9990 chunk 17 optimal weight: 0.9990 chunk 93 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 5 optimal weight: 7.9990 chunk 56 optimal weight: 5.9990 chunk 76 optimal weight: 20.0000 chunk 29 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.115110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.084713 restraints weight = 13558.076| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 3.18 r_work: 0.3082 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.5087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8212 Z= 0.165 Angle : 0.582 11.851 11174 Z= 0.293 Chirality : 0.046 0.424 1242 Planarity : 0.004 0.037 1398 Dihedral : 8.649 87.631 1349 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.55 % Allowed : 16.55 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 0.73 (0.27), residues: 984 helix: 1.41 (0.36), residues: 240 sheet: 0.93 (0.31), residues: 279 loop : -0.22 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 268 TYR 0.025 0.002 TYR C 90 PHE 0.027 0.002 PHE B 92 TRP 0.007 0.001 TRP C 47 HIS 0.002 0.001 HIS A 355 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.16 ( 8190) covalent geometry : angle 0.55679 / 0.29 (11121) SS BOND : bond 0.00244 / 0.15 ( 13) SS BOND : angle 1.21426 / 0.80 ( 26) hydrogen bonds : bond 0.02741 / 1.85 ( 214) hydrogen bonds : angle 4.63498 / 3.17 ( 585) link_NAG-ASN : bond 0.00352 / 0.22 ( 9) link_NAG-ASN : angle 3.35953 / 2.60 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 67 time to evaluate : 0.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 ARG cc_start: 0.8509 (mtp-110) cc_final: 0.8291 (mtp85) REVERT: A 304 ARG cc_start: 0.7999 (OUTLIER) cc_final: 0.7506 (mtt-85) REVERT: B 181 GLU cc_start: 0.8590 (mt-10) cc_final: 0.8116 (tt0) REVERT: C 283 LYS cc_start: 0.7793 (mmtt) cc_final: 0.7426 (ttpp) outliers start: 30 outliers final: 15 residues processed: 88 average time/residue: 0.3091 time to fit residues: 29.3905 Evaluate side-chains 77 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 61 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 199 LYS Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 304 ARG Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 132 CYS Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 99 SER Chi-restraints excluded: chain C residue 132 CYS Chi-restraints excluded: chain C residue 210 ASN Chi-restraints excluded: chain C residue 258 ASP Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 328 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 11 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 87 optimal weight: 0.8980 chunk 36 optimal weight: 5.9990 chunk 82 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 32 optimal weight: 20.0000 chunk 3 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 277 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.115378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.085065 restraints weight = 13703.283| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 3.18 r_work: 0.3083 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.5224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8212 Z= 0.147 Angle : 0.573 11.538 11174 Z= 0.289 Chirality : 0.046 0.425 1242 Planarity : 0.004 0.032 1398 Dihedral : 8.508 85.018 1349 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.84 % Allowed : 17.73 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 0.67 (0.27), residues: 984 helix: 1.36 (0.36), residues: 240 sheet: 0.93 (0.31), residues: 279 loop : -0.30 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 197 TYR 0.024 0.001 TYR C 90 PHE 0.024 0.002 PHE B 92 TRP 0.013 0.001 TRP A 47 HIS 0.002 0.001 HIS A 355 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 ( 8190) covalent geometry : angle 0.55082 / 0.28 (11121) SS BOND : bond 0.00231 / 0.15 ( 13) SS BOND : angle 1.21851 / 0.80 ( 26) hydrogen bonds : bond 0.02618 / 1.78 ( 214) hydrogen bonds : angle 4.60906 / 3.17 ( 585) link_NAG-ASN : bond 0.00353 / 0.22 ( 9) link_NAG-ASN : angle 3.04966 / 2.46 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 68 time to evaluate : 0.193 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 SER cc_start: 0.8248 (m) cc_final: 0.7577 (t) REVERT: A 244 ARG cc_start: 0.8473 (mtp-110) cc_final: 0.8259 (mtp85) REVERT: A 304 ARG cc_start: 0.7927 (OUTLIER) cc_final: 0.7442 (mtt-85) REVERT: B 181 GLU cc_start: 0.8546 (mt-10) cc_final: 0.8183 (tt0) REVERT: C 283 LYS cc_start: 0.7817 (mmtt) cc_final: 0.7498 (ttpp) outliers start: 24 outliers final: 13 residues processed: 86 average time/residue: 0.3814 time to fit residues: 35.4683 Evaluate side-chains 75 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 61 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 304 ARG Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 132 CYS Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 132 CYS Chi-restraints excluded: chain C residue 258 ASP Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 328 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 54 optimal weight: 0.7980 chunk 94 optimal weight: 5.9990 chunk 52 optimal weight: 0.9990 chunk 79 optimal weight: 9.9990 chunk 87 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.115224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.085260 restraints weight = 13626.649| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 3.20 r_work: 0.3090 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.5245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8212 Z= 0.137 Angle : 0.576 11.340 11174 Z= 0.290 Chirality : 0.046 0.420 1242 Planarity : 0.004 0.032 1398 Dihedral : 8.328 83.247 1347 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.60 % Allowed : 18.44 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 0.70 (0.27), residues: 984 helix: 1.38 (0.36), residues: 240 sheet: 0.96 (0.31), residues: 279 loop : -0.28 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 268 TYR 0.024 0.002 TYR C 43 PHE 0.025 0.002 PHE B 326 TRP 0.008 0.001 TRP A 47 HIS 0.002 0.000 HIS A 355 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 ( 8190) covalent geometry : angle 0.55592 / 0.29 (11121) SS BOND : bond 0.00228 / 0.14 ( 13) SS BOND : angle 1.16177 / 0.77 ( 26) hydrogen bonds : bond 0.02579 / 1.74 ( 214) hydrogen bonds : angle 4.61451 / 3.17 ( 585) link_NAG-ASN : bond 0.00344 / 0.20 ( 9) link_NAG-ASN : angle 2.93126 / 2.39 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 72 time to evaluate : 0.208 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 SER cc_start: 0.8224 (m) cc_final: 0.7566 (t) REVERT: A 304 ARG cc_start: 0.7910 (OUTLIER) cc_final: 0.7432 (mtt-85) REVERT: B 181 GLU cc_start: 0.8550 (mt-10) cc_final: 0.8328 (mt-10) REVERT: C 172 LYS cc_start: 0.8547 (tppp) cc_final: 0.8251 (mmmt) REVERT: C 208 GLU cc_start: 0.7758 (mp0) cc_final: 0.7438 (mp0) REVERT: C 283 LYS cc_start: 0.7791 (mmtt) cc_final: 0.7457 (ttpp) outliers start: 22 outliers final: 12 residues processed: 88 average time/residue: 0.3657 time to fit residues: 34.8672 Evaluate side-chains 76 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 63 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 304 ARG Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 108 MET Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 99 SER Chi-restraints excluded: chain C residue 132 CYS Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 328 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 77 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 36 optimal weight: 7.9990 chunk 12 optimal weight: 7.9990 chunk 78 optimal weight: 0.9980 chunk 56 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.115149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.084922 restraints weight = 13555.966| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 3.18 r_work: 0.3092 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.5372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8212 Z= 0.146 Angle : 0.592 11.303 11174 Z= 0.300 Chirality : 0.046 0.416 1242 Planarity : 0.004 0.062 1398 Dihedral : 8.279 82.570 1347 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.60 % Allowed : 19.03 % Favored : 78.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 0.70 (0.27), residues: 984 helix: 1.39 (0.36), residues: 240 sheet: 0.85 (0.31), residues: 273 loop : -0.19 (0.29), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 244 TYR 0.021 0.001 TYR B 90 PHE 0.024 0.002 PHE B 92 TRP 0.015 0.001 TRP A 47 HIS 0.002 0.001 HIS A 355 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 ( 8190) covalent geometry : angle 0.57293 / 0.30 (11121) SS BOND : bond 0.00220 / 0.14 ( 13) SS BOND : angle 1.16781 / 0.78 ( 26) hydrogen bonds : bond 0.02588 / 1.75 ( 214) hydrogen bonds : angle 4.63827 / 3.18 ( 585) link_NAG-ASN : bond 0.00575 / 0.42 ( 9) link_NAG-ASN : angle 2.88295 / 2.36 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 68 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLU cc_start: 0.9024 (mm-30) cc_final: 0.8646 (mp0) REVERT: A 66 SER cc_start: 0.8241 (m) cc_final: 0.7581 (t) REVERT: A 304 ARG cc_start: 0.8024 (OUTLIER) cc_final: 0.7538 (mtt-85) REVERT: B 181 GLU cc_start: 0.8577 (mt-10) cc_final: 0.8218 (tt0) REVERT: C 172 LYS cc_start: 0.8583 (tppp) cc_final: 0.8291 (mmmt) REVERT: C 208 GLU cc_start: 0.7802 (mp0) cc_final: 0.7475 (mp0) REVERT: C 283 LYS cc_start: 0.7886 (mmtt) cc_final: 0.7572 (ttpp) outliers start: 22 outliers final: 14 residues processed: 85 average time/residue: 0.3987 time to fit residues: 36.8159 Evaluate side-chains 78 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 63 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 304 ARG Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 108 MET Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 99 SER Chi-restraints excluded: chain C residue 132 CYS Chi-restraints excluded: chain C residue 258 ASP Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 328 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 26 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 1 optimal weight: 6.9990 chunk 81 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 73 optimal weight: 0.9990 chunk 39 optimal weight: 0.4980 chunk 68 optimal weight: 3.9990 chunk 98 optimal weight: 9.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.115932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.086893 restraints weight = 13591.581| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 3.18 r_work: 0.3118 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.5345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8212 Z= 0.123 Angle : 0.585 10.895 11174 Z= 0.297 Chirality : 0.046 0.411 1242 Planarity : 0.004 0.039 1398 Dihedral : 8.178 81.701 1347 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.01 % Allowed : 19.62 % Favored : 78.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 0.69 (0.27), residues: 984 helix: 1.29 (0.36), residues: 240 sheet: 0.88 (0.31), residues: 273 loop : -0.16 (0.29), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 244 TYR 0.025 0.002 TYR C 90 PHE 0.028 0.002 PHE B 326 TRP 0.013 0.001 TRP A 47 HIS 0.002 0.000 HIS A 355 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 ( 8190) covalent geometry : angle 0.56807 / 0.29 (11121) SS BOND : bond 0.00220 / 0.14 ( 13) SS BOND : angle 1.11721 / 0.75 ( 26) hydrogen bonds : bond 0.02557 / 1.71 ( 214) hydrogen bonds : angle 4.67028 / 3.20 ( 585) link_NAG-ASN : bond 0.00507 / 0.34 ( 9) link_NAG-ASN : angle 2.76284 / 2.28 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 69 time to evaluate : 0.293 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLU cc_start: 0.9005 (mm-30) cc_final: 0.8591 (mp0) REVERT: A 66 SER cc_start: 0.8195 (m) cc_final: 0.7603 (t) REVERT: B 181 GLU cc_start: 0.8545 (mt-10) cc_final: 0.8315 (mt-10) REVERT: C 172 LYS cc_start: 0.8586 (tppp) cc_final: 0.8300 (mmmt) REVERT: C 208 GLU cc_start: 0.7825 (mp0) cc_final: 0.7495 (mp0) REVERT: C 283 LYS cc_start: 0.7892 (mmtt) cc_final: 0.7655 (ttpp) outliers start: 17 outliers final: 14 residues processed: 83 average time/residue: 0.3764 time to fit residues: 34.0619 Evaluate side-chains 78 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 64 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 108 MET Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 99 SER Chi-restraints excluded: chain C residue 132 CYS Chi-restraints excluded: chain C residue 258 ASP Chi-restraints excluded: chain C residue 284 ASN Chi-restraints excluded: chain C residue 328 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 22 optimal weight: 0.3980 chunk 98 optimal weight: 6.9990 chunk 73 optimal weight: 2.9990 chunk 71 optimal weight: 0.0050 chunk 42 optimal weight: 0.0970 chunk 24 optimal weight: 1.9990 chunk 92 optimal weight: 0.0980 chunk 80 optimal weight: 5.9990 chunk 53 optimal weight: 0.7980 chunk 52 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 overall best weight: 0.2792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.118715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.090120 restraints weight = 13617.791| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 3.13 r_work: 0.3168 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.5363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 8212 Z= 0.102 Angle : 0.567 10.092 11174 Z= 0.286 Chirality : 0.045 0.392 1242 Planarity : 0.004 0.050 1398 Dihedral : 7.940 77.988 1347 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.18 % Allowed : 20.21 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 0.75 (0.27), residues: 984 helix: 1.35 (0.36), residues: 240 sheet: 0.96 (0.31), residues: 273 loop : -0.16 (0.29), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG A 244 TYR 0.021 0.001 TYR B 90 PHE 0.020 0.001 PHE A 326 TRP 0.024 0.001 TRP A 47 HIS 0.002 0.000 HIS A 355 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.10 ( 8190) covalent geometry : angle 0.55105 / 0.28 (11121) SS BOND : bond 0.00202 / 0.13 ( 13) SS BOND : angle 0.98824 / 0.68 ( 26) hydrogen bonds : bond 0.02235 / 1.51 ( 214) hydrogen bonds : angle 4.67048 / 3.19 ( 585) link_NAG-ASN : bond 0.00708 / 0.50 ( 9) link_NAG-ASN : angle 2.61031 / 2.15 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2254.27 seconds wall clock time: 39 minutes 13.20 seconds (2353.20 seconds total)