Starting phenix.real_space_refine on Wed Sep 17 16:49:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cra_45856/09_2025/9cra_45856.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cra_45856/09_2025/9cra_45856.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9cra_45856/09_2025/9cra_45856.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cra_45856/09_2025/9cra_45856.map" model { file = "/net/cci-nas-00/data/ceres_data/9cra_45856/09_2025/9cra_45856.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cra_45856/09_2025/9cra_45856.cif" } resolution = 2.34 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= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 52 5.16 5 C 6277 2.51 5 N 1659 2.21 5 O 1846 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9842 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2427 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 19, 'TRANS': 293} Chain breaks: 2 Chain: "B" Number of atoms: 2388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2388 Classifications: {'peptide': 309} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 19, 'TRANS': 289} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 2415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2415 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 19, 'TRANS': 291} Chain breaks: 2 Chain: "D" Number of atoms: 2436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2436 Classifications: {'peptide': 314} Link IDs: {'PTRANS': 19, 'TRANS': 294} Chain breaks: 2 Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.66, per 1000 atoms: 0.27 Number of scatterers: 9842 At special positions: 0 Unit cell: (107.687, 95.1405, 97.2315, 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 52 16.00 P 8 15.00 O 1846 8.00 N 1659 7.00 C 6277 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 1.02 Conformation dependent library (CDL) restraints added in 389.5 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2350 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 22 sheets defined 25.7% alpha, 25.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 118 through 130 removed outlier: 3.560A pdb=" N MET A 130 " --> pdb=" O CYS A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 144 removed outlier: 3.522A pdb=" N LEU A 143 " --> pdb=" O GLU A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 150 removed outlier: 4.238A pdb=" N ALA A 149 " --> pdb=" O ASP A 145 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N SER A 150 " --> pdb=" O PRO A 146 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 145 through 150' Processing helix chain 'A' and resid 154 through 159 removed outlier: 3.691A pdb=" N LYS A 159 " --> pdb=" O GLY A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 194 removed outlier: 3.839A pdb=" N LEU A 187 " --> pdb=" O GLY A 183 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N PHE A 194 " --> pdb=" O ALA A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 230 removed outlier: 3.705A pdb=" N GLN A 223 " --> pdb=" O ASN A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 324 Processing helix chain 'A' and resid 326 through 331 removed outlier: 3.580A pdb=" N ALA A 330 " --> pdb=" O ALA A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 424 Processing helix chain 'B' and resid 115 through 117 No H-bonds generated for 'chain 'B' and resid 115 through 117' Processing helix chain 'B' and resid 118 through 130 Processing helix chain 'B' and resid 139 through 144 removed outlier: 3.749A pdb=" N LEU B 143 " --> pdb=" O GLU B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 150 removed outlier: 4.145A pdb=" N ALA B 149 " --> pdb=" O ASP B 145 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N SER B 150 " --> pdb=" O PRO B 146 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 145 through 150' Processing helix chain 'B' and resid 152 through 159 removed outlier: 4.056A pdb=" N ALA B 156 " --> pdb=" O GLU B 152 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N VAL B 157 " --> pdb=" O SER B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 194 removed outlier: 3.866A pdb=" N LEU B 187 " --> pdb=" O GLY B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 230 removed outlier: 3.674A pdb=" N GLN B 223 " --> pdb=" O ASN B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 325 removed outlier: 3.993A pdb=" N THR B 325 " --> pdb=" O THR B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 331 Processing helix chain 'B' and resid 412 through 424 Processing helix chain 'C' and resid 118 through 130 Processing helix chain 'C' and resid 140 through 144 Processing helix chain 'C' and resid 145 through 150 Processing helix chain 'C' and resid 151 through 159 removed outlier: 3.588A pdb=" N GLY C 155 " --> pdb=" O ASP C 151 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA C 156 " --> pdb=" O GLU C 152 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N VAL C 157 " --> pdb=" O SER C 153 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS C 159 " --> pdb=" O GLY C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 194 removed outlier: 3.832A pdb=" N LEU C 187 " --> pdb=" O GLY C 183 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE C 194 " --> pdb=" O ALA C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 219 through 230 removed outlier: 3.763A pdb=" N GLN C 223 " --> pdb=" O ASN C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 325 removed outlier: 4.025A pdb=" N THR C 325 " --> pdb=" O THR C 322 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 331 removed outlier: 3.503A pdb=" N ALA C 331 " --> pdb=" O TYR C 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 412 through 424 Processing helix chain 'D' and resid 119 through 130 Processing helix chain 'D' and resid 139 through 144 removed outlier: 3.598A pdb=" N LEU D 143 " --> pdb=" O GLU D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 150 Processing helix chain 'D' and resid 154 through 159 removed outlier: 3.700A pdb=" N LYS D 159 " --> pdb=" O GLY D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 193 removed outlier: 3.660A pdb=" N LEU D 187 " --> pdb=" O GLY D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 219 through 230 removed outlier: 3.766A pdb=" N GLN D 223 " --> pdb=" O ASN D 219 " (cutoff:3.500A) Processing helix chain 'D' and resid 320 through 324 Processing helix chain 'D' and resid 326 through 331 Processing helix chain 'D' and resid 412 through 424 Processing sheet with id=AA1, first strand: chain 'A' and resid 135 through 137 removed outlier: 6.749A pdb=" N SER A 106 " --> pdb=" O PHE A 177 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N ILE A 179 " --> pdb=" O SER A 106 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N LEU A 108 " --> pdb=" O ILE A 179 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N LEU A 181 " --> pdb=" O LEU A 108 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ILE A 110 " --> pdb=" O LEU A 181 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ILE A 178 " --> pdb=" O MET A 202 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N PHE A 204 " --> pdb=" O ILE A 178 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N CYS A 180 " --> pdb=" O PHE A 204 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE A 215 " --> pdb=" O ALA A 203 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 233 through 237 removed outlier: 4.507A pdb=" N ALA A 233 " --> pdb=" O CYS A 409 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 278 through 282 removed outlier: 3.633A pdb=" N THR A 309 " --> pdb=" O VAL A 301 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N LEU A 303 " --> pdb=" O LEU A 307 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N LEU A 307 " --> pdb=" O LEU A 303 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N GLN A 312 " --> pdb=" O PRO A 350 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ILE A 348 " --> pdb=" O ASP A 314 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 278 through 282 removed outlier: 3.633A pdb=" N THR A 309 " --> pdb=" O VAL A 301 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N LEU A 303 " --> pdb=" O LEU A 307 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N LEU A 307 " --> pdb=" O LEU A 303 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 342 through 345 Processing sheet with id=AA6, first strand: chain 'B' and resid 135 through 137 removed outlier: 6.650A pdb=" N VAL B 107 " --> pdb=" O TYR B 137 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N SER B 106 " --> pdb=" O PHE B 177 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N ILE B 179 " --> pdb=" O SER B 106 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N LEU B 108 " --> pdb=" O ILE B 179 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N LEU B 181 " --> pdb=" O LEU B 108 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N ILE B 110 " --> pdb=" O LEU B 181 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ILE B 178 " --> pdb=" O MET B 202 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N PHE B 204 " --> pdb=" O ILE B 178 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N CYS B 180 " --> pdb=" O PHE B 204 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 234 through 237 Processing sheet with id=AA8, first strand: chain 'B' and resid 278 through 282 removed outlier: 5.887A pdb=" N SER B 297 " --> pdb=" O GLN B 312 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLN B 312 " --> pdb=" O SER B 297 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N VAL B 299 " --> pdb=" O THR B 310 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N THR B 310 " --> pdb=" O VAL B 299 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N VAL B 301 " --> pdb=" O ILE B 308 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 286 through 289 removed outlier: 3.545A pdb=" N ALA B 378 " --> pdb=" O ILE B 390 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 343 through 345 Processing sheet with id=AB2, first strand: chain 'C' and resid 162 through 164 removed outlier: 3.631A pdb=" N PHE C 164 " --> pdb=" O VAL C 138 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N GLU C 139 " --> pdb=" O VAL C 109 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N SER C 106 " --> pdb=" O PHE C 177 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N ILE C 179 " --> pdb=" O SER C 106 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N LEU C 108 " --> pdb=" O ILE C 179 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N LEU C 181 " --> pdb=" O LEU C 108 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ILE C 110 " --> pdb=" O LEU C 181 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 234 through 237 Processing sheet with id=AB4, first strand: chain 'C' and resid 280 through 282 removed outlier: 3.838A pdb=" N THR C 309 " --> pdb=" O VAL C 301 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LEU C 303 " --> pdb=" O LEU C 307 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N LEU C 307 " --> pdb=" O LEU C 303 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 286 through 289 Processing sheet with id=AB6, first strand: chain 'C' and resid 315 through 316 removed outlier: 3.855A pdb=" N GLY C 315 " --> pdb=" O ILE C 348 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 335 through 336 removed outlier: 6.507A pdb=" N MET C 335 " --> pdb=" O VAL D 359 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 342 through 345 Processing sheet with id=AB9, first strand: chain 'D' and resid 135 through 137 removed outlier: 6.834A pdb=" N VAL D 107 " --> pdb=" O TYR D 137 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N SER D 106 " --> pdb=" O PHE D 177 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N ILE D 179 " --> pdb=" O SER D 106 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N LEU D 108 " --> pdb=" O ILE D 179 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N LEU D 181 " --> pdb=" O LEU D 108 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ILE D 110 " --> pdb=" O LEU D 181 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ILE D 178 " --> pdb=" O MET D 202 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N PHE D 204 " --> pdb=" O ILE D 178 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N CYS D 180 " --> pdb=" O PHE D 204 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 233 through 237 removed outlier: 4.573A pdb=" N ALA D 233 " --> pdb=" O CYS D 409 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 280 through 282 removed outlier: 5.689A pdb=" N SER D 297 " --> pdb=" O GLN D 312 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLN D 312 " --> pdb=" O SER D 297 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N VAL D 299 " --> pdb=" O THR D 310 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N THR D 310 " --> pdb=" O VAL D 299 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N VAL D 301 " --> pdb=" O ILE D 308 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 286 through 289 removed outlier: 6.789A pdb=" N ALA D 378 " --> pdb=" O GLU D 389 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N GLU D 389 " --> pdb=" O ALA D 378 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N VAL D 380 " --> pdb=" O ARG D 387 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ARG D 387 " --> pdb=" O VAL D 380 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 315 through 316 removed outlier: 3.840A pdb=" N GLY D 315 " --> pdb=" O ILE D 348 " (cutoff:3.500A) 353 hydrogen bonds defined for protein. 918 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: 1.68 Time building geometry restraints manager: 1.31 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: 3138 1.34 - 1.46: 1821 1.46 - 1.58: 5013 1.58 - 1.69: 16 1.69 - 1.81: 84 Bond restraints: 10072 Sorted by residual: bond pdb=" C MET A 113 " pdb=" N ARG A 114 " ideal model delta sigma weight residual 1.330 1.307 0.023 1.43e-02 4.89e+03 2.60e+00 bond pdb=" C LYS A 112 " pdb=" N MET A 113 " ideal model delta sigma weight residual 1.332 1.311 0.021 1.38e-02 5.25e+03 2.31e+00 bond pdb=" CA THR B 162 " pdb=" CB THR B 162 " ideal model delta sigma weight residual 1.523 1.540 -0.016 1.27e-02 6.20e+03 1.68e+00 bond pdb=" CA THR A 162 " pdb=" CB THR A 162 " ideal model delta sigma weight residual 1.524 1.540 -0.016 1.37e-02 5.33e+03 1.44e+00 bond pdb=" CA THR D 162 " pdb=" CB THR D 162 " ideal model delta sigma weight residual 1.524 1.540 -0.017 1.41e-02 5.03e+03 1.39e+00 ... (remaining 10067 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.80: 13440 1.80 - 3.60: 244 3.60 - 5.41: 26 5.41 - 7.21: 8 7.21 - 9.01: 2 Bond angle restraints: 13720 Sorted by residual: angle pdb=" N TYR C 168 " pdb=" CA TYR C 168 " pdb=" C TYR C 168 " ideal model delta sigma weight residual 114.56 109.63 4.93 1.27e+00 6.20e-01 1.51e+01 angle pdb=" CG1 ILE D 317 " pdb=" CB ILE D 317 " pdb=" CG2 ILE D 317 " ideal model delta sigma weight residual 110.70 101.69 9.01 3.00e+00 1.11e-01 9.02e+00 angle pdb=" OG1 THR A 79 " pdb=" CB THR A 79 " pdb=" CG2 THR A 79 " ideal model delta sigma weight residual 109.30 103.29 6.01 2.00e+00 2.50e-01 9.02e+00 angle pdb=" OG1 THR B 162 " pdb=" CB THR B 162 " pdb=" CG2 THR B 162 " ideal model delta sigma weight residual 109.30 103.31 5.99 2.00e+00 2.50e-01 8.96e+00 angle pdb=" OG1 THR A 162 " pdb=" CB THR A 162 " pdb=" CG2 THR A 162 " ideal model delta sigma weight residual 109.30 103.32 5.98 2.00e+00 2.50e-01 8.95e+00 ... (remaining 13715 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 5703 17.68 - 35.35: 380 35.35 - 53.03: 61 53.03 - 70.71: 20 70.71 - 88.38: 8 Dihedral angle restraints: 6172 sinusoidal: 2557 harmonic: 3615 Sorted by residual: dihedral pdb=" CA VAL C 318 " pdb=" C VAL C 318 " pdb=" N SER C 319 " pdb=" CA SER C 319 " ideal model delta harmonic sigma weight residual -180.00 -160.09 -19.91 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" CA VAL B 318 " pdb=" C VAL B 318 " pdb=" N SER B 319 " pdb=" CA SER B 319 " ideal model delta harmonic sigma weight residual -180.00 -160.60 -19.40 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CA VAL A 318 " pdb=" C VAL A 318 " pdb=" N SER A 319 " pdb=" CA SER A 319 " ideal model delta harmonic sigma weight residual 180.00 -160.67 -19.33 0 5.00e+00 4.00e-02 1.49e+01 ... (remaining 6169 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1165 0.047 - 0.094: 315 0.094 - 0.141: 105 0.141 - 0.188: 12 0.188 - 0.235: 2 Chirality restraints: 1599 Sorted by residual: chirality pdb=" CB ILE D 317 " pdb=" CA ILE D 317 " pdb=" CG1 ILE D 317 " pdb=" CG2 ILE D 317 " both_signs ideal model delta sigma weight residual False 2.64 2.88 -0.24 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CB ILE A 317 " pdb=" CA ILE A 317 " pdb=" CG1 ILE A 317 " pdb=" CG2 ILE A 317 " both_signs ideal model delta sigma weight residual False 2.64 2.86 -0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CA GLN B 312 " pdb=" N GLN B 312 " pdb=" C GLN B 312 " pdb=" CB GLN B 312 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.04e-01 ... (remaining 1596 not shown) Planarity restraints: 1716 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY C 75 " 0.032 5.00e-02 4.00e+02 4.91e-02 3.86e+00 pdb=" N PRO C 76 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO C 76 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 76 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 145 " 0.029 5.00e-02 4.00e+02 4.47e-02 3.20e+00 pdb=" N PRO C 146 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO C 146 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 146 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 317 " -0.008 2.00e-02 2.50e+03 1.59e-02 2.53e+00 pdb=" C ILE A 317 " 0.028 2.00e-02 2.50e+03 pdb=" O ILE A 317 " -0.010 2.00e-02 2.50e+03 pdb=" N VAL A 318 " -0.009 2.00e-02 2.50e+03 ... (remaining 1713 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 786 2.74 - 3.28: 9441 3.28 - 3.82: 15810 3.82 - 4.36: 19527 4.36 - 4.90: 32929 Nonbonded interactions: 78493 Sorted by model distance: nonbonded pdb=" O LEU A 283 " pdb=" OG1 THR A 320 " model vdw 2.203 3.040 nonbonded pdb=" O PHE C 74 " pdb=" OG SER C 197 " model vdw 2.230 3.040 nonbonded pdb=" OE2 GLU A 166 " pdb=" OH TYR A 189 " model vdw 2.239 3.040 nonbonded pdb=" O ALA B 362 " pdb=" OG1 THR B 400 " model vdw 2.252 3.040 nonbonded pdb=" OE2 GLU C 285 " pdb=" O2D NAD C 501 " model vdw 2.252 3.040 ... (remaining 78488 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 74 through 78 or resid 96 through 165 or resid 172 through \ 501)) selection = (chain 'B' and (resid 74 through 78 or resid 96 through 246 or resid 277 through \ 501)) selection = (chain 'C' and (resid 74 through 165 or resid 172 through 246 or resid 277 throu \ gh 501)) selection = (chain 'D' and (resid 74 through 78 or resid 96 through 165 or resid 172 through \ 246 or resid 277 through 501)) } 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: 1.190 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.500 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 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 : 0.003 0.037 10072 Z= 0.121 Angle : 0.603 9.012 13720 Z= 0.321 Chirality : 0.048 0.235 1599 Planarity : 0.005 0.049 1716 Dihedral : 12.612 88.383 3822 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.84 (0.24), residues: 1221 helix: 0.03 (0.34), residues: 253 sheet: 0.73 (0.28), residues: 325 loop : -1.54 (0.24), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 165 TYR 0.025 0.002 TYR A 327 PHE 0.011 0.001 PHE D 177 TRP 0.010 0.001 TRP B 427 HIS 0.004 0.001 HIS A 128 Details of bonding type rmsd covalent geometry : bond 0.00255 (10072) covalent geometry : angle 0.60269 (13720) hydrogen bonds : bond 0.18208 ( 328) hydrogen bonds : angle 6.87549 ( 918) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 251 time to evaluate : 0.396 Fit side-chains REVERT: A 298 ASN cc_start: 0.7056 (m-40) cc_final: 0.6834 (m-40) REVERT: B 212 LEU cc_start: 0.7945 (mt) cc_final: 0.7652 (mt) REVERT: C 298 ASN cc_start: 0.6818 (m-40) cc_final: 0.6607 (m110) REVERT: C 387 ARG cc_start: 0.7413 (mtp85) cc_final: 0.6989 (mtp180) REVERT: D 202 MET cc_start: 0.8879 (ttt) cc_final: 0.8431 (ttm) outliers start: 0 outliers final: 0 residues processed: 251 average time/residue: 0.8469 time to fit residues: 223.3278 Evaluate side-chains 233 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 233 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 0.4980 chunk 97 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 117 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 GLN A 339 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.149135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.130846 restraints weight = 12462.332| |-----------------------------------------------------------------------------| r_work (start): 0.3854 rms_B_bonded: 1.79 r_work: 0.3758 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3607 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.1212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 10072 Z= 0.193 Angle : 0.636 6.642 13720 Z= 0.330 Chirality : 0.050 0.175 1599 Planarity : 0.006 0.044 1716 Dihedral : 8.824 87.883 1541 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 2.57 % Allowed : 8.72 % Favored : 88.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.82 (0.24), residues: 1221 helix: 0.02 (0.32), residues: 273 sheet: 0.84 (0.29), residues: 305 loop : -1.55 (0.24), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 97 TYR 0.034 0.002 TYR A 327 PHE 0.019 0.002 PHE D 177 TRP 0.008 0.001 TRP D 379 HIS 0.004 0.001 HIS D 128 Details of bonding type rmsd covalent geometry : bond 0.00478 (10072) covalent geometry : angle 0.63557 (13720) hydrogen bonds : bond 0.04244 ( 328) hydrogen bonds : angle 5.05817 ( 918) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 243 time to evaluate : 0.384 Fit side-chains REVERT: B 106 SER cc_start: 0.8234 (m) cc_final: 0.7935 (p) REVERT: B 212 LEU cc_start: 0.7924 (mt) cc_final: 0.7644 (mt) REVERT: B 241 LYS cc_start: 0.8364 (tttp) cc_final: 0.8106 (tttp) REVERT: C 391 ARG cc_start: 0.7558 (mpp80) cc_final: 0.7021 (mpp80) REVERT: D 140 LYS cc_start: 0.7550 (tptt) cc_final: 0.7287 (tptt) REVERT: D 158 LYS cc_start: 0.8152 (OUTLIER) cc_final: 0.7824 (ttpt) REVERT: D 389 GLU cc_start: 0.8393 (tt0) cc_final: 0.8119 (tt0) REVERT: D 391 ARG cc_start: 0.7524 (mtt90) cc_final: 0.7303 (mtt90) outliers start: 28 outliers final: 14 residues processed: 253 average time/residue: 0.8404 time to fit residues: 223.5461 Evaluate side-chains 248 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 233 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LYS Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain B residue 298 ASN Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 409 CYS Chi-restraints excluded: chain D residue 130 MET Chi-restraints excluded: chain D residue 148 ILE Chi-restraints excluded: chain D residue 158 LYS Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 419 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 26 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 298 ASN D 226 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.147643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.129327 restraints weight = 12480.576| |-----------------------------------------------------------------------------| r_work (start): 0.3835 rms_B_bonded: 1.79 r_work: 0.3739 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3586 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 10072 Z= 0.218 Angle : 0.638 6.459 13720 Z= 0.332 Chirality : 0.051 0.179 1599 Planarity : 0.006 0.045 1716 Dihedral : 8.984 89.571 1541 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 3.58 % Allowed : 10.46 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.82 (0.24), residues: 1221 helix: 0.18 (0.32), residues: 272 sheet: 0.73 (0.29), residues: 324 loop : -1.63 (0.24), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 243 TYR 0.030 0.002 TYR D 327 PHE 0.020 0.002 PHE D 177 TRP 0.008 0.001 TRP D 379 HIS 0.004 0.001 HIS A 205 Details of bonding type rmsd covalent geometry : bond 0.00548 (10072) covalent geometry : angle 0.63760 (13720) hydrogen bonds : bond 0.04167 ( 328) hydrogen bonds : angle 4.82886 ( 918) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 225 time to evaluate : 0.398 Fit side-chains REVERT: B 106 SER cc_start: 0.8251 (m) cc_final: 0.7980 (p) REVERT: B 335 MET cc_start: 0.8309 (OUTLIER) cc_final: 0.6160 (mpp) REVERT: C 391 ARG cc_start: 0.7688 (mpp80) cc_final: 0.7200 (mpp80) REVERT: D 158 LYS cc_start: 0.8134 (OUTLIER) cc_final: 0.7779 (ttpt) outliers start: 39 outliers final: 26 residues processed: 246 average time/residue: 0.7452 time to fit residues: 192.5365 Evaluate side-chains 249 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 221 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LYS Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 335 MET Chi-restraints excluded: chain B residue 354 SER Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 409 CYS Chi-restraints excluded: chain B residue 411 ARG Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 409 CYS Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 158 LYS Chi-restraints excluded: chain D residue 192 SER Chi-restraints excluded: chain D residue 311 VAL Chi-restraints excluded: chain D residue 312 GLN Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 419 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 46 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 23 optimal weight: 0.4980 chunk 93 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 120 optimal weight: 1.9990 chunk 84 optimal weight: 0.0970 chunk 34 optimal weight: 0.7980 chunk 98 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 114 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 298 ASN B 351 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.148122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.129814 restraints weight = 12574.067| |-----------------------------------------------------------------------------| r_work (start): 0.3838 rms_B_bonded: 1.79 r_work: 0.3742 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3591 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10072 Z= 0.175 Angle : 0.599 6.296 13720 Z= 0.313 Chirality : 0.049 0.170 1599 Planarity : 0.006 0.045 1716 Dihedral : 8.890 89.568 1541 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 3.94 % Allowed : 12.02 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.78 (0.24), residues: 1221 helix: 0.26 (0.32), residues: 274 sheet: 0.71 (0.29), residues: 324 loop : -1.61 (0.24), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 243 TYR 0.022 0.002 TYR A 327 PHE 0.017 0.002 PHE D 177 TRP 0.006 0.001 TRP B 427 HIS 0.004 0.001 HIS A 205 Details of bonding type rmsd covalent geometry : bond 0.00436 (10072) covalent geometry : angle 0.59931 (13720) hydrogen bonds : bond 0.03759 ( 328) hydrogen bonds : angle 4.70397 ( 918) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 225 time to evaluate : 0.285 Fit side-chains REVERT: B 416 ASP cc_start: 0.7983 (m-30) cc_final: 0.7770 (m-30) REVERT: C 335 MET cc_start: 0.8486 (OUTLIER) cc_final: 0.7261 (mmp) REVERT: C 391 ARG cc_start: 0.7646 (mpp80) cc_final: 0.7193 (mpp80) REVERT: D 140 LYS cc_start: 0.7478 (tptt) cc_final: 0.7223 (tptt) outliers start: 43 outliers final: 27 residues processed: 252 average time/residue: 0.7601 time to fit residues: 201.4755 Evaluate side-chains 255 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 227 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LYS Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 354 SER Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 409 CYS Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 335 MET Chi-restraints excluded: chain C residue 409 CYS Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 311 VAL Chi-restraints excluded: chain D residue 312 GLN Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 340 VAL Chi-restraints excluded: chain D residue 419 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 111 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 85 optimal weight: 0.6980 chunk 75 optimal weight: 3.9990 chunk 118 optimal weight: 0.7980 chunk 41 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 31 optimal weight: 5.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 298 ASN B 279 GLN ** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 226 GLN ** D 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.147921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.129712 restraints weight = 12488.928| |-----------------------------------------------------------------------------| r_work (start): 0.3842 rms_B_bonded: 1.78 r_work: 0.3744 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3593 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10072 Z= 0.165 Angle : 0.589 6.409 13720 Z= 0.308 Chirality : 0.048 0.165 1599 Planarity : 0.006 0.043 1716 Dihedral : 8.826 89.358 1541 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 3.76 % Allowed : 13.03 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.71 (0.24), residues: 1221 helix: 0.34 (0.33), residues: 275 sheet: 0.76 (0.29), residues: 316 loop : -1.55 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 356 TYR 0.019 0.002 TYR B 327 PHE 0.016 0.002 PHE D 177 TRP 0.006 0.001 TRP B 427 HIS 0.004 0.001 HIS A 205 Details of bonding type rmsd covalent geometry : bond 0.00409 (10072) covalent geometry : angle 0.58927 (13720) hydrogen bonds : bond 0.03666 ( 328) hydrogen bonds : angle 4.64621 ( 918) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 227 time to evaluate : 0.427 Fit side-chains REVERT: B 279 GLN cc_start: 0.7930 (OUTLIER) cc_final: 0.7602 (tp40) REVERT: B 416 ASP cc_start: 0.7976 (m-30) cc_final: 0.7766 (m-30) REVERT: C 145 ASP cc_start: 0.8004 (t0) cc_final: 0.7798 (t0) REVERT: C 391 ARG cc_start: 0.7623 (mpp80) cc_final: 0.7171 (mtp85) REVERT: D 140 LYS cc_start: 0.7473 (tptt) cc_final: 0.7213 (tptt) REVERT: D 416 ASP cc_start: 0.8062 (m-30) cc_final: 0.7855 (m-30) outliers start: 41 outliers final: 27 residues processed: 252 average time/residue: 0.7573 time to fit residues: 200.8370 Evaluate side-chains 246 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 218 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LYS Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 140 LYS Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 354 SER Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 409 CYS Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 192 SER Chi-restraints excluded: chain D residue 311 VAL Chi-restraints excluded: chain D residue 312 GLN Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 340 VAL Chi-restraints excluded: chain D residue 419 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 116 optimal weight: 0.0010 chunk 80 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 122 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 97 optimal weight: 0.7980 chunk 56 optimal weight: 0.0980 chunk 26 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 67 optimal weight: 0.3980 overall best weight: 0.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.149252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.131119 restraints weight = 12484.081| |-----------------------------------------------------------------------------| r_work (start): 0.3857 rms_B_bonded: 1.79 r_work: 0.3763 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3614 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10072 Z= 0.117 Angle : 0.562 7.265 13720 Z= 0.294 Chirality : 0.046 0.152 1599 Planarity : 0.005 0.040 1716 Dihedral : 8.630 88.614 1541 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 3.30 % Allowed : 14.13 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.58 (0.24), residues: 1221 helix: 0.49 (0.33), residues: 275 sheet: 0.78 (0.29), residues: 322 loop : -1.48 (0.24), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 243 TYR 0.013 0.001 TYR B 327 PHE 0.011 0.001 PHE D 177 TRP 0.005 0.001 TRP B 427 HIS 0.004 0.001 HIS A 205 Details of bonding type rmsd covalent geometry : bond 0.00279 (10072) covalent geometry : angle 0.56229 (13720) hydrogen bonds : bond 0.03312 ( 328) hydrogen bonds : angle 4.54339 ( 918) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 220 time to evaluate : 0.390 Fit side-chains REVERT: B 416 ASP cc_start: 0.7952 (m-30) cc_final: 0.7747 (m-30) REVERT: C 391 ARG cc_start: 0.7561 (mpp80) cc_final: 0.7111 (mtp85) REVERT: D 140 LYS cc_start: 0.7407 (tptt) cc_final: 0.7181 (tptt) outliers start: 36 outliers final: 30 residues processed: 243 average time/residue: 0.8218 time to fit residues: 209.8729 Evaluate side-chains 254 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 224 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LYS Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 140 LYS Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 411 ARG Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 409 CYS Chi-restraints excluded: chain D residue 112 LYS Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 192 SER Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 311 VAL Chi-restraints excluded: chain D residue 312 GLN Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 320 THR Chi-restraints excluded: chain D residue 340 VAL Chi-restraints excluded: chain D residue 419 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 53 optimal weight: 0.5980 chunk 19 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 98 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 90 optimal weight: 0.0060 chunk 22 optimal weight: 0.8980 chunk 65 optimal weight: 0.3980 chunk 32 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.148954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.130836 restraints weight = 12560.915| |-----------------------------------------------------------------------------| r_work (start): 0.3858 rms_B_bonded: 1.79 r_work: 0.3761 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3609 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10072 Z= 0.132 Angle : 0.579 9.658 13720 Z= 0.300 Chirality : 0.047 0.175 1599 Planarity : 0.005 0.040 1716 Dihedral : 8.602 88.990 1541 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 3.94 % Allowed : 14.40 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.52 (0.24), residues: 1221 helix: 0.48 (0.33), residues: 276 sheet: 0.93 (0.29), residues: 314 loop : -1.45 (0.24), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 290 TYR 0.014 0.001 TYR B 327 PHE 0.013 0.001 PHE D 177 TRP 0.007 0.001 TRP D 379 HIS 0.004 0.001 HIS A 205 Details of bonding type rmsd covalent geometry : bond 0.00323 (10072) covalent geometry : angle 0.57874 (13720) hydrogen bonds : bond 0.03369 ( 328) hydrogen bonds : angle 4.53106 ( 918) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 224 time to evaluate : 0.316 Fit side-chains REVERT: B 416 ASP cc_start: 0.7991 (m-30) cc_final: 0.7772 (m-30) REVERT: C 391 ARG cc_start: 0.7587 (mpp80) cc_final: 0.7137 (mtp85) REVERT: D 140 LYS cc_start: 0.7455 (tptt) cc_final: 0.7214 (tptt) outliers start: 43 outliers final: 34 residues processed: 252 average time/residue: 0.8077 time to fit residues: 214.0559 Evaluate side-chains 255 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 221 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LYS Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain B residue 140 LYS Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 354 SER Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 411 ARG Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 409 CYS Chi-restraints excluded: chain D residue 112 LYS Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 192 SER Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 311 VAL Chi-restraints excluded: chain D residue 312 GLN Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 320 THR Chi-restraints excluded: chain D residue 340 VAL Chi-restraints excluded: chain D residue 411 ARG Chi-restraints excluded: chain D residue 419 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 93 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 69 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 26 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 388 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.147320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.129196 restraints weight = 12449.764| |-----------------------------------------------------------------------------| r_work (start): 0.3833 rms_B_bonded: 1.78 r_work: 0.3737 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3585 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 10072 Z= 0.200 Angle : 0.638 11.297 13720 Z= 0.330 Chirality : 0.050 0.210 1599 Planarity : 0.006 0.043 1716 Dihedral : 8.839 89.368 1541 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 4.04 % Allowed : 15.14 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.62 (0.24), residues: 1221 helix: 0.38 (0.32), residues: 275 sheet: 0.74 (0.29), residues: 330 loop : -1.46 (0.24), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 243 TYR 0.020 0.002 TYR D 327 PHE 0.019 0.002 PHE D 177 TRP 0.011 0.001 TRP D 379 HIS 0.004 0.001 HIS A 205 Details of bonding type rmsd covalent geometry : bond 0.00502 (10072) covalent geometry : angle 0.63846 (13720) hydrogen bonds : bond 0.03761 ( 328) hydrogen bonds : angle 4.65158 ( 918) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 224 time to evaluate : 0.421 Fit side-chains REVERT: B 416 ASP cc_start: 0.8011 (m-30) cc_final: 0.7785 (m-30) REVERT: C 391 ARG cc_start: 0.7634 (mpp80) cc_final: 0.7193 (mtp85) outliers start: 44 outliers final: 37 residues processed: 250 average time/residue: 0.7705 time to fit residues: 202.7373 Evaluate side-chains 260 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 223 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LYS Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain B residue 140 LYS Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 354 SER Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 409 CYS Chi-restraints excluded: chain B residue 411 ARG Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 409 CYS Chi-restraints excluded: chain D residue 112 LYS Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 192 SER Chi-restraints excluded: chain D residue 311 VAL Chi-restraints excluded: chain D residue 312 GLN Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 320 THR Chi-restraints excluded: chain D residue 340 VAL Chi-restraints excluded: chain D residue 411 ARG Chi-restraints excluded: chain D residue 419 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 4 optimal weight: 0.2980 chunk 34 optimal weight: 0.6980 chunk 24 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 83 optimal weight: 0.4980 chunk 80 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 98 optimal weight: 0.3980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 GLN B 284 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.148801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.130676 restraints weight = 12490.824| |-----------------------------------------------------------------------------| r_work (start): 0.3850 rms_B_bonded: 1.80 r_work: 0.3755 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3605 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10072 Z= 0.133 Angle : 0.596 11.961 13720 Z= 0.308 Chirality : 0.047 0.181 1599 Planarity : 0.005 0.042 1716 Dihedral : 8.657 88.267 1541 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 4.04 % Allowed : 15.23 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.54 (0.24), residues: 1221 helix: 0.57 (0.33), residues: 270 sheet: 0.87 (0.29), residues: 316 loop : -1.47 (0.24), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 243 TYR 0.013 0.001 TYR B 327 PHE 0.012 0.001 PHE D 177 TRP 0.010 0.001 TRP D 379 HIS 0.004 0.001 HIS A 205 Details of bonding type rmsd covalent geometry : bond 0.00327 (10072) covalent geometry : angle 0.59645 (13720) hydrogen bonds : bond 0.03354 ( 328) hydrogen bonds : angle 4.55241 ( 918) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 219 time to evaluate : 0.386 Fit side-chains REVERT: B 416 ASP cc_start: 0.8000 (m-30) cc_final: 0.7775 (m-30) REVERT: C 290 ARG cc_start: 0.8379 (ptt90) cc_final: 0.8164 (ptt90) REVERT: C 391 ARG cc_start: 0.7550 (mpp80) cc_final: 0.7115 (mtp85) REVERT: D 298 ASN cc_start: 0.8117 (m110) cc_final: 0.7910 (m-40) outliers start: 44 outliers final: 37 residues processed: 245 average time/residue: 0.7451 time to fit residues: 192.1609 Evaluate side-chains 267 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 230 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ARG Chi-restraints excluded: chain A residue 111 LYS Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain B residue 140 LYS Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 354 SER Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 409 CYS Chi-restraints excluded: chain B residue 411 ARG Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 409 CYS Chi-restraints excluded: chain D residue 112 LYS Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 192 SER Chi-restraints excluded: chain D residue 311 VAL Chi-restraints excluded: chain D residue 312 GLN Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 320 THR Chi-restraints excluded: chain D residue 340 VAL Chi-restraints excluded: chain D residue 419 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 61 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 7 optimal weight: 0.0370 chunk 81 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 27 optimal weight: 0.4980 chunk 50 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 overall best weight: 0.8862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.147871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.129835 restraints weight = 12408.213| |-----------------------------------------------------------------------------| r_work (start): 0.3838 rms_B_bonded: 1.78 r_work: 0.3743 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3594 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10072 Z= 0.177 Angle : 0.635 12.368 13720 Z= 0.327 Chirality : 0.049 0.188 1599 Planarity : 0.005 0.043 1716 Dihedral : 8.749 89.073 1541 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 3.58 % Allowed : 15.87 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.55 (0.24), residues: 1221 helix: 0.53 (0.33), residues: 270 sheet: 0.85 (0.29), residues: 316 loop : -1.46 (0.24), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 243 TYR 0.018 0.001 TYR D 327 PHE 0.016 0.002 PHE D 177 TRP 0.010 0.001 TRP D 379 HIS 0.004 0.001 HIS A 205 Details of bonding type rmsd covalent geometry : bond 0.00443 (10072) covalent geometry : angle 0.63484 (13720) hydrogen bonds : bond 0.03594 ( 328) hydrogen bonds : angle 4.58864 ( 918) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 223 time to evaluate : 0.394 Fit side-chains REVERT: B 416 ASP cc_start: 0.8012 (m-30) cc_final: 0.7762 (m-30) REVERT: C 391 ARG cc_start: 0.7604 (mpp80) cc_final: 0.7173 (mtp85) REVERT: D 298 ASN cc_start: 0.8105 (m110) cc_final: 0.7895 (m-40) outliers start: 39 outliers final: 38 residues processed: 248 average time/residue: 0.7711 time to fit residues: 201.2801 Evaluate side-chains 269 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 231 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ARG Chi-restraints excluded: chain A residue 111 LYS Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain B residue 140 LYS Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 354 SER Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 409 CYS Chi-restraints excluded: chain B residue 411 ARG Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 409 CYS Chi-restraints excluded: chain D residue 112 LYS Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 192 SER Chi-restraints excluded: chain D residue 309 THR Chi-restraints excluded: chain D residue 311 VAL Chi-restraints excluded: chain D residue 312 GLN Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 320 THR Chi-restraints excluded: chain D residue 340 VAL Chi-restraints excluded: chain D residue 411 ARG Chi-restraints excluded: chain D residue 419 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 102 optimal weight: 0.9990 chunk 2 optimal weight: 0.1980 chunk 6 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 chunk 105 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 chunk 109 optimal weight: 0.8980 chunk 88 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 GLN C 388 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.148009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.129909 restraints weight = 12552.518| |-----------------------------------------------------------------------------| r_work (start): 0.3839 rms_B_bonded: 1.79 r_work: 0.3743 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3593 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10072 Z= 0.168 Angle : 0.628 12.358 13720 Z= 0.323 Chirality : 0.049 0.183 1599 Planarity : 0.005 0.043 1716 Dihedral : 8.762 88.935 1541 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 3.94 % Allowed : 15.60 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.54 (0.24), residues: 1221 helix: 0.55 (0.33), residues: 270 sheet: 0.86 (0.29), residues: 316 loop : -1.45 (0.24), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 243 TYR 0.017 0.001 TYR D 327 PHE 0.015 0.002 PHE D 177 TRP 0.009 0.001 TRP D 379 HIS 0.004 0.001 HIS A 205 Details of bonding type rmsd covalent geometry : bond 0.00420 (10072) covalent geometry : angle 0.62769 (13720) hydrogen bonds : bond 0.03559 ( 328) hydrogen bonds : angle 4.58856 ( 918) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5093.55 seconds wall clock time: 87 minutes 15.38 seconds (5235.38 seconds total)