Starting phenix.real_space_refine on Fri Jul 25 17:10:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ztd_60458/07_2025/8ztd_60458.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ztd_60458/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8ztd_60458/07_2025/8ztd_60458.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ztd_60458/07_2025/8ztd_60458.map" model { file = "/net/cci-nas-00/data/ceres_data/8ztd_60458/07_2025/8ztd_60458.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ztd_60458/07_2025/8ztd_60458.cif" } resolution = 2.63 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 5.41, per 1000 atoms: 0.68 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: 2.06 Conformation dependent library (CDL) restraints added in 864.7 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: 0.92 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: 1.88 Time building geometry restraints manager: 2.45 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: 1.890 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: 0.410 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 21.470 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.030 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:12.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.320 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.007 0.001 TRP A 164 HIS 0.005 0.000 HIS A 355 PHE 0.006 0.001 PHE B 342 TYR 0.010 0.001 TYR B 90 ARG 0.001 0.000 ARG A 244 Details of bonding type rmsd link_NAG-ASN : bond 0.00826 ( 9) link_NAG-ASN : angle 3.17332 ( 27) hydrogen bonds : bond 0.20908 ( 214) hydrogen bonds : angle 7.55817 ( 585) SS BOND : bond 0.00321 ( 13) SS BOND : angle 0.69076 ( 26) covalent geometry : bond 0.00440 ( 8190) covalent geometry : angle 0.79943 (11121) *********************** 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 : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 242 ASP cc_start: 0.6724 (t70) cc_final: 0.6515 (t0) outliers start: 12 outliers final: 1 residues processed: 246 average time/residue: 1.0702 time to fit residues: 279.8363 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 : 0.917 ------------------------------------------------------------------------------- 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 83 optimal weight: 3.9990 chunk 75 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 50 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 30 optimal weight: 6.9990 chunk 47 optimal weight: 0.0370 chunk 57 optimal weight: 0.9980 chunk 89 optimal weight: 0.9980 overall best weight: 1.0062 ------------------------------------------------------------------------------- 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 B 76 GLN B 112 GLN B 180 HIS B 191 ASN B 220 HIS C 56 GLN C 191 ASN C 220 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.131086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.103390 restraints weight = 13503.098| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 3.19 r_work: 0.3388 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.2904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8212 Z= 0.140 Angle : 0.599 9.156 11174 Z= 0.299 Chirality : 0.047 0.326 1242 Planarity : 0.004 0.043 1398 Dihedral : 8.270 84.120 1349 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.19 % Allowed : 13.95 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.27), residues: 984 helix: 0.84 (0.36), residues: 240 sheet: 1.07 (0.30), residues: 279 loop : -0.51 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 47 HIS 0.007 0.001 HIS B 180 PHE 0.020 0.002 PHE C 92 TYR 0.035 0.002 TYR C 90 ARG 0.008 0.001 ARG A 244 Details of bonding type rmsd link_NAG-ASN : bond 0.01128 ( 9) link_NAG-ASN : angle 3.64837 ( 27) hydrogen bonds : bond 0.03052 ( 214) hydrogen bonds : angle 5.10831 ( 585) SS BOND : bond 0.00567 ( 13) SS BOND : angle 1.42136 ( 26) covalent geometry : bond 0.00312 ( 8190) covalent geometry : angle 0.56843 (11121) *********************** 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 142 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 115 time to evaluate : 1.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 GLU cc_start: 0.8345 (mp0) cc_final: 0.7928 (mp0) REVERT: B 80 LEU cc_start: 0.8355 (mp) cc_final: 0.8104 (pp) REVERT: B 83 GLN cc_start: 0.7834 (tt0) cc_final: 0.7618 (tt0) REVERT: B 185 PHE cc_start: 0.6249 (m-10) cc_final: 0.5827 (m-10) REVERT: B 260 GLU cc_start: 0.8412 (tp30) cc_final: 0.8146 (mm-30) REVERT: B 341 ILE cc_start: 0.8115 (mt) cc_final: 0.7889 (tt) REVERT: C 129 ASP cc_start: 0.8569 (OUTLIER) cc_final: 0.8248 (m-30) REVERT: C 270 CYS cc_start: 0.6758 (OUTLIER) cc_final: 0.6354 (m) REVERT: C 292 ARG cc_start: 0.8824 (mtm-85) cc_final: 0.8509 (mtm180) outliers start: 27 outliers final: 5 residues processed: 134 average time/residue: 0.9213 time to fit residues: 133.5553 Evaluate side-chains 91 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 84 time to evaluate : 0.782 ------------------------------------------------------------------------------- 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 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 14 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 43 optimal weight: 8.9990 chunk 66 optimal weight: 30.0000 chunk 89 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 83 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 76 GLN B 116 HIS B 180 HIS C 114 GLN C 241 GLN C 290 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.116718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.087205 restraints weight = 14007.309| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 3.18 r_work: 0.3080 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.4590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 8212 Z= 0.252 Angle : 0.693 12.642 11174 Z= 0.353 Chirality : 0.051 0.396 1242 Planarity : 0.004 0.048 1398 Dihedral : 9.124 89.054 1349 Min Nonbonded Distance : 1.771 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 4.37 % Allowed : 14.18 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.27), residues: 984 helix: 1.09 (0.36), residues: 240 sheet: 1.03 (0.31), residues: 267 loop : -0.24 (0.28), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 47 HIS 0.010 0.001 HIS B 180 PHE 0.037 0.002 PHE C 92 TYR 0.031 0.002 TYR C 90 ARG 0.010 0.001 ARG C 244 Details of bonding type rmsd link_NAG-ASN : bond 0.00741 ( 9) link_NAG-ASN : angle 4.44813 ( 27) hydrogen bonds : bond 0.03491 ( 214) hydrogen bonds : angle 4.86451 ( 585) SS BOND : bond 0.00393 ( 13) SS BOND : angle 1.63725 ( 26) covalent geometry : bond 0.00574 ( 8190) covalent geometry : angle 0.65456 (11121) *********************** 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 123 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 86 time to evaluate : 0.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 304 ARG cc_start: 0.8019 (OUTLIER) cc_final: 0.7586 (mtt-85) REVERT: B 181 GLU cc_start: 0.8562 (mt-10) cc_final: 0.8189 (tt0) REVERT: B 260 GLU cc_start: 0.8480 (tp30) cc_final: 0.8243 (mm-30) REVERT: C 138 GLU cc_start: 0.8630 (pm20) cc_final: 0.8415 (mp0) REVERT: C 170 ASP cc_start: 0.7477 (OUTLIER) cc_final: 0.6977 (m-30) outliers start: 37 outliers final: 15 residues processed: 116 average time/residue: 0.8217 time to fit residues: 103.7579 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 : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 304 ARG 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 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 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 37 optimal weight: 3.9990 chunk 43 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 chunk 38 optimal weight: 0.0370 chunk 76 optimal weight: 30.0000 chunk 82 optimal weight: 3.9990 chunk 65 optimal weight: 20.0000 chunk 41 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 overall best weight: 3.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 26 ASN B 114 GLN B 277 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.112614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.082111 restraints weight = 13653.303| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 3.18 r_work: 0.3041 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.5064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 8212 Z= 0.275 Angle : 0.704 13.374 11174 Z= 0.352 Chirality : 0.052 0.453 1242 Planarity : 0.004 0.049 1398 Dihedral : 9.378 88.943 1349 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 4.73 % Allowed : 15.01 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.27), residues: 984 helix: 1.29 (0.36), residues: 240 sheet: 0.75 (0.31), residues: 261 loop : -0.26 (0.28), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 47 HIS 0.004 0.001 HIS A 220 PHE 0.039 0.002 PHE C 92 TYR 0.027 0.002 TYR C 90 ARG 0.007 0.001 ARG A 244 Details of bonding type rmsd link_NAG-ASN : bond 0.00318 ( 9) link_NAG-ASN : angle 4.75960 ( 27) hydrogen bonds : bond 0.03278 ( 214) hydrogen bonds : angle 4.75332 ( 585) SS BOND : bond 0.00468 ( 13) SS BOND : angle 1.64344 ( 26) covalent geometry : bond 0.00630 ( 8190) covalent geometry : angle 0.66094 (11121) *********************** 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 114 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 74 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 ARG cc_start: 0.8514 (mtp-110) cc_final: 0.8304 (mtp85) REVERT: A 304 ARG cc_start: 0.8080 (OUTLIER) cc_final: 0.7620 (mtt-85) REVERT: B 70 LYS cc_start: 0.8542 (OUTLIER) cc_final: 0.8284 (mttm) REVERT: B 181 GLU cc_start: 0.8669 (mt-10) cc_final: 0.8399 (tt0) REVERT: B 260 GLU cc_start: 0.8535 (tp30) cc_final: 0.8287 (mm-30) REVERT: C 138 GLU cc_start: 0.8613 (pm20) cc_final: 0.8395 (mp0) REVERT: C 170 ASP cc_start: 0.7592 (OUTLIER) cc_final: 0.7140 (m-30) REVERT: C 197 ARG cc_start: 0.8740 (mtp85) cc_final: 0.8449 (mtp-110) REVERT: C 208 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7794 (mp0) REVERT: C 260 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7883 (tm-30) REVERT: C 283 LYS cc_start: 0.7593 (mmtt) cc_final: 0.7260 (ttpp) outliers start: 40 outliers final: 19 residues processed: 102 average time/residue: 0.8926 time to fit residues: 98.6954 Evaluate side-chains 91 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 67 time to evaluate : 0.903 ------------------------------------------------------------------------------- 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 328 ILE 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 70 LYS 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 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 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 260 GLU 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 41 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 5 optimal weight: 9.9990 chunk 27 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 88 optimal weight: 0.9990 chunk 77 optimal weight: 8.9990 chunk 18 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 1 optimal weight: 6.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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 = 0.3618 r_free = 0.3618 target = 0.113628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.083519 restraints weight = 13570.125| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 3.14 r_work: 0.3057 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.5167 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= 0.184 Angle : 0.624 12.618 11174 Z= 0.313 Chirality : 0.049 0.461 1242 Planarity : 0.004 0.032 1398 Dihedral : 9.023 85.434 1349 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.90 % Allowed : 16.90 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.27), residues: 984 helix: 1.37 (0.36), residues: 240 sheet: 0.61 (0.31), residues: 279 loop : -0.30 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 47 HIS 0.003 0.001 HIS A 355 PHE 0.030 0.002 PHE B 92 TYR 0.026 0.002 TYR C 90 ARG 0.005 0.001 ARG A 244 Details of bonding type rmsd link_NAG-ASN : bond 0.00349 ( 9) link_NAG-ASN : angle 4.28068 ( 27) hydrogen bonds : bond 0.02837 ( 214) hydrogen bonds : angle 4.72053 ( 585) SS BOND : bond 0.00276 ( 13) SS BOND : angle 1.39563 ( 26) covalent geometry : bond 0.00423 ( 8190) covalent geometry : angle 0.58456 (11121) *********************** 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 110 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 77 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 70 LYS cc_start: 0.8378 (OUTLIER) cc_final: 0.8037 (mttm) REVERT: B 181 GLU cc_start: 0.8626 (mt-10) cc_final: 0.8381 (tt0) REVERT: B 260 GLU cc_start: 0.8532 (tp30) cc_final: 0.8287 (mm-30) REVERT: C 138 GLU cc_start: 0.8597 (pm20) cc_final: 0.8396 (mp0) REVERT: C 170 ASP cc_start: 0.7511 (OUTLIER) cc_final: 0.7128 (m-30) REVERT: C 197 ARG cc_start: 0.8710 (mtp85) cc_final: 0.8489 (mtp-110) REVERT: C 283 LYS cc_start: 0.7760 (mmtt) cc_final: 0.7339 (ttpp) outliers start: 33 outliers final: 16 residues processed: 98 average time/residue: 0.8035 time to fit residues: 86.1417 Evaluate side-chains 85 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 67 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 70 LYS 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 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 87 VAL Chi-restraints excluded: chain C residue 99 SER Chi-restraints excluded: chain C residue 170 ASP 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 81 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 86 optimal weight: 5.9990 chunk 59 optimal weight: 0.6980 chunk 13 optimal weight: 8.9990 chunk 56 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 63 optimal weight: 8.9990 chunk 67 optimal weight: 0.7980 chunk 90 optimal weight: 0.8980 chunk 55 optimal weight: 0.0170 overall best weight: 0.6618 ------------------------------------------------------------------------------- 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 = 0.3660 r_free = 0.3660 target = 0.116403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.086472 restraints weight = 13447.047| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 3.23 r_work: 0.3105 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.5112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8212 Z= 0.110 Angle : 0.566 11.379 11174 Z= 0.284 Chirality : 0.047 0.438 1242 Planarity : 0.004 0.046 1398 Dihedral : 8.617 86.657 1349 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.72 % Allowed : 18.09 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.27), residues: 984 helix: 1.38 (0.36), residues: 240 sheet: 0.84 (0.31), residues: 261 loop : -0.32 (0.28), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 47 HIS 0.002 0.000 HIS A 355 PHE 0.026 0.002 PHE B 326 TYR 0.024 0.002 TYR C 90 ARG 0.008 0.000 ARG A 244 Details of bonding type rmsd link_NAG-ASN : bond 0.00467 ( 9) link_NAG-ASN : angle 3.74294 ( 27) hydrogen bonds : bond 0.02385 ( 214) hydrogen bonds : angle 4.64253 ( 585) SS BOND : bond 0.00241 ( 13) SS BOND : angle 1.09636 ( 26) covalent geometry : bond 0.00249 ( 8190) covalent geometry : angle 0.53443 (11121) *********************** 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: 23 poor density : 77 time to evaluate : 0.919 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 70 LYS cc_start: 0.8267 (OUTLIER) cc_final: 0.8061 (mttm) REVERT: B 181 GLU cc_start: 0.8583 (mt-10) cc_final: 0.8148 (tt0) REVERT: B 260 GLU cc_start: 0.8525 (tp30) cc_final: 0.8292 (mm-30) REVERT: C 138 GLU cc_start: 0.8578 (pm20) cc_final: 0.8370 (mp0) REVERT: C 283 LYS cc_start: 0.7792 (mmtt) cc_final: 0.7408 (ttpp) outliers start: 23 outliers final: 9 residues processed: 92 average time/residue: 0.8339 time to fit residues: 83.9874 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 : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain B residue 70 LYS 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 66 SER Chi-restraints excluded: chain C residue 87 VAL 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 25 optimal weight: 0.9990 chunk 72 optimal weight: 0.7980 chunk 61 optimal weight: 6.9990 chunk 34 optimal weight: 0.8980 chunk 93 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 56 optimal weight: 7.9990 chunk 26 optimal weight: 0.8980 chunk 20 optimal weight: 0.3980 chunk 11 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3662 r_free = 0.3662 target = 0.116696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.086747 restraints weight = 13636.927| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 3.22 r_work: 0.3108 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.5147 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= 0.114 Angle : 0.576 11.183 11174 Z= 0.285 Chirality : 0.046 0.424 1242 Planarity : 0.004 0.035 1398 Dihedral : 8.438 83.654 1347 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.25 % Allowed : 18.91 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.27), residues: 984 helix: 1.37 (0.36), residues: 240 sheet: 0.92 (0.31), residues: 261 loop : -0.33 (0.28), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 47 HIS 0.002 0.000 HIS A 355 PHE 0.020 0.001 PHE A 326 TYR 0.018 0.001 TYR B 90 ARG 0.008 0.000 ARG C 197 Details of bonding type rmsd link_NAG-ASN : bond 0.00631 ( 9) link_NAG-ASN : angle 3.70211 ( 27) hydrogen bonds : bond 0.02434 ( 214) hydrogen bonds : angle 4.62030 ( 585) SS BOND : bond 0.00219 ( 13) SS BOND : angle 1.15474 ( 26) covalent geometry : bond 0.00257 ( 8190) covalent geometry : angle 0.54500 (11121) *********************** 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: 19 poor density : 73 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 181 GLU cc_start: 0.8451 (mt-10) cc_final: 0.8098 (tt0) REVERT: B 260 GLU cc_start: 0.8517 (tp30) cc_final: 0.8277 (mm-30) REVERT: C 283 LYS cc_start: 0.7788 (mmtt) cc_final: 0.7416 (ttpp) outliers start: 19 outliers final: 8 residues processed: 87 average time/residue: 0.8235 time to fit residues: 78.3769 Evaluate side-chains 75 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 time to evaluate : 0.834 ------------------------------------------------------------------------------- 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 335 ILE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain C residue 186 THR 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 65 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 0 optimal weight: 40.0000 chunk 55 optimal weight: 0.9980 chunk 56 optimal weight: 4.9990 chunk 58 optimal weight: 0.9990 chunk 34 optimal weight: 9.9990 chunk 48 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 78 optimal weight: 9.9990 chunk 81 optimal weight: 4.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 = 0.3638 r_free = 0.3638 target = 0.115019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.084908 restraints weight = 13737.065| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 3.23 r_work: 0.3090 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.5252 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 : 0.585 11.448 11174 Z= 0.295 Chirality : 0.046 0.421 1242 Planarity : 0.004 0.037 1398 Dihedral : 8.389 83.841 1347 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.36 % Allowed : 18.79 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.27), residues: 984 helix: 1.37 (0.36), residues: 240 sheet: 0.91 (0.32), residues: 261 loop : -0.31 (0.28), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 47 HIS 0.002 0.001 HIS A 355 PHE 0.026 0.002 PHE B 326 TYR 0.029 0.002 TYR A 90 ARG 0.008 0.001 ARG A 244 Details of bonding type rmsd link_NAG-ASN : bond 0.00654 ( 9) link_NAG-ASN : angle 3.24572 ( 27) hydrogen bonds : bond 0.02623 ( 214) hydrogen bonds : angle 4.60316 ( 585) SS BOND : bond 0.00221 ( 13) SS BOND : angle 1.24345 ( 26) covalent geometry : bond 0.00333 ( 8190) covalent geometry : angle 0.56103 (11121) *********************** 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: 20 poor density : 74 time to evaluate : 1.131 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLU cc_start: 0.9037 (mm-30) cc_final: 0.8584 (mp0) REVERT: A 304 ARG cc_start: 0.8007 (OUTLIER) cc_final: 0.7506 (mtt-85) REVERT: B 172 LYS cc_start: 0.8617 (pttm) cc_final: 0.8203 (pmtt) REVERT: B 181 GLU cc_start: 0.8479 (mt-10) cc_final: 0.8122 (tt0) REVERT: B 260 GLU cc_start: 0.8532 (tp30) cc_final: 0.8300 (mm-30) REVERT: C 170 ASP cc_start: 0.7538 (OUTLIER) cc_final: 0.7196 (m-30) REVERT: C 172 LYS cc_start: 0.8460 (tppp) cc_final: 0.8246 (mmmt) REVERT: C 283 LYS cc_start: 0.7788 (mmtt) cc_final: 0.7417 (ttpp) outliers start: 20 outliers final: 11 residues processed: 89 average time/residue: 0.9311 time to fit residues: 89.9193 Evaluate side-chains 83 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 70 time to evaluate : 0.963 ------------------------------------------------------------------------------- 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 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 170 ASP Chi-restraints excluded: chain C residue 186 THR 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 8 optimal weight: 0.9980 chunk 47 optimal weight: 6.9990 chunk 26 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 chunk 6 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 36 optimal weight: 6.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.3650 r_free = 0.3650 target = 0.115922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.085687 restraints weight = 13778.827| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 3.27 r_work: 0.3096 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.5302 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= 0.122 Angle : 0.576 11.110 11174 Z= 0.292 Chirality : 0.046 0.419 1242 Planarity : 0.004 0.052 1398 Dihedral : 8.273 81.353 1347 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.89 % Allowed : 19.27 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.27), residues: 984 helix: 1.29 (0.36), residues: 240 sheet: 0.96 (0.32), residues: 261 loop : -0.29 (0.28), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 47 HIS 0.002 0.000 HIS A 355 PHE 0.021 0.001 PHE B 92 TYR 0.028 0.002 TYR A 90 ARG 0.005 0.000 ARG C 197 Details of bonding type rmsd link_NAG-ASN : bond 0.00499 ( 9) link_NAG-ASN : angle 3.02359 ( 27) hydrogen bonds : bond 0.02540 ( 214) hydrogen bonds : angle 4.63065 ( 585) SS BOND : bond 0.00221 ( 13) SS BOND : angle 1.14946 ( 26) covalent geometry : bond 0.00276 ( 8190) covalent geometry : angle 0.55527 (11121) *********************** 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: 16 poor density : 74 time to evaluate : 0.836 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLU cc_start: 0.9042 (mm-30) cc_final: 0.8618 (mp0) REVERT: B 70 LYS cc_start: 0.8381 (OUTLIER) cc_final: 0.7967 (mttm) REVERT: B 172 LYS cc_start: 0.8614 (pttm) cc_final: 0.8176 (pmtt) REVERT: B 181 GLU cc_start: 0.8436 (mt-10) cc_final: 0.8072 (tt0) REVERT: B 260 GLU cc_start: 0.8516 (tp30) cc_final: 0.8280 (mm-30) REVERT: C 172 LYS cc_start: 0.8435 (tppp) cc_final: 0.8215 (mmmt) REVERT: C 283 LYS cc_start: 0.7777 (mmtt) cc_final: 0.7407 (ttpp) outliers start: 16 outliers final: 10 residues processed: 85 average time/residue: 0.9137 time to fit residues: 84.3452 Evaluate side-chains 78 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 67 time to evaluate : 0.815 ------------------------------------------------------------------------------- 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 335 ILE Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 192 SER 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 40 optimal weight: 0.9990 chunk 92 optimal weight: 3.9990 chunk 5 optimal weight: 0.0870 chunk 89 optimal weight: 5.9990 chunk 69 optimal weight: 4.9990 chunk 44 optimal weight: 0.8980 chunk 95 optimal weight: 2.9990 chunk 32 optimal weight: 20.0000 chunk 47 optimal weight: 6.9990 chunk 75 optimal weight: 5.9990 chunk 51 optimal weight: 0.5980 overall best weight: 1.1162 ------------------------------------------------------------------------------- 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 = 0.3648 r_free = 0.3648 target = 0.115611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.085444 restraints weight = 13558.899| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 3.22 r_work: 0.3095 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.5367 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= 0.134 Angle : 0.589 11.079 11174 Z= 0.298 Chirality : 0.046 0.412 1242 Planarity : 0.004 0.054 1398 Dihedral : 8.200 80.606 1347 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.89 % Allowed : 19.27 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.27), residues: 984 helix: 0.83 (0.35), residues: 258 sheet: 0.96 (0.32), residues: 261 loop : -0.47 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 47 HIS 0.002 0.000 HIS A 355 PHE 0.028 0.002 PHE B 326 TYR 0.025 0.002 TYR C 90 ARG 0.018 0.001 ARG A 244 Details of bonding type rmsd link_NAG-ASN : bond 0.00432 ( 9) link_NAG-ASN : angle 2.97643 ( 27) hydrogen bonds : bond 0.02510 ( 214) hydrogen bonds : angle 4.62688 ( 585) SS BOND : bond 0.00219 ( 13) SS BOND : angle 1.19083 ( 26) covalent geometry : bond 0.00308 ( 8190) covalent geometry : angle 0.56875 (11121) ********************** 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: 16 poor density : 70 time to evaluate : 0.925 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLU cc_start: 0.9028 (mm-30) cc_final: 0.8661 (mp0) REVERT: A 304 ARG cc_start: 0.8001 (OUTLIER) cc_final: 0.7511 (mtt-85) REVERT: B 70 LYS cc_start: 0.8479 (OUTLIER) cc_final: 0.8069 (mttm) REVERT: B 172 LYS cc_start: 0.8562 (pttm) cc_final: 0.8158 (pmtt) REVERT: B 260 GLU cc_start: 0.8525 (tp30) cc_final: 0.8293 (mm-30) REVERT: C 170 ASP cc_start: 0.7543 (OUTLIER) cc_final: 0.7250 (m-30) REVERT: C 172 LYS cc_start: 0.8460 (tppp) cc_final: 0.8231 (mmmt) REVERT: C 283 LYS cc_start: 0.7796 (mmtt) cc_final: 0.7425 (ttpp) outliers start: 16 outliers final: 9 residues processed: 82 average time/residue: 0.9276 time to fit residues: 82.6748 Evaluate side-chains 77 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 65 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 335 ILE Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 170 ASP Chi-restraints excluded: chain C residue 318 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 44 optimal weight: 0.0040 chunk 73 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 77 optimal weight: 5.9990 chunk 74 optimal weight: 0.9990 chunk 38 optimal weight: 0.0370 chunk 24 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 19 optimal weight: 0.0970 chunk 54 optimal weight: 0.7980 chunk 36 optimal weight: 4.9990 overall best weight: 0.3870 ------------------------------------------------------------------------------- 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 = 0.3684 r_free = 0.3684 target = 0.118174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.088458 restraints weight = 13709.826| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 3.16 r_work: 0.3141 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.5326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 8212 Z= 0.099 Angle : 0.554 10.279 11174 Z= 0.281 Chirality : 0.045 0.398 1242 Planarity : 0.004 0.055 1398 Dihedral : 7.932 78.377 1347 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.30 % Allowed : 19.86 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.27), residues: 984 helix: 0.91 (0.35), residues: 258 sheet: 0.86 (0.31), residues: 273 loop : -0.42 (0.28), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 47 HIS 0.002 0.000 HIS A 355 PHE 0.020 0.001 PHE A 326 TYR 0.033 0.002 TYR A 90 ARG 0.012 0.001 ARG B 197 Details of bonding type rmsd link_NAG-ASN : bond 0.00497 ( 9) link_NAG-ASN : angle 2.75706 ( 27) hydrogen bonds : bond 0.02320 ( 214) hydrogen bonds : angle 4.61876 ( 585) SS BOND : bond 0.00208 ( 13) SS BOND : angle 1.06285 ( 26) covalent geometry : bond 0.00223 ( 8190) covalent geometry : angle 0.53649 (11121) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5586.41 seconds wall clock time: 95 minutes 54.01 seconds (5754.01 seconds total)