Starting phenix.real_space_refine on Wed Sep 17 14:17:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xwq_38741/09_2025/8xwq_38741.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xwq_38741/09_2025/8xwq_38741.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xwq_38741/09_2025/8xwq_38741.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xwq_38741/09_2025/8xwq_38741.map" model { file = "/net/cci-nas-00/data/ceres_data/8xwq_38741/09_2025/8xwq_38741.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xwq_38741/09_2025/8xwq_38741.cif" } resolution = 4.6 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= 0.000 sd= 0.006 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: 4 Type Number sf(0) Gaussians S 70 5.16 5 C 5795 2.51 5 N 1527 2.21 5 O 1684 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9076 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2404 Classifications: {'peptide': 302} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 13, 'TRANS': 288} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "L" Number of atoms: 171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 171 Classifications: {'peptide': 21} Modifications used: {'COO': 1} Link IDs: {'TRANS': 20} Chain: "A" Number of atoms: 1751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1751 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 2584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2584 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 404 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 48} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 1762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1762 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Time building chain proxies: 2.93, per 1000 atoms: 0.32 Number of scatterers: 9076 At special positions: 0 Unit cell: (120.34, 126.904, 109.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 70 16.00 O 1684 8.00 N 1527 7.00 C 5795 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS R 90 " - pdb=" SG CYS R 358 " distance=2.03 Simple disulfide: pdb=" SG CYS R 174 " - pdb=" SG CYS R 255 " distance=2.03 Simple disulfide: pdb=" SG CYS L 1 " - pdb=" SG CYS L 15 " distance=2.03 Simple disulfide: pdb=" SG CYS L 3 " - pdb=" SG CYS L 11 " distance=2.03 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.04 Simple disulfide: pdb=" SG CYS D 147 " - pdb=" SG CYS D 217 " distance=2.03 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: 0.88 Conformation dependent library (CDL) restraints added in 271.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2180 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 14 sheets defined 37.4% alpha, 19.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'R' and resid 97 through 129 removed outlier: 3.633A pdb=" N VAL R 106 " --> pdb=" O TYR R 102 " (cutoff:3.500A) Processing helix chain 'R' and resid 134 through 162 Proline residue: R 156 - end of helix removed outlier: 3.729A pdb=" N LEU R 162 " --> pdb=" O ASN R 158 " (cutoff:3.500A) Processing helix chain 'R' and resid 170 through 205 Proline residue: R 178 - end of helix removed outlier: 4.603A pdb=" N VAL R 203 " --> pdb=" O ARG R 199 " (cutoff:3.500A) Processing helix chain 'R' and resid 217 through 238 removed outlier: 3.752A pdb=" N VAL R 230 " --> pdb=" O TRP R 226 " (cutoff:3.500A) Proline residue: R 235 - end of helix removed outlier: 3.611A pdb=" N ILE R 238 " --> pdb=" O VAL R 234 " (cutoff:3.500A) Processing helix chain 'R' and resid 263 through 272 removed outlier: 4.154A pdb=" N ALA R 272 " --> pdb=" O PHE R 268 " (cutoff:3.500A) Processing helix chain 'R' and resid 272 through 282 removed outlier: 3.675A pdb=" N TRP R 276 " --> pdb=" O ALA R 272 " (cutoff:3.500A) Processing helix chain 'R' and resid 282 through 301 Processing helix chain 'R' and resid 313 through 349 Proline residue: R 338 - end of helix Processing helix chain 'R' and resid 356 through 388 removed outlier: 3.745A pdb=" N ASN R 382 " --> pdb=" O ASN R 378 " (cutoff:3.500A) Proline residue: R 383 - end of helix Processing helix chain 'R' and resid 390 through 398 Processing helix chain 'L' and resid 10 through 18 Processing helix chain 'A' and resid 6 through 32 Processing helix chain 'A' and resid 45 through 53 Processing helix chain 'A' and resid 211 through 216 Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 242 through 255 Processing helix chain 'A' and resid 270 through 281 Processing helix chain 'A' and resid 295 through 310 removed outlier: 3.676A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 351 Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 30 through 35 removed outlier: 3.553A pdb=" N ASN B 35 " --> pdb=" O SER B 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 24 Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.651A pdb=" N PHE D 32 " --> pdb=" O PHE D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 56 Processing helix chain 'D' and resid 62 through 65 removed outlier: 3.742A pdb=" N LYS D 65 " --> pdb=" O ASP D 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 62 through 65' Processing helix chain 'D' and resid 74 through 76 No H-bonds generated for 'chain 'D' and resid 74 through 76' Processing sheet with id=AA1, first strand: chain 'R' and resid 240 through 243 Processing sheet with id=AA2, first strand: chain 'R' and resid 246 through 247 Processing sheet with id=AA3, first strand: chain 'A' and resid 185 through 188 removed outlier: 3.630A pdb=" N LEU A 38 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N CYS A 224 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.722A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU B 336 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 58 through 63 removed outlier: 4.132A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 100 through 105 removed outlier: 3.778A pdb=" N CYS B 121 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.656A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.134A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.856A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.588A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AB3, first strand: chain 'D' and resid 58 through 60 removed outlier: 6.478A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N TYR D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N MET D 34 " --> pdb=" O TYR D 50 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 128 through 129 Processing sheet with id=AB5, first strand: chain 'D' and resid 134 through 136 removed outlier: 6.429A pdb=" N VAL D 135 " --> pdb=" O GLU D 234 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N LEU D 162 " --> pdb=" O TYR D 178 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N TYR D 178 " --> pdb=" O LEU D 162 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N TRP D 164 " --> pdb=" O LEU D 176 " (cutoff:3.500A) 449 hydrogen bonds defined for protein. 1269 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: 1.35 Time building geometry restraints manager: 1.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2906 1.35 - 1.47: 2282 1.47 - 1.59: 3980 1.59 - 1.71: 0 1.71 - 1.83: 98 Bond restraints: 9266 Sorted by residual: bond pdb=" CA ARG R 208 " pdb=" CB ARG R 208 " ideal model delta sigma weight residual 1.523 1.541 -0.018 1.21e-02 6.83e+03 2.19e+00 bond pdb=" CA LYS L 9 " pdb=" C LYS L 9 " ideal model delta sigma weight residual 1.522 1.504 0.018 1.38e-02 5.25e+03 1.67e+00 bond pdb=" CA VAL R 234 " pdb=" C VAL R 234 " ideal model delta sigma weight residual 1.520 1.530 -0.010 8.80e-03 1.29e+04 1.34e+00 bond pdb=" CB ARG R 208 " pdb=" CG ARG R 208 " ideal model delta sigma weight residual 1.520 1.550 -0.030 3.00e-02 1.11e+03 1.01e+00 bond pdb=" CA ALA B 92 " pdb=" C ALA B 92 " ideal model delta sigma weight residual 1.528 1.518 0.010 1.18e-02 7.18e+03 7.90e-01 ... (remaining 9261 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.22: 12053 1.22 - 2.43: 419 2.43 - 3.65: 66 3.65 - 4.87: 11 4.87 - 6.08: 5 Bond angle restraints: 12554 Sorted by residual: angle pdb=" C VAL R 234 " pdb=" CA VAL R 234 " pdb=" CB VAL R 234 " ideal model delta sigma weight residual 114.35 109.69 4.66 1.06e+00 8.90e-01 1.94e+01 angle pdb=" N MET L 7 " pdb=" CA MET L 7 " pdb=" C MET L 7 " ideal model delta sigma weight residual 114.39 110.35 4.04 1.45e+00 4.76e-01 7.77e+00 angle pdb=" CA ARG R 208 " pdb=" CB ARG R 208 " pdb=" CG ARG R 208 " ideal model delta sigma weight residual 114.10 119.44 -5.34 2.00e+00 2.50e-01 7.13e+00 angle pdb=" C ALA R 233 " pdb=" N VAL R 234 " pdb=" CA VAL R 234 " ideal model delta sigma weight residual 120.24 121.90 -1.66 6.30e-01 2.52e+00 6.94e+00 angle pdb=" C ARG D 179 " pdb=" N MET D 180 " pdb=" CA MET D 180 " ideal model delta sigma weight residual 121.54 125.90 -4.36 1.91e+00 2.74e-01 5.22e+00 ... (remaining 12549 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.60: 5086 17.60 - 35.19: 325 35.19 - 52.79: 89 52.79 - 70.38: 14 70.38 - 87.98: 2 Dihedral angle restraints: 5516 sinusoidal: 2140 harmonic: 3376 Sorted by residual: dihedral pdb=" CB CYS R 174 " pdb=" SG CYS R 174 " pdb=" SG CYS R 255 " pdb=" CB CYS R 255 " ideal model delta sinusoidal sigma weight residual -86.00 -126.43 40.43 1 1.00e+01 1.00e-02 2.29e+01 dihedral pdb=" CA LEU R 256 " pdb=" C LEU R 256 " pdb=" N LEU R 257 " pdb=" CA LEU R 257 " ideal model delta harmonic sigma weight residual 180.00 161.11 18.89 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" CA ARG A 208 " pdb=" C ARG A 208 " pdb=" N LYS A 209 " pdb=" CA LYS A 209 " ideal model delta harmonic sigma weight residual -180.00 -162.59 -17.41 0 5.00e+00 4.00e-02 1.21e+01 ... (remaining 5513 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 871 0.026 - 0.053: 339 0.053 - 0.079: 128 0.079 - 0.106: 70 0.106 - 0.132: 24 Chirality restraints: 1432 Sorted by residual: chirality pdb=" CA ILE D 51 " pdb=" N ILE D 51 " pdb=" C ILE D 51 " pdb=" CB ILE D 51 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.36e-01 chirality pdb=" CA PRO R 338 " pdb=" N PRO R 338 " pdb=" C PRO R 338 " pdb=" CB PRO R 338 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.12e-01 chirality pdb=" CA ILE D 145 " pdb=" N ILE D 145 " pdb=" C ILE D 145 " pdb=" CB ILE D 145 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.10e-01 ... (remaining 1429 not shown) Planarity restraints: 1579 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE R 370 " 0.008 2.00e-02 2.50e+03 1.68e-02 2.83e+00 pdb=" C ILE R 370 " -0.029 2.00e-02 2.50e+03 pdb=" O ILE R 370 " 0.011 2.00e-02 2.50e+03 pdb=" N GLY R 371 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR R 369 " -0.008 2.00e-02 2.50e+03 1.57e-02 2.47e+00 pdb=" C TYR R 369 " 0.027 2.00e-02 2.50e+03 pdb=" O TYR R 369 " -0.010 2.00e-02 2.50e+03 pdb=" N ILE R 370 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER R 279 " 0.007 2.00e-02 2.50e+03 1.46e-02 2.14e+00 pdb=" C SER R 279 " -0.025 2.00e-02 2.50e+03 pdb=" O SER R 279 " 0.010 2.00e-02 2.50e+03 pdb=" N PHE R 280 " 0.008 2.00e-02 2.50e+03 ... (remaining 1576 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.70: 304 2.70 - 3.25: 9489 3.25 - 3.80: 15106 3.80 - 4.35: 18987 4.35 - 4.90: 31340 Nonbonded interactions: 75226 Sorted by model distance: nonbonded pdb=" O GLN B 75 " pdb=" OG SER B 98 " model vdw 2.145 3.040 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.174 3.040 nonbonded pdb=" OE2 GLU R 236 " pdb=" OH TYR R 269 " model vdw 2.191 3.040 nonbonded pdb=" O GLU R 359 " pdb=" OG SER R 362 " model vdw 2.217 3.040 nonbonded pdb=" OG1 THR B 65 " pdb=" O PRO B 107 " model vdw 2.217 3.040 ... (remaining 75221 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 group one per residue 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: 0.470 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: 0.030 Set scattering table: 0.030 Process input model: 10.470 Find NCS groups from input model: 0.050 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:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9272 Z= 0.137 Angle : 0.547 6.083 12566 Z= 0.323 Chirality : 0.038 0.132 1432 Planarity : 0.003 0.036 1579 Dihedral : 12.776 87.977 3318 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 7.98 % Allowed : 9.19 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.12 (0.25), residues: 1143 helix: 1.47 (0.27), residues: 413 sheet: -0.12 (0.35), residues: 228 loop : -1.40 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 68 TYR 0.009 0.001 TYR D 223 PHE 0.014 0.001 PHE R 291 TRP 0.012 0.001 TRP R 336 HIS 0.003 0.001 HIS B 266 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 9266) covalent geometry : angle 0.54649 (12554) SS BOND : bond 0.00354 ( 6) SS BOND : angle 1.12114 ( 12) hydrogen bonds : bond 0.13916 ( 449) hydrogen bonds : angle 6.05158 ( 1269) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 425 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 94 ILE cc_start: 0.8348 (mt) cc_final: 0.6448 (pt) REVERT: R 126 ILE cc_start: 0.8485 (mp) cc_final: 0.8267 (mp) REVERT: R 134 ASN cc_start: 0.7224 (p0) cc_final: 0.6939 (t0) REVERT: R 138 ILE cc_start: 0.8766 (mt) cc_final: 0.8507 (pt) REVERT: R 175 LYS cc_start: 0.7442 (tttp) cc_final: 0.6964 (pttt) REVERT: R 190 LEU cc_start: 0.9594 (mt) cc_final: 0.9379 (mt) REVERT: R 236 GLU cc_start: 0.8157 (mp0) cc_final: 0.7310 (mp0) REVERT: R 240 PHE cc_start: 0.8987 (m-80) cc_final: 0.8201 (m-80) REVERT: R 280 PHE cc_start: 0.8633 (t80) cc_final: 0.8129 (m-10) REVERT: R 293 TYR cc_start: 0.8758 (m-10) cc_final: 0.8526 (m-10) REVERT: R 295 LEU cc_start: 0.9002 (mt) cc_final: 0.8802 (mt) REVERT: R 313 ASP cc_start: 0.8472 (t70) cc_final: 0.8260 (t70) REVERT: R 319 ARG cc_start: 0.7525 (mtt180) cc_final: 0.7059 (tmt170) REVERT: R 323 LYS cc_start: 0.5326 (OUTLIER) cc_final: 0.5108 (pttt) REVERT: R 326 PHE cc_start: 0.8362 (m-10) cc_final: 0.7703 (t80) REVERT: R 327 CYS cc_start: 0.9019 (OUTLIER) cc_final: 0.8459 (t) REVERT: R 336 TRP cc_start: 0.8793 (m100) cc_final: 0.8519 (m100) REVERT: R 370 ILE cc_start: 0.9045 (mm) cc_final: 0.8651 (tt) REVERT: L 8 ASP cc_start: 0.4458 (OUTLIER) cc_final: 0.3732 (p0) REVERT: L 10 GLU cc_start: 0.8476 (mp0) cc_final: 0.8112 (pm20) REVERT: A 21 ARG cc_start: 0.8954 (mtm110) cc_final: 0.8592 (ptm160) REVERT: A 43 GLU cc_start: 0.6963 (pm20) cc_final: 0.5884 (tt0) REVERT: A 213 HIS cc_start: 0.8726 (p90) cc_final: 0.7710 (p90) REVERT: A 215 PHE cc_start: 0.8907 (m-80) cc_final: 0.8705 (m-80) REVERT: A 216 GLU cc_start: 0.8803 (tt0) cc_final: 0.8313 (tp30) REVERT: A 224 CYS cc_start: 0.9306 (m) cc_final: 0.7989 (t) REVERT: A 230 TYR cc_start: 0.5349 (OUTLIER) cc_final: 0.4791 (p90) REVERT: A 242 ARG cc_start: 0.8426 (mtp85) cc_final: 0.8048 (mmp-170) REVERT: A 250 PHE cc_start: 0.9485 (t80) cc_final: 0.9023 (t80) REVERT: A 256 ASN cc_start: 0.9127 (m-40) cc_final: 0.8829 (t0) REVERT: A 269 ASN cc_start: 0.8824 (OUTLIER) cc_final: 0.8517 (p0) REVERT: A 298 GLU cc_start: 0.9023 (OUTLIER) cc_final: 0.8735 (pp20) REVERT: A 304 GLN cc_start: 0.9405 (tt0) cc_final: 0.9114 (tm-30) REVERT: A 320 TYR cc_start: 0.8764 (m-80) cc_final: 0.7256 (m-80) REVERT: A 348 LEU cc_start: 0.9593 (mt) cc_final: 0.9101 (tp) REVERT: A 349 LYS cc_start: 0.9402 (ttmm) cc_final: 0.9182 (mtmm) REVERT: B 45 MET cc_start: 0.8663 (mmm) cc_final: 0.8282 (mmm) REVERT: B 57 LYS cc_start: 0.9067 (pttp) cc_final: 0.8465 (ptpt) REVERT: B 59 TYR cc_start: 0.8001 (m-80) cc_final: 0.7097 (m-80) REVERT: B 63 TRP cc_start: 0.9314 (m100) cc_final: 0.8928 (m100) REVERT: B 81 ILE cc_start: 0.9529 (mt) cc_final: 0.9224 (tp) REVERT: B 89 LYS cc_start: 0.8889 (mptt) cc_final: 0.8529 (mmtp) REVERT: B 119 ASN cc_start: 0.8559 (OUTLIER) cc_final: 0.8208 (m-40) REVERT: B 146 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8063 (tp) REVERT: B 157 ILE cc_start: 0.9489 (tt) cc_final: 0.9187 (tt) REVERT: B 180 PHE cc_start: 0.8319 (m-80) cc_final: 0.7890 (m-80) REVERT: B 192 LEU cc_start: 0.8573 (mt) cc_final: 0.8077 (pt) REVERT: B 222 PHE cc_start: 0.8236 (m-80) cc_final: 0.7955 (m-80) REVERT: B 234 PHE cc_start: 0.8234 (OUTLIER) cc_final: 0.7976 (t80) REVERT: B 243 THR cc_start: 0.8301 (p) cc_final: 0.8059 (t) REVERT: B 267 ASP cc_start: 0.9042 (OUTLIER) cc_final: 0.8652 (p0) REVERT: B 278 PHE cc_start: 0.8340 (m-80) cc_final: 0.8108 (m-80) REVERT: B 289 TYR cc_start: 0.8087 (m-80) cc_final: 0.6523 (m-80) REVERT: B 335 PHE cc_start: 0.6297 (OUTLIER) cc_final: 0.5703 (m-10) REVERT: C 24 ASN cc_start: 0.9216 (t0) cc_final: 0.8784 (p0) REVERT: C 36 ASP cc_start: 0.9132 (m-30) cc_final: 0.8893 (m-30) REVERT: D 35 HIS cc_start: 0.9054 (m-70) cc_final: 0.8486 (m-70) REVERT: D 36 TRP cc_start: 0.8295 (m100) cc_final: 0.7440 (m100) REVERT: D 73 ASP cc_start: 0.8855 (t70) cc_final: 0.8636 (t0) REVERT: D 74 ASP cc_start: 0.9082 (m-30) cc_final: 0.8808 (m-30) REVERT: D 77 ASN cc_start: 0.8784 (m-40) cc_final: 0.8424 (p0) REVERT: D 78 THR cc_start: 0.9066 (m) cc_final: 0.8624 (p) REVERT: D 79 LEU cc_start: 0.9500 (tp) cc_final: 0.9213 (tp) REVERT: D 108 PHE cc_start: 0.9011 (m-80) cc_final: 0.8763 (m-80) REVERT: D 111 TRP cc_start: 0.8265 (m100) cc_final: 0.7502 (m-10) REVERT: D 165 PHE cc_start: 0.9072 (m-80) cc_final: 0.8729 (m-80) outliers start: 79 outliers final: 24 residues processed: 470 average time/residue: 0.1163 time to fit residues: 72.2720 Evaluate side-chains 311 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 276 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 7.9990 chunk 113 optimal weight: 7.9990 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 5.9990 chunk 100 optimal weight: 0.9980 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 150 HIS R 181 GLN R 258 HIS R 317 GLN A 188 HIS A 195 HIS A 244 HIS ** A 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 ASN A 294 ASN A 304 GLN B 32 GLN B 156 GLN B 268 ASN D 167 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.073949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.057973 restraints weight = 41302.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.060108 restraints weight = 27271.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.061671 restraints weight = 19929.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.062803 restraints weight = 15676.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.063653 restraints weight = 13010.947| |-----------------------------------------------------------------------------| r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.3564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 9272 Z= 0.236 Angle : 0.691 7.970 12566 Z= 0.375 Chirality : 0.045 0.232 1432 Planarity : 0.005 0.054 1579 Dihedral : 4.929 25.293 1251 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 18.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.30 % Allowed : 4.85 % Favored : 94.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.39 (0.25), residues: 1143 helix: 1.04 (0.25), residues: 401 sheet: -0.28 (0.33), residues: 244 loop : -1.29 (0.28), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 357 TYR 0.019 0.002 TYR L 13 PHE 0.021 0.002 PHE R 397 TRP 0.016 0.002 TRP R 336 HIS 0.014 0.002 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00487 ( 9266) covalent geometry : angle 0.68624 (12554) SS BOND : bond 0.00756 ( 6) SS BOND : angle 2.82505 ( 12) hydrogen bonds : bond 0.04541 ( 449) hydrogen bonds : angle 5.40481 ( 1269) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 334 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 94 ILE cc_start: 0.8026 (mt) cc_final: 0.7492 (mp) REVERT: R 134 ASN cc_start: 0.7055 (p0) cc_final: 0.6453 (t0) REVERT: R 176 LEU cc_start: 0.8512 (tp) cc_final: 0.8304 (pp) REVERT: R 210 LYS cc_start: 0.7358 (tptp) cc_final: 0.7151 (tptp) REVERT: R 245 MET cc_start: 0.8996 (mpp) cc_final: 0.8590 (mpp) REVERT: R 257 LEU cc_start: 0.9053 (mm) cc_final: 0.8760 (mm) REVERT: R 280 PHE cc_start: 0.8583 (t80) cc_final: 0.7868 (m-80) REVERT: R 286 LEU cc_start: 0.9278 (tt) cc_final: 0.9051 (mm) REVERT: R 326 PHE cc_start: 0.8387 (m-10) cc_final: 0.7693 (t80) REVERT: R 381 ILE cc_start: 0.8951 (tp) cc_final: 0.8711 (tp) REVERT: L 7 MET cc_start: 0.7866 (tmm) cc_final: 0.7566 (tmm) REVERT: L 10 GLU cc_start: 0.8320 (mp0) cc_final: 0.7867 (pm20) REVERT: L 13 TYR cc_start: 0.8354 (t80) cc_final: 0.7933 (t80) REVERT: A 24 ARG cc_start: 0.7909 (mtt180) cc_final: 0.7356 (mmm160) REVERT: A 32 ARG cc_start: 0.7992 (mtm180) cc_final: 0.7627 (mtp-110) REVERT: A 188 HIS cc_start: 0.8416 (OUTLIER) cc_final: 0.8147 (t-90) REVERT: A 213 HIS cc_start: 0.8666 (p90) cc_final: 0.7708 (p90) REVERT: A 216 GLU cc_start: 0.8704 (tt0) cc_final: 0.8247 (tp30) REVERT: A 223 PHE cc_start: 0.8693 (t80) cc_final: 0.8370 (t80) REVERT: A 224 CYS cc_start: 0.9217 (m) cc_final: 0.7646 (t) REVERT: A 243 MET cc_start: 0.9202 (ttp) cc_final: 0.8345 (tmm) REVERT: A 247 MET cc_start: 0.9164 (mtm) cc_final: 0.8141 (mtm) REVERT: A 248 LYS cc_start: 0.9342 (mtmm) cc_final: 0.9129 (mttt) REVERT: A 256 ASN cc_start: 0.9107 (m-40) cc_final: 0.8902 (m110) REVERT: A 269 ASN cc_start: 0.9263 (m-40) cc_final: 0.7788 (m-40) REVERT: A 304 GLN cc_start: 0.9427 (tt0) cc_final: 0.9059 (tm-30) REVERT: A 317 LYS cc_start: 0.8300 (pttt) cc_final: 0.8008 (pttp) REVERT: A 332 VAL cc_start: 0.9496 (t) cc_final: 0.9238 (t) REVERT: A 333 GLN cc_start: 0.8878 (mp10) cc_final: 0.8461 (mp10) REVERT: A 348 LEU cc_start: 0.9505 (mt) cc_final: 0.9220 (tp) REVERT: B 38 ASP cc_start: 0.9038 (p0) cc_final: 0.8837 (t70) REVERT: B 45 MET cc_start: 0.8264 (mmm) cc_final: 0.8052 (mmm) REVERT: B 51 LEU cc_start: 0.9089 (mp) cc_final: 0.8799 (mp) REVERT: B 57 LYS cc_start: 0.9083 (pttp) cc_final: 0.8720 (ptpt) REVERT: B 101 MET cc_start: 0.8565 (mtp) cc_final: 0.8308 (mtm) REVERT: B 146 LEU cc_start: 0.7630 (mp) cc_final: 0.7232 (mp) REVERT: B 192 LEU cc_start: 0.8600 (mt) cc_final: 0.8209 (pt) REVERT: B 222 PHE cc_start: 0.8229 (m-80) cc_final: 0.8001 (m-80) REVERT: B 252 LEU cc_start: 0.9734 (tt) cc_final: 0.9334 (mt) REVERT: B 254 ASP cc_start: 0.7513 (t70) cc_final: 0.7192 (t0) REVERT: B 283 ARG cc_start: 0.8987 (tpt170) cc_final: 0.8755 (tpt170) REVERT: B 289 TYR cc_start: 0.7979 (m-80) cc_final: 0.6654 (m-80) REVERT: D 73 ASP cc_start: 0.9179 (t70) cc_final: 0.8551 (t0) REVERT: D 78 THR cc_start: 0.9167 (m) cc_final: 0.8792 (p) REVERT: D 111 TRP cc_start: 0.8441 (m100) cc_final: 0.7841 (m-10) REVERT: D 159 ASN cc_start: 0.9254 (m110) cc_final: 0.9044 (m110) REVERT: D 164 TRP cc_start: 0.8293 (m100) cc_final: 0.7804 (m-10) REVERT: D 202 LEU cc_start: 0.9195 (tt) cc_final: 0.8575 (tt) outliers start: 3 outliers final: 1 residues processed: 334 average time/residue: 0.1100 time to fit residues: 49.2209 Evaluate side-chains 251 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 249 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 71 optimal weight: 10.0000 chunk 2 optimal weight: 10.0000 chunk 34 optimal weight: 5.9990 chunk 80 optimal weight: 20.0000 chunk 99 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 47 optimal weight: 20.0000 chunk 69 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 150 HIS R 181 GLN R 258 HIS R 340 HIS A 195 HIS B 32 GLN C 44 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.075191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.058786 restraints weight = 39790.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.061085 restraints weight = 25462.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.062742 restraints weight = 18218.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.064014 restraints weight = 14099.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.064964 restraints weight = 11462.135| |-----------------------------------------------------------------------------| r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.4361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9272 Z= 0.181 Angle : 0.647 8.559 12566 Z= 0.345 Chirality : 0.044 0.198 1432 Planarity : 0.004 0.048 1579 Dihedral : 4.872 30.199 1251 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 16.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 0.40 % Allowed : 4.55 % Favored : 95.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.53 (0.25), residues: 1143 helix: 0.84 (0.25), residues: 402 sheet: -0.46 (0.33), residues: 247 loop : -1.24 (0.28), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG R 343 TYR 0.017 0.002 TYR R 369 PHE 0.031 0.002 PHE D 68 TRP 0.022 0.002 TRP D 36 HIS 0.005 0.001 HIS R 258 Details of bonding type rmsd covalent geometry : bond 0.00395 ( 9266) covalent geometry : angle 0.64368 (12554) SS BOND : bond 0.00821 ( 6) SS BOND : angle 2.14605 ( 12) hydrogen bonds : bond 0.04127 ( 449) hydrogen bonds : angle 5.23012 ( 1269) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 319 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 119 ASN cc_start: 0.8550 (m-40) cc_final: 0.8036 (m110) REVERT: R 245 MET cc_start: 0.8994 (mpp) cc_final: 0.8682 (mpp) REVERT: R 257 LEU cc_start: 0.9182 (mm) cc_final: 0.8946 (mm) REVERT: R 280 PHE cc_start: 0.8537 (t80) cc_final: 0.7770 (m-80) REVERT: R 286 LEU cc_start: 0.9217 (tt) cc_final: 0.8979 (mm) REVERT: R 293 TYR cc_start: 0.8480 (m-10) cc_final: 0.8235 (m-80) REVERT: R 295 LEU cc_start: 0.8547 (mt) cc_final: 0.8229 (mt) REVERT: R 299 GLU cc_start: 0.6371 (mp0) cc_final: 0.6129 (mp0) REVERT: R 320 GLU cc_start: 0.8717 (mt-10) cc_final: 0.8389 (mt-10) REVERT: R 326 PHE cc_start: 0.8533 (m-10) cc_final: 0.7698 (t80) REVERT: L 7 MET cc_start: 0.7878 (tmm) cc_final: 0.7554 (tmm) REVERT: L 10 GLU cc_start: 0.8303 (mp0) cc_final: 0.7867 (pm20) REVERT: L 13 TYR cc_start: 0.8489 (t80) cc_final: 0.8176 (t80) REVERT: A 5 LEU cc_start: 0.7952 (mm) cc_final: 0.7565 (pt) REVERT: A 24 ARG cc_start: 0.7932 (mtt180) cc_final: 0.7409 (mmm-85) REVERT: A 198 MET cc_start: 0.8382 (ttm) cc_final: 0.8121 (ttp) REVERT: A 223 PHE cc_start: 0.8686 (t80) cc_final: 0.8217 (t80) REVERT: A 224 CYS cc_start: 0.9258 (m) cc_final: 0.7670 (t) REVERT: A 248 LYS cc_start: 0.9360 (mtmm) cc_final: 0.9144 (mttt) REVERT: A 256 ASN cc_start: 0.9182 (m-40) cc_final: 0.8874 (m110) REVERT: A 269 ASN cc_start: 0.9212 (m-40) cc_final: 0.7739 (m-40) REVERT: A 304 GLN cc_start: 0.9358 (tt0) cc_final: 0.9115 (tt0) REVERT: A 348 LEU cc_start: 0.9465 (mt) cc_final: 0.9187 (tp) REVERT: A 349 LYS cc_start: 0.9453 (ttmm) cc_final: 0.8768 (tmtt) REVERT: B 49 ARG cc_start: 0.8771 (mmt180) cc_final: 0.8500 (mmt90) REVERT: B 57 LYS cc_start: 0.9074 (pttp) cc_final: 0.8553 (ptpt) REVERT: B 69 LEU cc_start: 0.9482 (mt) cc_final: 0.8598 (pp) REVERT: B 101 MET cc_start: 0.8531 (mtp) cc_final: 0.7953 (mtm) REVERT: B 146 LEU cc_start: 0.7914 (mp) cc_final: 0.7432 (mp) REVERT: B 192 LEU cc_start: 0.8485 (mt) cc_final: 0.8186 (pt) REVERT: B 199 PHE cc_start: 0.8881 (p90) cc_final: 0.8574 (p90) REVERT: B 252 LEU cc_start: 0.9759 (tt) cc_final: 0.9378 (mt) REVERT: B 254 ASP cc_start: 0.7647 (t70) cc_final: 0.7319 (t0) REVERT: B 283 ARG cc_start: 0.8977 (tpt170) cc_final: 0.8681 (tpt170) REVERT: B 289 TYR cc_start: 0.7921 (m-80) cc_final: 0.6718 (m-80) REVERT: C 21 MET cc_start: 0.9121 (mmm) cc_final: 0.8688 (mmm) REVERT: D 37 VAL cc_start: 0.9603 (m) cc_final: 0.9356 (p) REVERT: D 45 LEU cc_start: 0.9491 (mt) cc_final: 0.8837 (mt) REVERT: D 73 ASP cc_start: 0.9119 (t70) cc_final: 0.8527 (t0) REVERT: D 78 THR cc_start: 0.9019 (m) cc_final: 0.8383 (p) REVERT: D 80 PHE cc_start: 0.8599 (m-80) cc_final: 0.8230 (m-10) REVERT: D 111 TRP cc_start: 0.8460 (m100) cc_final: 0.8061 (m-10) REVERT: D 159 ASN cc_start: 0.9244 (m110) cc_final: 0.8840 (t0) REVERT: D 164 TRP cc_start: 0.8458 (m100) cc_final: 0.7430 (m-10) REVERT: D 165 PHE cc_start: 0.8737 (m-80) cc_final: 0.8433 (m-80) REVERT: D 202 LEU cc_start: 0.9234 (tt) cc_final: 0.8638 (tt) REVERT: D 218 MET cc_start: 0.8522 (tmm) cc_final: 0.8306 (tmm) outliers start: 4 outliers final: 0 residues processed: 321 average time/residue: 0.1070 time to fit residues: 46.4817 Evaluate side-chains 244 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 244 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 31 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 2 optimal weight: 10.0000 chunk 75 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 61 optimal weight: 7.9990 chunk 99 optimal weight: 0.9990 chunk 81 optimal weight: 7.9990 chunk 16 optimal weight: 0.9980 chunk 91 optimal weight: 6.9990 chunk 78 optimal weight: 0.0070 overall best weight: 1.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 137 ASN R 150 HIS R 340 HIS R 378 ASN A 188 HIS A 195 HIS A 294 ASN A 304 GLN B 32 GLN B 142 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.077497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.061325 restraints weight = 39448.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.063663 restraints weight = 25310.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.065338 restraints weight = 18128.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.066616 restraints weight = 13975.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.067571 restraints weight = 11357.358| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.4712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9272 Z= 0.131 Angle : 0.612 6.918 12566 Z= 0.323 Chirality : 0.043 0.176 1432 Planarity : 0.004 0.047 1579 Dihedral : 4.733 32.470 1251 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 0.30 % Allowed : 4.24 % Favored : 95.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.52 (0.25), residues: 1143 helix: 0.68 (0.25), residues: 409 sheet: -0.38 (0.33), residues: 252 loop : -1.15 (0.29), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 206 TYR 0.019 0.001 TYR R 369 PHE 0.033 0.002 PHE A 307 TRP 0.022 0.002 TRP D 36 HIS 0.006 0.001 HIS R 150 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 9266) covalent geometry : angle 0.61009 (12554) SS BOND : bond 0.00355 ( 6) SS BOND : angle 1.51974 ( 12) hydrogen bonds : bond 0.03888 ( 449) hydrogen bonds : angle 5.08953 ( 1269) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 313 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 119 ASN cc_start: 0.8495 (m-40) cc_final: 0.7866 (m110) REVERT: R 190 LEU cc_start: 0.9537 (mt) cc_final: 0.9314 (mt) REVERT: R 280 PHE cc_start: 0.8439 (t80) cc_final: 0.7751 (m-80) REVERT: R 286 LEU cc_start: 0.9212 (tt) cc_final: 0.9006 (mm) REVERT: R 293 TYR cc_start: 0.8594 (m-10) cc_final: 0.8301 (m-80) REVERT: R 295 LEU cc_start: 0.8401 (mt) cc_final: 0.8166 (mt) REVERT: R 299 GLU cc_start: 0.6093 (mp0) cc_final: 0.5853 (mp0) REVERT: R 320 GLU cc_start: 0.8688 (mt-10) cc_final: 0.8346 (mt-10) REVERT: R 326 PHE cc_start: 0.7925 (m-10) cc_final: 0.7716 (t80) REVERT: L 7 MET cc_start: 0.7866 (tmm) cc_final: 0.7366 (tmm) REVERT: L 13 TYR cc_start: 0.8411 (t80) cc_final: 0.8159 (t80) REVERT: A 5 LEU cc_start: 0.7966 (mm) cc_final: 0.7474 (pt) REVERT: A 24 ARG cc_start: 0.7903 (mtt180) cc_final: 0.7368 (mmm-85) REVERT: A 188 HIS cc_start: 0.8385 (OUTLIER) cc_final: 0.8144 (t-90) REVERT: A 223 PHE cc_start: 0.8661 (t80) cc_final: 0.8239 (t80) REVERT: A 224 CYS cc_start: 0.9176 (m) cc_final: 0.7912 (t) REVERT: A 248 LYS cc_start: 0.9344 (mtmm) cc_final: 0.9108 (mttt) REVERT: A 256 ASN cc_start: 0.9181 (m-40) cc_final: 0.8812 (m110) REVERT: A 304 GLN cc_start: 0.9360 (tt0) cc_final: 0.8659 (tm-30) REVERT: A 348 LEU cc_start: 0.9433 (mt) cc_final: 0.9129 (tp) REVERT: B 45 MET cc_start: 0.8443 (mmm) cc_final: 0.8019 (mmp) REVERT: B 63 TRP cc_start: 0.9430 (m100) cc_final: 0.8891 (m100) REVERT: B 69 LEU cc_start: 0.9486 (mt) cc_final: 0.8608 (pp) REVERT: B 101 MET cc_start: 0.8612 (mtp) cc_final: 0.8150 (mtm) REVERT: B 127 LYS cc_start: 0.9221 (mtpp) cc_final: 0.8948 (mttp) REVERT: B 190 LEU cc_start: 0.8471 (tp) cc_final: 0.8146 (tt) REVERT: B 192 LEU cc_start: 0.8476 (mt) cc_final: 0.8195 (pt) REVERT: B 199 PHE cc_start: 0.8862 (p90) cc_final: 0.8368 (p90) REVERT: B 219 ARG cc_start: 0.8167 (tpt90) cc_final: 0.7950 (tpt90) REVERT: B 222 PHE cc_start: 0.8126 (m-80) cc_final: 0.7760 (m-10) REVERT: B 254 ASP cc_start: 0.7595 (t70) cc_final: 0.7392 (t0) REVERT: B 283 ARG cc_start: 0.8882 (tpt170) cc_final: 0.8567 (tpt170) REVERT: B 289 TYR cc_start: 0.7766 (m-80) cc_final: 0.6230 (m-80) REVERT: B 296 VAL cc_start: 0.9562 (t) cc_final: 0.9263 (p) REVERT: B 332 TRP cc_start: 0.7830 (m-10) cc_final: 0.7617 (m-10) REVERT: C 38 MET cc_start: 0.9236 (ptp) cc_final: 0.8996 (ptp) REVERT: D 73 ASP cc_start: 0.9075 (t70) cc_final: 0.8601 (t0) REVERT: D 78 THR cc_start: 0.8966 (m) cc_final: 0.8177 (p) REVERT: D 80 PHE cc_start: 0.8388 (m-80) cc_final: 0.8039 (m-10) REVERT: D 93 MET cc_start: 0.7739 (tpt) cc_final: 0.7473 (tpp) REVERT: D 111 TRP cc_start: 0.8238 (m100) cc_final: 0.7888 (m-10) REVERT: D 159 ASN cc_start: 0.9269 (m110) cc_final: 0.8897 (t0) REVERT: D 164 TRP cc_start: 0.8212 (m100) cc_final: 0.7433 (m-10) REVERT: D 165 PHE cc_start: 0.8522 (m-80) cc_final: 0.8033 (m-80) REVERT: D 202 LEU cc_start: 0.9168 (tt) cc_final: 0.8664 (tt) REVERT: D 218 MET cc_start: 0.8472 (tmm) cc_final: 0.7989 (tmm) REVERT: D 227 PHE cc_start: 0.8497 (m-80) cc_final: 0.8254 (m-10) outliers start: 3 outliers final: 0 residues processed: 313 average time/residue: 0.1046 time to fit residues: 44.1915 Evaluate side-chains 250 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 249 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 53 optimal weight: 4.9990 chunk 13 optimal weight: 9.9990 chunk 23 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 14 optimal weight: 10.0000 chunk 3 optimal weight: 6.9990 chunk 64 optimal weight: 20.0000 chunk 5 optimal weight: 6.9990 chunk 46 optimal weight: 0.0980 chunk 11 optimal weight: 10.0000 chunk 87 optimal weight: 5.9990 overall best weight: 3.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 150 HIS R 181 GLN A 195 HIS ** A 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN D 35 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.075280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.059227 restraints weight = 40528.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.061498 restraints weight = 26132.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.063174 restraints weight = 18750.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.064388 restraints weight = 14492.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.065242 restraints weight = 11818.405| |-----------------------------------------------------------------------------| r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.4879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9272 Z= 0.177 Angle : 0.636 6.367 12566 Z= 0.338 Chirality : 0.043 0.178 1432 Planarity : 0.004 0.053 1579 Dihedral : 4.831 23.702 1251 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 15.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 0.10 % Allowed : 3.23 % Favored : 96.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.53 (0.25), residues: 1143 helix: 0.65 (0.25), residues: 409 sheet: -0.39 (0.33), residues: 252 loop : -1.13 (0.29), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 206 TYR 0.018 0.002 TYR R 369 PHE 0.028 0.002 PHE A 307 TRP 0.023 0.002 TRP B 211 HIS 0.008 0.002 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00384 ( 9266) covalent geometry : angle 0.63388 (12554) SS BOND : bond 0.00513 ( 6) SS BOND : angle 1.91193 ( 12) hydrogen bonds : bond 0.03873 ( 449) hydrogen bonds : angle 5.18342 ( 1269) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 303 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 119 ASN cc_start: 0.8557 (m-40) cc_final: 0.8004 (m110) REVERT: R 190 LEU cc_start: 0.9552 (mt) cc_final: 0.9329 (mt) REVERT: R 280 PHE cc_start: 0.8486 (t80) cc_final: 0.7757 (m-80) REVERT: R 293 TYR cc_start: 0.8585 (m-10) cc_final: 0.8264 (m-80) REVERT: R 320 GLU cc_start: 0.8602 (mt-10) cc_final: 0.8227 (mt-10) REVERT: R 326 PHE cc_start: 0.8028 (m-10) cc_final: 0.7698 (t80) REVERT: R 374 MET cc_start: 0.5155 (mmt) cc_final: 0.4648 (mmt) REVERT: L 7 MET cc_start: 0.7892 (tmm) cc_final: 0.7366 (tmm) REVERT: L 13 TYR cc_start: 0.8605 (t80) cc_final: 0.8393 (t80) REVERT: A 5 LEU cc_start: 0.8140 (mm) cc_final: 0.7638 (pt) REVERT: A 24 ARG cc_start: 0.7967 (mtt180) cc_final: 0.7451 (mmm160) REVERT: A 223 PHE cc_start: 0.8653 (t80) cc_final: 0.8138 (t80) REVERT: A 224 CYS cc_start: 0.9177 (m) cc_final: 0.7890 (t) REVERT: A 243 MET cc_start: 0.8960 (ttp) cc_final: 0.8438 (tmm) REVERT: A 248 LYS cc_start: 0.9371 (mtmm) cc_final: 0.9107 (mttm) REVERT: A 256 ASN cc_start: 0.9188 (m-40) cc_final: 0.8807 (m110) REVERT: A 304 GLN cc_start: 0.9371 (tt0) cc_final: 0.8691 (tm-30) REVERT: A 348 LEU cc_start: 0.9441 (mt) cc_final: 0.9193 (tp) REVERT: B 50 THR cc_start: 0.8874 (m) cc_final: 0.8646 (t) REVERT: B 57 LYS cc_start: 0.9086 (pttp) cc_final: 0.8577 (ptpt) REVERT: B 101 MET cc_start: 0.8671 (mtp) cc_final: 0.8184 (mtm) REVERT: B 138 GLU cc_start: 0.8706 (pt0) cc_final: 0.7986 (pm20) REVERT: B 146 LEU cc_start: 0.7626 (mp) cc_final: 0.7009 (mp) REVERT: B 190 LEU cc_start: 0.8579 (tp) cc_final: 0.8315 (tt) REVERT: B 192 LEU cc_start: 0.8499 (mt) cc_final: 0.8189 (pt) REVERT: B 199 PHE cc_start: 0.8987 (p90) cc_final: 0.8700 (p90) REVERT: B 222 PHE cc_start: 0.8161 (m-80) cc_final: 0.7893 (m-10) REVERT: B 254 ASP cc_start: 0.7666 (t70) cc_final: 0.7455 (t0) REVERT: B 262 MET cc_start: 0.8524 (ptp) cc_final: 0.8282 (ptm) REVERT: B 283 ARG cc_start: 0.8981 (tpt170) cc_final: 0.8763 (tpt170) REVERT: B 289 TYR cc_start: 0.7776 (m-80) cc_final: 0.6333 (m-80) REVERT: D 73 ASP cc_start: 0.9115 (t70) cc_final: 0.8516 (t0) REVERT: D 78 THR cc_start: 0.8850 (m) cc_final: 0.8133 (p) REVERT: D 80 PHE cc_start: 0.8539 (m-80) cc_final: 0.8041 (m-10) REVERT: D 81 LEU cc_start: 0.8608 (tp) cc_final: 0.8207 (tp) REVERT: D 83 MET cc_start: 0.8659 (mmp) cc_final: 0.8307 (mmp) REVERT: D 93 MET cc_start: 0.7909 (tpt) cc_final: 0.7588 (tpp) REVERT: D 111 TRP cc_start: 0.8505 (m100) cc_final: 0.8171 (m-10) REVERT: D 159 ASN cc_start: 0.9350 (m110) cc_final: 0.8950 (t0) REVERT: D 164 TRP cc_start: 0.8280 (m100) cc_final: 0.7768 (m-10) REVERT: D 165 PHE cc_start: 0.8435 (m-80) cc_final: 0.8127 (m-80) REVERT: D 202 LEU cc_start: 0.9167 (tt) cc_final: 0.8667 (tt) REVERT: D 218 MET cc_start: 0.8527 (tmm) cc_final: 0.7977 (tmm) REVERT: D 225 LEU cc_start: 0.7622 (mt) cc_final: 0.7322 (mt) outliers start: 1 outliers final: 0 residues processed: 303 average time/residue: 0.1048 time to fit residues: 43.3691 Evaluate side-chains 224 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 224 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 2 optimal weight: 9.9990 chunk 12 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 109 optimal weight: 7.9990 chunk 5 optimal weight: 4.9990 chunk 85 optimal weight: 9.9990 chunk 97 optimal weight: 10.0000 chunk 20 optimal weight: 6.9990 chunk 71 optimal weight: 5.9990 chunk 92 optimal weight: 20.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 150 HIS R 181 GLN R 378 ASN A 188 HIS A 195 HIS A 294 ASN ** A 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 35 HIS D 77 ASN D 219 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.073786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.057849 restraints weight = 41470.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.060071 restraints weight = 26946.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.061677 restraints weight = 19449.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.062872 restraints weight = 15135.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.063784 restraints weight = 12411.679| |-----------------------------------------------------------------------------| r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.5159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 9272 Z= 0.210 Angle : 0.678 7.298 12566 Z= 0.359 Chirality : 0.044 0.165 1432 Planarity : 0.005 0.055 1579 Dihedral : 5.032 25.147 1251 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 17.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 0.40 % Allowed : 3.64 % Favored : 95.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.74 (0.25), residues: 1143 helix: 0.46 (0.25), residues: 408 sheet: -0.52 (0.33), residues: 253 loop : -1.23 (0.28), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 206 TYR 0.023 0.002 TYR B 124 PHE 0.027 0.002 PHE D 227 TRP 0.018 0.002 TRP R 217 HIS 0.008 0.002 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00450 ( 9266) covalent geometry : angle 0.67702 (12554) SS BOND : bond 0.00507 ( 6) SS BOND : angle 1.55287 ( 12) hydrogen bonds : bond 0.03886 ( 449) hydrogen bonds : angle 5.41105 ( 1269) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 280 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 119 ASN cc_start: 0.8697 (m-40) cc_final: 0.8225 (m-40) REVERT: R 190 LEU cc_start: 0.9572 (mt) cc_final: 0.9358 (mt) REVERT: R 253 ARG cc_start: 0.8023 (tpp-160) cc_final: 0.7749 (mtt180) REVERT: R 257 LEU cc_start: 0.9333 (mm) cc_final: 0.9112 (mm) REVERT: R 280 PHE cc_start: 0.8525 (t80) cc_final: 0.7735 (m-80) REVERT: R 320 GLU cc_start: 0.8583 (mt-10) cc_final: 0.8211 (mt-10) REVERT: R 326 PHE cc_start: 0.8293 (m-10) cc_final: 0.7744 (t80) REVERT: R 344 ILE cc_start: 0.9407 (mt) cc_final: 0.9133 (mt) REVERT: R 374 MET cc_start: 0.5304 (mmt) cc_final: 0.4854 (mmt) REVERT: L 7 MET cc_start: 0.7991 (tmm) cc_final: 0.7450 (tmm) REVERT: L 13 TYR cc_start: 0.8695 (t80) cc_final: 0.8444 (t80) REVERT: A 5 LEU cc_start: 0.8310 (mm) cc_final: 0.7753 (pt) REVERT: A 188 HIS cc_start: 0.8501 (OUTLIER) cc_final: 0.8227 (t-90) REVERT: A 223 PHE cc_start: 0.8669 (t80) cc_final: 0.8153 (t80) REVERT: A 248 LYS cc_start: 0.9490 (mtmm) cc_final: 0.9289 (mttt) REVERT: A 256 ASN cc_start: 0.9224 (m-40) cc_final: 0.8765 (m110) REVERT: A 304 GLN cc_start: 0.9412 (tt0) cc_final: 0.8760 (tm-30) REVERT: A 349 LYS cc_start: 0.9280 (tttm) cc_final: 0.8833 (tmtt) REVERT: B 50 THR cc_start: 0.8875 (m) cc_final: 0.8670 (t) REVERT: B 57 LYS cc_start: 0.9113 (pttp) cc_final: 0.8578 (ptpt) REVERT: B 101 MET cc_start: 0.8693 (mtp) cc_final: 0.8212 (mtm) REVERT: B 138 GLU cc_start: 0.8688 (pt0) cc_final: 0.7971 (pm20) REVERT: B 146 LEU cc_start: 0.7852 (mp) cc_final: 0.7122 (mp) REVERT: B 192 LEU cc_start: 0.8440 (mt) cc_final: 0.8183 (pt) REVERT: B 199 PHE cc_start: 0.9037 (p90) cc_final: 0.8674 (p90) REVERT: B 219 ARG cc_start: 0.8381 (tpt90) cc_final: 0.8115 (tpt90) REVERT: B 283 ARG cc_start: 0.8987 (tpt170) cc_final: 0.8668 (tpt170) REVERT: B 289 TYR cc_start: 0.7767 (m-80) cc_final: 0.6402 (m-80) REVERT: C 38 MET cc_start: 0.9225 (ptp) cc_final: 0.8918 (ptp) REVERT: D 73 ASP cc_start: 0.9158 (t70) cc_final: 0.8416 (t0) REVERT: D 78 THR cc_start: 0.9004 (m) cc_final: 0.8290 (p) REVERT: D 80 PHE cc_start: 0.8568 (m-80) cc_final: 0.8091 (m-10) REVERT: D 93 MET cc_start: 0.7957 (tpt) cc_final: 0.7739 (tpt) REVERT: D 111 TRP cc_start: 0.8586 (m100) cc_final: 0.8119 (m-10) REVERT: D 159 ASN cc_start: 0.9279 (m110) cc_final: 0.8814 (t0) REVERT: D 164 TRP cc_start: 0.8301 (m100) cc_final: 0.7606 (m-10) REVERT: D 202 LEU cc_start: 0.9259 (tt) cc_final: 0.8843 (tt) REVERT: D 218 MET cc_start: 0.8186 (tmm) cc_final: 0.7928 (tmm) REVERT: D 225 LEU cc_start: 0.7562 (mt) cc_final: 0.7327 (mt) outliers start: 4 outliers final: 1 residues processed: 282 average time/residue: 0.1073 time to fit residues: 41.1989 Evaluate side-chains 217 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 215 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 63 optimal weight: 7.9990 chunk 96 optimal weight: 6.9990 chunk 12 optimal weight: 8.9990 chunk 65 optimal weight: 7.9990 chunk 103 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 92 optimal weight: 20.0000 chunk 53 optimal weight: 7.9990 chunk 93 optimal weight: 2.9990 chunk 82 optimal weight: 10.0000 chunk 81 optimal weight: 0.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 137 ASN R 150 HIS R 181 GLN ** R 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 HIS A 195 HIS A 213 HIS ** A 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.074248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.058316 restraints weight = 41050.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.060559 restraints weight = 26664.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.062234 restraints weight = 19175.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.063482 restraints weight = 14804.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.064419 restraints weight = 12027.181| |-----------------------------------------------------------------------------| r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.5402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9272 Z= 0.186 Angle : 0.682 8.362 12566 Z= 0.358 Chirality : 0.045 0.158 1432 Planarity : 0.005 0.076 1579 Dihedral : 5.034 24.981 1251 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 16.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.78 (0.25), residues: 1143 helix: 0.39 (0.25), residues: 411 sheet: -0.40 (0.35), residues: 234 loop : -1.29 (0.28), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG R 343 TYR 0.020 0.002 TYR R 369 PHE 0.031 0.002 PHE A 307 TRP 0.018 0.002 TRP R 206 HIS 0.006 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00405 ( 9266) covalent geometry : angle 0.68141 (12554) SS BOND : bond 0.00419 ( 6) SS BOND : angle 1.38607 ( 12) hydrogen bonds : bond 0.03950 ( 449) hydrogen bonds : angle 5.42130 ( 1269) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 280 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 119 ASN cc_start: 0.8654 (m-40) cc_final: 0.8195 (m-40) REVERT: R 280 PHE cc_start: 0.8432 (t80) cc_final: 0.7680 (m-80) REVERT: R 293 TYR cc_start: 0.8393 (m-10) cc_final: 0.8133 (m-80) REVERT: R 320 GLU cc_start: 0.8623 (mt-10) cc_final: 0.8263 (mt-10) REVERT: R 326 PHE cc_start: 0.8290 (m-10) cc_final: 0.7650 (t80) REVERT: R 374 MET cc_start: 0.5055 (mmt) cc_final: 0.4599 (mmt) REVERT: L 7 MET cc_start: 0.7923 (tmm) cc_final: 0.7338 (tmm) REVERT: L 13 TYR cc_start: 0.8732 (t80) cc_final: 0.8532 (t80) REVERT: A 18 MET cc_start: 0.9118 (tmm) cc_final: 0.8805 (ptp) REVERT: A 24 ARG cc_start: 0.7962 (mtt180) cc_final: 0.7615 (mmm160) REVERT: A 223 PHE cc_start: 0.8714 (t80) cc_final: 0.8345 (t80) REVERT: A 243 MET cc_start: 0.9040 (ttp) cc_final: 0.8540 (tmm) REVERT: A 247 MET cc_start: 0.9199 (mtm) cc_final: 0.8563 (mtm) REVERT: A 248 LYS cc_start: 0.9497 (mtmm) cc_final: 0.9273 (mttt) REVERT: A 256 ASN cc_start: 0.9214 (m-40) cc_final: 0.8746 (m110) REVERT: A 304 GLN cc_start: 0.9390 (tt0) cc_final: 0.8661 (tm-30) REVERT: B 57 LYS cc_start: 0.8954 (pttp) cc_final: 0.8450 (ptpt) REVERT: B 59 TYR cc_start: 0.7238 (m-10) cc_final: 0.6218 (m-10) REVERT: B 69 LEU cc_start: 0.9448 (mt) cc_final: 0.8622 (pp) REVERT: B 101 MET cc_start: 0.8740 (mtp) cc_final: 0.8230 (mtm) REVERT: B 192 LEU cc_start: 0.8513 (mt) cc_final: 0.8198 (pt) REVERT: B 199 PHE cc_start: 0.8919 (p90) cc_final: 0.8638 (p90) REVERT: B 219 ARG cc_start: 0.8358 (tpt90) cc_final: 0.8151 (tpt90) REVERT: B 254 ASP cc_start: 0.7446 (t0) cc_final: 0.7159 (t0) REVERT: B 283 ARG cc_start: 0.8974 (tpt170) cc_final: 0.8672 (tpt170) REVERT: B 289 TYR cc_start: 0.7672 (m-80) cc_final: 0.6421 (m-80) REVERT: C 21 MET cc_start: 0.8744 (mmp) cc_final: 0.8222 (mmm) REVERT: C 38 MET cc_start: 0.9186 (ptp) cc_final: 0.8861 (ptp) REVERT: D 29 PHE cc_start: 0.9048 (t80) cc_final: 0.8661 (t80) REVERT: D 73 ASP cc_start: 0.9169 (t70) cc_final: 0.8326 (t0) REVERT: D 111 TRP cc_start: 0.8503 (m100) cc_final: 0.7948 (m-10) REVERT: D 126 ILE cc_start: 0.6797 (mm) cc_final: 0.6590 (mm) REVERT: D 159 ASN cc_start: 0.9259 (m110) cc_final: 0.8733 (t0) REVERT: D 164 TRP cc_start: 0.8215 (m100) cc_final: 0.7661 (m-10) REVERT: D 202 LEU cc_start: 0.9190 (tt) cc_final: 0.8805 (tt) REVERT: D 218 MET cc_start: 0.8064 (tmm) cc_final: 0.7849 (tmm) outliers start: 0 outliers final: 0 residues processed: 280 average time/residue: 0.1029 time to fit residues: 39.1574 Evaluate side-chains 225 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 225 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 41 optimal weight: 0.7980 chunk 23 optimal weight: 5.9990 chunk 65 optimal weight: 10.0000 chunk 7 optimal weight: 0.9980 chunk 68 optimal weight: 4.9990 chunk 109 optimal weight: 0.8980 chunk 81 optimal weight: 7.9990 chunk 43 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 70 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 137 ASN R 150 HIS A 188 HIS A 195 HIS ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN C 44 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.076441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.060603 restraints weight = 40201.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.062822 restraints weight = 26477.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.064470 restraints weight = 19274.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.065665 restraints weight = 15021.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.066604 restraints weight = 12324.409| |-----------------------------------------------------------------------------| r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.5585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9272 Z= 0.139 Angle : 0.685 7.431 12566 Z= 0.354 Chirality : 0.045 0.166 1432 Planarity : 0.004 0.054 1579 Dihedral : 4.862 22.788 1251 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 0.20 % Allowed : 1.41 % Favored : 98.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.74 (0.25), residues: 1143 helix: 0.37 (0.25), residues: 412 sheet: -0.56 (0.33), residues: 251 loop : -1.12 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG R 343 TYR 0.023 0.002 TYR R 369 PHE 0.020 0.001 PHE R 332 TRP 0.015 0.002 TRP R 167 HIS 0.005 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 9266) covalent geometry : angle 0.68358 (12554) SS BOND : bond 0.00507 ( 6) SS BOND : angle 1.49033 ( 12) hydrogen bonds : bond 0.03886 ( 449) hydrogen bonds : angle 5.32425 ( 1269) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 286 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 119 ASN cc_start: 0.8516 (m-40) cc_final: 0.8198 (m-40) REVERT: R 190 LEU cc_start: 0.9588 (mt) cc_final: 0.9367 (mt) REVERT: R 253 ARG cc_start: 0.7150 (mtp180) cc_final: 0.6893 (mtp180) REVERT: R 280 PHE cc_start: 0.8368 (t80) cc_final: 0.7724 (m-80) REVERT: R 316 LYS cc_start: 0.8492 (mtmt) cc_final: 0.8279 (mmtt) REVERT: R 320 GLU cc_start: 0.8614 (mt-10) cc_final: 0.8254 (mt-10) REVERT: R 326 PHE cc_start: 0.8075 (m-10) cc_final: 0.7353 (t80) REVERT: R 343 ARG cc_start: 0.8809 (ttp-110) cc_final: 0.8458 (ttp-170) REVERT: R 374 MET cc_start: 0.4798 (mmt) cc_final: 0.4301 (mmt) REVERT: L 7 MET cc_start: 0.7698 (tmm) cc_final: 0.7095 (tmm) REVERT: L 13 TYR cc_start: 0.8645 (t80) cc_final: 0.8404 (t80) REVERT: A 18 MET cc_start: 0.9051 (tmm) cc_final: 0.8788 (ptp) REVERT: A 24 ARG cc_start: 0.7917 (mtt180) cc_final: 0.7527 (mmm160) REVERT: A 188 HIS cc_start: 0.8409 (OUTLIER) cc_final: 0.8169 (t-90) REVERT: A 223 PHE cc_start: 0.8517 (t80) cc_final: 0.8025 (t80) REVERT: A 243 MET cc_start: 0.8941 (ttp) cc_final: 0.8449 (tmm) REVERT: A 247 MET cc_start: 0.9135 (mtm) cc_final: 0.8328 (mtm) REVERT: A 256 ASN cc_start: 0.9242 (m-40) cc_final: 0.8754 (m110) REVERT: A 275 GLU cc_start: 0.9185 (tm-30) cc_final: 0.8774 (tm-30) REVERT: A 304 GLN cc_start: 0.9360 (tt0) cc_final: 0.8655 (tm-30) REVERT: A 349 LYS cc_start: 0.9334 (tttm) cc_final: 0.8903 (tptm) REVERT: B 57 LYS cc_start: 0.9073 (pttp) cc_final: 0.8612 (ptmt) REVERT: B 101 MET cc_start: 0.8619 (mtp) cc_final: 0.8229 (mtm) REVERT: B 192 LEU cc_start: 0.8537 (mt) cc_final: 0.8171 (pt) REVERT: B 198 LEU cc_start: 0.9244 (mt) cc_final: 0.9016 (mt) REVERT: B 219 ARG cc_start: 0.8305 (tpt90) cc_final: 0.8067 (tpt90) REVERT: B 283 ARG cc_start: 0.8874 (tpt170) cc_final: 0.8604 (tpt170) REVERT: B 289 TYR cc_start: 0.7475 (m-80) cc_final: 0.6245 (m-80) REVERT: B 292 PHE cc_start: 0.9184 (m-10) cc_final: 0.8559 (m-80) REVERT: C 27 ARG cc_start: 0.7814 (ptp90) cc_final: 0.7456 (ptp90) REVERT: C 38 MET cc_start: 0.9122 (ptp) cc_final: 0.8793 (ptp) REVERT: D 45 LEU cc_start: 0.9095 (mt) cc_final: 0.8510 (mt) REVERT: D 73 ASP cc_start: 0.8909 (t70) cc_final: 0.8439 (t0) REVERT: D 111 TRP cc_start: 0.8102 (m100) cc_final: 0.7601 (m-10) REVERT: D 126 ILE cc_start: 0.6763 (mm) cc_final: 0.6537 (mm) REVERT: D 159 ASN cc_start: 0.9315 (m110) cc_final: 0.8831 (t0) REVERT: D 164 TRP cc_start: 0.8033 (m100) cc_final: 0.7495 (m-10) REVERT: D 202 LEU cc_start: 0.9107 (tt) cc_final: 0.8578 (tt) REVERT: D 225 LEU cc_start: 0.7400 (mt) cc_final: 0.7181 (mt) outliers start: 2 outliers final: 1 residues processed: 287 average time/residue: 0.1079 time to fit residues: 41.8987 Evaluate side-chains 238 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 236 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 25 optimal weight: 6.9990 chunk 37 optimal weight: 20.0000 chunk 28 optimal weight: 0.0060 chunk 22 optimal weight: 7.9990 chunk 55 optimal weight: 6.9990 chunk 4 optimal weight: 9.9990 chunk 60 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 overall best weight: 2.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 137 ASN A 188 HIS A 195 HIS ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 GLN ** A 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 44 HIS D 219 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.075799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.060292 restraints weight = 40638.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.062449 restraints weight = 27085.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.064035 restraints weight = 19806.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.065210 restraints weight = 15477.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.066083 restraints weight = 12727.454| |-----------------------------------------------------------------------------| r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.5823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 9272 Z= 0.153 Angle : 0.675 7.930 12566 Z= 0.351 Chirality : 0.044 0.170 1432 Planarity : 0.004 0.064 1579 Dihedral : 4.871 24.783 1251 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 0.20 % Allowed : 0.71 % Favored : 99.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.73 (0.25), residues: 1143 helix: 0.42 (0.25), residues: 413 sheet: -0.42 (0.33), residues: 251 loop : -1.24 (0.29), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 205 TYR 0.025 0.002 TYR B 59 PHE 0.019 0.002 PHE A 307 TRP 0.014 0.002 TRP R 167 HIS 0.008 0.001 HIS D 35 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 9266) covalent geometry : angle 0.67379 (12554) SS BOND : bond 0.00387 ( 6) SS BOND : angle 1.39654 ( 12) hydrogen bonds : bond 0.03874 ( 449) hydrogen bonds : angle 5.32366 ( 1269) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 283 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 119 ASN cc_start: 0.8637 (m-40) cc_final: 0.8200 (m110) REVERT: R 190 LEU cc_start: 0.9581 (mt) cc_final: 0.9346 (mt) REVERT: R 253 ARG cc_start: 0.7094 (mtp180) cc_final: 0.6258 (mtp180) REVERT: R 280 PHE cc_start: 0.8352 (t80) cc_final: 0.7617 (m-80) REVERT: R 288 ILE cc_start: 0.8357 (mm) cc_final: 0.8073 (mm) REVERT: R 289 THR cc_start: 0.9286 (p) cc_final: 0.9080 (p) REVERT: R 292 PHE cc_start: 0.8629 (m-80) cc_final: 0.8296 (m-80) REVERT: R 316 LYS cc_start: 0.8497 (mtmt) cc_final: 0.8252 (mmtt) REVERT: R 320 GLU cc_start: 0.8594 (mt-10) cc_final: 0.8332 (mt-10) REVERT: R 326 PHE cc_start: 0.8017 (m-10) cc_final: 0.7321 (t80) REVERT: R 343 ARG cc_start: 0.8592 (ttp-110) cc_final: 0.8239 (ttp-170) REVERT: R 374 MET cc_start: 0.4888 (mmt) cc_final: 0.4324 (mmt) REVERT: R 393 PHE cc_start: 0.8636 (m-80) cc_final: 0.8395 (m-80) REVERT: L 7 MET cc_start: 0.7631 (tmm) cc_final: 0.7052 (tmm) REVERT: L 17 LEU cc_start: 0.9012 (pp) cc_final: 0.8695 (pp) REVERT: A 14 GLU cc_start: 0.8774 (tm-30) cc_final: 0.8561 (tm-30) REVERT: A 18 MET cc_start: 0.8995 (tmm) cc_final: 0.8750 (ptp) REVERT: A 24 ARG cc_start: 0.7889 (mtt180) cc_final: 0.7464 (mmm160) REVERT: A 200 ASP cc_start: 0.8295 (t0) cc_final: 0.8069 (t0) REVERT: A 223 PHE cc_start: 0.8441 (t80) cc_final: 0.8031 (t80) REVERT: A 243 MET cc_start: 0.8896 (ttp) cc_final: 0.8438 (tmm) REVERT: A 247 MET cc_start: 0.9103 (mtm) cc_final: 0.8399 (mtp) REVERT: A 248 LYS cc_start: 0.9467 (mtmm) cc_final: 0.9259 (mttt) REVERT: A 253 ILE cc_start: 0.9622 (pt) cc_final: 0.9364 (pt) REVERT: A 256 ASN cc_start: 0.9253 (m-40) cc_final: 0.8784 (m110) REVERT: A 274 PHE cc_start: 0.9111 (t80) cc_final: 0.8634 (t80) REVERT: A 296 TYR cc_start: 0.8402 (t80) cc_final: 0.7824 (t80) REVERT: A 304 GLN cc_start: 0.9475 (tt0) cc_final: 0.8856 (tm-30) REVERT: B 57 LYS cc_start: 0.9134 (pttp) cc_final: 0.8735 (ptmt) REVERT: B 69 LEU cc_start: 0.9560 (mt) cc_final: 0.8714 (pp) REVERT: B 101 MET cc_start: 0.8696 (mtp) cc_final: 0.8356 (mtp) REVERT: B 146 LEU cc_start: 0.8279 (mp) cc_final: 0.7781 (mp) REVERT: B 190 LEU cc_start: 0.8582 (tp) cc_final: 0.8141 (tp) REVERT: B 192 LEU cc_start: 0.8565 (mt) cc_final: 0.8172 (pt) REVERT: B 283 ARG cc_start: 0.8805 (tpt170) cc_final: 0.8531 (tpt170) REVERT: B 289 TYR cc_start: 0.7657 (m-80) cc_final: 0.6340 (m-80) REVERT: B 292 PHE cc_start: 0.9166 (m-10) cc_final: 0.8568 (m-80) REVERT: C 38 MET cc_start: 0.9075 (ptp) cc_final: 0.8739 (ptp) REVERT: D 43 LYS cc_start: 0.8905 (pttp) cc_final: 0.8663 (pptt) REVERT: D 73 ASP cc_start: 0.8895 (t70) cc_final: 0.8381 (t0) REVERT: D 111 TRP cc_start: 0.8105 (m100) cc_final: 0.7637 (m-10) REVERT: D 159 ASN cc_start: 0.9247 (m110) cc_final: 0.8783 (t0) REVERT: D 164 TRP cc_start: 0.8026 (m100) cc_final: 0.7503 (m-10) REVERT: D 202 LEU cc_start: 0.9161 (tt) cc_final: 0.8627 (tt) REVERT: D 225 LEU cc_start: 0.7267 (mt) cc_final: 0.6952 (mt) outliers start: 2 outliers final: 0 residues processed: 285 average time/residue: 0.1051 time to fit residues: 40.8863 Evaluate side-chains 236 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 236 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 95 optimal weight: 0.8980 chunk 21 optimal weight: 20.0000 chunk 19 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 chunk 76 optimal weight: 4.9990 chunk 111 optimal weight: 6.9990 chunk 44 optimal weight: 9.9990 chunk 85 optimal weight: 5.9990 chunk 102 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 137 ASN R 150 HIS A 188 HIS ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 44 HIS D 219 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.074656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.059092 restraints weight = 41150.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.061186 restraints weight = 27676.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.062719 restraints weight = 20365.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.063878 restraints weight = 16049.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.064763 restraints weight = 13268.067| |-----------------------------------------------------------------------------| r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.5940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9272 Z= 0.167 Angle : 0.688 7.403 12566 Z= 0.359 Chirality : 0.044 0.158 1432 Planarity : 0.005 0.060 1579 Dihedral : 4.937 25.423 1251 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.30 % Allowed : 0.61 % Favored : 99.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.72 (0.25), residues: 1143 helix: 0.41 (0.25), residues: 411 sheet: -0.44 (0.33), residues: 252 loop : -1.19 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 206 TYR 0.025 0.002 TYR B 59 PHE 0.016 0.002 PHE R 291 TRP 0.019 0.002 TRP R 206 HIS 0.007 0.001 HIS D 35 Details of bonding type rmsd covalent geometry : bond 0.00370 ( 9266) covalent geometry : angle 0.68730 (12554) SS BOND : bond 0.00460 ( 6) SS BOND : angle 1.17856 ( 12) hydrogen bonds : bond 0.03879 ( 449) hydrogen bonds : angle 5.33428 ( 1269) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 265 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 119 ASN cc_start: 0.8670 (m-40) cc_final: 0.8224 (m-40) REVERT: R 253 ARG cc_start: 0.7168 (mtp180) cc_final: 0.6517 (mtp180) REVERT: R 280 PHE cc_start: 0.8366 (t80) cc_final: 0.7994 (m-80) REVERT: R 281 TYR cc_start: 0.8743 (m-80) cc_final: 0.8287 (m-10) REVERT: R 316 LYS cc_start: 0.8489 (mtmt) cc_final: 0.8252 (mmtt) REVERT: R 320 GLU cc_start: 0.8591 (mt-10) cc_final: 0.8264 (mt-10) REVERT: R 326 PHE cc_start: 0.7861 (m-10) cc_final: 0.7205 (t80) REVERT: R 343 ARG cc_start: 0.8549 (ttp-110) cc_final: 0.8221 (ttp-170) REVERT: R 374 MET cc_start: 0.4819 (mmt) cc_final: 0.4278 (mmt) REVERT: L 7 MET cc_start: 0.7719 (tmm) cc_final: 0.7292 (tmm) REVERT: A 14 GLU cc_start: 0.8741 (tm-30) cc_final: 0.8496 (tm-30) REVERT: A 18 MET cc_start: 0.9031 (tmm) cc_final: 0.8778 (ptp) REVERT: A 188 HIS cc_start: 0.8327 (OUTLIER) cc_final: 0.8118 (t-90) REVERT: A 200 ASP cc_start: 0.8410 (t0) cc_final: 0.8204 (t0) REVERT: A 223 PHE cc_start: 0.8502 (t80) cc_final: 0.8033 (t80) REVERT: A 248 LYS cc_start: 0.9467 (mtmm) cc_final: 0.9253 (mttt) REVERT: A 274 PHE cc_start: 0.9079 (t80) cc_final: 0.8801 (t80) REVERT: A 275 GLU cc_start: 0.9209 (tm-30) cc_final: 0.8977 (tm-30) REVERT: A 304 GLN cc_start: 0.9435 (tt0) cc_final: 0.8748 (tm-30) REVERT: A 320 TYR cc_start: 0.8337 (m-80) cc_final: 0.7991 (m-80) REVERT: A 349 LYS cc_start: 0.9274 (tttm) cc_final: 0.8878 (tptm) REVERT: B 57 LYS cc_start: 0.9153 (pttp) cc_final: 0.8785 (ptmt) REVERT: B 146 LEU cc_start: 0.8136 (mp) cc_final: 0.7909 (mp) REVERT: B 192 LEU cc_start: 0.8572 (mt) cc_final: 0.8161 (pt) REVERT: B 289 TYR cc_start: 0.7553 (m-80) cc_final: 0.6334 (m-80) REVERT: B 325 MET cc_start: 0.9058 (mtp) cc_final: 0.8702 (ttt) REVERT: C 38 MET cc_start: 0.9096 (ptp) cc_final: 0.8763 (ptp) REVERT: D 73 ASP cc_start: 0.8954 (t70) cc_final: 0.8420 (t0) REVERT: D 81 LEU cc_start: 0.8902 (pp) cc_final: 0.8263 (pp) REVERT: D 111 TRP cc_start: 0.8181 (m100) cc_final: 0.7744 (m-10) REVERT: D 153 LEU cc_start: 0.9124 (mt) cc_final: 0.8909 (mt) REVERT: D 159 ASN cc_start: 0.9205 (m110) cc_final: 0.8738 (t0) REVERT: D 164 TRP cc_start: 0.7984 (m100) cc_final: 0.7499 (m-10) REVERT: D 202 LEU cc_start: 0.9138 (tt) cc_final: 0.8670 (tt) REVERT: D 225 LEU cc_start: 0.7252 (mt) cc_final: 0.7048 (mt) outliers start: 3 outliers final: 1 residues processed: 267 average time/residue: 0.1004 time to fit residues: 36.8960 Evaluate side-chains 220 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 218 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 53 optimal weight: 9.9990 chunk 77 optimal weight: 5.9990 chunk 21 optimal weight: 8.9990 chunk 46 optimal weight: 10.0000 chunk 18 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 92 optimal weight: 9.9990 chunk 25 optimal weight: 0.0000 chunk 90 optimal weight: 4.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 137 ASN R 150 HIS A 188 HIS ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 GLN ** A 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 44 HIS D 219 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.075922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.060458 restraints weight = 40318.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.062491 restraints weight = 27083.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.064040 restraints weight = 20137.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.065216 restraints weight = 15805.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.066053 restraints weight = 13013.715| |-----------------------------------------------------------------------------| r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.6041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9272 Z= 0.143 Angle : 0.677 7.239 12566 Z= 0.351 Chirality : 0.044 0.194 1432 Planarity : 0.004 0.059 1579 Dihedral : 4.860 24.103 1251 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 15.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 0.20 % Allowed : 0.61 % Favored : 99.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.68 (0.25), residues: 1143 helix: 0.43 (0.25), residues: 416 sheet: -0.42 (0.33), residues: 251 loop : -1.18 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG D 206 TYR 0.025 0.002 TYR L 13 PHE 0.017 0.001 PHE A 307 TRP 0.015 0.002 TRP B 297 HIS 0.007 0.001 HIS D 35 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 9266) covalent geometry : angle 0.67629 (12554) SS BOND : bond 0.00368 ( 6) SS BOND : angle 1.10716 ( 12) hydrogen bonds : bond 0.03823 ( 449) hydrogen bonds : angle 5.22894 ( 1269) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1668.37 seconds wall clock time: 29 minutes 56.56 seconds (1796.56 seconds total)