Starting phenix.real_space_refine on Sat Aug 23 02:03:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jlq_36404/08_2025/8jlq_36404.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jlq_36404/08_2025/8jlq_36404.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jlq_36404/08_2025/8jlq_36404.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jlq_36404/08_2025/8jlq_36404.map" model { file = "/net/cci-nas-00/data/ceres_data/8jlq_36404/08_2025/8jlq_36404.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jlq_36404/08_2025/8jlq_36404.cif" } resolution = 2.84 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.006 sd= 0.121 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 S 67 5.16 5 Cl 1 4.86 5 C 5767 2.51 5 N 1541 2.21 5 O 1657 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9033 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1902 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 6, 'TRANS': 221} Chain breaks: 3 Chain: "B" Number of atoms: 2587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2587 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "R" Number of atoms: 2294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2294 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 11, 'TRANS': 271} Chain breaks: 1 Chain: "S" Number of atoms: 1784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1784 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 10, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "Y" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 445 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "R" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'G3C': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.97, per 1000 atoms: 0.22 Number of scatterers: 9033 At special positions: 0 Unit cell: (107.12, 128.96, 101.92, 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) Cl 1 17.00 S 67 16.00 O 1657 8.00 N 1541 7.00 C 5767 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.04 Simple disulfide: pdb=" SG CYS R 96 " - pdb=" SG CYS R 182 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.02 Conformation dependent library (CDL) restraints added in 372.8 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2140 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 15 sheets defined 38.9% alpha, 22.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 13 through 39 Processing helix chain 'A' and resid 52 through 62 Processing helix chain 'A' and resid 233 through 238 Processing helix chain 'A' and resid 264 through 278 removed outlier: 3.534A pdb=" N ALA A 268 " --> pdb=" O ASN A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 283 Processing helix chain 'A' and resid 293 through 302 removed outlier: 3.525A pdb=" N LYS A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 351 removed outlier: 4.572A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N SER A 349 " --> pdb=" O PHE A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 391 removed outlier: 3.708A pdb=" N ARG A 373 " --> pdb=" O THR A 369 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLN A 384 " --> pdb=" O ARG A 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.574A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 23 through 51 Processing helix chain 'R' and resid 52 through 55 removed outlier: 3.509A pdb=" N HIS R 55 " --> pdb=" O LYS R 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 52 through 55' Processing helix chain 'R' and resid 56 through 87 removed outlier: 4.269A pdb=" N MET R 77 " --> pdb=" O GLY R 73 " (cutoff:3.500A) Proline residue: R 78 - end of helix Processing helix chain 'R' and resid 92 through 124 Processing helix chain 'R' and resid 127 through 129 No H-bonds generated for 'chain 'R' and resid 127 through 129' Processing helix chain 'R' and resid 130 through 135 Processing helix chain 'R' and resid 136 through 160 Proline residue: R 151 - end of helix Processing helix chain 'R' and resid 168 through 180 removed outlier: 4.201A pdb=" N ARG R 179 " --> pdb=" O HIS R 175 " (cutoff:3.500A) Processing helix chain 'R' and resid 187 through 199 Processing helix chain 'R' and resid 199 through 232 removed outlier: 3.871A pdb=" N ILE R 224 " --> pdb=" O GLN R 220 " (cutoff:3.500A) Processing helix chain 'R' and resid 249 through 277 Proline residue: R 266 - end of helix Proline residue: R 275 - end of helix Processing helix chain 'R' and resid 282 through 305 Proline residue: R 301 - end of helix Processing helix chain 'R' and resid 308 through 319 Processing helix chain 'S' and resid 220 through 224 Processing helix chain 'Y' and resid 7 through 24 removed outlier: 3.966A pdb=" N ASN Y 24 " --> pdb=" O LYS Y 20 " (cutoff:3.500A) Processing helix chain 'Y' and resid 29 through 44 Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 4.330A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N GLY A 47 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 9.368A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.348A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 48 through 52 removed outlier: 3.809A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.911A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.554A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.547A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 4.446A pdb=" N ALA B 203 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.240A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.744A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7 removed outlier: 5.457A pdb=" N GLY S 16 " --> pdb=" O SER S 85 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 11 through 12 Processing sheet with id=AB2, first strand: chain 'S' and resid 58 through 60 removed outlier: 6.910A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 58 through 60 removed outlier: 6.910A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 140 through 142 Processing sheet with id=AB5, first strand: chain 'S' and resid 146 through 148 removed outlier: 4.143A pdb=" N GLU S 246 " --> pdb=" O VAL S 147 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'S' and resid 194 through 195 removed outlier: 3.899A pdb=" N ASN S 194 " --> pdb=" O TYR S 190 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE S 189 " --> pdb=" O TRP S 176 " (cutoff:3.500A) 463 hydrogen bonds defined for protein. 1326 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.30 Time building geometry restraints manager: 1.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1446 1.30 - 1.44: 2616 1.44 - 1.57: 5074 1.57 - 1.71: 0 1.71 - 1.84: 101 Bond restraints: 9237 Sorted by residual: bond pdb=" CA HIS R 99 " pdb=" CB HIS R 99 " ideal model delta sigma weight residual 1.530 1.447 0.083 1.57e-02 4.06e+03 2.79e+01 bond pdb=" C ARG B 134 " pdb=" O ARG B 134 " ideal model delta sigma weight residual 1.234 1.170 0.063 1.26e-02 6.30e+03 2.52e+01 bond pdb=" N ARG A 347 " pdb=" CA ARG A 347 " ideal model delta sigma weight residual 1.457 1.393 0.064 1.29e-02 6.01e+03 2.48e+01 bond pdb=" C ARG A 283 " pdb=" O ARG A 283 " ideal model delta sigma weight residual 1.236 1.180 0.057 1.16e-02 7.43e+03 2.39e+01 bond pdb=" CA PHE R 154 " pdb=" C PHE R 154 " ideal model delta sigma weight residual 1.524 1.461 0.063 1.32e-02 5.74e+03 2.28e+01 ... (remaining 9232 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.44: 12243 2.44 - 4.88: 228 4.88 - 7.31: 29 7.31 - 9.75: 4 9.75 - 12.19: 1 Bond angle restraints: 12505 Sorted by residual: angle pdb=" C ARG A 283 " pdb=" N ASP A 284 " pdb=" CA ASP A 284 " ideal model delta sigma weight residual 122.21 110.02 12.19 1.48e+00 4.57e-01 6.78e+01 angle pdb=" C GLU S 234 " pdb=" N TYR S 235 " pdb=" CA TYR S 235 " ideal model delta sigma weight residual 122.89 115.22 7.67 1.12e+00 7.97e-01 4.69e+01 angle pdb=" N VAL R 184 " pdb=" CA VAL R 184 " pdb=" C VAL R 184 " ideal model delta sigma weight residual 109.37 116.64 -7.27 1.35e+00 5.49e-01 2.90e+01 angle pdb=" N TYR A 358 " pdb=" CA TYR A 358 " pdb=" CB TYR A 358 " ideal model delta sigma weight residual 111.43 103.57 7.86 1.59e+00 3.96e-01 2.44e+01 angle pdb=" N THR B 223 " pdb=" CA THR B 223 " pdb=" C THR B 223 " ideal model delta sigma weight residual 110.17 102.80 7.37 1.51e+00 4.39e-01 2.38e+01 ... (remaining 12500 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.77: 4954 16.77 - 33.53: 412 33.53 - 50.30: 101 50.30 - 67.07: 9 67.07 - 83.84: 6 Dihedral angle restraints: 5482 sinusoidal: 2165 harmonic: 3317 Sorted by residual: dihedral pdb=" CB CYS R 96 " pdb=" SG CYS R 96 " pdb=" SG CYS R 182 " pdb=" CB CYS R 182 " ideal model delta sinusoidal sigma weight residual -86.00 -148.00 62.00 1 1.00e+01 1.00e-02 5.09e+01 dihedral pdb=" C ARG B 134 " pdb=" N ARG B 134 " pdb=" CA ARG B 134 " pdb=" CB ARG B 134 " ideal model delta harmonic sigma weight residual -122.60 -110.44 -12.16 0 2.50e+00 1.60e-01 2.37e+01 dihedral pdb=" CA TYR S 235 " pdb=" C TYR S 235 " pdb=" N PRO S 236 " pdb=" CA PRO S 236 " ideal model delta harmonic sigma weight residual 180.00 158.91 21.09 0 5.00e+00 4.00e-02 1.78e+01 ... (remaining 5479 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1085 0.054 - 0.108: 265 0.108 - 0.162: 35 0.162 - 0.216: 7 0.216 - 0.270: 1 Chirality restraints: 1393 Sorted by residual: chirality pdb=" CA ARG B 134 " pdb=" N ARG B 134 " pdb=" C ARG B 134 " pdb=" CB ARG B 134 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" CA ILE B 338 " pdb=" N ILE B 338 " pdb=" C ILE B 338 " pdb=" CB ILE B 338 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.19 2.00e-01 2.50e+01 9.30e-01 chirality pdb=" CA ILE B 229 " pdb=" N ILE B 229 " pdb=" C ILE B 229 " pdb=" CB ILE B 229 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.74e-01 ... (remaining 1390 not shown) Planarity restraints: 1577 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN R 220 " 0.019 2.00e-02 2.50e+03 3.84e-02 1.48e+01 pdb=" C GLN R 220 " -0.066 2.00e-02 2.50e+03 pdb=" O GLN R 220 " 0.024 2.00e-02 2.50e+03 pdb=" N ALA R 221 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS R 99 " -0.028 2.00e-02 2.50e+03 2.33e-02 8.16e+00 pdb=" CG HIS R 99 " 0.048 2.00e-02 2.50e+03 pdb=" ND1 HIS R 99 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 HIS R 99 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 HIS R 99 " -0.008 2.00e-02 2.50e+03 pdb=" NE2 HIS R 99 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE R 292 " 0.014 2.00e-02 2.50e+03 2.84e-02 8.06e+00 pdb=" C PHE R 292 " -0.049 2.00e-02 2.50e+03 pdb=" O PHE R 292 " 0.019 2.00e-02 2.50e+03 pdb=" N GLY R 293 " 0.016 2.00e-02 2.50e+03 ... (remaining 1574 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 827 2.74 - 3.28: 9477 3.28 - 3.82: 16137 3.82 - 4.36: 19073 4.36 - 4.90: 32353 Nonbonded interactions: 77867 Sorted by model distance: nonbonded pdb=" OE2 GLU A 15 " pdb=" OH TYR S 175 " model vdw 2.203 3.040 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.210 3.040 nonbonded pdb=" ND1 HIS A 387 " pdb=" O ALA R 124 " model vdw 2.230 3.120 nonbonded pdb=" OD2 ASP B 83 " pdb=" OG1 THR B 86 " model vdw 2.241 3.040 nonbonded pdb=" OG SER B 108 " pdb=" OD1 ASP B 154 " model vdw 2.261 3.040 ... (remaining 77862 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.950 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: 0.160 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 8.920 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6613 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 : 0.005 0.083 9241 Z= 0.328 Angle : 0.783 12.189 12513 Z= 0.475 Chirality : 0.047 0.270 1393 Planarity : 0.005 0.044 1577 Dihedral : 13.144 83.836 3330 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 18.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 0.41 % Allowed : 1.02 % Favored : 98.57 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.45 (0.25), residues: 1120 helix: 0.90 (0.26), residues: 403 sheet: -0.51 (0.32), residues: 270 loop : -1.19 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 20 TYR 0.029 0.002 TYR A 358 PHE 0.018 0.001 PHE R 154 TRP 0.020 0.002 TRP B 82 HIS 0.016 0.001 HIS R 99 Details of bonding type rmsd covalent geometry : bond 0.00481 ( 9237) covalent geometry : angle 0.78206 (12505) SS BOND : bond 0.00727 ( 4) SS BOND : angle 1.62150 ( 8) hydrogen bonds : bond 0.15097 ( 458) hydrogen bonds : angle 7.02175 ( 1326) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 170 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 65 MET cc_start: 0.7214 (ttp) cc_final: 0.6995 (mtp) REVERT: Y 32 LYS cc_start: 0.8155 (tttm) cc_final: 0.7781 (tppt) outliers start: 4 outliers final: 3 residues processed: 173 average time/residue: 0.5052 time to fit residues: 93.8694 Evaluate side-chains 140 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 137 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 229 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 10.0000 chunk 53 optimal weight: 0.2980 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.0980 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 chunk 100 optimal weight: 5.9990 chunk 106 optimal weight: 20.0000 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN ** R 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 164 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4601 r_free = 0.4601 target = 0.240803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.185686 restraints weight = 10105.321| |-----------------------------------------------------------------------------| r_work (start): 0.4085 rms_B_bonded: 2.38 r_work: 0.3901 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3763 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7100 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9241 Z= 0.167 Angle : 0.645 7.938 12513 Z= 0.339 Chirality : 0.045 0.202 1393 Planarity : 0.005 0.043 1577 Dihedral : 4.849 50.698 1261 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 14.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.04 % Allowed : 10.69 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.07 (0.26), residues: 1120 helix: 1.40 (0.25), residues: 398 sheet: -0.41 (0.33), residues: 269 loop : -1.08 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 38 TYR 0.019 0.002 TYR A 37 PHE 0.015 0.002 PHE B 253 TRP 0.020 0.002 TRP B 211 HIS 0.006 0.002 HIS R 55 Details of bonding type rmsd covalent geometry : bond 0.00385 ( 9237) covalent geometry : angle 0.64351 (12505) SS BOND : bond 0.00836 ( 4) SS BOND : angle 1.64210 ( 8) hydrogen bonds : bond 0.04255 ( 458) hydrogen bonds : angle 5.56115 ( 1326) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 149 time to evaluate : 0.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 132 ASN cc_start: 0.6695 (m-40) cc_final: 0.6064 (p0) REVERT: B 134 ARG cc_start: 0.7812 (ptp-170) cc_final: 0.7411 (ptp90) REVERT: R 32 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7923 (pt) REVERT: R 65 MET cc_start: 0.7935 (ttp) cc_final: 0.7647 (ttp) REVERT: R 220 GLN cc_start: 0.7366 (OUTLIER) cc_final: 0.7102 (mp10) REVERT: S 38 ARG cc_start: 0.5566 (ptt180) cc_final: 0.5184 (ptt180) REVERT: S 93 MET cc_start: 0.6520 (mmm) cc_final: 0.6306 (mmm) REVERT: Y 32 LYS cc_start: 0.8205 (tttm) cc_final: 0.7424 (tppt) outliers start: 20 outliers final: 6 residues processed: 156 average time/residue: 0.5066 time to fit residues: 85.5759 Evaluate side-chains 143 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 135 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 126 CYS Chi-restraints excluded: chain R residue 138 LEU Chi-restraints excluded: chain R residue 220 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 107 optimal weight: 8.9990 chunk 82 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 69 optimal weight: 7.9990 chunk 22 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 98 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS A 357 HIS ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 183 HIS B 268 ASN ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 164 ASN ** R 296 ASN ** 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 = 0.4589 r_free = 0.4589 target = 0.239254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.181546 restraints weight = 10091.437| |-----------------------------------------------------------------------------| r_work (start): 0.4035 rms_B_bonded: 2.48 r_work: 0.3845 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7043 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9241 Z= 0.157 Angle : 0.609 7.640 12513 Z= 0.319 Chirality : 0.044 0.174 1393 Planarity : 0.004 0.042 1577 Dihedral : 4.770 52.317 1258 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.56 % Allowed : 13.65 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.07 (0.26), residues: 1120 helix: 1.53 (0.25), residues: 398 sheet: -0.28 (0.33), residues: 267 loop : -1.06 (0.30), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 38 TYR 0.014 0.002 TYR R 200 PHE 0.014 0.002 PHE B 253 TRP 0.014 0.002 TRP B 211 HIS 0.006 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 9237) covalent geometry : angle 0.60850 (12505) SS BOND : bond 0.00769 ( 4) SS BOND : angle 1.13725 ( 8) hydrogen bonds : bond 0.04093 ( 458) hydrogen bonds : angle 5.37245 ( 1326) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 135 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 ARG cc_start: 0.7509 (mmt-90) cc_final: 0.7202 (mmt-90) REVERT: B 132 ASN cc_start: 0.6608 (m-40) cc_final: 0.6045 (p0) REVERT: B 134 ARG cc_start: 0.7723 (ptp-170) cc_final: 0.7492 (ptp-170) REVERT: B 249 THR cc_start: 0.7880 (p) cc_final: 0.7624 (p) REVERT: R 32 LEU cc_start: 0.8020 (OUTLIER) cc_final: 0.7778 (pt) REVERT: R 65 MET cc_start: 0.7828 (ttp) cc_final: 0.7608 (ttp) REVERT: R 123 TYR cc_start: 0.8342 (m-80) cc_final: 0.8110 (m-80) REVERT: R 158 MET cc_start: 0.6652 (OUTLIER) cc_final: 0.6278 (ttm) REVERT: S 38 ARG cc_start: 0.5403 (ptt180) cc_final: 0.5199 (ptt180) REVERT: S 172 THR cc_start: 0.6554 (OUTLIER) cc_final: 0.6254 (t) REVERT: Y 32 LYS cc_start: 0.8315 (tttm) cc_final: 0.7536 (tppt) outliers start: 35 outliers final: 14 residues processed: 154 average time/residue: 0.5417 time to fit residues: 89.9760 Evaluate side-chains 134 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 117 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 76 VAL Chi-restraints excluded: chain R residue 126 CYS Chi-restraints excluded: chain R residue 138 LEU Chi-restraints excluded: chain R residue 158 MET Chi-restraints excluded: chain R residue 209 VAL Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 172 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 61 optimal weight: 7.9990 chunk 94 optimal weight: 5.9990 chunk 99 optimal weight: 8.9990 chunk 20 optimal weight: 2.9990 chunk 14 optimal weight: 9.9990 chunk 90 optimal weight: 6.9990 chunk 57 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 87 optimal weight: 6.9990 chunk 1 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 50 HIS R 63 HIS ** R 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 164 ASN ** R 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.231209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.172167 restraints weight = 10179.592| |-----------------------------------------------------------------------------| r_work (start): 0.3938 rms_B_bonded: 2.53 r_work: 0.3740 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7192 moved from start: 0.2895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 9241 Z= 0.294 Angle : 0.744 11.028 12513 Z= 0.387 Chirality : 0.048 0.252 1393 Planarity : 0.005 0.046 1577 Dihedral : 5.266 54.077 1258 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 18.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.56 % Allowed : 15.48 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.17 (0.26), residues: 1120 helix: 1.30 (0.25), residues: 397 sheet: -0.54 (0.31), residues: 277 loop : -1.06 (0.31), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 283 TYR 0.035 0.003 TYR B 105 PHE 0.018 0.002 PHE A 212 TRP 0.016 0.003 TRP B 82 HIS 0.014 0.002 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00688 ( 9237) covalent geometry : angle 0.74171 (12505) SS BOND : bond 0.01617 ( 4) SS BOND : angle 2.33160 ( 8) hydrogen bonds : bond 0.04746 ( 458) hydrogen bonds : angle 5.63126 ( 1326) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 139 time to evaluate : 0.368 Fit side-chains revert: symmetry clash REVERT: A 20 ARG cc_start: 0.7645 (mmt-90) cc_final: 0.7317 (mmt-90) REVERT: A 338 LYS cc_start: 0.6509 (OUTLIER) cc_final: 0.6039 (ptmt) REVERT: B 180 PHE cc_start: 0.7006 (OUTLIER) cc_final: 0.4630 (p90) REVERT: R 59 ASN cc_start: 0.8149 (m-40) cc_final: 0.7945 (m-40) REVERT: R 65 MET cc_start: 0.8067 (ttp) cc_final: 0.7811 (ttp) REVERT: R 158 MET cc_start: 0.6967 (OUTLIER) cc_final: 0.6517 (ttm) REVERT: R 220 GLN cc_start: 0.7382 (OUTLIER) cc_final: 0.6996 (mp10) REVERT: R 272 VAL cc_start: 0.8617 (m) cc_final: 0.8376 (p) REVERT: S 38 ARG cc_start: 0.5554 (ptt180) cc_final: 0.5336 (ptt180) REVERT: S 172 THR cc_start: 0.6696 (OUTLIER) cc_final: 0.6401 (t) REVERT: Y 32 LYS cc_start: 0.8432 (tttm) cc_final: 0.7717 (tppt) outliers start: 35 outliers final: 18 residues processed: 161 average time/residue: 0.4739 time to fit residues: 82.3742 Evaluate side-chains 150 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 127 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 338 LYS Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 180 PHE Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 76 VAL Chi-restraints excluded: chain R residue 126 CYS Chi-restraints excluded: chain R residue 138 LEU Chi-restraints excluded: chain R residue 158 MET Chi-restraints excluded: chain R residue 209 VAL Chi-restraints excluded: chain R residue 220 GLN Chi-restraints excluded: chain S residue 23 SER Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 172 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 26 optimal weight: 4.9990 chunk 74 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 58 optimal weight: 6.9990 chunk 54 optimal weight: 0.9980 chunk 103 optimal weight: 20.0000 chunk 108 optimal weight: 10.0000 chunk 53 optimal weight: 0.9990 chunk 85 optimal weight: 0.5980 chunk 37 optimal weight: 0.7980 chunk 65 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS A 357 HIS ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 164 ASN ** R 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4562 r_free = 0.4562 target = 0.236017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.178450 restraints weight = 10122.357| |-----------------------------------------------------------------------------| r_work (start): 0.4003 rms_B_bonded: 2.46 r_work: 0.3827 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3689 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.2832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9241 Z= 0.147 Angle : 0.622 8.299 12513 Z= 0.322 Chirality : 0.044 0.183 1393 Planarity : 0.004 0.043 1577 Dihedral : 4.948 56.153 1258 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 14.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.87 % Allowed : 17.41 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.04 (0.26), residues: 1120 helix: 1.47 (0.25), residues: 397 sheet: -0.48 (0.31), residues: 278 loop : -1.05 (0.31), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 283 TYR 0.013 0.002 TYR R 123 PHE 0.013 0.001 PHE A 212 TRP 0.015 0.002 TRP B 211 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 9237) covalent geometry : angle 0.62040 (12505) SS BOND : bond 0.00903 ( 4) SS BOND : angle 1.64692 ( 8) hydrogen bonds : bond 0.04024 ( 458) hydrogen bonds : angle 5.38679 ( 1326) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 136 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 MET cc_start: 0.7017 (mpt) cc_final: 0.6698 (mpt) REVERT: B 197 ARG cc_start: 0.6877 (mmm-85) cc_final: 0.6590 (mmm-85) REVERT: B 225 HIS cc_start: 0.7628 (OUTLIER) cc_final: 0.5852 (t-90) REVERT: B 249 THR cc_start: 0.7810 (p) cc_final: 0.7550 (p) REVERT: R 59 ASN cc_start: 0.8154 (m-40) cc_final: 0.7932 (m-40) REVERT: R 123 TYR cc_start: 0.8378 (m-80) cc_final: 0.8070 (m-80) REVERT: R 158 MET cc_start: 0.7043 (OUTLIER) cc_final: 0.6574 (ttm) REVERT: R 272 VAL cc_start: 0.8572 (m) cc_final: 0.8297 (p) REVERT: S 38 ARG cc_start: 0.5423 (ptt180) cc_final: 0.5010 (ptt180) REVERT: S 101 TYR cc_start: 0.7240 (m-80) cc_final: 0.7029 (m-80) REVERT: S 172 THR cc_start: 0.6555 (OUTLIER) cc_final: 0.6345 (t) REVERT: Y 32 LYS cc_start: 0.8311 (tttm) cc_final: 0.7575 (tppt) outliers start: 38 outliers final: 13 residues processed: 155 average time/residue: 0.4751 time to fit residues: 79.8244 Evaluate side-chains 139 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 123 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 96 CYS Chi-restraints excluded: chain R residue 126 CYS Chi-restraints excluded: chain R residue 138 LEU Chi-restraints excluded: chain R residue 158 MET Chi-restraints excluded: chain R residue 209 VAL Chi-restraints excluded: chain S residue 23 SER Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 172 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 6 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 92 optimal weight: 10.0000 chunk 30 optimal weight: 2.9990 chunk 66 optimal weight: 0.5980 chunk 96 optimal weight: 50.0000 chunk 48 optimal weight: 0.7980 chunk 55 optimal weight: 6.9990 chunk 40 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS ** A 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN ** B 293 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 = 0.4560 r_free = 0.4560 target = 0.235488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.178203 restraints weight = 10153.411| |-----------------------------------------------------------------------------| r_work (start): 0.4013 rms_B_bonded: 2.39 r_work: 0.3812 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7107 moved from start: 0.2930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9241 Z= 0.161 Angle : 0.636 8.756 12513 Z= 0.325 Chirality : 0.044 0.203 1393 Planarity : 0.004 0.044 1577 Dihedral : 4.903 54.489 1258 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 4.07 % Allowed : 18.23 % Favored : 77.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.03 (0.26), residues: 1120 helix: 1.49 (0.25), residues: 398 sheet: -0.41 (0.32), residues: 277 loop : -0.99 (0.32), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 283 TYR 0.012 0.002 TYR S 190 PHE 0.014 0.001 PHE A 212 TRP 0.013 0.002 TRP B 211 HIS 0.008 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00373 ( 9237) covalent geometry : angle 0.63477 (12505) SS BOND : bond 0.00886 ( 4) SS BOND : angle 1.43127 ( 8) hydrogen bonds : bond 0.04012 ( 458) hydrogen bonds : angle 5.29409 ( 1326) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 135 time to evaluate : 0.292 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 MET cc_start: 0.6818 (mpt) cc_final: 0.6527 (mpt) REVERT: B 180 PHE cc_start: 0.6737 (OUTLIER) cc_final: 0.4406 (p90) REVERT: B 225 HIS cc_start: 0.7688 (OUTLIER) cc_final: 0.5934 (t-90) REVERT: B 249 THR cc_start: 0.7842 (p) cc_final: 0.7579 (p) REVERT: B 262 MET cc_start: 0.7649 (OUTLIER) cc_final: 0.7411 (ttm) REVERT: R 59 ASN cc_start: 0.8103 (m-40) cc_final: 0.7890 (m-40) REVERT: R 65 MET cc_start: 0.7768 (ttp) cc_final: 0.7445 (ttp) REVERT: R 123 TYR cc_start: 0.8327 (m-80) cc_final: 0.7921 (m-80) REVERT: R 158 MET cc_start: 0.7040 (OUTLIER) cc_final: 0.6593 (ttm) REVERT: R 220 GLN cc_start: 0.7253 (OUTLIER) cc_final: 0.6980 (mp10) REVERT: R 262 ILE cc_start: 0.8809 (OUTLIER) cc_final: 0.8587 (mt) REVERT: R 272 VAL cc_start: 0.8538 (m) cc_final: 0.8260 (p) REVERT: S 38 ARG cc_start: 0.5436 (ptt180) cc_final: 0.5034 (ptt180) REVERT: S 172 THR cc_start: 0.6558 (OUTLIER) cc_final: 0.6312 (t) REVERT: Y 32 LYS cc_start: 0.8349 (tttm) cc_final: 0.7602 (tppt) outliers start: 40 outliers final: 24 residues processed: 158 average time/residue: 0.4458 time to fit residues: 76.0401 Evaluate side-chains 161 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 130 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 180 PHE Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 96 CYS Chi-restraints excluded: chain R residue 126 CYS Chi-restraints excluded: chain R residue 138 LEU Chi-restraints excluded: chain R residue 158 MET Chi-restraints excluded: chain R residue 209 VAL Chi-restraints excluded: chain R residue 220 GLN Chi-restraints excluded: chain R residue 253 LEU Chi-restraints excluded: chain R residue 262 ILE Chi-restraints excluded: chain S residue 23 SER Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 189 ILE Chi-restraints excluded: chain S residue 195 LEU Chi-restraints excluded: chain S residue 210 THR Chi-restraints excluded: chain S residue 213 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 73 optimal weight: 0.9990 chunk 68 optimal weight: 0.9980 chunk 24 optimal weight: 7.9990 chunk 16 optimal weight: 0.9990 chunk 54 optimal weight: 5.9990 chunk 3 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 103 optimal weight: 6.9990 chunk 21 optimal weight: 0.9980 chunk 71 optimal weight: 7.9990 chunk 32 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS A 357 HIS ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 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 = 0.4564 r_free = 0.4564 target = 0.236005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.178732 restraints weight = 10218.006| |-----------------------------------------------------------------------------| r_work (start): 0.4006 rms_B_bonded: 2.46 r_work: 0.3825 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3684 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9241 Z= 0.156 Angle : 0.641 10.350 12513 Z= 0.327 Chirality : 0.044 0.174 1393 Planarity : 0.004 0.056 1577 Dihedral : 4.866 52.743 1258 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 14.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 4.58 % Allowed : 18.43 % Favored : 76.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.07 (0.26), residues: 1120 helix: 1.53 (0.25), residues: 398 sheet: -0.40 (0.32), residues: 277 loop : -0.98 (0.32), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 283 TYR 0.014 0.001 TYR S 190 PHE 0.014 0.001 PHE A 212 TRP 0.012 0.002 TRP B 211 HIS 0.006 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 9237) covalent geometry : angle 0.64015 (12505) SS BOND : bond 0.00839 ( 4) SS BOND : angle 1.67521 ( 8) hydrogen bonds : bond 0.03967 ( 458) hydrogen bonds : angle 5.25939 ( 1326) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 141 time to evaluate : 0.266 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 MET cc_start: 0.6883 (mpt) cc_final: 0.6587 (mpt) REVERT: B 180 PHE cc_start: 0.6812 (OUTLIER) cc_final: 0.4243 (p90) REVERT: B 199 PHE cc_start: 0.8559 (p90) cc_final: 0.8213 (p90) REVERT: B 219 ARG cc_start: 0.7381 (mmp80) cc_final: 0.7167 (mmp80) REVERT: B 225 HIS cc_start: 0.7613 (OUTLIER) cc_final: 0.6000 (t-90) REVERT: B 245 SER cc_start: 0.8628 (m) cc_final: 0.8355 (t) REVERT: B 249 THR cc_start: 0.7883 (p) cc_final: 0.7639 (p) REVERT: R 32 LEU cc_start: 0.8036 (OUTLIER) cc_final: 0.7782 (pt) REVERT: R 59 ASN cc_start: 0.8203 (m-40) cc_final: 0.7996 (m-40) REVERT: R 65 MET cc_start: 0.7869 (ttp) cc_final: 0.7527 (ttp) REVERT: R 123 TYR cc_start: 0.8410 (m-80) cc_final: 0.7980 (m-80) REVERT: R 158 MET cc_start: 0.7063 (OUTLIER) cc_final: 0.6582 (ttm) REVERT: R 220 GLN cc_start: 0.7388 (OUTLIER) cc_final: 0.7073 (mp10) REVERT: R 262 ILE cc_start: 0.8856 (OUTLIER) cc_final: 0.8625 (mt) REVERT: R 272 VAL cc_start: 0.8544 (m) cc_final: 0.8256 (p) REVERT: S 38 ARG cc_start: 0.5389 (ptt180) cc_final: 0.4964 (ptt180) REVERT: S 93 MET cc_start: 0.6773 (mmm) cc_final: 0.6158 (mmm) REVERT: S 172 THR cc_start: 0.6524 (OUTLIER) cc_final: 0.6291 (t) REVERT: Y 32 LYS cc_start: 0.8276 (tttm) cc_final: 0.7533 (tppt) outliers start: 45 outliers final: 18 residues processed: 167 average time/residue: 0.4389 time to fit residues: 79.5368 Evaluate side-chains 157 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 132 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 180 PHE Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 96 CYS Chi-restraints excluded: chain R residue 126 CYS Chi-restraints excluded: chain R residue 138 LEU Chi-restraints excluded: chain R residue 158 MET Chi-restraints excluded: chain R residue 209 VAL Chi-restraints excluded: chain R residue 220 GLN Chi-restraints excluded: chain R residue 262 ILE Chi-restraints excluded: chain S residue 23 SER Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 189 ILE Chi-restraints excluded: chain S residue 210 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 47 optimal weight: 0.0980 chunk 91 optimal weight: 20.0000 chunk 42 optimal weight: 0.9990 chunk 75 optimal weight: 4.9990 chunk 30 optimal weight: 0.4980 chunk 26 optimal weight: 5.9990 chunk 57 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 88 optimal weight: 0.7980 chunk 110 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS A 357 HIS B 32 GLN ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 183 HIS B 268 ASN ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 231 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 = 0.4577 r_free = 0.4577 target = 0.237496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.182365 restraints weight = 10206.763| |-----------------------------------------------------------------------------| r_work (start): 0.4060 rms_B_bonded: 2.32 r_work: 0.3846 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.3708 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.3053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9241 Z= 0.136 Angle : 0.642 15.031 12513 Z= 0.323 Chirality : 0.044 0.353 1393 Planarity : 0.004 0.046 1577 Dihedral : 4.782 52.948 1258 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 14.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.67 % Allowed : 19.35 % Favored : 76.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.11 (0.26), residues: 1120 helix: 1.58 (0.25), residues: 400 sheet: -0.28 (0.32), residues: 270 loop : -1.04 (0.31), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 283 TYR 0.014 0.001 TYR S 190 PHE 0.014 0.001 PHE A 212 TRP 0.014 0.002 TRP B 211 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 9237) covalent geometry : angle 0.64027 (12505) SS BOND : bond 0.00564 ( 4) SS BOND : angle 1.74302 ( 8) hydrogen bonds : bond 0.03853 ( 458) hydrogen bonds : angle 5.18560 ( 1326) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 140 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 MET cc_start: 0.6835 (mpt) cc_final: 0.6581 (mpt) REVERT: A 221 MET cc_start: 0.8600 (ttp) cc_final: 0.8336 (ttm) REVERT: B 46 ARG cc_start: 0.7090 (ptm160) cc_final: 0.6824 (ptm-80) REVERT: B 180 PHE cc_start: 0.6739 (OUTLIER) cc_final: 0.4265 (p90) REVERT: B 199 PHE cc_start: 0.8547 (p90) cc_final: 0.8192 (p90) REVERT: B 219 ARG cc_start: 0.7509 (mmp80) cc_final: 0.7129 (mmp80) REVERT: B 225 HIS cc_start: 0.7609 (OUTLIER) cc_final: 0.6000 (t-90) REVERT: B 245 SER cc_start: 0.8605 (m) cc_final: 0.8367 (t) REVERT: B 249 THR cc_start: 0.7849 (p) cc_final: 0.7628 (p) REVERT: R 32 LEU cc_start: 0.8119 (OUTLIER) cc_final: 0.7886 (pt) REVERT: R 59 ASN cc_start: 0.8174 (m-40) cc_final: 0.7955 (m-40) REVERT: R 65 MET cc_start: 0.7827 (ttp) cc_final: 0.7400 (ttp) REVERT: R 123 TYR cc_start: 0.8322 (m-80) cc_final: 0.8099 (m-80) REVERT: R 158 MET cc_start: 0.7061 (OUTLIER) cc_final: 0.6586 (ttm) REVERT: R 220 GLN cc_start: 0.7395 (OUTLIER) cc_final: 0.7135 (mp10) REVERT: R 262 ILE cc_start: 0.8876 (OUTLIER) cc_final: 0.8565 (mt) REVERT: S 38 ARG cc_start: 0.5337 (ptt180) cc_final: 0.5028 (ptt180) REVERT: S 172 THR cc_start: 0.6439 (OUTLIER) cc_final: 0.6216 (t) REVERT: Y 32 LYS cc_start: 0.8291 (tttm) cc_final: 0.7564 (tppt) outliers start: 36 outliers final: 18 residues processed: 163 average time/residue: 0.5177 time to fit residues: 90.8986 Evaluate side-chains 157 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 132 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 180 PHE Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 96 CYS Chi-restraints excluded: chain R residue 126 CYS Chi-restraints excluded: chain R residue 138 LEU Chi-restraints excluded: chain R residue 158 MET Chi-restraints excluded: chain R residue 220 GLN Chi-restraints excluded: chain R residue 253 LEU Chi-restraints excluded: chain R residue 262 ILE Chi-restraints excluded: chain R residue 318 MET Chi-restraints excluded: chain S residue 23 SER Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 189 ILE Chi-restraints excluded: chain S residue 210 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 88 optimal weight: 0.0570 chunk 92 optimal weight: 2.9990 chunk 83 optimal weight: 20.0000 chunk 99 optimal weight: 7.9990 chunk 28 optimal weight: 0.7980 chunk 42 optimal weight: 0.3980 chunk 71 optimal weight: 10.0000 chunk 17 optimal weight: 0.9990 chunk 24 optimal weight: 5.9990 chunk 3 optimal weight: 0.9990 chunk 81 optimal weight: 0.7980 overall best weight: 0.6100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS A 357 HIS ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 183 HIS B 239 ASN B 268 ASN ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 231 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 = 0.4583 r_free = 0.4583 target = 0.238375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.178933 restraints weight = 10169.408| |-----------------------------------------------------------------------------| r_work (start): 0.4020 rms_B_bonded: 2.45 r_work: 0.3867 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3729 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7199 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9241 Z= 0.135 Angle : 0.646 12.771 12513 Z= 0.324 Chirality : 0.045 0.341 1393 Planarity : 0.004 0.044 1577 Dihedral : 4.751 52.649 1258 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 3.56 % Allowed : 19.96 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.16 (0.26), residues: 1120 helix: 1.65 (0.25), residues: 398 sheet: -0.31 (0.33), residues: 256 loop : -0.98 (0.30), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 283 TYR 0.014 0.001 TYR S 190 PHE 0.014 0.001 PHE A 212 TRP 0.016 0.002 TRP R 60 HIS 0.006 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 9237) covalent geometry : angle 0.64450 (12505) SS BOND : bond 0.00673 ( 4) SS BOND : angle 1.61825 ( 8) hydrogen bonds : bond 0.03842 ( 458) hydrogen bonds : angle 5.12719 ( 1326) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 132 time to evaluate : 0.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 MET cc_start: 0.6827 (mpt) cc_final: 0.6560 (mpt) REVERT: A 221 MET cc_start: 0.8597 (ttp) cc_final: 0.8353 (ttm) REVERT: A 283 ARG cc_start: 0.7951 (mtp-110) cc_final: 0.7580 (ptm160) REVERT: B 180 PHE cc_start: 0.6732 (OUTLIER) cc_final: 0.4259 (p90) REVERT: B 199 PHE cc_start: 0.8529 (p90) cc_final: 0.8187 (p90) REVERT: B 219 ARG cc_start: 0.7598 (mmp80) cc_final: 0.7080 (mmp80) REVERT: B 225 HIS cc_start: 0.7656 (OUTLIER) cc_final: 0.6002 (t-90) REVERT: B 239 ASN cc_start: 0.8112 (OUTLIER) cc_final: 0.7901 (p0) REVERT: B 245 SER cc_start: 0.8607 (m) cc_final: 0.8365 (t) REVERT: B 249 THR cc_start: 0.7869 (p) cc_final: 0.7630 (p) REVERT: B 262 MET cc_start: 0.7751 (OUTLIER) cc_final: 0.7539 (ttm) REVERT: R 59 ASN cc_start: 0.8186 (m-40) cc_final: 0.7971 (m-40) REVERT: R 65 MET cc_start: 0.7809 (ttp) cc_final: 0.7462 (ttp) REVERT: R 123 TYR cc_start: 0.8313 (m-80) cc_final: 0.8101 (m-80) REVERT: R 158 MET cc_start: 0.7053 (OUTLIER) cc_final: 0.6585 (ttm) REVERT: R 220 GLN cc_start: 0.7372 (OUTLIER) cc_final: 0.7113 (mp10) REVERT: R 262 ILE cc_start: 0.8907 (OUTLIER) cc_final: 0.8494 (tt) REVERT: S 38 ARG cc_start: 0.5422 (ptt180) cc_final: 0.5117 (ptt180) REVERT: S 172 THR cc_start: 0.6473 (OUTLIER) cc_final: 0.6252 (t) REVERT: Y 32 LYS cc_start: 0.8277 (tttm) cc_final: 0.7506 (tppt) outliers start: 35 outliers final: 15 residues processed: 153 average time/residue: 0.4922 time to fit residues: 81.0799 Evaluate side-chains 153 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 130 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 180 PHE Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 239 ASN Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 96 CYS Chi-restraints excluded: chain R residue 126 CYS Chi-restraints excluded: chain R residue 138 LEU Chi-restraints excluded: chain R residue 158 MET Chi-restraints excluded: chain R residue 220 GLN Chi-restraints excluded: chain R residue 253 LEU Chi-restraints excluded: chain R residue 262 ILE Chi-restraints excluded: chain S residue 23 SER Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 210 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 23 optimal weight: 7.9990 chunk 15 optimal weight: 0.0980 chunk 79 optimal weight: 0.2980 chunk 69 optimal weight: 8.9990 chunk 85 optimal weight: 1.9990 chunk 20 optimal weight: 0.4980 chunk 48 optimal weight: 4.9990 chunk 81 optimal weight: 0.1980 chunk 37 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 overall best weight: 0.3580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS A 357 HIS ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 183 HIS B 239 ASN B 268 ASN B 293 ASN ** S 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4598 r_free = 0.4598 target = 0.240146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.179247 restraints weight = 10132.532| |-----------------------------------------------------------------------------| r_work (start): 0.4023 rms_B_bonded: 2.25 r_work: 0.3896 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3760 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7156 moved from start: 0.3120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9241 Z= 0.123 Angle : 0.646 12.441 12513 Z= 0.324 Chirality : 0.045 0.343 1393 Planarity : 0.004 0.046 1577 Dihedral : 4.714 52.816 1258 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.95 % Allowed : 20.67 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.16 (0.26), residues: 1120 helix: 1.65 (0.25), residues: 398 sheet: -0.28 (0.33), residues: 254 loop : -1.01 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 283 TYR 0.015 0.001 TYR S 190 PHE 0.014 0.001 PHE A 212 TRP 0.019 0.002 TRP R 60 HIS 0.006 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 9237) covalent geometry : angle 0.64487 (12505) SS BOND : bond 0.00588 ( 4) SS BOND : angle 1.44693 ( 8) hydrogen bonds : bond 0.03799 ( 458) hydrogen bonds : angle 5.10707 ( 1326) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 131 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 MET cc_start: 0.6832 (mpt) cc_final: 0.6600 (mpt) REVERT: A 221 MET cc_start: 0.8602 (ttp) cc_final: 0.8371 (ttm) REVERT: A 283 ARG cc_start: 0.7953 (mtp-110) cc_final: 0.7640 (ptm160) REVERT: B 180 PHE cc_start: 0.6611 (OUTLIER) cc_final: 0.4314 (p90) REVERT: B 219 ARG cc_start: 0.7548 (mmp80) cc_final: 0.7031 (mmp80) REVERT: B 225 HIS cc_start: 0.7622 (OUTLIER) cc_final: 0.6090 (t-90) REVERT: B 245 SER cc_start: 0.8592 (m) cc_final: 0.8347 (t) REVERT: B 249 THR cc_start: 0.7858 (p) cc_final: 0.7638 (p) REVERT: B 262 MET cc_start: 0.7781 (OUTLIER) cc_final: 0.7566 (ttm) REVERT: R 59 ASN cc_start: 0.8160 (m-40) cc_final: 0.7947 (m-40) REVERT: R 65 MET cc_start: 0.7719 (ttp) cc_final: 0.7285 (ttp) REVERT: R 158 MET cc_start: 0.7032 (OUTLIER) cc_final: 0.6565 (ttm) REVERT: R 220 GLN cc_start: 0.7333 (OUTLIER) cc_final: 0.7106 (mp10) REVERT: R 262 ILE cc_start: 0.8890 (OUTLIER) cc_final: 0.8475 (tt) REVERT: R 318 MET cc_start: 0.5681 (OUTLIER) cc_final: 0.4851 (ttt) REVERT: S 38 ARG cc_start: 0.5332 (ptt180) cc_final: 0.5097 (ptt180) REVERT: S 93 MET cc_start: 0.6745 (mmm) cc_final: 0.6159 (mmm) REVERT: S 101 TYR cc_start: 0.7152 (m-80) cc_final: 0.6825 (m-80) REVERT: S 172 THR cc_start: 0.6479 (OUTLIER) cc_final: 0.6250 (t) REVERT: S 213 THR cc_start: 0.7363 (OUTLIER) cc_final: 0.7155 (t) REVERT: Y 32 LYS cc_start: 0.8285 (tttm) cc_final: 0.7498 (tppt) outliers start: 29 outliers final: 13 residues processed: 152 average time/residue: 0.5161 time to fit residues: 84.1009 Evaluate side-chains 149 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 127 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 180 PHE Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 96 CYS Chi-restraints excluded: chain R residue 126 CYS Chi-restraints excluded: chain R residue 138 LEU Chi-restraints excluded: chain R residue 158 MET Chi-restraints excluded: chain R residue 220 GLN Chi-restraints excluded: chain R residue 262 ILE Chi-restraints excluded: chain R residue 318 MET Chi-restraints excluded: chain S residue 23 SER Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 210 THR Chi-restraints excluded: chain S residue 213 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 0.7980 chunk 68 optimal weight: 5.9990 chunk 31 optimal weight: 0.7980 chunk 78 optimal weight: 0.6980 chunk 72 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 89 optimal weight: 6.9990 chunk 37 optimal weight: 0.6980 chunk 97 optimal weight: 30.0000 chunk 91 optimal weight: 20.0000 chunk 6 optimal weight: 2.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS A 357 HIS ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 183 HIS B 220 GLN B 237 ASN B 268 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4566 r_free = 0.4566 target = 0.236120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.179640 restraints weight = 10037.440| |-----------------------------------------------------------------------------| r_work (start): 0.4017 rms_B_bonded: 2.41 r_work: 0.3822 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3681 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.3223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9241 Z= 0.174 Angle : 0.672 12.355 12513 Z= 0.341 Chirality : 0.046 0.332 1393 Planarity : 0.004 0.044 1577 Dihedral : 4.808 51.524 1258 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 15.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 3.16 % Allowed : 20.88 % Favored : 75.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.17 (0.26), residues: 1120 helix: 1.65 (0.25), residues: 398 sheet: -0.31 (0.31), residues: 271 loop : -0.97 (0.31), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 283 TYR 0.016 0.002 TYR S 190 PHE 0.016 0.002 PHE A 212 TRP 0.018 0.002 TRP R 60 HIS 0.011 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00405 ( 9237) covalent geometry : angle 0.67045 (12505) SS BOND : bond 0.00892 ( 4) SS BOND : angle 1.89115 ( 8) hydrogen bonds : bond 0.04080 ( 458) hydrogen bonds : angle 5.18670 ( 1326) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4106.80 seconds wall clock time: 70 minutes 45.46 seconds (4245.46 seconds total)