Starting phenix.real_space_refine on Wed Apr 30 19:46:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cra_45856/04_2025/9cra_45856.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cra_45856/04_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_45856/04_2025/9cra_45856.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cra_45856/04_2025/9cra_45856.map" model { file = "/net/cci-nas-00/data/ceres_data/9cra_45856/04_2025/9cra_45856.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cra_45856/04_2025/9cra_45856.cif" } resolution = 2.34 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.025 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-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: 6.79, per 1000 atoms: 0.69 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: 2.83 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 1.49 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: 4.18 Time building geometry restraints manager: 3.35 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 \ 430 or resid 501)) selection = (chain 'B' and (resid 74 through 78 or resid 96 through 246 or resid 277 through \ 430 or resid 501)) selection = (chain 'C' and (resid 74 through 165 or resid 172 through 246 or resid 277 throu \ gh 430 or resid 501)) selection = (chain 'D' and (resid 74 through 78 or resid 96 through 165 or resid 172 through \ 246 or resid 277 through 430 or resid 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: 80.390 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: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 30.150 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.050 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:21.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 133.120 ------------------------------------------------------------------------------- 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 : 10.41 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (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 TRP 0.010 0.001 TRP B 427 HIS 0.004 0.001 HIS A 128 PHE 0.011 0.001 PHE D 177 TYR 0.025 0.002 TYR A 327 ARG 0.001 0.000 ARG D 165 Details of bonding type rmsd hydrogen bonds : bond 0.18208 ( 328) hydrogen bonds : angle 6.87549 ( 918) covalent geometry : bond 0.00255 (10072) covalent geometry : angle 0.60269 (13720) *********************** 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 : 1.060 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: 1.6595 time to fit residues: 439.8187 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 : 1.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 31 optimal weight: 8.9990 chunk 62 optimal weight: 1.9990 chunk 49 optimal weight: 0.4980 chunk 96 optimal weight: 0.8980 chunk 37 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 71 optimal weight: 0.4980 chunk 111 optimal weight: 3.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 ** B 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.149992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.131786 restraints weight = 12338.950| |-----------------------------------------------------------------------------| r_work (start): 0.3866 rms_B_bonded: 1.78 r_work: 0.3770 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3619 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.1172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10072 Z= 0.163 Angle : 0.612 6.472 13720 Z= 0.319 Chirality : 0.049 0.175 1599 Planarity : 0.006 0.043 1716 Dihedral : 8.709 86.494 1541 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 2.57 % Allowed : 8.44 % Favored : 88.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.24), residues: 1221 helix: 0.04 (0.32), residues: 273 sheet: 0.83 (0.28), residues: 321 loop : -1.60 (0.24), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 379 HIS 0.004 0.001 HIS D 128 PHE 0.017 0.002 PHE D 177 TYR 0.032 0.002 TYR A 327 ARG 0.003 0.000 ARG D 239 Details of bonding type rmsd hydrogen bonds : bond 0.04032 ( 328) hydrogen bonds : angle 5.01970 ( 918) covalent geometry : bond 0.00399 (10072) covalent geometry : angle 0.61246 (13720) *********************** 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 : 1.024 Fit side-chains REVERT: B 106 SER cc_start: 0.8227 (m) cc_final: 0.7913 (p) REVERT: B 212 LEU cc_start: 0.7907 (mt) cc_final: 0.7621 (mt) REVERT: B 241 LYS cc_start: 0.8350 (tttp) cc_final: 0.8117 (tttp) REVERT: C 391 ARG cc_start: 0.7524 (mpp80) cc_final: 0.6977 (mpp80) REVERT: D 140 LYS cc_start: 0.7539 (tptt) cc_final: 0.7272 (tptt) REVERT: D 158 LYS cc_start: 0.8097 (OUTLIER) cc_final: 0.7790 (ttpt) outliers start: 28 outliers final: 13 residues processed: 253 average time/residue: 1.7130 time to fit residues: 456.2391 Evaluate side-chains 244 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 230 time to evaluate : 1.118 ------------------------------------------------------------------------------- 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 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 132 GLU 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 6 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 16 optimal weight: 0.5980 chunk 72 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 80 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 14 optimal weight: 5.9990 chunk 45 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 298 ASN B 312 GLN D 226 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.149356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.130922 restraints weight = 12587.442| |-----------------------------------------------------------------------------| r_work (start): 0.3857 rms_B_bonded: 1.81 r_work: 0.3760 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3609 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10072 Z= 0.156 Angle : 0.590 5.980 13720 Z= 0.308 Chirality : 0.048 0.167 1599 Planarity : 0.005 0.040 1716 Dihedral : 8.714 87.721 1541 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 3.30 % Allowed : 11.10 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.24), residues: 1221 helix: 0.28 (0.33), residues: 273 sheet: 0.85 (0.29), residues: 321 loop : -1.57 (0.24), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 379 HIS 0.004 0.001 HIS A 205 PHE 0.016 0.001 PHE D 177 TYR 0.026 0.002 TYR D 327 ARG 0.004 0.000 ARG A 243 Details of bonding type rmsd hydrogen bonds : bond 0.03797 ( 328) hydrogen bonds : angle 4.71375 ( 918) covalent geometry : bond 0.00386 (10072) covalent geometry : angle 0.59023 (13720) *********************** 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 260 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 224 time to evaluate : 1.105 Fit side-chains revert: symmetry clash REVERT: B 106 SER cc_start: 0.8243 (m) cc_final: 0.7957 (p) REVERT: C 391 ARG cc_start: 0.7567 (mpp80) cc_final: 0.7073 (mpp80) REVERT: D 140 LYS cc_start: 0.7492 (tptt) cc_final: 0.7233 (tptt) REVERT: D 158 LYS cc_start: 0.8069 (OUTLIER) cc_final: 0.7737 (ttpt) outliers start: 36 outliers final: 24 residues processed: 242 average time/residue: 1.6609 time to fit residues: 423.1647 Evaluate side-chains 252 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 227 time to evaluate : 1.162 ------------------------------------------------------------------------------- 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 243 ARG Chi-restraints excluded: chain B residue 298 ASN 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 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 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 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 5 optimal weight: 4.9990 chunk 8 optimal weight: 5.9990 chunk 9 optimal weight: 0.5980 chunk 38 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 31 optimal weight: 8.9990 chunk 48 optimal weight: 6.9990 chunk 122 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 298 ASN B 312 GLN B 351 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.147479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.129264 restraints weight = 12433.538| |-----------------------------------------------------------------------------| r_work (start): 0.3835 rms_B_bonded: 1.78 r_work: 0.3739 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3586 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 10072 Z= 0.224 Angle : 0.631 6.518 13720 Z= 0.328 Chirality : 0.050 0.176 1599 Planarity : 0.006 0.045 1716 Dihedral : 8.970 89.442 1541 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 4.40 % Allowed : 11.19 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.24), residues: 1221 helix: 0.23 (0.32), residues: 273 sheet: 0.74 (0.29), residues: 324 loop : -1.59 (0.24), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 427 HIS 0.004 0.001 HIS A 205 PHE 0.020 0.002 PHE D 177 TYR 0.027 0.002 TYR D 327 ARG 0.004 0.000 ARG D 391 Details of bonding type rmsd hydrogen bonds : bond 0.04021 ( 328) hydrogen bonds : angle 4.74131 ( 918) covalent geometry : bond 0.00562 (10072) covalent geometry : angle 0.63067 (13720) *********************** 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 278 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 230 time to evaluate : 1.144 Fit side-chains REVERT: B 241 LYS cc_start: 0.8350 (tttp) cc_final: 0.8117 (tttp) REVERT: C 391 ARG cc_start: 0.7640 (mpp80) cc_final: 0.7186 (mpp80) REVERT: D 416 ASP cc_start: 0.8035 (m-30) cc_final: 0.7823 (m-30) outliers start: 48 outliers final: 30 residues processed: 258 average time/residue: 1.6715 time to fit residues: 454.8449 Evaluate side-chains 252 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 222 time to evaluate : 1.467 ------------------------------------------------------------------------------- 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 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 243 ARG Chi-restraints excluded: chain B residue 298 ASN 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 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 318 VAL Chi-restraints excluded: chain C residue 409 CYS Chi-restraints excluded: chain D residue 97 ARG 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 86 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 115 optimal weight: 0.2980 chunk 71 optimal weight: 0.8980 chunk 105 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 52 optimal weight: 0.0870 chunk 107 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 overall best weight: 0.6358 ------------------------------------------------------------------------------- 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 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 226 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.148582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.130379 restraints weight = 12443.647| |-----------------------------------------------------------------------------| r_work (start): 0.3851 rms_B_bonded: 1.79 r_work: 0.3755 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3603 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10072 Z= 0.142 Angle : 0.575 6.326 13720 Z= 0.301 Chirality : 0.047 0.166 1599 Planarity : 0.005 0.042 1716 Dihedral : 8.769 89.335 1541 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 3.85 % Allowed : 12.94 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.24), residues: 1221 helix: 0.37 (0.33), residues: 274 sheet: 0.76 (0.29), residues: 322 loop : -1.52 (0.24), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 427 HIS 0.004 0.001 HIS A 205 PHE 0.014 0.001 PHE D 177 TYR 0.018 0.001 TYR B 327 ARG 0.003 0.000 ARG D 391 Details of bonding type rmsd hydrogen bonds : bond 0.03524 ( 328) hydrogen bonds : angle 4.61272 ( 918) covalent geometry : bond 0.00348 (10072) covalent geometry : angle 0.57546 (13720) *********************** 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 263 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 221 time to evaluate : 1.165 Fit side-chains revert: symmetry clash REVERT: B 241 LYS cc_start: 0.8332 (tttp) cc_final: 0.8121 (tttp) REVERT: C 391 ARG cc_start: 0.7570 (mpp80) cc_final: 0.7134 (mpp80) REVERT: D 140 LYS cc_start: 0.7475 (tptt) cc_final: 0.7221 (tptt) REVERT: D 365 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.7382 (tm-30) outliers start: 42 outliers final: 29 residues processed: 242 average time/residue: 1.6412 time to fit residues: 417.7761 Evaluate side-chains 247 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 217 time to evaluate : 1.131 ------------------------------------------------------------------------------- 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 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 140 LYS Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain B residue 243 ARG 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 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 365 GLU 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 4 optimal weight: 2.9990 chunk 54 optimal weight: 0.0970 chunk 45 optimal weight: 3.9990 chunk 118 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 3 optimal weight: 0.5980 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 388 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.146691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.128439 restraints weight = 12454.458| |-----------------------------------------------------------------------------| r_work (start): 0.3820 rms_B_bonded: 1.78 r_work: 0.3724 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3572 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 10072 Z= 0.245 Angle : 0.653 7.181 13720 Z= 0.338 Chirality : 0.051 0.174 1599 Planarity : 0.006 0.045 1716 Dihedral : 9.064 89.923 1541 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 4.31 % Allowed : 13.30 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.24), residues: 1221 helix: 0.30 (0.32), residues: 274 sheet: 0.67 (0.28), residues: 323 loop : -1.58 (0.24), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 427 HIS 0.004 0.001 HIS A 205 PHE 0.020 0.002 PHE D 177 TYR 0.026 0.002 TYR C 327 ARG 0.004 0.000 ARG D 243 Details of bonding type rmsd hydrogen bonds : bond 0.04077 ( 328) hydrogen bonds : angle 4.73839 ( 918) covalent geometry : bond 0.00615 (10072) covalent geometry : angle 0.65305 (13720) *********************** 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 272 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 225 time to evaluate : 1.017 Fit side-chains revert: symmetry clash REVERT: C 145 ASP cc_start: 0.8014 (t0) cc_final: 0.7814 (t0) REVERT: C 285 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.7123 (pm20) REVERT: D 365 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7490 (tm-30) outliers start: 47 outliers final: 33 residues processed: 255 average time/residue: 1.5865 time to fit residues: 426.5893 Evaluate side-chains 259 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 224 time to evaluate : 1.042 ------------------------------------------------------------------------------- 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 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 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 192 SER Chi-restraints excluded: chain C residue 285 GLU 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 97 ARG 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 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 365 GLU 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 19 optimal weight: 0.7980 chunk 92 optimal weight: 10.0000 chunk 64 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 91 optimal weight: 0.8980 chunk 78 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 284 ASN D 226 GLN D 392 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.147763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.129595 restraints weight = 12523.253| |-----------------------------------------------------------------------------| r_work (start): 0.3841 rms_B_bonded: 1.79 r_work: 0.3744 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: 0.7932 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10072 Z= 0.160 Angle : 0.604 9.769 13720 Z= 0.314 Chirality : 0.048 0.192 1599 Planarity : 0.006 0.044 1716 Dihedral : 8.873 89.684 1541 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 4.13 % Allowed : 14.13 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.24), residues: 1221 helix: 0.34 (0.32), residues: 276 sheet: 0.74 (0.29), residues: 315 loop : -1.53 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 379 HIS 0.004 0.001 HIS A 205 PHE 0.015 0.002 PHE D 177 TYR 0.017 0.001 TYR C 327 ARG 0.005 0.000 ARG D 243 Details of bonding type rmsd hydrogen bonds : bond 0.03586 ( 328) hydrogen bonds : angle 4.64623 ( 918) covalent geometry : bond 0.00396 (10072) covalent geometry : angle 0.60447 (13720) *********************** 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 278 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 233 time to evaluate : 1.103 Fit side-chains revert: symmetry clash REVERT: D 365 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7443 (tm-30) outliers start: 45 outliers final: 35 residues processed: 260 average time/residue: 1.5071 time to fit residues: 413.7702 Evaluate side-chains 266 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 230 time to evaluate : 1.103 ------------------------------------------------------------------------------- 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 A residue 414 VAL Chi-restraints excluded: chain B residue 111 LYS 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 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 316 VAL Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 409 CYS Chi-restraints excluded: chain D residue 97 ARG 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 365 GLU 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 119 optimal weight: 1.9990 chunk 95 optimal weight: 0.5980 chunk 65 optimal weight: 2.9990 chunk 113 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 109 optimal weight: 0.6980 chunk 99 optimal weight: 0.5980 chunk 0 optimal weight: 8.9990 chunk 30 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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** D 392 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.147161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.129039 restraints weight = 12484.673| |-----------------------------------------------------------------------------| r_work (start): 0.3833 rms_B_bonded: 1.79 r_work: 0.3736 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3583 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 10072 Z= 0.185 Angle : 0.631 10.935 13720 Z= 0.327 Chirality : 0.049 0.183 1599 Planarity : 0.006 0.045 1716 Dihedral : 8.892 89.763 1541 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 4.40 % Allowed : 14.95 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.24), residues: 1221 helix: 0.49 (0.33), residues: 270 sheet: 0.65 (0.28), residues: 329 loop : -1.56 (0.24), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 427 HIS 0.004 0.001 HIS A 205 PHE 0.018 0.002 PHE D 177 TYR 0.019 0.001 TYR C 327 ARG 0.005 0.000 ARG D 243 Details of bonding type rmsd hydrogen bonds : bond 0.03729 ( 328) hydrogen bonds : angle 4.65903 ( 918) covalent geometry : bond 0.00463 (10072) covalent geometry : angle 0.63140 (13720) *********************** 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 280 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 232 time to evaluate : 1.143 Fit side-chains revert: symmetry clash REVERT: C 391 ARG cc_start: 0.7584 (mpp80) cc_final: 0.7369 (ptp90) REVERT: D 365 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.7453 (tm-30) outliers start: 48 outliers final: 37 residues processed: 261 average time/residue: 1.5713 time to fit residues: 432.6216 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 : 1.151 ------------------------------------------------------------------------------- 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 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 111 LYS 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 97 ARG 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 311 VAL 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 365 GLU 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: 0.1980 chunk 117 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 31 optimal weight: 7.9990 chunk 101 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 40 optimal weight: 0.9990 chunk 100 optimal weight: 4.9990 chunk 68 optimal weight: 0.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- 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 428 ASN D 392 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.147766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.129540 restraints weight = 12568.726| |-----------------------------------------------------------------------------| r_work (start): 0.3841 rms_B_bonded: 1.81 r_work: 0.3742 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3590 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10072 Z= 0.157 Angle : 0.617 12.087 13720 Z= 0.320 Chirality : 0.048 0.181 1599 Planarity : 0.006 0.044 1716 Dihedral : 8.787 89.451 1541 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 4.13 % Allowed : 15.50 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.24), residues: 1221 helix: 0.55 (0.33), residues: 271 sheet: 0.73 (0.29), residues: 316 loop : -1.51 (0.24), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 379 HIS 0.004 0.001 HIS A 205 PHE 0.015 0.002 PHE D 177 TYR 0.016 0.001 TYR D 327 ARG 0.006 0.000 ARG D 243 Details of bonding type rmsd hydrogen bonds : bond 0.03539 ( 328) hydrogen bonds : angle 4.59957 ( 918) covalent geometry : bond 0.00391 (10072) covalent geometry : angle 0.61664 (13720) *********************** 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 278 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 233 time to evaluate : 1.101 Fit side-chains revert: symmetry clash REVERT: B 416 ASP cc_start: 0.8010 (m-30) cc_final: 0.7773 (m-30) REVERT: C 391 ARG cc_start: 0.7562 (mpp80) cc_final: 0.7259 (ptp90) REVERT: D 365 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.7450 (tm-30) outliers start: 45 outliers final: 38 residues processed: 260 average time/residue: 1.8610 time to fit residues: 510.3161 Evaluate side-chains 273 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 234 time to evaluate : 1.066 ------------------------------------------------------------------------------- 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 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 394 ASP 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 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 97 ARG 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 286 VAL Chi-restraints excluded: chain D residue 311 VAL 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 365 GLU 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 103 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 95 optimal weight: 0.5980 chunk 67 optimal weight: 0.9990 chunk 68 optimal weight: 0.9980 chunk 50 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 31 optimal weight: 8.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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** D 392 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.146697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.128621 restraints weight = 12471.308| |-----------------------------------------------------------------------------| r_work (start): 0.3828 rms_B_bonded: 1.79 r_work: 0.3730 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3577 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 10072 Z= 0.206 Angle : 0.658 11.494 13720 Z= 0.340 Chirality : 0.050 0.208 1599 Planarity : 0.006 0.045 1716 Dihedral : 8.928 89.709 1541 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 3.76 % Allowed : 16.24 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.24), residues: 1221 helix: 0.51 (0.32), residues: 270 sheet: 0.65 (0.29), residues: 324 loop : -1.55 (0.24), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 379 HIS 0.004 0.001 HIS A 205 PHE 0.019 0.002 PHE D 177 TYR 0.020 0.002 TYR D 327 ARG 0.006 0.000 ARG D 243 Details of bonding type rmsd hydrogen bonds : bond 0.03809 ( 328) hydrogen bonds : angle 4.68777 ( 918) covalent geometry : bond 0.00516 (10072) covalent geometry : angle 0.65775 (13720) ********************** 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 276 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 235 time to evaluate : 1.144 Fit side-chains revert: symmetry clash REVERT: B 416 ASP cc_start: 0.8030 (m-30) cc_final: 0.7815 (m-30) REVERT: D 365 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.7448 (tm-30) outliers start: 41 outliers final: 38 residues processed: 259 average time/residue: 1.5975 time to fit residues: 436.4976 Evaluate side-chains 274 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 235 time to evaluate : 1.107 ------------------------------------------------------------------------------- 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 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 134 MET Chi-restraints excluded: chain B residue 140 LYS Chi-restraints excluded: chain B residue 163 THR 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 367 LYS Chi-restraints excluded: chain C residue 409 CYS Chi-restraints excluded: chain D residue 97 ARG 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 365 GLU 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 39 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 115 optimal weight: 0.0070 chunk 80 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 56 optimal weight: 0.0770 chunk 105 optimal weight: 0.7980 chunk 43 optimal weight: 0.5980 chunk 122 optimal weight: 0.5980 chunk 27 optimal weight: 0.0980 chunk 55 optimal weight: 0.4980 overall best weight: 0.2556 ------------------------------------------------------------------------------- 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** C 388 GLN D 392 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.150204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.132067 restraints weight = 12518.053| |-----------------------------------------------------------------------------| r_work (start): 0.3870 rms_B_bonded: 1.81 r_work: 0.3774 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3625 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10072 Z= 0.107 Angle : 0.581 11.228 13720 Z= 0.301 Chirality : 0.046 0.176 1599 Planarity : 0.005 0.042 1716 Dihedral : 8.465 84.809 1541 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 2.39 % Allowed : 17.80 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.24), residues: 1221 helix: 0.65 (0.33), residues: 271 sheet: 0.91 (0.30), residues: 297 loop : -1.43 (0.24), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 379 HIS 0.004 0.001 HIS A 128 PHE 0.009 0.001 PHE B 194 TYR 0.013 0.001 TYR D 280 ARG 0.006 0.000 ARG D 243 Details of bonding type rmsd hydrogen bonds : bond 0.03109 ( 328) hydrogen bonds : angle 4.44522 ( 918) covalent geometry : bond 0.00250 (10072) covalent geometry : angle 0.58130 (13720) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10326.19 seconds wall clock time: 179 minutes 51.40 seconds (10791.40 seconds total)