Starting phenix.real_space_refine on Thu Jul 2 15:11:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8jlq_36404/07_2026/8jlq_36404.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jlq_36404/07_2026/8jlq_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 { model { file = "/net/cci-nas-00/data/ceres_data/8jlq_36404/07_2026/8jlq_36404.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jlq_36404/07_2026/8jlq_36404.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jlq_36404/07_2026/8jlq_36404.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jlq_36404/07_2026/8jlq_36404.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8jlq_36404/07_2026/8jlq_36404.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8jlq_36404/07_2026/8jlq_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 1.75, per 1000 atoms: 0.19 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: 0.67 Conformation dependent library (CDL) restraints added in 302.2 milliseconds 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: 0.17 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: 1.11 Time building geometry restraints manager: 0.87 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: 4939 16.77 - 33.53: 412 33.53 - 50.30: 101 50.30 - 67.07: 9 67.07 - 83.84: 6 Dihedral angle restraints: 5467 sinusoidal: 2150 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 5464 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: 0.530 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: 0.130 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 7.760 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:5.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6856 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 : 13.167 83.836 3315 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 are 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/Z covalent geometry : bond 0.00481 / 0.33 ( 9237) covalent geometry : angle 0.78206 / 0.47 (12505) SS BOND : bond 0.00727 / 0.38 ( 4) SS BOND : angle 1.62150 / 0.86 ( 8) hydrogen bonds : bond 0.15097 / 9.91 ( 458) hydrogen bonds : angle 7.02175 / 4.97 ( 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 : 0.198 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: 0.3936 time to fit residues: 73.4159 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 : 0.195 ------------------------------------------------------------------------------- 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... 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 = 0.4605 r_free = 0.4605 target = 0.241346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.184992 restraints weight = 10129.523| |-----------------------------------------------------------------------------| r_work (start): 0.4072 rms_B_bonded: 2.52 r_work: 0.3892 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 moved from start: 0.1657 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= 0.168 Angle : 0.641 7.975 12513 Z= 0.337 Chirality : 0.045 0.204 1393 Planarity : 0.005 0.043 1577 Dihedral : 4.812 50.570 1246 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 14.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.04 % Allowed : 10.39 % Favored : 87.58 % 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 are not related in a simple way. whole: -0.05 (0.26), residues: 1120 helix: 1.43 (0.25), residues: 397 sheet: -0.42 (0.33), residues: 269 loop : -1.06 (0.30), residues: 454 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 R 299 TRP 0.019 0.002 TRP B 211 HIS 0.006 0.002 HIS R 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.17 ( 9237) covalent geometry : angle 0.63970 / 0.34 (12505) SS BOND : bond 0.00823 / 0.43 ( 4) SS BOND : angle 1.64123 / 0.89 ( 8) hydrogen bonds : bond 0.04359 / 2.96 ( 458) hydrogen bonds : angle 5.59213 / 3.98 ( 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 170 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 150 time to evaluate : 0.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 132 ASN cc_start: 0.6554 (m-40) cc_final: 0.5917 (p0) REVERT: B 134 ARG cc_start: 0.7623 (ptp-170) cc_final: 0.7314 (ptt-90) REVERT: R 32 LEU cc_start: 0.8013 (OUTLIER) cc_final: 0.7794 (pt) REVERT: R 65 MET cc_start: 0.7802 (ttp) cc_final: 0.7522 (ttp) REVERT: R 220 GLN cc_start: 0.7154 (OUTLIER) cc_final: 0.6939 (mp10) REVERT: S 38 ARG cc_start: 0.5628 (ptt180) cc_final: 0.5230 (ptt180) REVERT: Y 32 LYS cc_start: 0.8287 (tttm) cc_final: 0.7489 (tppt) outliers start: 20 outliers final: 6 residues processed: 157 average time/residue: 0.3783 time to fit residues: 64.3419 Evaluate side-chains 142 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 134 time to evaluate : 0.231 ------------------------------------------------------------------------------- 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: 8.9990 chunk 8 optimal weight: 0.9990 chunk 75 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 69 optimal weight: 10.0000 chunk 22 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 98 optimal weight: 7.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4564 r_free = 0.4564 target = 0.236052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.178499 restraints weight = 10078.736| |-----------------------------------------------------------------------------| r_work (start): 0.4018 rms_B_bonded: 2.37 r_work: 0.3815 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 9241 Z= 0.200 Angle : 0.648 8.938 12513 Z= 0.340 Chirality : 0.045 0.191 1393 Planarity : 0.004 0.042 1577 Dihedral : 4.893 51.451 1243 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 3.26 % Allowed : 13.54 % Favored : 83.20 % 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 are not related in a simple way. whole: -0.01 (0.26), residues: 1120 helix: 1.44 (0.25), residues: 398 sheet: -0.31 (0.32), residues: 268 loop : -1.08 (0.31), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 38 TYR 0.014 0.002 TYR B 59 PHE 0.014 0.002 PHE B 180 TRP 0.013 0.002 TRP B 211 HIS 0.007 0.002 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.20 ( 9237) covalent geometry : angle 0.64730 / 0.34 (12505) SS BOND : bond 0.00917 / 0.48 ( 4) SS BOND : angle 1.36553 / 0.73 ( 8) hydrogen bonds : bond 0.04330 / 2.93 ( 458) hydrogen bonds : angle 5.48348 / 3.89 ( 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 172 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 140 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 ARG cc_start: 0.7566 (mmt-90) cc_final: 0.7231 (mmt-90) REVERT: B 132 ASN cc_start: 0.6758 (m-40) cc_final: 0.6175 (p0) REVERT: B 134 ARG cc_start: 0.7728 (ptp-170) cc_final: 0.7315 (ptp90) REVERT: B 249 THR cc_start: 0.7947 (p) cc_final: 0.7644 (p) REVERT: R 59 ASN cc_start: 0.8013 (m-40) cc_final: 0.7787 (m-40) REVERT: R 65 MET cc_start: 0.7937 (ttp) cc_final: 0.7697 (ttp) REVERT: R 123 TYR cc_start: 0.8450 (m-80) cc_final: 0.7969 (m-80) REVERT: R 158 MET cc_start: 0.7043 (OUTLIER) cc_final: 0.6631 (ttm) REVERT: R 220 GLN cc_start: 0.7254 (OUTLIER) cc_final: 0.7018 (mp10) REVERT: S 38 ARG cc_start: 0.5415 (ptt180) cc_final: 0.5159 (ptt180) REVERT: S 172 THR cc_start: 0.6597 (OUTLIER) cc_final: 0.6295 (t) REVERT: Y 32 LYS cc_start: 0.8340 (tttm) cc_final: 0.7570 (tppt) outliers start: 32 outliers final: 15 residues processed: 158 average time/residue: 0.4030 time to fit residues: 68.9161 Evaluate side-chains 144 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 126 time to evaluate : 0.193 ------------------------------------------------------------------------------- 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 55 LEU 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 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 172 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 61 optimal weight: 9.9990 chunk 94 optimal weight: 7.9990 chunk 99 optimal weight: 7.9990 chunk 20 optimal weight: 0.9990 chunk 14 optimal weight: 0.4980 chunk 90 optimal weight: 6.9990 chunk 57 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 3 optimal weight: 0.4980 chunk 87 optimal weight: 10.0000 chunk 1 optimal weight: 0.7980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 ** 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 = 0.4577 r_free = 0.4577 target = 0.237742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.181800 restraints weight = 10231.474| |-----------------------------------------------------------------------------| r_work (start): 0.4046 rms_B_bonded: 2.30 r_work: 0.3851 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3715 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.2394 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= 0.155 Angle : 0.620 7.819 12513 Z= 0.321 Chirality : 0.044 0.177 1393 Planarity : 0.004 0.043 1577 Dihedral : 4.826 56.057 1243 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.97 % Allowed : 15.38 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.26), residues: 1120 helix: 1.57 (0.25), residues: 398 sheet: -0.24 (0.33), residues: 268 loop : -1.00 (0.31), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 283 TYR 0.014 0.002 TYR A 37 PHE 0.014 0.002 PHE A 212 TRP 0.014 0.002 TRP B 211 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 ( 9237) covalent geometry : angle 0.61914 / 0.32 (12505) SS BOND : bond 0.01123 / 0.59 ( 4) SS BOND : angle 1.46496 / 0.77 ( 8) hydrogen bonds : bond 0.04022 / 2.75 ( 458) hydrogen bonds : angle 5.32970 / 3.77 ( 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 172 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 133 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 ARG cc_start: 0.7687 (mmt-90) cc_final: 0.7390 (mmt-90) REVERT: B 134 ARG cc_start: 0.8004 (ptp-170) cc_final: 0.7787 (ptp-170) REVERT: B 249 THR cc_start: 0.7791 (p) cc_final: 0.7552 (p) REVERT: R 32 LEU cc_start: 0.8092 (OUTLIER) cc_final: 0.7847 (pt) REVERT: R 59 ASN cc_start: 0.8078 (m-40) cc_final: 0.7870 (m-40) REVERT: R 65 MET cc_start: 0.7883 (ttp) cc_final: 0.7667 (ttp) REVERT: R 123 TYR cc_start: 0.8396 (m-80) cc_final: 0.8186 (m-80) REVERT: R 158 MET cc_start: 0.7015 (OUTLIER) cc_final: 0.6591 (ttm) REVERT: R 220 GLN cc_start: 0.7373 (OUTLIER) cc_final: 0.7143 (mp10) REVERT: S 38 ARG cc_start: 0.5357 (ptt180) cc_final: 0.5114 (ptt180) REVERT: S 93 MET cc_start: 0.6648 (mmm) cc_final: 0.6428 (mmm) REVERT: S 172 THR cc_start: 0.6533 (OUTLIER) cc_final: 0.6257 (t) REVERT: Y 32 LYS cc_start: 0.8299 (tttm) cc_final: 0.7524 (tppt) outliers start: 39 outliers final: 16 residues processed: 158 average time/residue: 0.5170 time to fit residues: 88.2172 Evaluate side-chains 142 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 122 time to evaluate : 0.335 ------------------------------------------------------------------------------- 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 55 LEU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 101 MET 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 91 THR Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 189 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 26 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 103 optimal weight: 30.0000 chunk 108 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 85 optimal weight: 7.9990 chunk 37 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 R 63 HIS 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 = 0.4538 r_free = 0.4538 target = 0.233186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.174236 restraints weight = 10052.004| |-----------------------------------------------------------------------------| r_work (start): 0.3969 rms_B_bonded: 2.48 r_work: 0.3783 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 9241 Z= 0.239 Angle : 0.703 10.516 12513 Z= 0.361 Chirality : 0.046 0.208 1393 Planarity : 0.005 0.045 1577 Dihedral : 5.041 54.655 1243 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 17.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.46 % Allowed : 16.70 % Favored : 79.84 % 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 are not related in a simple way. whole: -0.05 (0.26), residues: 1120 helix: 1.44 (0.25), residues: 397 sheet: -0.55 (0.31), residues: 279 loop : -0.98 (0.32), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 283 TYR 0.023 0.002 TYR B 105 PHE 0.017 0.002 PHE A 212 TRP 0.013 0.002 TRP B 82 HIS 0.011 0.002 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00563 / 0.24 ( 9237) covalent geometry : angle 0.70173 / 0.36 (12505) SS BOND : bond 0.01181 / 0.62 ( 4) SS BOND : angle 1.79420 / 0.95 ( 8) hydrogen bonds : bond 0.04428 / 3.01 ( 458) hydrogen bonds : angle 5.46080 / 3.85 ( 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 173 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 139 time to evaluate : 0.384 Fit side-chains revert: symmetry clash REVERT: A 338 LYS cc_start: 0.6494 (OUTLIER) cc_final: 0.5929 (ptmt) REVERT: A 370 GLU cc_start: 0.6273 (pm20) cc_final: 0.6050 (mm-30) REVERT: B 55 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.8125 (mp) REVERT: B 134 ARG cc_start: 0.7828 (ptp-170) cc_final: 0.7582 (ptp-170) REVERT: B 180 PHE cc_start: 0.6985 (OUTLIER) cc_final: 0.4616 (p90) REVERT: B 249 THR cc_start: 0.7936 (p) cc_final: 0.7657 (p) REVERT: R 65 MET cc_start: 0.7899 (ttp) cc_final: 0.7634 (ttp) REVERT: R 123 TYR cc_start: 0.8443 (m-80) cc_final: 0.8000 (m-80) REVERT: R 158 MET cc_start: 0.7072 (OUTLIER) cc_final: 0.6613 (ttm) REVERT: R 272 VAL cc_start: 0.8529 (m) cc_final: 0.8311 (p) REVERT: S 38 ARG cc_start: 0.5514 (ptt180) cc_final: 0.5087 (ptt180) REVERT: S 93 MET cc_start: 0.6539 (mmm) cc_final: 0.6296 (mmm) REVERT: S 140 MET cc_start: 0.5375 (mmm) cc_final: 0.4537 (mmm) REVERT: S 172 THR cc_start: 0.6595 (OUTLIER) cc_final: 0.6343 (t) REVERT: Y 32 LYS cc_start: 0.8425 (tttm) cc_final: 0.7703 (tppt) outliers start: 34 outliers final: 17 residues processed: 160 average time/residue: 0.4893 time to fit residues: 84.7811 Evaluate side-chains 152 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 130 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 338 LYS Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 180 PHE 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 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 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 Chi-restraints excluded: chain S residue 189 ILE 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: 1.9990 chunk 52 optimal weight: 4.9990 chunk 92 optimal weight: 7.9990 chunk 30 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 chunk 96 optimal weight: 50.0000 chunk 48 optimal weight: 7.9990 chunk 55 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 59 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 220 HIS A 357 HIS ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 GLN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4565 r_free = 0.4565 target = 0.236235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.178557 restraints weight = 10116.440| |-----------------------------------------------------------------------------| r_work (start): 0.4012 rms_B_bonded: 2.46 r_work: 0.3823 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9241 Z= 0.155 Angle : 0.645 9.402 12513 Z= 0.331 Chirality : 0.044 0.182 1393 Planarity : 0.004 0.044 1577 Dihedral : 4.917 56.706 1243 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 15.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 3.87 % Allowed : 18.13 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.26), residues: 1120 helix: 1.55 (0.25), residues: 398 sheet: -0.41 (0.32), residues: 275 loop : -1.05 (0.31), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 283 TYR 0.016 0.002 TYR A 37 PHE 0.014 0.001 PHE A 212 TRP 0.012 0.002 TRP B 211 HIS 0.007 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.15 ( 9237) covalent geometry : angle 0.64431 / 0.33 (12505) SS BOND : bond 0.00850 / 0.45 ( 4) SS BOND : angle 1.54281 / 0.80 ( 8) hydrogen bonds : bond 0.04052 / 2.77 ( 458) hydrogen bonds : angle 5.33388 / 3.76 ( 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 172 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 134 time to evaluate : 0.344 Fit side-chains revert: symmetry clash REVERT: B 134 ARG cc_start: 0.7810 (ptp-170) cc_final: 0.7324 (ptt-90) REVERT: B 180 PHE cc_start: 0.6756 (OUTLIER) cc_final: 0.4464 (p90) REVERT: B 219 ARG cc_start: 0.7295 (mmp80) cc_final: 0.7042 (mmp80) REVERT: B 225 HIS cc_start: 0.7664 (OUTLIER) cc_final: 0.5967 (t-90) REVERT: B 249 THR cc_start: 0.7774 (p) cc_final: 0.7540 (p) REVERT: R 32 LEU cc_start: 0.7684 (OUTLIER) cc_final: 0.7398 (pt) REVERT: R 123 TYR cc_start: 0.8343 (m-80) cc_final: 0.7887 (m-80) REVERT: R 158 MET cc_start: 0.7013 (OUTLIER) cc_final: 0.6571 (ttm) REVERT: R 220 GLN cc_start: 0.7088 (OUTLIER) cc_final: 0.6884 (mp10) REVERT: R 262 ILE cc_start: 0.8825 (OUTLIER) cc_final: 0.8608 (mt) REVERT: R 272 VAL cc_start: 0.8535 (m) cc_final: 0.8260 (p) REVERT: S 38 ARG cc_start: 0.5372 (ptt180) cc_final: 0.4967 (ptt180) REVERT: S 93 MET cc_start: 0.6521 (mmm) cc_final: 0.6277 (mmm) REVERT: S 140 MET cc_start: 0.5355 (mmm) cc_final: 0.4502 (mmm) REVERT: S 172 THR cc_start: 0.6524 (OUTLIER) cc_final: 0.6281 (t) REVERT: Y 32 LYS cc_start: 0.8343 (tttm) cc_final: 0.7587 (tppt) outliers start: 38 outliers final: 16 residues processed: 156 average time/residue: 0.5202 time to fit residues: 87.5855 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 : 0.354 ------------------------------------------------------------------------------- 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 69 LEU Chi-restraints excluded: chain B residue 180 PHE 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 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 156 SER Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 189 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 73 optimal weight: 0.6980 chunk 68 optimal weight: 2.9990 chunk 24 optimal weight: 8.9990 chunk 16 optimal weight: 7.9990 chunk 54 optimal weight: 6.9990 chunk 3 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 103 optimal weight: 20.0000 chunk 21 optimal weight: 0.7980 chunk 71 optimal weight: 8.9990 chunk 32 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 ** R 296 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 = 0.4559 r_free = 0.4559 target = 0.235126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.176950 restraints weight = 10184.856| |-----------------------------------------------------------------------------| r_work (start): 0.3994 rms_B_bonded: 2.55 r_work: 0.3798 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.2970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9241 Z= 0.183 Angle : 0.673 14.343 12513 Z= 0.341 Chirality : 0.046 0.362 1393 Planarity : 0.004 0.045 1577 Dihedral : 4.961 56.502 1243 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 15.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 3.77 % Allowed : 18.53 % 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 are not related in a simple way. whole: -0.01 (0.26), residues: 1120 helix: 1.49 (0.25), residues: 397 sheet: -0.44 (0.32), residues: 276 loop : -1.03 (0.31), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 283 TYR 0.014 0.002 TYR S 190 PHE 0.015 0.002 PHE A 212 TRP 0.012 0.002 TRP A 281 HIS 0.011 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.18 ( 9237) covalent geometry : angle 0.67190 / 0.34 (12505) SS BOND : bond 0.00862 / 0.45 ( 4) SS BOND : angle 1.92536 / 1.01 ( 8) hydrogen bonds : bond 0.04147 / 2.84 ( 458) hydrogen bonds : angle 5.33841 / 3.76 ( 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 174 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 137 time to evaluate : 0.366 Fit side-chains revert: symmetry clash REVERT: B 76 ASP cc_start: 0.7694 (OUTLIER) cc_final: 0.7454 (p0) REVERT: B 134 ARG cc_start: 0.7853 (ptp-170) cc_final: 0.7619 (ptp-170) REVERT: B 180 PHE cc_start: 0.6795 (OUTLIER) cc_final: 0.4588 (p90) REVERT: B 219 ARG cc_start: 0.7345 (mmp80) cc_final: 0.7128 (mmp80) REVERT: B 225 HIS cc_start: 0.7672 (OUTLIER) cc_final: 0.5856 (t-90) REVERT: B 249 THR cc_start: 0.7823 (p) cc_final: 0.7578 (p) REVERT: B 262 MET cc_start: 0.7555 (OUTLIER) cc_final: 0.7170 (ttm) REVERT: R 32 LEU cc_start: 0.7668 (OUTLIER) cc_final: 0.7256 (pt) REVERT: R 65 MET cc_start: 0.7796 (ttp) cc_final: 0.7463 (ttp) REVERT: R 123 TYR cc_start: 0.8403 (m-80) cc_final: 0.8004 (m-80) REVERT: R 158 MET cc_start: 0.7045 (OUTLIER) cc_final: 0.6580 (ttm) REVERT: R 220 GLN cc_start: 0.7230 (OUTLIER) cc_final: 0.6953 (mp10) REVERT: R 262 ILE cc_start: 0.8834 (OUTLIER) cc_final: 0.8606 (mt) REVERT: R 272 VAL cc_start: 0.8534 (m) cc_final: 0.8253 (p) REVERT: S 38 ARG cc_start: 0.5400 (ptt180) cc_final: 0.4968 (ptt180) REVERT: S 93 MET cc_start: 0.6508 (mmm) cc_final: 0.6250 (mmm) REVERT: S 140 MET cc_start: 0.5380 (mmm) cc_final: 0.4494 (mmm) REVERT: S 172 THR cc_start: 0.6511 (OUTLIER) cc_final: 0.6280 (t) REVERT: Y 32 LYS cc_start: 0.8331 (tttm) cc_final: 0.7586 (tppt) outliers start: 37 outliers final: 17 residues processed: 158 average time/residue: 0.4753 time to fit residues: 81.6983 Evaluate side-chains 159 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 133 time to evaluate : 0.351 ------------------------------------------------------------------------------- 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 291 LEU Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 76 ASP 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 47 optimal weight: 1.9990 chunk 91 optimal weight: 20.0000 chunk 42 optimal weight: 7.9990 chunk 75 optimal weight: 5.9990 chunk 30 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 57 optimal weight: 0.8980 chunk 76 optimal weight: 0.8980 chunk 88 optimal weight: 0.0010 chunk 110 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 overall best weight: 0.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 35 GLN 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 R 164 ASN ** 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 = 0.4571 r_free = 0.4571 target = 0.236426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.178445 restraints weight = 10207.251| |-----------------------------------------------------------------------------| r_work (start): 0.4010 rms_B_bonded: 2.53 r_work: 0.3826 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.2991 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= 0.153 Angle : 0.646 11.426 12513 Z= 0.328 Chirality : 0.044 0.203 1393 Planarity : 0.004 0.059 1577 Dihedral : 4.905 57.149 1243 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.87 % Allowed : 18.94 % Favored : 77.19 % 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 are not related in a simple way. whole: 0.06 (0.26), residues: 1120 helix: 1.61 (0.25), residues: 398 sheet: -0.42 (0.32), residues: 277 loop : -1.04 (0.31), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 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 A 281 HIS 0.008 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 ( 9237) covalent geometry : angle 0.64434 / 0.33 (12505) SS BOND : bond 0.00724 / 0.38 ( 4) SS BOND : angle 1.91210 / 1.02 ( 8) hydrogen bonds : bond 0.04002 / 2.75 ( 458) hydrogen bonds : angle 5.26002 / 3.71 ( 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 175 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 137 time to evaluate : 0.367 Fit side-chains revert: symmetry clash REVERT: B 76 ASP cc_start: 0.7591 (OUTLIER) cc_final: 0.7318 (p0) REVERT: B 78 LYS cc_start: 0.8320 (OUTLIER) cc_final: 0.8020 (ttmt) REVERT: B 180 PHE cc_start: 0.6695 (OUTLIER) cc_final: 0.4475 (p90) REVERT: B 219 ARG cc_start: 0.7412 (mmp80) cc_final: 0.6997 (mmp80) REVERT: B 225 HIS cc_start: 0.7663 (OUTLIER) cc_final: 0.5964 (t-90) REVERT: B 249 THR cc_start: 0.7754 (p) cc_final: 0.7543 (p) REVERT: B 262 MET cc_start: 0.7639 (OUTLIER) cc_final: 0.7268 (ttm) REVERT: R 65 MET cc_start: 0.7703 (ttp) cc_final: 0.7303 (ttp) REVERT: R 123 TYR cc_start: 0.8309 (m-80) cc_final: 0.7897 (m-80) REVERT: R 158 MET cc_start: 0.6946 (OUTLIER) cc_final: 0.6485 (ttm) REVERT: R 272 VAL cc_start: 0.8532 (m) cc_final: 0.8245 (p) REVERT: S 34 MET cc_start: 0.6732 (mmp) cc_final: 0.6464 (mmp) REVERT: S 38 ARG cc_start: 0.5482 (ptt180) cc_final: 0.5164 (ptt180) REVERT: S 93 MET cc_start: 0.6501 (mmm) cc_final: 0.6226 (mmm) REVERT: S 140 MET cc_start: 0.5522 (mmm) cc_final: 0.4699 (mmm) REVERT: S 172 THR cc_start: 0.6382 (OUTLIER) cc_final: 0.6152 (t) REVERT: Y 32 LYS cc_start: 0.8333 (tttm) cc_final: 0.7589 (tppt) outliers start: 38 outliers final: 18 residues processed: 158 average time/residue: 0.4916 time to fit residues: 84.0599 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 : 0.374 ------------------------------------------------------------------------------- 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 55 LEU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 78 LYS 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 B residue 336 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 253 LEU 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: 0.0870 chunk 92 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 chunk 99 optimal weight: 6.9990 chunk 28 optimal weight: 0.5980 chunk 42 optimal weight: 5.9990 chunk 71 optimal weight: 20.0000 chunk 17 optimal weight: 3.9990 chunk 24 optimal weight: 9.9990 chunk 3 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 overall best weight: 1.2962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 35 GLN 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4560 r_free = 0.4560 target = 0.235305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.176809 restraints weight = 10098.120| |-----------------------------------------------------------------------------| r_work (start): 0.3995 rms_B_bonded: 2.52 r_work: 0.3808 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.3102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9241 Z= 0.184 Angle : 0.701 11.723 12513 Z= 0.350 Chirality : 0.046 0.202 1393 Planarity : 0.005 0.051 1577 Dihedral : 4.965 56.253 1243 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 15.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 3.36 % Allowed : 19.76 % Favored : 76.88 % 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 are not related in a simple way. whole: -0.02 (0.26), residues: 1120 helix: 1.45 (0.25), residues: 399 sheet: -0.48 (0.32), residues: 279 loop : -0.99 (0.31), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 283 TYR 0.015 0.002 TYR S 190 PHE 0.015 0.002 PHE A 212 TRP 0.014 0.002 TRP A 281 HIS 0.011 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.18 ( 9237) covalent geometry : angle 0.69944 / 0.35 (12505) SS BOND : bond 0.00897 / 0.47 ( 4) SS BOND : angle 1.96166 / 1.04 ( 8) hydrogen bonds : bond 0.04220 / 2.89 ( 458) hydrogen bonds : angle 5.30588 / 3.74 ( 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 170 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 137 time to evaluate : 0.417 Fit side-chains revert: symmetry clash REVERT: B 46 ARG cc_start: 0.7018 (ptm160) cc_final: 0.6785 (ptm-80) REVERT: B 76 ASP cc_start: 0.7644 (OUTLIER) cc_final: 0.7376 (p0) REVERT: B 78 LYS cc_start: 0.8314 (OUTLIER) cc_final: 0.7976 (ttmt) REVERT: B 134 ARG cc_start: 0.7766 (ptp-170) cc_final: 0.7552 (ptp-170) REVERT: B 180 PHE cc_start: 0.6858 (OUTLIER) cc_final: 0.4594 (p90) REVERT: B 219 ARG cc_start: 0.7374 (mmp80) cc_final: 0.7039 (mmp80) REVERT: B 225 HIS cc_start: 0.7702 (OUTLIER) cc_final: 0.5947 (t-90) REVERT: B 249 THR cc_start: 0.7845 (p) cc_final: 0.7608 (p) REVERT: B 262 MET cc_start: 0.7642 (OUTLIER) cc_final: 0.7345 (ttm) REVERT: R 65 MET cc_start: 0.7773 (ttp) cc_final: 0.7358 (ttp) REVERT: R 123 TYR cc_start: 0.8368 (m-80) cc_final: 0.7961 (m-80) REVERT: R 158 MET cc_start: 0.6999 (OUTLIER) cc_final: 0.6538 (ttm) REVERT: R 272 VAL cc_start: 0.8553 (m) cc_final: 0.8251 (p) REVERT: S 38 ARG cc_start: 0.5432 (ptt180) cc_final: 0.4991 (ptt180) REVERT: S 93 MET cc_start: 0.6493 (mmm) cc_final: 0.6214 (mmm) REVERT: S 140 MET cc_start: 0.5519 (mmm) cc_final: 0.4724 (mmm) REVERT: S 172 THR cc_start: 0.6451 (OUTLIER) cc_final: 0.6211 (t) REVERT: Y 32 LYS cc_start: 0.8335 (tttm) cc_final: 0.7592 (tppt) outliers start: 33 outliers final: 18 residues processed: 154 average time/residue: 0.5309 time to fit residues: 88.1113 Evaluate side-chains 159 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 134 time to evaluate : 0.362 ------------------------------------------------------------------------------- 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 55 LEU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 180 PHE Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 260 GLU 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 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 253 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 23 optimal weight: 10.0000 chunk 15 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 69 optimal weight: 20.0000 chunk 85 optimal weight: 6.9990 chunk 20 optimal weight: 0.9990 chunk 48 optimal weight: 6.9990 chunk 81 optimal weight: 0.6980 chunk 37 optimal weight: 0.6980 chunk 77 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 35 GLN 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 220 GLN B 268 ASN ** B 293 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 = 0.4577 r_free = 0.4577 target = 0.237158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.179114 restraints weight = 10094.478| |-----------------------------------------------------------------------------| r_work (start): 0.4020 rms_B_bonded: 2.48 r_work: 0.3840 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.3140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9241 Z= 0.148 Angle : 0.671 10.953 12513 Z= 0.337 Chirality : 0.045 0.198 1393 Planarity : 0.004 0.048 1577 Dihedral : 4.926 56.988 1243 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 14.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 3.05 % Allowed : 20.16 % Favored : 76.78 % 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 are not related in a simple way. whole: 0.05 (0.26), residues: 1120 helix: 1.51 (0.25), residues: 399 sheet: -0.37 (0.32), residues: 269 loop : -1.01 (0.31), residues: 452 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 0.014 0.002 TRP R 60 HIS 0.010 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 ( 9237) covalent geometry : angle 0.66905 / 0.34 (12505) SS BOND : bond 0.00675 / 0.35 ( 4) SS BOND : angle 1.91540 / 1.02 ( 8) hydrogen bonds : bond 0.04012 / 2.76 ( 458) hydrogen bonds : angle 5.23386 / 3.69 ( 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 161 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 131 time to evaluate : 0.293 Fit side-chains revert: symmetry clash REVERT: A 221 MET cc_start: 0.8538 (ttp) cc_final: 0.8280 (ttm) REVERT: B 46 ARG cc_start: 0.6927 (ptm160) cc_final: 0.6690 (ptm-80) REVERT: B 76 ASP cc_start: 0.7719 (OUTLIER) cc_final: 0.7469 (p0) REVERT: B 78 LYS cc_start: 0.8310 (OUTLIER) cc_final: 0.7984 (ttmt) REVERT: B 180 PHE cc_start: 0.6638 (OUTLIER) cc_final: 0.4360 (p90) REVERT: B 219 ARG cc_start: 0.7377 (mmp80) cc_final: 0.7001 (mmp80) REVERT: B 225 HIS cc_start: 0.7656 (OUTLIER) cc_final: 0.5953 (t-90) REVERT: B 249 THR cc_start: 0.7850 (p) cc_final: 0.7601 (p) REVERT: B 262 MET cc_start: 0.7612 (OUTLIER) cc_final: 0.7232 (ttm) REVERT: R 65 MET cc_start: 0.7622 (ttp) cc_final: 0.7204 (ttp) REVERT: R 123 TYR cc_start: 0.8290 (m-80) cc_final: 0.8013 (m-80) REVERT: R 158 MET cc_start: 0.6940 (OUTLIER) cc_final: 0.6494 (ttm) REVERT: R 262 ILE cc_start: 0.8869 (OUTLIER) cc_final: 0.8432 (tt) REVERT: S 38 ARG cc_start: 0.5361 (ptt180) cc_final: 0.5063 (ptt180) REVERT: S 93 MET cc_start: 0.6609 (mmm) cc_final: 0.6339 (mmm) REVERT: S 105 SER cc_start: 0.7573 (p) cc_final: 0.7266 (t) REVERT: S 140 MET cc_start: 0.5490 (mmm) cc_final: 0.4673 (mmm) REVERT: S 172 THR cc_start: 0.6445 (OUTLIER) cc_final: 0.6199 (t) REVERT: Y 32 LYS cc_start: 0.8323 (tttm) cc_final: 0.7548 (tppt) outliers start: 30 outliers final: 20 residues processed: 148 average time/residue: 0.4977 time to fit residues: 79.1355 Evaluate side-chains 151 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 123 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 180 PHE Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 260 GLU 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 327 VAL Chi-restraints excluded: chain B residue 336 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 253 LEU Chi-restraints excluded: chain R residue 262 ILE Chi-restraints excluded: chain R residue 317 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 0.5980 chunk 68 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 78 optimal weight: 0.6980 chunk 72 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 chunk 89 optimal weight: 5.9990 chunk 37 optimal weight: 0.7980 chunk 97 optimal weight: 30.0000 chunk 91 optimal weight: 20.0000 chunk 6 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 35 GLN 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 239 ASN ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 164 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4576 r_free = 0.4576 target = 0.237218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.179768 restraints weight = 10023.381| |-----------------------------------------------------------------------------| r_work (start): 0.4024 rms_B_bonded: 2.49 r_work: 0.3840 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.3165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.223 9241 Z= 0.267 Angle : 1.059 59.200 12513 Z= 0.601 Chirality : 0.077 2.331 1393 Planarity : 0.005 0.054 1577 Dihedral : 5.223 56.981 1243 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 16.23 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.11 % Favored : 95.80 % Rotamer: Outliers : 3.46 % Allowed : 20.37 % Favored : 76.17 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.26), residues: 1120 helix: 1.44 (0.25), residues: 399 sheet: -0.38 (0.32), residues: 269 loop : -0.99 (0.31), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 134 TYR 0.013 0.001 TYR S 102 PHE 0.016 0.001 PHE A 363 TRP 0.017 0.002 TRP R 291 HIS 0.007 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00526 / 0.27 ( 9237) covalent geometry : angle 1.05809 / 0.60 (12505) SS BOND : bond 0.00754 / 0.40 ( 4) SS BOND : angle 1.85252 / 0.99 ( 8) hydrogen bonds : bond 0.04083 / 2.82 ( 458) hydrogen bonds : angle 5.28034 / 3.71 ( 1326) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3451.99 seconds wall clock time: 59 minutes 49.97 seconds (3589.97 seconds total)