Starting phenix.real_space_refine on Wed Sep 17 09:53:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ztd_60458/09_2025/8ztd_60458.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ztd_60458/09_2025/8ztd_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 { model { file = "/net/cci-nas-00/data/ceres_data/8ztd_60458/09_2025/8ztd_60458.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ztd_60458/09_2025/8ztd_60458.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ztd_60458/09_2025/8ztd_60458.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ztd_60458/09_2025/8ztd_60458.map" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/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, 106 Unusual residues: {' CA': 1, ' MG': 1, 'ATP': 2, 'NAG': 3} Classifications: {'undetermined': 7} Link IDs: {None: 6} 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, 44 Unusual residues: {' CA': 1, ' MG': 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: "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: 2.41, per 1000 atoms: 0.30 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: 0.70 Conformation dependent library (CDL) restraints added in 476.0 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 0.27 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: 1.38 Time building geometry restraints manager: 0.96 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: 1.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.210 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.020 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:8.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6341 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 aren 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 covalent geometry : bond 0.00440 ( 8190) covalent geometry : angle 0.79943 (11121) SS BOND : bond 0.00321 ( 13) SS BOND : angle 0.69076 ( 26) hydrogen bonds : bond 0.20908 ( 214) hydrogen bonds : angle 7.55817 ( 585) link_NAG-ASN : bond 0.00826 ( 9) link_NAG-ASN : angle 3.17332 ( 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 : 0.574 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: 0.5736 time to fit residues: 149.5154 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 : 0.321 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 56 GLN A 191 ASN A 220 HIS A 241 GLN A 275 GLN B 76 GLN B 112 GLN B 180 HIS B 191 ASN B 220 HIS C 56 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 = 0.3900 r_free = 0.3900 target = 0.134457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.107241 restraints weight = 13612.684| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 3.23 r_work: 0.3448 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8212 Z= 0.128 Angle : 0.603 8.864 11174 Z= 0.300 Chirality : 0.047 0.398 1242 Planarity : 0.004 0.042 1398 Dihedral : 9.236 100.458 1349 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.19 % Allowed : 14.07 % 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 aren not related in a simple way. whole: 0.34 (0.27), residues: 984 helix: 0.88 (0.35), residues: 240 sheet: 1.05 (0.30), residues: 279 loop : -0.60 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 244 TYR 0.030 0.002 TYR C 90 PHE 0.020 0.001 PHE A 326 TRP 0.008 0.001 TRP A 47 HIS 0.007 0.001 HIS B 180 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 8190) covalent geometry : angle 0.57342 (11121) SS BOND : bond 0.00623 ( 13) SS BOND : angle 1.84725 ( 26) hydrogen bonds : bond 0.03124 ( 214) hydrogen bonds : angle 5.21689 ( 585) link_NAG-ASN : bond 0.01124 ( 9) link_NAG-ASN : angle 3.45447 ( 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 151 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 124 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 GLU cc_start: 0.8291 (mp0) cc_final: 0.7864 (mp0) REVERT: B 80 LEU cc_start: 0.8349 (mp) cc_final: 0.8107 (pp) REVERT: B 83 GLN cc_start: 0.7785 (tt0) cc_final: 0.7561 (tt0) REVERT: B 181 GLU cc_start: 0.7818 (mt-10) cc_final: 0.7522 (mt-10) REVERT: B 185 PHE cc_start: 0.5514 (m-10) cc_final: 0.5080 (m-10) REVERT: C 129 ASP cc_start: 0.8539 (OUTLIER) cc_final: 0.8249 (m-30) REVERT: C 185 PHE cc_start: 0.5026 (m-10) cc_final: 0.4703 (m-10) outliers start: 27 outliers final: 5 residues processed: 141 average time/residue: 0.4544 time to fit residues: 68.9547 Evaluate side-chains 96 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 90 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 218 LEU 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 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: 3.9990 chunk 34 optimal weight: 0.9990 chunk 98 optimal weight: 4.9990 chunk 77 optimal weight: 0.0020 chunk 69 optimal weight: 6.9990 chunk 27 optimal weight: 4.9990 chunk 38 optimal weight: 7.9990 chunk 19 optimal weight: 6.9990 chunk 76 optimal weight: 10.0000 chunk 1 optimal weight: 5.9990 overall best weight: 2.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 116 HIS B 180 HIS C 114 GLN C 241 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.118472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.089417 restraints weight = 13835.070| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 3.14 r_work: 0.3117 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.4374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 8212 Z= 0.248 Angle : 0.713 11.598 11174 Z= 0.359 Chirality : 0.050 0.358 1242 Planarity : 0.004 0.047 1398 Dihedral : 9.176 87.574 1349 Min Nonbonded Distance : 1.778 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.43 % Allowed : 14.66 % Favored : 81.91 % 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 aren not related in a simple way. whole: 0.62 (0.27), residues: 984 helix: 1.15 (0.36), residues: 240 sheet: 1.08 (0.30), residues: 267 loop : -0.31 (0.28), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 244 TYR 0.030 0.002 TYR C 90 PHE 0.034 0.002 PHE C 92 TRP 0.012 0.001 TRP C 47 HIS 0.009 0.001 HIS B 180 Details of bonding type rmsd covalent geometry : bond 0.00565 ( 8190) covalent geometry : angle 0.67375 (11121) SS BOND : bond 0.00272 ( 13) SS BOND : angle 2.23899 ( 26) hydrogen bonds : bond 0.03367 ( 214) hydrogen bonds : angle 4.82316 ( 585) link_NAG-ASN : bond 0.00410 ( 9) link_NAG-ASN : angle 4.31625 ( 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 107 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 78 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 152 PHE cc_start: 0.7678 (t80) cc_final: 0.7462 (t80) REVERT: C 170 ASP cc_start: 0.7520 (OUTLIER) cc_final: 0.7053 (m-30) outliers start: 29 outliers final: 9 residues processed: 100 average time/residue: 0.4311 time to fit residues: 46.8081 Evaluate side-chains 76 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 LEU 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 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: 2.9990 chunk 24 optimal weight: 1.9990 chunk 66 optimal weight: 30.0000 chunk 11 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 92 optimal weight: 0.7980 chunk 33 optimal weight: 30.0000 chunk 59 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 67 optimal weight: 6.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 26 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.116367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.086483 restraints weight = 13811.760| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 3.16 r_work: 0.3081 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.4675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8212 Z= 0.180 Angle : 0.643 11.580 11174 Z= 0.318 Chirality : 0.047 0.412 1242 Planarity : 0.004 0.046 1398 Dihedral : 9.102 88.389 1349 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 4.02 % Allowed : 15.25 % Favored : 80.73 % 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 aren not related in a simple way. whole: 0.64 (0.27), residues: 984 helix: 1.32 (0.36), residues: 240 sheet: 0.98 (0.31), residues: 261 loop : -0.30 (0.28), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 244 TYR 0.028 0.002 TYR C 90 PHE 0.027 0.002 PHE C 92 TRP 0.008 0.001 TRP A 164 HIS 0.003 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00412 ( 8190) covalent geometry : angle 0.60510 (11121) SS BOND : bond 0.00355 ( 13) SS BOND : angle 2.09545 ( 26) hydrogen bonds : bond 0.02848 ( 214) hydrogen bonds : angle 4.64743 ( 585) link_NAG-ASN : bond 0.00443 ( 9) link_NAG-ASN : angle 4.03142 ( 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 110 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 76 time to evaluate : 0.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 ARG cc_start: 0.8509 (mtp-110) cc_final: 0.8299 (mtp85) REVERT: A 262 ASP cc_start: 0.8412 (t0) cc_final: 0.8201 (t0) REVERT: A 304 ARG cc_start: 0.7907 (OUTLIER) cc_final: 0.7464 (mtt-85) REVERT: B 181 GLU cc_start: 0.8452 (mt-10) cc_final: 0.8127 (tt0) REVERT: C 138 GLU cc_start: 0.8605 (pm20) cc_final: 0.8395 (mp0) REVERT: C 170 ASP cc_start: 0.7403 (OUTLIER) cc_final: 0.6984 (m-30) REVERT: C 208 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7652 (mp0) outliers start: 34 outliers final: 11 residues processed: 102 average time/residue: 0.4178 time to fit residues: 46.1018 Evaluate side-chains 81 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 67 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 304 ARG Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 99 SER Chi-restraints excluded: chain C residue 170 ASP Chi-restraints excluded: chain C residue 208 GLU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 19 optimal weight: 6.9990 chunk 56 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 31 optimal weight: 10.0000 chunk 57 optimal weight: 0.7980 chunk 83 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 84 optimal weight: 0.0970 chunk 98 optimal weight: 8.9990 chunk 26 optimal weight: 0.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 114 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.116976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.086781 restraints weight = 13813.573| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 3.27 r_work: 0.3122 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.4841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8212 Z= 0.136 Angle : 0.587 11.352 11174 Z= 0.293 Chirality : 0.046 0.414 1242 Planarity : 0.003 0.033 1398 Dihedral : 8.598 88.717 1349 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.19 % Allowed : 16.55 % Favored : 80.26 % 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 aren not related in a simple way. whole: 0.79 (0.27), residues: 984 helix: 1.51 (0.37), residues: 240 sheet: 1.08 (0.31), residues: 267 loop : -0.28 (0.28), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 244 TYR 0.027 0.002 TYR C 90 PHE 0.023 0.002 PHE B 326 TRP 0.009 0.001 TRP A 47 HIS 0.002 0.001 HIS A 355 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 8190) covalent geometry : angle 0.55816 (11121) SS BOND : bond 0.00276 ( 13) SS BOND : angle 1.77978 ( 26) hydrogen bonds : bond 0.02579 ( 214) hydrogen bonds : angle 4.62849 ( 585) link_NAG-ASN : bond 0.00391 ( 9) link_NAG-ASN : angle 3.31602 ( 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 106 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 79 time to evaluate : 0.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 SER cc_start: 0.8179 (OUTLIER) cc_final: 0.7525 (t) REVERT: A 248 GLU cc_start: 0.8587 (tt0) cc_final: 0.8291 (tt0) REVERT: A 304 ARG cc_start: 0.7918 (OUTLIER) cc_final: 0.7466 (mtt-85) REVERT: B 80 LEU cc_start: 0.8346 (mp) cc_final: 0.8072 (pp) REVERT: B 181 GLU cc_start: 0.8513 (mt-10) cc_final: 0.8200 (tt0) REVERT: C 283 LYS cc_start: 0.7676 (mmtt) cc_final: 0.7281 (ttpp) outliers start: 27 outliers final: 13 residues processed: 95 average time/residue: 0.4422 time to fit residues: 45.2676 Evaluate side-chains 85 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 70 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 66 SER 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 328 ILE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 99 SER 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: 5.9990 chunk 16 optimal weight: 1.9990 chunk 40 optimal weight: 7.9990 chunk 17 optimal weight: 0.8980 chunk 93 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 5 optimal weight: 10.0000 chunk 56 optimal weight: 2.9990 chunk 76 optimal weight: 0.0070 chunk 29 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 overall best weight: 1.1402 ------------------------------------------------------------------------------- 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 = 0.3665 r_free = 0.3665 target = 0.116829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.086627 restraints weight = 13598.043| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 3.26 r_work: 0.3116 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.5006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8212 Z= 0.134 Angle : 0.578 11.193 11174 Z= 0.292 Chirality : 0.046 0.411 1242 Planarity : 0.004 0.050 1398 Dihedral : 8.391 85.832 1349 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.43 % Allowed : 17.02 % Favored : 79.55 % 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 aren not related in a simple way. whole: 0.74 (0.27), residues: 984 helix: 1.42 (0.36), residues: 240 sheet: 1.05 (0.31), residues: 261 loop : -0.25 (0.28), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 244 TYR 0.023 0.002 TYR C 43 PHE 0.022 0.001 PHE B 92 TRP 0.014 0.001 TRP A 47 HIS 0.002 0.000 HIS A 355 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 8190) covalent geometry : angle 0.55215 (11121) SS BOND : bond 0.00254 ( 13) SS BOND : angle 1.82404 ( 26) hydrogen bonds : bond 0.02507 ( 214) hydrogen bonds : angle 4.58878 ( 585) link_NAG-ASN : bond 0.00371 ( 9) link_NAG-ASN : angle 3.10605 ( 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 100 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 71 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 SER cc_start: 0.8142 (m) cc_final: 0.7521 (t) REVERT: A 248 GLU cc_start: 0.8553 (tt0) cc_final: 0.8269 (tt0) REVERT: A 304 ARG cc_start: 0.7887 (OUTLIER) cc_final: 0.7431 (mtt-85) REVERT: B 181 GLU cc_start: 0.8543 (mt-10) cc_final: 0.8339 (mt-10) REVERT: C 248 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.8079 (mm-30) REVERT: C 283 LYS cc_start: 0.7746 (mmtt) cc_final: 0.7376 (ttpp) outliers start: 29 outliers final: 12 residues processed: 92 average time/residue: 0.4517 time to fit residues: 44.9863 Evaluate side-chains 80 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 66 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER 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 192 SER Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 99 SER Chi-restraints excluded: chain C residue 248 GLU 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: 0.7980 chunk 6 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 32 optimal weight: 20.0000 chunk 3 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- 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 = 0.3649 r_free = 0.3649 target = 0.115592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.085642 restraints weight = 13765.808| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 3.12 r_work: 0.3086 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.5113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8212 Z= 0.152 Angle : 0.587 11.438 11174 Z= 0.296 Chirality : 0.046 0.413 1242 Planarity : 0.004 0.039 1398 Dihedral : 8.283 85.294 1347 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.19 % Allowed : 17.38 % 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 aren not related in a simple way. whole: 0.71 (0.27), residues: 984 helix: 1.41 (0.36), residues: 240 sheet: 1.01 (0.31), residues: 261 loop : -0.27 (0.28), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 244 TYR 0.024 0.002 TYR C 90 PHE 0.025 0.002 PHE C 92 TRP 0.007 0.001 TRP A 47 HIS 0.002 0.001 HIS A 355 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 8190) covalent geometry : angle 0.56166 (11121) SS BOND : bond 0.00244 ( 13) SS BOND : angle 1.89190 ( 26) hydrogen bonds : bond 0.02627 ( 214) hydrogen bonds : angle 4.56945 ( 585) link_NAG-ASN : bond 0.00578 ( 9) link_NAG-ASN : angle 3.03937 ( 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 97 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 70 time to evaluate : 0.277 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 SER cc_start: 0.8204 (OUTLIER) cc_final: 0.7547 (t) REVERT: A 248 GLU cc_start: 0.8565 (tt0) cc_final: 0.8285 (tt0) REVERT: A 304 ARG cc_start: 0.7948 (OUTLIER) cc_final: 0.7465 (mtt-85) REVERT: C 248 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.8051 (mm-30) REVERT: C 283 LYS cc_start: 0.7808 (mmtt) cc_final: 0.7491 (ttpp) outliers start: 27 outliers final: 12 residues processed: 88 average time/residue: 0.4381 time to fit residues: 41.7501 Evaluate side-chains 79 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 64 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 72 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 192 SER Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 99 SER Chi-restraints excluded: chain C residue 248 GLU Chi-restraints excluded: chain C residue 258 ASP 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: 0.8980 chunk 94 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 = 0.3665 r_free = 0.3665 target = 0.116743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.087728 restraints weight = 13650.568| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 3.17 r_work: 0.3127 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.5189 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= 0.118 Angle : 0.558 10.860 11174 Z= 0.281 Chirality : 0.045 0.407 1242 Planarity : 0.003 0.032 1398 Dihedral : 8.085 81.469 1347 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.01 % Allowed : 18.91 % Favored : 79.08 % 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 aren not related in a simple way. whole: 0.47 (0.27), residues: 984 helix: 0.96 (0.35), residues: 258 sheet: 1.08 (0.31), residues: 261 loop : -0.47 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 244 TYR 0.026 0.002 TYR C 43 PHE 0.020 0.001 PHE B 92 TRP 0.007 0.001 TRP A 47 HIS 0.002 0.000 HIS A 355 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 8190) covalent geometry : angle 0.53604 (11121) SS BOND : bond 0.00229 ( 13) SS BOND : angle 1.69926 ( 26) hydrogen bonds : bond 0.02397 ( 214) hydrogen bonds : angle 4.55000 ( 585) link_NAG-ASN : bond 0.00472 ( 9) link_NAG-ASN : angle 2.79053 ( 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 88 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 71 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 SER cc_start: 0.8156 (m) cc_final: 0.7551 (t) REVERT: A 248 GLU cc_start: 0.8549 (tt0) cc_final: 0.8301 (tt0) REVERT: B 181 GLU cc_start: 0.8547 (mt-10) cc_final: 0.8152 (tt0) REVERT: C 283 LYS cc_start: 0.7853 (mmtt) cc_final: 0.7552 (ttpp) outliers start: 17 outliers final: 9 residues processed: 82 average time/residue: 0.4831 time to fit residues: 42.6778 Evaluate side-chains 74 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 65 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU 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 133 THR Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 66 SER 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: 9.9990 chunk 11 optimal weight: 9.9990 chunk 4 optimal weight: 5.9990 chunk 27 optimal weight: 0.7980 chunk 36 optimal weight: 6.9990 chunk 12 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 55 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 = 0.3651 r_free = 0.3651 target = 0.115757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.085529 restraints weight = 13609.245| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 3.24 r_work: 0.3096 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.5265 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= 0.145 Angle : 0.584 11.118 11174 Z= 0.294 Chirality : 0.046 0.405 1242 Planarity : 0.003 0.031 1398 Dihedral : 8.124 81.984 1347 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.25 % Allowed : 19.15 % 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 aren not related in a simple way. whole: 0.48 (0.27), residues: 984 helix: 0.93 (0.35), residues: 258 sheet: 1.06 (0.31), residues: 261 loop : -0.43 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 244 TYR 0.024 0.002 TYR C 90 PHE 0.027 0.002 PHE B 326 TRP 0.014 0.001 TRP A 47 HIS 0.002 0.001 HIS A 355 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 8190) covalent geometry : angle 0.56195 (11121) SS BOND : bond 0.00226 ( 13) SS BOND : angle 1.72569 ( 26) hydrogen bonds : bond 0.02603 ( 214) hydrogen bonds : angle 4.60238 ( 585) link_NAG-ASN : bond 0.00511 ( 9) link_NAG-ASN : angle 2.84581 ( 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 92 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 73 time to evaluate : 0.252 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLU cc_start: 0.9014 (mm-30) cc_final: 0.8660 (mp0) REVERT: A 66 SER cc_start: 0.8159 (m) cc_final: 0.7567 (t) REVERT: A 248 GLU cc_start: 0.8577 (tt0) cc_final: 0.8313 (tt0) REVERT: A 304 ARG cc_start: 0.8038 (OUTLIER) cc_final: 0.7561 (mtt-85) REVERT: B 181 GLU cc_start: 0.8572 (mt-10) cc_final: 0.8233 (tt0) REVERT: C 283 LYS cc_start: 0.7841 (mmtt) cc_final: 0.7606 (ttpp) outliers start: 19 outliers final: 13 residues processed: 87 average time/residue: 0.4708 time to fit residues: 44.1633 Evaluate side-chains 80 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 66 time to evaluate : 0.306 ------------------------------------------------------------------------------- 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 133 THR Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 99 SER 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: 0.7980 chunk 53 optimal weight: 6.9990 chunk 90 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 81 optimal weight: 0.8980 chunk 88 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 98 optimal weight: 10.0000 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 = 0.3655 r_free = 0.3655 target = 0.115949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.085945 restraints weight = 13677.132| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 3.20 r_work: 0.3108 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.5370 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= 0.137 Angle : 0.599 10.910 11174 Z= 0.304 Chirality : 0.046 0.404 1242 Planarity : 0.004 0.062 1398 Dihedral : 8.111 80.693 1347 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.01 % Allowed : 19.74 % Favored : 78.25 % 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 aren not related in a simple way. whole: 0.44 (0.27), residues: 984 helix: 0.85 (0.35), residues: 258 sheet: 1.08 (0.32), residues: 261 loop : -0.43 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 244 TYR 0.024 0.002 TYR C 43 PHE 0.023 0.001 PHE B 92 TRP 0.011 0.001 TRP A 47 HIS 0.002 0.000 HIS A 355 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 8190) covalent geometry : angle 0.57818 (11121) SS BOND : bond 0.00228 ( 13) SS BOND : angle 1.66370 ( 26) hydrogen bonds : bond 0.02623 ( 214) hydrogen bonds : angle 4.66300 ( 585) link_NAG-ASN : bond 0.00458 ( 9) link_NAG-ASN : angle 2.89275 ( 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 87 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 70 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLU cc_start: 0.9033 (mm-30) cc_final: 0.8591 (mp0) REVERT: A 66 SER cc_start: 0.8131 (m) cc_final: 0.7537 (t) REVERT: A 248 GLU cc_start: 0.8558 (tt0) cc_final: 0.8302 (tt0) REVERT: B 181 GLU cc_start: 0.8553 (mt-10) cc_final: 0.8133 (tt0) REVERT: C 283 LYS cc_start: 0.7855 (mmtt) cc_final: 0.7521 (ttpp) outliers start: 17 outliers final: 13 residues processed: 80 average time/residue: 0.4434 time to fit residues: 38.4405 Evaluate side-chains 80 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 67 time to evaluate : 0.326 ------------------------------------------------------------------------------- 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 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 133 THR Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 66 SER 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 22 optimal weight: 0.0980 chunk 98 optimal weight: 5.9990 chunk 73 optimal weight: 0.0870 chunk 71 optimal weight: 0.1980 chunk 42 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 80 optimal weight: 10.0000 chunk 53 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 84 optimal weight: 0.6980 overall best weight: 0.4160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.118234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.089328 restraints weight = 13652.396| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 3.16 r_work: 0.3156 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.5291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 8212 Z= 0.102 Angle : 0.571 10.226 11174 Z= 0.287 Chirality : 0.046 0.391 1242 Planarity : 0.003 0.031 1398 Dihedral : 7.987 78.372 1347 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.18 % Allowed : 20.57 % Favored : 78.25 % 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 aren not related in a simple way. whole: 0.49 (0.27), residues: 984 helix: 0.89 (0.35), residues: 258 sheet: 1.18 (0.32), residues: 261 loop : -0.47 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 244 TYR 0.025 0.001 TYR C 90 PHE 0.029 0.001 PHE B 326 TRP 0.021 0.001 TRP A 47 HIS 0.002 0.000 HIS A 355 Details of bonding type rmsd covalent geometry : bond 0.00233 ( 8190) covalent geometry : angle 0.55290 (11121) SS BOND : bond 0.00225 ( 13) SS BOND : angle 1.49025 ( 26) hydrogen bonds : bond 0.02351 ( 214) hydrogen bonds : angle 4.64871 ( 585) link_NAG-ASN : bond 0.00632 ( 9) link_NAG-ASN : angle 2.62298 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2719.08 seconds wall clock time: 47 minutes 6.64 seconds (2826.64 seconds total)