Starting phenix.real_space_refine on Thu Jul 2 08:09:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ux3_64571/07_2026/9ux3_64571_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ux3_64571/07_2026/9ux3_64571.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ux3_64571/07_2026/9ux3_64571.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ux3_64571/07_2026/9ux3_64571.map" model { file = "/net/cci-nas-00/data/ceres_data/9ux3_64571/07_2026/9ux3_64571_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ux3_64571/07_2026/9ux3_64571_neut.cif" } resolution = 2.64 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= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 9 5.49 5 S 42 5.16 5 C 4803 2.51 5 N 1246 2.21 5 O 1429 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7529 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2432 Classifications: {'peptide': 310} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 294} Chain: "B" Number of atoms: 2441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2441 Classifications: {'peptide': 313} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 297} Chain: "C" Number of atoms: 2441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2441 Classifications: {'peptide': 313} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 297} Chain: "A" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 73 Unusual residues: {'ATP': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} 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: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {'ATP': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 83 Unusual residues: {'AF9': 1, 'ATP': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 1.77, per 1000 atoms: 0.24 Number of scatterers: 7529 At special positions: 0 Unit cell: (88.35, 90.25, 117.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 42 16.00 P 9 15.00 O 1429 8.00 N 1246 7.00 C 4803 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 107 " - pdb=" SG CYS A 153 " distance=2.04 Simple disulfide: pdb=" SG CYS A 116 " - pdb=" SG CYS A 137 " distance=2.02 Simple disulfide: pdb=" SG CYS A 122 " - pdb=" SG CYS A 147 " distance=2.04 Simple disulfide: pdb=" SG CYS A 203 " - pdb=" SG CYS A 213 " distance=2.05 Simple disulfide: pdb=" SG CYS A 247 " - pdb=" SG CYS A 256 " distance=2.03 Simple disulfide: pdb=" SG CYS B 125 " - pdb=" SG CYS B 176 " distance=2.02 Simple disulfide: pdb=" SG CYS B 136 " - pdb=" SG CYS B 159 " distance=2.03 Simple disulfide: pdb=" SG CYS B 142 " - pdb=" SG CYS B 170 " distance=2.03 Simple disulfide: pdb=" SG CYS B 226 " - pdb=" SG CYS B 236 " distance=2.03 Simple disulfide: pdb=" SG CYS B 270 " - pdb=" SG CYS B 279 " distance=2.04 Simple disulfide: pdb=" SG CYS C 125 " - pdb=" SG CYS C 176 " distance=2.03 Simple disulfide: pdb=" SG CYS C 136 " - pdb=" SG CYS C 159 " distance=2.03 Simple disulfide: pdb=" SG CYS C 142 " - pdb=" SG CYS C 170 " distance=2.04 Simple disulfide: pdb=" SG CYS C 226 " - pdb=" SG CYS C 236 " distance=2.03 Simple disulfide: pdb=" SG CYS C 270 " - pdb=" SG CYS C 279 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 401 " - " ASN A 290 " " NAG A 402 " - " ASN A 170 " " NAG A 403 " - " ASN A 194 " " NAG B 501 " - " ASN B 133 " " NAG B 502 " - " ASN B 194 " " NAG C 503 " - " ASN C 133 " " NAG C 504 " - " ASN C 194 " Time building additional restraints: 0.64 Conformation dependent library (CDL) restraints added in 400.0 milliseconds 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1714 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 9 sheets defined 21.9% alpha, 26.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 30 through 42 Processing helix chain 'A' and resid 76 through 80 removed outlier: 3.532A pdb=" N TYR A 80 " --> pdb=" O ASP A 76 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 76 through 80' Processing helix chain 'A' and resid 165 through 170 removed outlier: 3.897A pdb=" N ALA A 168 " --> pdb=" O MET A 165 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLU A 169 " --> pdb=" O MET A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 203 removed outlier: 3.923A pdb=" N THR A 202 " --> pdb=" O ARG A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 225 Processing helix chain 'A' and resid 228 through 236 removed outlier: 3.823A pdb=" N ARG A 234 " --> pdb=" O ALA A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 256 removed outlier: 3.524A pdb=" N GLN A 255 " --> pdb=" O ALA A 252 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N CYS A 256 " --> pdb=" O TRP A 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 252 through 256' Processing helix chain 'A' and resid 318 through 338 Processing helix chain 'B' and resid 47 through 63 Processing helix chain 'B' and resid 94 through 98 removed outlier: 3.635A pdb=" N TYR B 98 " --> pdb=" O ASP B 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 94 through 98' Processing helix chain 'B' and resid 138 through 142 removed outlier: 3.893A pdb=" N CYS B 142 " --> pdb=" O ASP B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 194 Processing helix chain 'B' and resid 241 through 248 Processing helix chain 'B' and resid 251 through 259 Processing helix chain 'B' and resid 337 through 357 removed outlier: 3.590A pdb=" N THR B 341 " --> pdb=" O SER B 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 62 Processing helix chain 'C' and resid 94 through 98 removed outlier: 3.698A pdb=" N TYR C 98 " --> pdb=" O ASP C 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 94 through 98' Processing helix chain 'C' and resid 191 through 194 Processing helix chain 'C' and resid 241 through 248 Processing helix chain 'C' and resid 251 through 259 Processing helix chain 'C' and resid 337 through 357 Processing sheet with id=AA1, first strand: chain 'A' and resid 50 through 53 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 50 through 53 current: chain 'A' and resid 89 through 108 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 89 through 108 current: chain 'A' and resid 148 through 153 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 148 through 153 current: chain 'A' and resid 259 through 264 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 259 through 264 current: chain 'A' and resid 293 through 316 No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 57 through 65 Processing sheet with id=AA3, first strand: chain 'A' and resid 68 through 70 Processing sheet with id=AA4, first strand: chain 'A' and resid 138 through 139 removed outlier: 3.538A pdb=" N VAL A 138 " --> pdb=" O THR A 146 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR A 146 " --> pdb=" O VAL A 138 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 68 through 71 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 68 through 71 current: chain 'B' and resid 107 through 126 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 107 through 126 current: chain 'B' and resid 154 through 161 removed outlier: 9.701A pdb=" N LEU B 154 " --> pdb=" O TRP B 175 " (cutoff:3.500A) removed outlier: 9.339A pdb=" N TRP B 175 " --> pdb=" O LEU B 154 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N THR B 156 " --> pdb=" O PHE B 173 " (cutoff:3.500A) removed outlier: 8.261A pdb=" N PHE B 173 " --> pdb=" O THR B 156 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N ARG B 158 " --> pdb=" O GLU B 171 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 168 through 176 current: chain 'B' and resid 281 through 287 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 281 through 287 current: chain 'B' and resid 312 through 336 Processing sheet with id=AA6, first strand: chain 'B' and resid 75 through 83 Processing sheet with id=AA7, first strand: chain 'C' and resid 68 through 71 Processing sheet with id=AA8, first strand: chain 'C' and resid 75 through 83 Processing sheet with id=AA9, first strand: chain 'C' and resid 99 through 100 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 107 through 126 current: chain 'C' and resid 168 through 176 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 168 through 176 current: chain 'C' and resid 281 through 287 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 281 through 287 current: chain 'C' and resid 312 through 329 170 hydrogen bonds defined for protein. 462 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: 1.07 Time building geometry restraints manager: 0.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 1188 1.31 - 1.45: 2225 1.45 - 1.59: 4234 1.59 - 1.72: 16 1.72 - 1.86: 53 Bond restraints: 7716 Sorted by residual: bond pdb=" CA MET B 191 " pdb=" C MET B 191 " ideal model delta sigma weight residual 1.521 1.414 0.108 1.31e-02 5.83e+03 6.76e+01 bond pdb=" CA LEU C 147 " pdb=" C LEU C 147 " ideal model delta sigma weight residual 1.526 1.422 0.104 1.28e-02 6.10e+03 6.55e+01 bond pdb=" C4 ATP B 503 " pdb=" C5 ATP B 503 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.34e+01 bond pdb=" C4 ATP A 404 " pdb=" C5 ATP A 404 " ideal model delta sigma weight residual 1.388 1.464 -0.076 1.00e-02 1.00e+04 5.78e+01 bond pdb=" C4 ATP C 501 " pdb=" C5 ATP C 501 " ideal model delta sigma weight residual 1.388 1.464 -0.076 1.00e-02 1.00e+04 5.76e+01 ... (remaining 7711 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.60: 10372 3.60 - 7.20: 91 7.20 - 10.80: 22 10.80 - 14.40: 5 14.40 - 18.01: 3 Bond angle restraints: 10493 Sorted by residual: angle pdb=" PB ATP B 503 " pdb=" O3B ATP B 503 " pdb=" PG ATP B 503 " ideal model delta sigma weight residual 139.87 123.48 16.39 1.00e+00 1.00e+00 2.69e+02 angle pdb=" PB ATP C 501 " pdb=" O3B ATP C 501 " pdb=" PG ATP C 501 " ideal model delta sigma weight residual 139.87 124.17 15.70 1.00e+00 1.00e+00 2.47e+02 angle pdb=" PA ATP C 501 " pdb=" O3A ATP C 501 " pdb=" PB ATP C 501 " ideal model delta sigma weight residual 136.83 122.91 13.92 1.00e+00 1.00e+00 1.94e+02 angle pdb=" PA ATP B 503 " pdb=" O3A ATP B 503 " pdb=" PB ATP B 503 " ideal model delta sigma weight residual 136.83 123.93 12.90 1.00e+00 1.00e+00 1.67e+02 angle pdb=" PB ATP A 404 " pdb=" O3B ATP A 404 " pdb=" PG ATP A 404 " ideal model delta sigma weight residual 139.87 127.30 12.57 1.00e+00 1.00e+00 1.58e+02 ... (remaining 10488 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 4246 17.79 - 35.59: 363 35.59 - 53.38: 87 53.38 - 71.17: 25 71.17 - 88.96: 6 Dihedral angle restraints: 4727 sinusoidal: 2040 harmonic: 2687 Sorted by residual: dihedral pdb=" CB CYS A 122 " pdb=" SG CYS A 122 " pdb=" SG CYS A 147 " pdb=" CB CYS A 147 " ideal model delta sinusoidal sigma weight residual 93.00 174.19 -81.19 1 1.00e+01 1.00e-02 8.13e+01 dihedral pdb=" CB CYS A 247 " pdb=" SG CYS A 247 " pdb=" SG CYS A 256 " pdb=" CB CYS A 256 " ideal model delta sinusoidal sigma weight residual 93.00 166.93 -73.93 1 1.00e+01 1.00e-02 6.94e+01 dihedral pdb=" CB CYS B 270 " pdb=" SG CYS B 270 " pdb=" SG CYS B 279 " pdb=" CB CYS B 279 " ideal model delta sinusoidal sigma weight residual -86.00 -40.87 -45.13 1 1.00e+01 1.00e-02 2.83e+01 ... (remaining 4724 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 644 0.036 - 0.073: 336 0.073 - 0.109: 142 0.109 - 0.145: 57 0.145 - 0.182: 6 Chirality restraints: 1185 Sorted by residual: chirality pdb=" CA LYS C 65 " pdb=" N LYS C 65 " pdb=" C LYS C 65 " pdb=" CB LYS C 65 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.24e-01 chirality pdb=" CA ILE B 85 " pdb=" N ILE B 85 " pdb=" C ILE B 85 " pdb=" CB ILE B 85 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.58e-01 chirality pdb=" CA ILE A 303 " pdb=" N ILE A 303 " pdb=" C ILE A 303 " pdb=" CB ILE A 303 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.32e-01 ... (remaining 1182 not shown) Planarity restraints: 1310 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR B 190 " 0.020 2.00e-02 2.50e+03 3.78e-02 1.43e+01 pdb=" C THR B 190 " -0.065 2.00e-02 2.50e+03 pdb=" O THR B 190 " 0.024 2.00e-02 2.50e+03 pdb=" N MET B 191 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 223 " -0.012 2.00e-02 2.50e+03 2.40e-02 5.76e+00 pdb=" C LEU B 223 " 0.042 2.00e-02 2.50e+03 pdb=" O LEU B 223 " -0.015 2.00e-02 2.50e+03 pdb=" N LYS B 224 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG C 225 " -0.011 2.00e-02 2.50e+03 2.18e-02 4.75e+00 pdb=" C ARG C 225 " 0.038 2.00e-02 2.50e+03 pdb=" O ARG C 225 " -0.015 2.00e-02 2.50e+03 pdb=" N CYS C 226 " -0.012 2.00e-02 2.50e+03 ... (remaining 1307 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 59 2.61 - 3.18: 6220 3.18 - 3.76: 10683 3.76 - 4.33: 16044 4.33 - 4.90: 26154 Nonbonded interactions: 59160 Sorted by model distance: nonbonded pdb=" OE2 GLU B 97 " pdb=" NE1 TRP C 175 " model vdw 2.038 3.120 nonbonded pdb=" OH TYR C 235 " pdb=" OD1 ASN C 280 " model vdw 2.208 3.040 nonbonded pdb=" OH TYR C 222 " pdb=" OD1 ASP C 233 " model vdw 2.265 3.040 nonbonded pdb=" NH1 ARG A 217 " pdb=" OD1 ASP A 220 " model vdw 2.272 3.120 nonbonded pdb=" O LEU B 338 " pdb=" OG1 THR B 341 " model vdw 2.299 3.040 ... (remaining 59155 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 'B' and resid 46 through 358) selection = (chain 'C' and resid 46 through 358) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.560 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.350 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 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 : 0.007 0.108 7738 Z= 0.452 Angle : 1.063 18.005 10544 Z= 0.673 Chirality : 0.053 0.182 1185 Planarity : 0.006 0.048 1303 Dihedral : 14.710 88.964 2968 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 0.12 % Allowed : 5.82 % Favored : 94.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.24 (0.25), residues: 930 helix: -2.18 (0.32), residues: 179 sheet: -0.12 (0.28), residues: 327 loop : -2.27 (0.27), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 302 TYR 0.019 0.002 TYR A 260 PHE 0.022 0.002 PHE C 61 TRP 0.021 0.003 TRP C 58 HIS 0.003 0.001 HIS B 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00745 / 0.45 ( 7716) covalent geometry : angle 1.04965 / 0.67 (10493) SS BOND : bond 0.00718 / 0.37 ( 15) SS BOND : angle 2.65418 / 1.69 ( 30) hydrogen bonds : bond 0.11472 / 8.04 ( 170) hydrogen bonds : angle 6.29538 / 4.33 ( 462) link_NAG-ASN : bond 0.00406 / 0.27 ( 7) link_NAG-ASN : angle 2.62612 / 1.70 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 97 time to evaluate : 0.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 68 GLN cc_start: 0.8365 (pt0) cc_final: 0.8031 (pt0) outliers start: 1 outliers final: 0 residues processed: 98 average time/residue: 0.6952 time to fit residues: 71.4358 Evaluate side-chains 53 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.4980 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 6.9990 chunk 45 optimal weight: 0.9980 chunk 74 optimal weight: 0.6980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 104 GLN A 177 ASN A 185 ASN B 201 ASN B 204 HIS B 209 HIS C 132 HIS C 201 ASN C 209 HIS C 229 HIS C 344 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.116627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.085300 restraints weight = 15615.736| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 3.39 r_work: 0.3209 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 7738 Z= 0.170 Angle : 0.689 11.596 10544 Z= 0.349 Chirality : 0.050 0.366 1185 Planarity : 0.004 0.045 1303 Dihedral : 12.042 84.167 1277 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.61 % Allowed : 10.90 % Favored : 87.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.57 (0.26), residues: 930 helix: -1.15 (0.36), residues: 177 sheet: 0.10 (0.27), residues: 335 loop : -1.95 (0.28), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 115 TYR 0.013 0.001 TYR A 140 PHE 0.016 0.001 PHE C 252 TRP 0.018 0.002 TRP A 253 HIS 0.005 0.001 HIS B 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.17 ( 7716) covalent geometry : angle 0.66393 / 0.34 (10493) SS BOND : bond 0.00577 / 0.38 ( 15) SS BOND : angle 2.21552 / 1.39 ( 30) hydrogen bonds : bond 0.04395 / 3.03 ( 170) hydrogen bonds : angle 5.31382 / 3.59 ( 462) link_NAG-ASN : bond 0.01806 / 0.56 ( 7) link_NAG-ASN : angle 3.33758 / 1.71 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 62 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 HIS cc_start: 0.8095 (t-90) cc_final: 0.7871 (t70) REVERT: A 75 MET cc_start: 0.8688 (OUTLIER) cc_final: 0.8305 (mtm) REVERT: C 149 MET cc_start: 0.8183 (mmp) cc_final: 0.7867 (mmp) outliers start: 13 outliers final: 3 residues processed: 67 average time/residue: 0.5483 time to fit residues: 39.2163 Evaluate side-chains 61 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 57 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 MET Chi-restraints excluded: chain A residue 165 MET Chi-restraints excluded: chain B residue 55 TYR Chi-restraints excluded: chain B residue 291 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 83 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 71 optimal weight: 10.0000 chunk 44 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 85 GLN C 204 HIS C 344 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.112718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.081177 restraints weight = 15788.132| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 3.41 r_work: 0.3146 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 7738 Z= 0.309 Angle : 0.751 8.790 10544 Z= 0.385 Chirality : 0.053 0.291 1185 Planarity : 0.005 0.069 1303 Dihedral : 11.936 88.578 1277 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 2.73 % Allowed : 13.88 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.33 (0.26), residues: 930 helix: -0.73 (0.36), residues: 181 sheet: 0.18 (0.29), residues: 308 loop : -1.73 (0.28), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 198 TYR 0.013 0.002 TYR A 70 PHE 0.018 0.002 PHE C 252 TRP 0.020 0.003 TRP A 253 HIS 0.003 0.001 HIS C 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00740 / 0.31 ( 7716) covalent geometry : angle 0.73025 / 0.38 (10493) SS BOND : bond 0.00774 / 0.51 ( 15) SS BOND : angle 2.62985 / 1.69 ( 30) hydrogen bonds : bond 0.04539 / 3.16 ( 170) hydrogen bonds : angle 5.18889 / 3.50 ( 462) link_NAG-ASN : bond 0.00645 / 0.22 ( 7) link_NAG-ASN : angle 2.63839 / 1.77 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 60 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 MET cc_start: 0.8722 (OUTLIER) cc_final: 0.8427 (mtm) REVERT: A 242 LYS cc_start: 0.8497 (OUTLIER) cc_final: 0.7867 (mppt) REVERT: C 286 ARG cc_start: 0.8227 (OUTLIER) cc_final: 0.7638 (ptt-90) outliers start: 22 outliers final: 8 residues processed: 73 average time/residue: 0.5302 time to fit residues: 41.3274 Evaluate side-chains 61 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 50 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 75 MET Chi-restraints excluded: chain A residue 116 CYS Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 165 MET Chi-restraints excluded: chain A residue 242 LYS Chi-restraints excluded: chain B residue 55 TYR Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 291 LYS Chi-restraints excluded: chain C residue 286 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 89 optimal weight: 0.7980 chunk 72 optimal weight: 0.6980 chunk 78 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 2 optimal weight: 0.2980 chunk 20 optimal weight: 1.9990 chunk 15 optimal weight: 0.0670 chunk 33 optimal weight: 2.9990 chunk 70 optimal weight: 0.5980 chunk 41 optimal weight: 0.6980 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 45 HIS C 344 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.116141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.084561 restraints weight = 15739.167| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 3.41 r_work: 0.3208 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 7738 Z= 0.127 Angle : 0.636 11.651 10544 Z= 0.320 Chirality : 0.048 0.265 1185 Planarity : 0.004 0.057 1303 Dihedral : 10.772 89.436 1277 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.35 % Allowed : 15.24 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.27), residues: 930 helix: -0.23 (0.38), residues: 182 sheet: 0.47 (0.29), residues: 306 loop : -1.45 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 315 TYR 0.010 0.001 TYR A 140 PHE 0.016 0.001 PHE B 61 TRP 0.020 0.002 TRP A 253 HIS 0.005 0.001 HIS C 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 ( 7716) covalent geometry : angle 0.60719 / 0.31 (10493) SS BOND : bond 0.00420 / 0.25 ( 15) SS BOND : angle 1.63826 / 1.02 ( 30) hydrogen bonds : bond 0.03518 / 2.41 ( 170) hydrogen bonds : angle 4.77707 / 3.23 ( 462) link_NAG-ASN : bond 0.00364 / 0.16 ( 7) link_NAG-ASN : angle 3.90075 / 2.28 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 66 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 MET cc_start: 0.8647 (OUTLIER) cc_final: 0.8247 (mtm) REVERT: A 165 MET cc_start: 0.8151 (OUTLIER) cc_final: 0.7894 (ttp) REVERT: C 127 GLU cc_start: 0.8666 (tp30) cc_final: 0.8317 (tp30) REVERT: C 324 ARG cc_start: 0.9306 (OUTLIER) cc_final: 0.7911 (ttm170) outliers start: 19 outliers final: 6 residues processed: 78 average time/residue: 0.5390 time to fit residues: 44.7808 Evaluate side-chains 65 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 75 MET Chi-restraints excluded: chain A residue 116 CYS Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 165 MET Chi-restraints excluded: chain B residue 55 TYR Chi-restraints excluded: chain B residue 291 LYS Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 324 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 87 optimal weight: 0.8980 chunk 82 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 64 optimal weight: 7.9990 chunk 61 optimal weight: 5.9990 chunk 88 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 81 optimal weight: 0.1980 chunk 42 optimal weight: 0.4980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 85 GLN C 344 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.114687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.082901 restraints weight = 15751.676| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 3.45 r_work: 0.3185 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7738 Z= 0.177 Angle : 0.669 12.185 10544 Z= 0.335 Chirality : 0.048 0.196 1185 Planarity : 0.004 0.050 1303 Dihedral : 10.732 87.190 1277 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.22 % Allowed : 15.61 % Favored : 81.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.27), residues: 930 helix: -0.11 (0.38), residues: 182 sheet: 0.48 (0.28), residues: 322 loop : -1.47 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 315 TYR 0.009 0.001 TYR C 321 PHE 0.015 0.001 PHE C 252 TRP 0.024 0.002 TRP A 253 HIS 0.005 0.001 HIS C 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.18 ( 7716) covalent geometry : angle 0.64891 / 0.33 (10493) SS BOND : bond 0.00586 / 0.38 ( 15) SS BOND : angle 1.97122 / 1.25 ( 30) hydrogen bonds : bond 0.03814 / 2.62 ( 170) hydrogen bonds : angle 4.75206 / 3.20 ( 462) link_NAG-ASN : bond 0.00177 / 0.08 ( 7) link_NAG-ASN : angle 2.96592 / 1.82 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 58 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 MET cc_start: 0.8706 (OUTLIER) cc_final: 0.8363 (mtm) REVERT: C 127 GLU cc_start: 0.8705 (tp30) cc_final: 0.8340 (tp30) REVERT: C 324 ARG cc_start: 0.9338 (OUTLIER) cc_final: 0.7956 (ttm170) outliers start: 26 outliers final: 10 residues processed: 72 average time/residue: 0.4418 time to fit residues: 34.4032 Evaluate side-chains 68 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 56 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 75 MET Chi-restraints excluded: chain A residue 116 CYS Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 165 MET Chi-restraints excluded: chain B residue 55 TYR Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 291 LYS Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 296 SER Chi-restraints excluded: chain C residue 324 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 24 optimal weight: 0.0870 chunk 61 optimal weight: 5.9990 chunk 23 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 chunk 9 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 overall best weight: 0.7362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.115280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.083440 restraints weight = 15662.447| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 3.43 r_work: 0.3204 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7738 Z= 0.138 Angle : 0.630 11.528 10544 Z= 0.315 Chirality : 0.048 0.198 1185 Planarity : 0.004 0.047 1303 Dihedral : 10.381 84.146 1277 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.73 % Allowed : 16.60 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.27), residues: 930 helix: 0.03 (0.38), residues: 184 sheet: 0.62 (0.28), residues: 322 loop : -1.45 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 286 TYR 0.014 0.001 TYR A 140 PHE 0.014 0.001 PHE C 252 TRP 0.024 0.002 TRP A 253 HIS 0.008 0.001 HIS A 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 ( 7716) covalent geometry : angle 0.61049 / 0.31 (10493) SS BOND : bond 0.00460 / 0.29 ( 15) SS BOND : angle 1.71451 / 1.07 ( 30) hydrogen bonds : bond 0.03486 / 2.34 ( 170) hydrogen bonds : angle 4.55417 / 3.05 ( 462) link_NAG-ASN : bond 0.00236 / 0.11 ( 7) link_NAG-ASN : angle 2.93488 / 1.73 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 66 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 MET cc_start: 0.8667 (OUTLIER) cc_final: 0.8277 (mtm) REVERT: A 111 GLU cc_start: 0.8466 (OUTLIER) cc_final: 0.8245 (tm-30) REVERT: B 115 GLU cc_start: 0.8921 (OUTLIER) cc_final: 0.8667 (mt-10) REVERT: C 68 GLN cc_start: 0.8747 (tt0) cc_final: 0.8165 (tp-100) REVERT: C 127 GLU cc_start: 0.8672 (tp30) cc_final: 0.8316 (tp30) REVERT: C 149 MET cc_start: 0.8194 (OUTLIER) cc_final: 0.7431 (tpt) REVERT: C 209 HIS cc_start: 0.8330 (OUTLIER) cc_final: 0.8097 (m-70) REVERT: C 324 ARG cc_start: 0.9324 (OUTLIER) cc_final: 0.7963 (ttm170) outliers start: 22 outliers final: 8 residues processed: 79 average time/residue: 0.4774 time to fit residues: 40.5049 Evaluate side-chains 71 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 57 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 75 MET Chi-restraints excluded: chain A residue 111 GLU Chi-restraints excluded: chain A residue 116 CYS Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain B residue 55 TYR Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 291 LYS Chi-restraints excluded: chain C residue 149 MET Chi-restraints excluded: chain C residue 209 HIS Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 296 SER Chi-restraints excluded: chain C residue 324 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 28 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 63 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 80 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 152 ASN C 344 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.114069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.082424 restraints weight = 15852.469| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 3.42 r_work: 0.3180 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 7738 Z= 0.198 Angle : 0.690 10.803 10544 Z= 0.347 Chirality : 0.049 0.187 1185 Planarity : 0.004 0.048 1303 Dihedral : 10.426 82.921 1277 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 3.10 % Allowed : 16.98 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.27), residues: 930 helix: 0.01 (0.38), residues: 185 sheet: 0.49 (0.27), residues: 316 loop : -1.36 (0.30), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 115 TYR 0.010 0.001 TYR B 59 PHE 0.015 0.001 PHE C 252 TRP 0.027 0.002 TRP A 253 HIS 0.005 0.001 HIS C 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00479 / 0.20 ( 7716) covalent geometry : angle 0.66802 / 0.34 (10493) SS BOND : bond 0.00591 / 0.39 ( 15) SS BOND : angle 2.28447 / 1.42 ( 30) hydrogen bonds : bond 0.03831 / 2.60 ( 170) hydrogen bonds : angle 4.68830 / 3.13 ( 462) link_NAG-ASN : bond 0.00165 / 0.08 ( 7) link_NAG-ASN : angle 2.98959 / 1.78 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 59 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 MET cc_start: 0.8703 (OUTLIER) cc_final: 0.8345 (mtm) REVERT: A 111 GLU cc_start: 0.8457 (OUTLIER) cc_final: 0.8198 (tm-30) REVERT: B 115 GLU cc_start: 0.8942 (OUTLIER) cc_final: 0.8669 (mt-10) REVERT: C 68 GLN cc_start: 0.8710 (tt0) cc_final: 0.8255 (tp-100) REVERT: C 127 GLU cc_start: 0.8708 (tp30) cc_final: 0.8323 (tp30) REVERT: C 149 MET cc_start: 0.8232 (OUTLIER) cc_final: 0.7909 (tpt) REVERT: C 324 ARG cc_start: 0.9350 (OUTLIER) cc_final: 0.7895 (ttm170) outliers start: 25 outliers final: 9 residues processed: 72 average time/residue: 0.4799 time to fit residues: 37.2685 Evaluate side-chains 71 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 57 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 75 MET Chi-restraints excluded: chain A residue 111 GLU Chi-restraints excluded: chain A residue 116 CYS Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain B residue 55 TYR Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain B residue 291 LYS Chi-restraints excluded: chain C residue 149 MET Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 296 SER Chi-restraints excluded: chain C residue 324 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 83 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 9 optimal weight: 0.0070 chunk 29 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 85 optimal weight: 0.0060 chunk 16 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 overall best weight: 0.8018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 45 HIS B 152 ASN C 344 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.115221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.083640 restraints weight = 15877.989| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 3.43 r_work: 0.3200 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 7738 Z= 0.146 Angle : 0.656 10.506 10544 Z= 0.329 Chirality : 0.048 0.176 1185 Planarity : 0.004 0.047 1303 Dihedral : 10.051 84.524 1277 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.97 % Allowed : 17.10 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.27), residues: 930 helix: 0.09 (0.39), residues: 184 sheet: 0.59 (0.27), residues: 322 loop : -1.44 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 295 TYR 0.015 0.001 TYR A 140 PHE 0.015 0.001 PHE C 252 TRP 0.029 0.002 TRP A 253 HIS 0.005 0.001 HIS C 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 ( 7716) covalent geometry : angle 0.63584 / 0.32 (10493) SS BOND : bond 0.00455 / 0.29 ( 15) SS BOND : angle 2.01283 / 1.23 ( 30) hydrogen bonds : bond 0.03514 / 2.36 ( 170) hydrogen bonds : angle 4.59145 / 3.06 ( 462) link_NAG-ASN : bond 0.00225 / 0.12 ( 7) link_NAG-ASN : angle 2.81955 / 1.66 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 61 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 MET cc_start: 0.8682 (OUTLIER) cc_final: 0.8314 (mtm) REVERT: A 111 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.8140 (tm-30) REVERT: B 115 GLU cc_start: 0.8917 (OUTLIER) cc_final: 0.8639 (mt-10) REVERT: C 68 GLN cc_start: 0.8737 (tt0) cc_final: 0.8348 (tp-100) REVERT: C 127 GLU cc_start: 0.8644 (tp30) cc_final: 0.8252 (tp30) REVERT: C 324 ARG cc_start: 0.9329 (OUTLIER) cc_final: 0.7993 (ttm170) outliers start: 24 outliers final: 11 residues processed: 74 average time/residue: 0.4625 time to fit residues: 36.8651 Evaluate side-chains 71 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 56 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 75 MET Chi-restraints excluded: chain A residue 111 GLU Chi-restraints excluded: chain A residue 116 CYS Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain B residue 55 TYR Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 291 LYS Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 296 SER Chi-restraints excluded: chain C residue 324 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 8 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 70 optimal weight: 0.1980 chunk 21 optimal weight: 1.9990 chunk 24 optimal weight: 0.0050 chunk 43 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 37 optimal weight: 0.7980 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 152 ASN C 344 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.116053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.084453 restraints weight = 15724.011| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 3.45 r_work: 0.3215 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.3016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 7738 Z= 0.128 Angle : 0.658 10.338 10544 Z= 0.331 Chirality : 0.048 0.215 1185 Planarity : 0.004 0.046 1303 Dihedral : 9.640 72.998 1277 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.23 % Allowed : 18.34 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.28), residues: 930 helix: 0.28 (0.39), residues: 178 sheet: 0.66 (0.27), residues: 322 loop : -1.35 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 198 TYR 0.016 0.001 TYR A 140 PHE 0.015 0.001 PHE C 252 TRP 0.032 0.002 TRP A 253 HIS 0.004 0.001 HIS B 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 ( 7716) covalent geometry : angle 0.64108 / 0.33 (10493) SS BOND : bond 0.00396 / 0.25 ( 15) SS BOND : angle 1.79560 / 1.09 ( 30) hydrogen bonds : bond 0.03338 / 2.20 ( 170) hydrogen bonds : angle 4.55086 / 3.03 ( 462) link_NAG-ASN : bond 0.00255 / 0.13 ( 7) link_NAG-ASN : angle 2.68814 / 1.57 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 59 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 MET cc_start: 0.8656 (OUTLIER) cc_final: 0.8272 (mtm) REVERT: A 111 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.8011 (tm-30) REVERT: B 115 GLU cc_start: 0.8935 (OUTLIER) cc_final: 0.8629 (mt-10) REVERT: C 68 GLN cc_start: 0.8776 (tt0) cc_final: 0.8401 (tp-100) REVERT: C 127 GLU cc_start: 0.8635 (tp30) cc_final: 0.8244 (tp30) REVERT: C 324 ARG cc_start: 0.9314 (OUTLIER) cc_final: 0.7985 (ttm170) outliers start: 18 outliers final: 10 residues processed: 72 average time/residue: 0.4207 time to fit residues: 32.7354 Evaluate side-chains 70 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 56 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 75 MET Chi-restraints excluded: chain A residue 111 GLU Chi-restraints excluded: chain A residue 116 CYS Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain B residue 55 TYR Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 291 LYS Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 296 SER Chi-restraints excluded: chain C residue 324 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 16 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 81 optimal weight: 0.0870 chunk 24 optimal weight: 0.8980 chunk 84 optimal weight: 0.4980 chunk 89 optimal weight: 1.9990 chunk 62 optimal weight: 0.0670 chunk 4 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 overall best weight: 0.5096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 85 GLN B 152 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.116512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.084950 restraints weight = 15695.587| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 3.43 r_work: 0.3229 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7738 Z= 0.125 Angle : 0.639 10.318 10544 Z= 0.322 Chirality : 0.047 0.189 1185 Planarity : 0.004 0.046 1303 Dihedral : 9.074 72.763 1277 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.23 % Allowed : 18.59 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.28), residues: 930 helix: 0.43 (0.40), residues: 178 sheet: 0.69 (0.27), residues: 330 loop : -1.29 (0.31), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 295 TYR 0.011 0.001 TYR A 140 PHE 0.014 0.001 PHE C 252 TRP 0.033 0.002 TRP A 253 HIS 0.003 0.001 HIS B 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.12 ( 7716) covalent geometry : angle 0.62330 / 0.32 (10493) SS BOND : bond 0.00373 / 0.24 ( 15) SS BOND : angle 1.75293 / 1.06 ( 30) hydrogen bonds : bond 0.03266 / 2.12 ( 170) hydrogen bonds : angle 4.47662 / 2.95 ( 462) link_NAG-ASN : bond 0.00250 / 0.12 ( 7) link_NAG-ASN : angle 2.59716 / 1.52 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 59 time to evaluate : 0.207 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 MET cc_start: 0.8649 (OUTLIER) cc_final: 0.8244 (mtm) REVERT: A 111 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7964 (tm-30) REVERT: B 338 LEU cc_start: 0.8520 (pp) cc_final: 0.8318 (tt) REVERT: C 68 GLN cc_start: 0.8805 (tt0) cc_final: 0.8520 (tp-100) REVERT: C 127 GLU cc_start: 0.8621 (tp30) cc_final: 0.8233 (tp30) REVERT: C 149 MET cc_start: 0.8287 (mmt) cc_final: 0.7921 (tpt) REVERT: C 324 ARG cc_start: 0.9308 (OUTLIER) cc_final: 0.7972 (ttm170) outliers start: 18 outliers final: 10 residues processed: 72 average time/residue: 0.3911 time to fit residues: 30.4381 Evaluate side-chains 68 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 55 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 75 MET Chi-restraints excluded: chain A residue 111 GLU Chi-restraints excluded: chain A residue 116 CYS Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain B residue 55 TYR Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 291 LYS Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 296 SER Chi-restraints excluded: chain C residue 324 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 0.5980 chunk 7 optimal weight: 0.8980 chunk 73 optimal weight: 0.0040 chunk 40 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 chunk 77 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 64 GLN B 152 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.116314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.084699 restraints weight = 15847.006| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 3.45 r_work: 0.3222 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 7738 Z= 0.131 Angle : 0.654 10.523 10544 Z= 0.331 Chirality : 0.048 0.233 1185 Planarity : 0.004 0.060 1303 Dihedral : 8.815 72.793 1277 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.11 % Allowed : 18.71 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.28), residues: 930 helix: 0.46 (0.40), residues: 178 sheet: 0.78 (0.27), residues: 324 loop : -1.30 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 315 TYR 0.009 0.001 TYR B 222 PHE 0.014 0.001 PHE C 252 TRP 0.037 0.002 TRP A 253 HIS 0.005 0.001 HIS C 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.13 ( 7716) covalent geometry : angle 0.63849 / 0.33 (10493) SS BOND : bond 0.00414 / 0.28 ( 15) SS BOND : angle 1.77027 / 1.08 ( 30) hydrogen bonds : bond 0.03243 / 2.12 ( 170) hydrogen bonds : angle 4.48556 / 2.97 ( 462) link_NAG-ASN : bond 0.00235 / 0.12 ( 7) link_NAG-ASN : angle 2.56984 / 1.51 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2574.39 seconds wall clock time: 44 minutes 49.77 seconds (2689.77 seconds total)