Starting phenix.real_space_refine on Fri Feb 14 06:05:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cra_45856/02_2025/9cra_45856.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cra_45856/02_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_45856/02_2025/9cra_45856.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cra_45856/02_2025/9cra_45856.map" model { file = "/net/cci-nas-00/data/ceres_data/9cra_45856/02_2025/9cra_45856.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cra_45856/02_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-5592/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: 6.62, per 1000 atoms: 0.67 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: 2.47 Conformation dependent library (CDL) restraints added in 1.2 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: 1.24 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: 2.74 Time building geometry restraints manager: 2.81 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: 0.900 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: 0.350 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 24.830 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.130 ------------------------------------------------------------------------------- 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= 0.173 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 *********************** 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 : 1.049 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: 1.6925 time to fit residues: 447.1237 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 : 1.167 ------------------------------------------------------------------------------- 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 = 0.150013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.131767 restraints weight = 12338.191| |-----------------------------------------------------------------------------| 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: 0.3620 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3620 ------------------------------------------------------------------------------- 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= 0.268 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 *********************** 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 : 1.035 Fit side-chains REVERT: B 106 SER cc_start: 0.8224 (m) cc_final: 0.7911 (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: 0.8116 (tttp) REVERT: C 391 ARG cc_start: 0.7520 (mpp80) cc_final: 0.6973 (mpp80) REVERT: D 140 LYS cc_start: 0.7535 (tptt) cc_final: 0.7270 (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: 1.6868 time to fit residues: 448.9311 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 : 1.131 ------------------------------------------------------------------------------- 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: 0.4980 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: 0.8980 chunk 80 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 14 optimal weight: 5.9990 chunk 45 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 A 428 ASN ** B 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 298 ASN B 312 GLN D 226 GLN ** D 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.149830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.131395 restraints weight = 12599.025| |-----------------------------------------------------------------------------| r_work (start): 0.3863 rms_B_bonded: 1.81 r_work: 0.3766 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3616 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10072 Z= 0.234 Angle : 0.579 5.828 13720 Z= 0.303 Chirality : 0.048 0.163 1599 Planarity : 0.005 0.040 1716 Dihedral : 8.664 86.775 1541 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 3.21 % Allowed : 11.19 % 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: -0.68 (0.24), residues: 1221 helix: 0.30 (0.33), residues: 273 sheet: 0.82 (0.29), residues: 327 loop : -1.55 (0.24), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 427 HIS 0.004 0.001 HIS A 205 PHE 0.015 0.001 PHE D 177 TYR 0.024 0.002 TYR D 327 ARG 0.004 0.000 ARG A 243 *********************** 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: 35 poor density : 225 time to evaluate : 1.061 Fit side-chains REVERT: B 106 SER cc_start: 0.8235 (m) cc_final: 0.7998 (p) REVERT: B 212 LEU cc_start: 0.7909 (mt) cc_final: 0.7623 (mt) REVERT: C 391 ARG cc_start: 0.7542 (mpp80) cc_final: 0.7052 (mpp80) REVERT: D 140 LYS cc_start: 0.7486 (tptt) cc_final: 0.7226 (tptt) REVERT: D 158 LYS cc_start: 0.8113 (OUTLIER) cc_final: 0.7795 (ttpt) outliers start: 35 outliers final: 25 residues processed: 243 average time/residue: 1.6680 time to fit residues: 426.8975 Evaluate side-chains 254 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 228 time to evaluate : 1.285 ------------------------------------------------------------------------------- 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 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 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 311 VAL Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 409 CYS Chi-restraints excluded: chain D residue 132 GLU 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: 3.9990 chunk 9 optimal weight: 0.3980 chunk 38 optimal weight: 0.6980 chunk 29 optimal weight: 0.3980 chunk 31 optimal weight: 8.9990 chunk 48 optimal weight: 0.0980 chunk 122 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 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 = 0.4083 r_free = 0.4083 target = 0.149105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.130899 restraints weight = 12431.666| |-----------------------------------------------------------------------------| r_work (start): 0.3859 rms_B_bonded: 1.79 r_work: 0.3761 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3610 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.1588 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= 0.250 Angle : 0.573 5.899 13720 Z= 0.299 Chirality : 0.048 0.167 1599 Planarity : 0.005 0.041 1716 Dihedral : 8.671 88.049 1541 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 3.67 % Allowed : 11.93 % 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: -0.63 (0.24), residues: 1221 helix: 0.34 (0.33), residues: 274 sheet: 0.85 (0.29), residues: 322 loop : -1.51 (0.24), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 427 HIS 0.004 0.001 HIS A 205 PHE 0.016 0.001 PHE D 177 TYR 0.022 0.002 TYR D 327 ARG 0.003 0.000 ARG D 391 *********************** 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 263 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 223 time to evaluate : 1.205 Fit side-chains REVERT: C 391 ARG cc_start: 0.7572 (mpp80) cc_final: 0.7102 (mpp80) REVERT: D 140 LYS cc_start: 0.7445 (tptt) cc_final: 0.7201 (tptt) REVERT: D 158 LYS cc_start: 0.8110 (OUTLIER) cc_final: 0.7800 (ttpt) outliers start: 40 outliers final: 25 residues processed: 244 average time/residue: 1.6598 time to fit residues: 426.6395 Evaluate side-chains 245 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 219 time to evaluate : 1.174 ------------------------------------------------------------------------------- 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 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 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 97 ARG Chi-restraints excluded: chain D residue 158 LYS 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 419 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 86 optimal weight: 2.9990 chunk 46 optimal weight: 0.0980 chunk 40 optimal weight: 1.9990 chunk 115 optimal weight: 0.0870 chunk 71 optimal weight: 0.7980 chunk 105 optimal weight: 0.0370 chunk 5 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 52 optimal weight: 0.4980 chunk 107 optimal weight: 0.9990 chunk 42 optimal weight: 0.6980 overall best weight: 0.2836 ------------------------------------------------------------------------------- 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 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.151287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.133094 restraints weight = 12468.112| |-----------------------------------------------------------------------------| r_work (start): 0.3888 rms_B_bonded: 1.79 r_work: 0.3792 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3643 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10072 Z= 0.151 Angle : 0.526 6.444 13720 Z= 0.276 Chirality : 0.046 0.153 1599 Planarity : 0.005 0.038 1716 Dihedral : 8.437 85.476 1541 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 2.94 % Allowed : 13.94 % Favored : 83.12 % 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: -0.53 (0.24), residues: 1221 helix: 0.47 (0.33), residues: 276 sheet: 1.01 (0.29), residues: 313 loop : -1.50 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP B 427 HIS 0.004 0.001 HIS A 205 PHE 0.009 0.001 PHE D 177 TYR 0.014 0.001 TYR B 327 ARG 0.004 0.000 ARG D 290 *********************** 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 264 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 232 time to evaluate : 1.088 Fit side-chains REVERT: B 301 VAL cc_start: 0.8492 (OUTLIER) cc_final: 0.8270 (t) REVERT: C 391 ARG cc_start: 0.7467 (mpp80) cc_final: 0.7232 (ptp90) REVERT: D 140 LYS cc_start: 0.7430 (tptt) cc_final: 0.7163 (tptt) REVERT: D 297 SER cc_start: 0.7572 (t) cc_final: 0.7365 (p) REVERT: D 365 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7333 (tm-30) outliers start: 32 outliers final: 19 residues processed: 250 average time/residue: 1.7056 time to fit residues: 449.0139 Evaluate side-chains 252 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 231 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 301 VAL 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 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 286 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: 1.9990 chunk 54 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 chunk 118 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 93 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 120 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 3 optimal weight: 0.4980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 A 428 ASN ** B 284 ASN ** 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 = 0.4080 r_free = 0.4080 target = 0.148842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.130661 restraints weight = 12502.967| |-----------------------------------------------------------------------------| r_work (start): 0.3855 rms_B_bonded: 1.79 r_work: 0.3759 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3608 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.1872 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= 0.267 Angle : 0.594 8.864 13720 Z= 0.305 Chirality : 0.048 0.176 1599 Planarity : 0.005 0.040 1716 Dihedral : 8.637 88.821 1541 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 3.94 % Allowed : 14.50 % Favored : 81.56 % 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: 0.47 (0.33), residues: 275 sheet: 0.99 (0.29), residues: 312 loop : -1.45 (0.24), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 379 HIS 0.004 0.001 HIS A 205 PHE 0.017 0.001 PHE D 177 TYR 0.022 0.002 TYR A 327 ARG 0.003 0.000 ARG D 391 *********************** 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 278 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 235 time to evaluate : 0.974 Fit side-chains REVERT: A 369 MET cc_start: 0.8503 (mtp) cc_final: 0.8302 (mtm) REVERT: B 241 LYS cc_start: 0.8270 (tttp) cc_final: 0.8049 (tttp) REVERT: C 391 ARG cc_start: 0.7521 (mpp80) cc_final: 0.7080 (mpp80) REVERT: D 140 LYS cc_start: 0.7466 (tptt) cc_final: 0.7209 (tptt) REVERT: D 365 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7420 (tm-30) outliers start: 43 outliers final: 26 residues processed: 258 average time/residue: 1.6530 time to fit residues: 449.0136 Evaluate side-chains 255 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 228 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LYS 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 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 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 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: 3.9990 chunk 92 optimal weight: 10.0000 chunk 64 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.147590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.129334 restraints weight = 12493.182| |-----------------------------------------------------------------------------| r_work (start): 0.3835 rms_B_bonded: 1.80 r_work: 0.3737 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3584 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 10072 Z= 0.336 Angle : 0.630 10.655 13720 Z= 0.325 Chirality : 0.050 0.175 1599 Planarity : 0.005 0.042 1716 Dihedral : 8.867 89.310 1541 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 3.94 % Allowed : 15.05 % Favored : 81.01 % 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: -0.60 (0.24), residues: 1221 helix: 0.41 (0.32), residues: 275 sheet: 0.83 (0.29), residues: 324 loop : -1.49 (0.24), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 379 HIS 0.004 0.001 HIS A 205 PHE 0.018 0.002 PHE D 177 TYR 0.023 0.002 TYR C 327 ARG 0.003 0.000 ARG D 243 *********************** 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 : 1.157 Fit side-chains REVERT: C 387 ARG cc_start: 0.7856 (mtp180) cc_final: 0.7401 (mtp180) REVERT: D 365 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.7491 (tm-30) outliers start: 43 outliers final: 35 residues processed: 252 average time/residue: 1.6532 time to fit residues: 438.7834 Evaluate side-chains 262 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 226 time to evaluate : 1.079 ------------------------------------------------------------------------------- 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 402 THR 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 134 MET Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain C residue 278 MET 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 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 365 GLU 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: 1.9990 chunk 113 optimal weight: 2.9990 chunk 86 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 99 optimal weight: 0.3980 chunk 0 optimal weight: 8.9990 chunk 30 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- 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 = 0.4051 r_free = 0.4051 target = 0.146504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.128403 restraints weight = 12425.225| |-----------------------------------------------------------------------------| r_work (start): 0.3822 rms_B_bonded: 1.78 r_work: 0.3724 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3572 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.2192 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= 0.427 Angle : 0.684 11.319 13720 Z= 0.353 Chirality : 0.052 0.193 1599 Planarity : 0.006 0.046 1716 Dihedral : 9.136 89.914 1541 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 4.40 % Allowed : 15.05 % 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 (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: -0.75 (0.24), residues: 1221 helix: 0.30 (0.32), residues: 276 sheet: 0.74 (0.29), residues: 318 loop : -1.59 (0.24), residues: 627 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 0.027 0.002 TYR C 327 ARG 0.012 0.001 ARG D 387 *********************** 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 274 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 226 time to evaluate : 1.065 Fit side-chains outliers start: 48 outliers final: 37 residues processed: 253 average time/residue: 1.6166 time to fit residues: 431.3632 Evaluate side-chains 259 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 222 time to evaluate : 1.029 ------------------------------------------------------------------------------- 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 318 VAL Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 402 THR 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 C residue 134 MET Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain C residue 278 MET 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 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 148 ILE Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 192 SER Chi-restraints excluded: chain D residue 299 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 419 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 4 optimal weight: 0.9990 chunk 117 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 31 optimal weight: 7.9990 chunk 101 optimal weight: 0.8980 chunk 65 optimal weight: 0.8980 chunk 88 optimal weight: 0.0670 chunk 13 optimal weight: 0.8980 chunk 40 optimal weight: 0.5980 chunk 100 optimal weight: 0.9990 chunk 68 optimal weight: 0.8980 overall best weight: 0.6718 ------------------------------------------------------------------------------- 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 D 392 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.148064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.129896 restraints weight = 12544.230| |-----------------------------------------------------------------------------| r_work (start): 0.3842 rms_B_bonded: 1.80 r_work: 0.3744 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3592 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.2136 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= 0.255 Angle : 0.617 11.954 13720 Z= 0.320 Chirality : 0.048 0.172 1599 Planarity : 0.005 0.043 1716 Dihedral : 8.874 89.449 1541 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 3.58 % Allowed : 16.06 % 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: -0.61 (0.24), residues: 1221 helix: 0.60 (0.33), residues: 269 sheet: 0.77 (0.29), residues: 316 loop : -1.52 (0.24), residues: 636 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 0.015 0.001 PHE D 177 TYR 0.017 0.001 TYR D 327 ARG 0.006 0.000 ARG D 243 *********************** 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 260 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 221 time to evaluate : 1.147 Fit side-chains REVERT: A 416 ASP cc_start: 0.7901 (m-30) cc_final: 0.7651 (m-30) REVERT: B 279 GLN cc_start: 0.7801 (OUTLIER) cc_final: 0.7462 (tp-100) outliers start: 39 outliers final: 33 residues processed: 247 average time/residue: 1.7174 time to fit residues: 448.4508 Evaluate side-chains 256 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 222 time to evaluate : 1.104 ------------------------------------------------------------------------------- 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 318 VAL Chi-restraints excluded: chain A residue 402 THR 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 C residue 157 VAL Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain C residue 278 MET 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 157 VAL Chi-restraints excluded: chain D residue 192 SER Chi-restraints excluded: chain D residue 299 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 chunk 95 optimal weight: 0.0980 chunk 67 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 19 optimal weight: 0.0670 chunk 94 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 31 optimal weight: 8.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- 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 = 0.4076 r_free = 0.4076 target = 0.148591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.130428 restraints weight = 12441.168| |-----------------------------------------------------------------------------| r_work (start): 0.3846 rms_B_bonded: 1.80 r_work: 0.3751 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3601 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10072 Z= 0.223 Angle : 0.611 11.580 13720 Z= 0.317 Chirality : 0.048 0.212 1599 Planarity : 0.005 0.043 1716 Dihedral : 8.754 88.859 1541 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 3.39 % Allowed : 16.33 % Favored : 80.28 % 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: -0.58 (0.24), residues: 1221 helix: 0.64 (0.33), residues: 269 sheet: 0.77 (0.29), residues: 313 loop : -1.49 (0.24), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 427 HIS 0.004 0.001 HIS B 205 PHE 0.013 0.001 PHE D 177 TYR 0.015 0.001 TYR D 327 ARG 0.006 0.000 ARG D 243 ********************** 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: 37 poor density : 225 time to evaluate : 1.124 Fit side-chains REVERT: A 416 ASP cc_start: 0.7879 (m-30) cc_final: 0.7622 (m-30) REVERT: D 297 SER cc_start: 0.7722 (t) cc_final: 0.7504 (p) outliers start: 37 outliers final: 34 residues processed: 250 average time/residue: 1.6502 time to fit residues: 434.2783 Evaluate side-chains 259 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 225 time to evaluate : 1.156 ------------------------------------------------------------------------------- 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 318 VAL Chi-restraints excluded: chain A residue 402 THR 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 278 MET 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 157 VAL Chi-restraints excluded: chain D residue 192 SER Chi-restraints excluded: chain D residue 299 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 39 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 115 optimal weight: 0.0010 chunk 80 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 122 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 overall best weight: 1.1190 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.147207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.129002 restraints weight = 12478.693| |-----------------------------------------------------------------------------| r_work (start): 0.3831 rms_B_bonded: 1.79 r_work: 0.3732 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3580 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 10072 Z= 0.355 Angle : 0.657 11.224 13720 Z= 0.340 Chirality : 0.050 0.217 1599 Planarity : 0.006 0.045 1716 Dihedral : 8.948 89.599 1541 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 3.67 % Allowed : 16.33 % 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: -0.64 (0.24), residues: 1221 helix: 0.57 (0.32), residues: 269 sheet: 0.63 (0.29), residues: 330 loop : -1.52 (0.24), residues: 622 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 0.020 0.002 PHE D 177 TYR 0.023 0.002 TYR C 327 ARG 0.006 0.000 ARG D 243 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9987.56 seconds wall clock time: 176 minutes 10.69 seconds (10570.69 seconds total)