Starting phenix.real_space_refine on Mon May 12 14:50:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xwq_38741/05_2025/8xwq_38741.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xwq_38741/05_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_38741/05_2025/8xwq_38741.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xwq_38741/05_2025/8xwq_38741.map" model { file = "/net/cci-nas-00/data/ceres_data/8xwq_38741/05_2025/8xwq_38741.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xwq_38741/05_2025/8xwq_38741.cif" } resolution = 4.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 5.16, per 1000 atoms: 0.57 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: 2.21 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 1.04 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: 2.41 Time building geometry restraints manager: 2.58 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: 0.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 21.680 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.420 ------------------------------------------------------------------------------- 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 : 14.35 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (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 TRP 0.012 0.001 TRP R 336 HIS 0.003 0.001 HIS B 266 PHE 0.014 0.001 PHE R 291 TYR 0.009 0.001 TYR D 223 ARG 0.002 0.000 ARG B 68 Details of bonding type rmsd hydrogen bonds : bond 0.13916 ( 449) hydrogen bonds : angle 6.05158 ( 1269) SS BOND : bond 0.00354 ( 6) SS BOND : angle 1.12114 ( 12) covalent geometry : bond 0.00258 ( 9266) covalent geometry : angle 0.54649 (12554) *********************** 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 : 0.941 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: 0.6938 (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: 0.6965 (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: 0.7704 (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: 0.5885 (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: 0.4792 (p90) REVERT: A 242 ARG cc_start: 0.8426 (mtp85) cc_final: 0.8029 (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: 0.9225 (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: 0.7891 (m-80) REVERT: B 192 LEU cc_start: 0.8573 (mt) cc_final: 0.8076 (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: 0.7977 (t80) REVERT: B 243 THR cc_start: 0.8301 (p) cc_final: 0.8062 (t) REVERT: B 267 ASP cc_start: 0.9042 (OUTLIER) cc_final: 0.8651 (p0) REVERT: B 278 PHE cc_start: 0.8340 (m-80) cc_final: 0.8108 (m-80) REVERT: B 283 ARG cc_start: 0.8593 (tpt90) cc_final: 0.8339 (tpt170) REVERT: B 289 TYR cc_start: 0.8087 (m-80) cc_final: 0.6525 (m-80) REVERT: B 335 PHE cc_start: 0.6297 (OUTLIER) cc_final: 0.5704 (m-10) REVERT: C 24 ASN cc_start: 0.9216 (t0) cc_final: 0.8783 (p0) REVERT: C 36 ASP cc_start: 0.9132 (m-30) cc_final: 0.8891 (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: 0.2359 time to fit residues: 145.3214 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 : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 1.9990 chunk 86 optimal weight: 7.9990 chunk 47 optimal weight: 6.9990 chunk 29 optimal weight: 0.9990 chunk 58 optimal weight: 5.9990 chunk 46 optimal weight: 10.0000 chunk 89 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 54 optimal weight: 9.9990 chunk 66 optimal weight: 0.9990 chunk 103 optimal weight: 20.0000 overall best weight: 1.9990 ------------------------------------------------------------------------------- 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 317 GLN A 188 HIS A 195 HIS A 244 HIS 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.076476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.060186 restraints weight = 40231.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.062439 restraints weight = 26425.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.064051 restraints weight = 19190.461| |-----------------------------------------------------------------------------| r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.3409 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= 0.160 Angle : 0.652 7.683 12566 Z= 0.349 Chirality : 0.044 0.223 1432 Planarity : 0.005 0.054 1579 Dihedral : 4.669 30.178 1251 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 15.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 0.20 % Allowed : 4.14 % Favored : 95.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.25), residues: 1143 helix: 1.26 (0.25), residues: 401 sheet: -0.23 (0.33), residues: 239 loop : -1.17 (0.28), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 36 HIS 0.013 0.002 HIS B 225 PHE 0.016 0.002 PHE R 397 TYR 0.019 0.002 TYR D 161 ARG 0.007 0.001 ARG R 392 Details of bonding type rmsd hydrogen bonds : bond 0.04407 ( 449) hydrogen bonds : angle 5.23887 ( 1269) SS BOND : bond 0.00488 ( 6) SS BOND : angle 2.38273 ( 12) covalent geometry : bond 0.00342 ( 9266) covalent geometry : angle 0.64782 (12554) *********************** 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 350 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 348 time to evaluate : 1.037 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: R 94 ILE cc_start: 0.8135 (mt) cc_final: 0.7678 (mp) REVERT: R 134 ASN cc_start: 0.7036 (p0) cc_final: 0.6358 (t0) REVERT: R 138 ILE cc_start: 0.8710 (mt) cc_final: 0.8502 (pt) REVERT: R 257 LEU cc_start: 0.8945 (mm) cc_final: 0.8633 (mm) REVERT: R 280 PHE cc_start: 0.8510 (t80) cc_final: 0.7844 (m-80) REVERT: R 326 PHE cc_start: 0.8326 (m-10) cc_final: 0.7666 (t80) REVERT: L 7 MET cc_start: 0.7710 (tmm) cc_final: 0.7375 (tmm) REVERT: L 10 GLU cc_start: 0.8322 (mp0) cc_final: 0.7901 (pm20) REVERT: L 13 TYR cc_start: 0.8214 (t80) cc_final: 0.7803 (t80) REVERT: A 5 LEU cc_start: 0.7830 (mt) cc_final: 0.7598 (pt) REVERT: A 24 ARG cc_start: 0.7862 (mtt180) cc_final: 0.7402 (mmm-85) REVERT: A 188 HIS cc_start: 0.8369 (OUTLIER) cc_final: 0.8081 (t-90) REVERT: A 213 HIS cc_start: 0.8667 (p90) cc_final: 0.7586 (p90) REVERT: A 215 PHE cc_start: 0.8991 (m-80) cc_final: 0.8782 (m-80) REVERT: A 216 GLU cc_start: 0.8771 (tt0) cc_final: 0.8284 (tp30) REVERT: A 223 PHE cc_start: 0.8666 (t80) cc_final: 0.8366 (t80) REVERT: A 224 CYS cc_start: 0.9164 (m) cc_final: 0.7647 (t) REVERT: A 243 MET cc_start: 0.9214 (ttp) cc_final: 0.8404 (tmm) REVERT: A 247 MET cc_start: 0.9179 (mtm) cc_final: 0.8324 (mtm) REVERT: A 248 LYS cc_start: 0.9296 (mtmm) cc_final: 0.9072 (mttt) REVERT: A 256 ASN cc_start: 0.9068 (m-40) cc_final: 0.8850 (m110) REVERT: A 269 ASN cc_start: 0.9151 (m110) cc_final: 0.7608 (m-40) REVERT: A 304 GLN cc_start: 0.9439 (tt0) cc_final: 0.9152 (tm-30) REVERT: A 317 LYS cc_start: 0.8342 (pttt) cc_final: 0.8135 (pttp) REVERT: A 348 LEU cc_start: 0.9502 (mt) cc_final: 0.9186 (tp) REVERT: B 51 LEU cc_start: 0.9023 (mp) cc_final: 0.8585 (tp) REVERT: B 57 LYS cc_start: 0.9052 (pttp) cc_final: 0.8737 (ptpt) REVERT: B 63 TRP cc_start: 0.9346 (m100) cc_final: 0.9033 (m100) REVERT: B 69 LEU cc_start: 0.9534 (mt) cc_final: 0.8661 (pp) REVERT: B 146 LEU cc_start: 0.7427 (mp) cc_final: 0.6963 (mp) REVERT: B 180 PHE cc_start: 0.8432 (m-80) cc_final: 0.8039 (m-80) REVERT: B 192 LEU cc_start: 0.8508 (mt) cc_final: 0.8116 (pt) REVERT: B 222 PHE cc_start: 0.8203 (m-80) cc_final: 0.7990 (m-80) REVERT: B 254 ASP cc_start: 0.7482 (t70) cc_final: 0.7262 (t0) REVERT: B 283 ARG cc_start: 0.9067 (tpt90) cc_final: 0.8828 (tpt170) REVERT: B 289 TYR cc_start: 0.7868 (m-80) cc_final: 0.6371 (m-80) REVERT: C 24 ASN cc_start: 0.8942 (t0) cc_final: 0.8549 (p0) REVERT: D 35 HIS cc_start: 0.8920 (m-70) cc_final: 0.8320 (m-70) REVERT: D 46 GLU cc_start: 0.9031 (mm-30) cc_final: 0.8730 (mm-30) REVERT: D 73 ASP cc_start: 0.9090 (t70) cc_final: 0.8586 (t0) REVERT: D 78 THR cc_start: 0.9155 (m) cc_final: 0.8737 (p) REVERT: D 89 GLU cc_start: 0.8835 (mp0) cc_final: 0.8318 (pm20) REVERT: D 111 TRP cc_start: 0.8314 (m100) cc_final: 0.7752 (m-10) REVERT: D 145 ILE cc_start: 0.8624 (pt) cc_final: 0.8379 (pt) REVERT: D 164 TRP cc_start: 0.8124 (m100) cc_final: 0.7391 (m-10) REVERT: D 165 PHE cc_start: 0.8907 (m-80) cc_final: 0.8566 (m-80) REVERT: D 202 LEU cc_start: 0.9190 (tt) cc_final: 0.8483 (tt) outliers start: 2 outliers final: 1 residues processed: 348 average time/residue: 0.2251 time to fit residues: 104.3150 Evaluate side-chains 259 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 257 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 73 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 13 optimal weight: 6.9990 chunk 22 optimal weight: 9.9990 chunk 51 optimal weight: 0.9990 chunk 65 optimal weight: 9.9990 chunk 99 optimal weight: 5.9990 chunk 24 optimal weight: 7.9990 chunk 28 optimal weight: 9.9990 chunk 77 optimal weight: 0.0040 chunk 19 optimal weight: 7.9990 overall best weight: 3.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 119 ASN R 150 HIS R 181 GLN R 258 HIS A 195 HIS B 32 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.075310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.058993 restraints weight = 41157.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.061215 restraints weight = 26834.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.062862 restraints weight = 19478.974| |-----------------------------------------------------------------------------| r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.4068 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= 0.188 Angle : 0.647 8.694 12566 Z= 0.341 Chirality : 0.044 0.178 1432 Planarity : 0.004 0.041 1579 Dihedral : 4.777 24.919 1251 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 15.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.51 % Allowed : 4.65 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.25), residues: 1143 helix: 1.05 (0.25), residues: 402 sheet: -0.32 (0.34), residues: 240 loop : -1.22 (0.27), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP R 336 HIS 0.006 0.001 HIS R 258 PHE 0.030 0.002 PHE D 68 TYR 0.013 0.002 TYR R 251 ARG 0.007 0.001 ARG D 206 Details of bonding type rmsd hydrogen bonds : bond 0.04097 ( 449) hydrogen bonds : angle 5.16245 ( 1269) SS BOND : bond 0.00996 ( 6) SS BOND : angle 2.28188 ( 12) covalent geometry : bond 0.00396 ( 9266) covalent geometry : angle 0.64392 (12554) *********************** 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 315 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 310 time to evaluate : 1.057 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 242 ILE cc_start: 0.8726 (tp) cc_final: 0.8348 (mt) REVERT: R 245 MET cc_start: 0.9046 (mpp) cc_final: 0.8725 (mpp) REVERT: R 280 PHE cc_start: 0.8517 (t80) cc_final: 0.7877 (m-80) REVERT: R 293 TYR cc_start: 0.8551 (m-10) cc_final: 0.8300 (m-80) REVERT: R 295 LEU cc_start: 0.8591 (mt) cc_final: 0.8290 (mt) REVERT: R 320 GLU cc_start: 0.8684 (mt-10) cc_final: 0.8381 (mt-10) REVERT: R 326 PHE cc_start: 0.8403 (m-10) cc_final: 0.7701 (t80) REVERT: L 7 MET cc_start: 0.7773 (tmm) cc_final: 0.7320 (tmm) REVERT: L 10 GLU cc_start: 0.8404 (mp0) cc_final: 0.7941 (pm20) REVERT: L 13 TYR cc_start: 0.8368 (t80) cc_final: 0.8098 (t80) REVERT: A 213 HIS cc_start: 0.8708 (p90) cc_final: 0.7628 (p90) REVERT: A 223 PHE cc_start: 0.8722 (t80) cc_final: 0.8276 (t80) REVERT: A 224 CYS cc_start: 0.9281 (m) cc_final: 0.7729 (t) REVERT: A 225 VAL cc_start: 0.9170 (OUTLIER) cc_final: 0.8899 (m) REVERT: A 256 ASN cc_start: 0.9126 (m-40) cc_final: 0.8862 (m110) REVERT: A 269 ASN cc_start: 0.9245 (m110) cc_final: 0.7864 (m-40) REVERT: A 304 GLN cc_start: 0.9414 (tt0) cc_final: 0.9109 (tm-30) REVERT: A 317 LYS cc_start: 0.8344 (pttt) cc_final: 0.7989 (pttp) REVERT: A 332 VAL cc_start: 0.9498 (t) cc_final: 0.9170 (t) REVERT: A 333 GLN cc_start: 0.8739 (mp10) cc_final: 0.8348 (mp10) REVERT: B 57 LYS cc_start: 0.9157 (pttp) cc_final: 0.8690 (ptpt) REVERT: B 63 TRP cc_start: 0.9421 (m100) cc_final: 0.8993 (m100) REVERT: B 192 LEU cc_start: 0.8564 (mt) cc_final: 0.8191 (pt) REVERT: B 222 PHE cc_start: 0.8181 (m-80) cc_final: 0.7745 (m-80) REVERT: B 252 LEU cc_start: 0.9697 (tt) cc_final: 0.9324 (mt) REVERT: B 254 ASP cc_start: 0.7610 (t70) cc_final: 0.7303 (t0) REVERT: B 283 ARG cc_start: 0.9056 (tpt90) cc_final: 0.8808 (tpt170) REVERT: B 289 TYR cc_start: 0.7779 (m-80) cc_final: 0.6308 (m-80) REVERT: D 19 LYS cc_start: 0.9108 (ttmm) cc_final: 0.8715 (tttm) REVERT: D 35 HIS cc_start: 0.8827 (m-70) cc_final: 0.8516 (m-70) REVERT: D 37 VAL cc_start: 0.9615 (m) cc_final: 0.9341 (p) REVERT: D 45 LEU cc_start: 0.9413 (mt) cc_final: 0.8732 (mt) REVERT: D 73 ASP cc_start: 0.9119 (t70) cc_final: 0.8600 (t0) REVERT: D 78 THR cc_start: 0.9098 (m) cc_final: 0.8470 (p) REVERT: D 80 PHE cc_start: 0.8769 (m-80) cc_final: 0.8511 (m-10) REVERT: D 111 TRP cc_start: 0.8402 (m100) cc_final: 0.7851 (m-10) REVERT: D 159 ASN cc_start: 0.9205 (m110) cc_final: 0.8814 (t0) REVERT: D 164 TRP cc_start: 0.8189 (m100) cc_final: 0.7197 (m-10) REVERT: D 165 PHE cc_start: 0.8466 (m-80) cc_final: 0.8012 (m-80) REVERT: D 202 LEU cc_start: 0.9203 (tt) cc_final: 0.8544 (tt) outliers start: 5 outliers final: 0 residues processed: 312 average time/residue: 0.2136 time to fit residues: 90.2183 Evaluate side-chains 235 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 234 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 101 optimal weight: 0.3980 chunk 83 optimal weight: 20.0000 chunk 2 optimal weight: 9.9990 chunk 14 optimal weight: 20.0000 chunk 104 optimal weight: 7.9990 chunk 91 optimal weight: 20.0000 chunk 108 optimal weight: 6.9990 chunk 44 optimal weight: 5.9990 chunk 97 optimal weight: 0.8980 chunk 109 optimal weight: 10.0000 chunk 70 optimal weight: 20.0000 overall best weight: 4.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 150 HIS R 181 GLN A 188 HIS A 195 HIS A 294 ASN B 32 GLN ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 219 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.073464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.057627 restraints weight = 42137.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.059675 restraints weight = 28165.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.061197 restraints weight = 20839.848| |-----------------------------------------------------------------------------| r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.4559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 9272 Z= 0.233 Angle : 0.684 6.627 12566 Z= 0.366 Chirality : 0.045 0.200 1432 Planarity : 0.005 0.047 1579 Dihedral : 5.125 23.907 1251 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 18.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 0.40 % Allowed : 5.15 % Favored : 94.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.24), residues: 1143 helix: 0.49 (0.25), residues: 401 sheet: -0.36 (0.33), residues: 257 loop : -1.26 (0.28), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP R 217 HIS 0.009 0.002 HIS B 142 PHE 0.024 0.002 PHE D 68 TYR 0.017 0.002 TYR R 369 ARG 0.010 0.001 ARG D 206 Details of bonding type rmsd hydrogen bonds : bond 0.04208 ( 449) hydrogen bonds : angle 5.34622 ( 1269) SS BOND : bond 0.00340 ( 6) SS BOND : angle 1.72401 ( 12) covalent geometry : bond 0.00490 ( 9266) covalent geometry : angle 0.68260 (12554) *********************** 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 283 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 279 time to evaluate : 1.159 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: R 132 MET cc_start: 0.6400 (ttt) cc_final: 0.6115 (ttt) REVERT: R 190 LEU cc_start: 0.9549 (mt) cc_final: 0.9342 (mt) REVERT: R 236 GLU cc_start: 0.8271 (mp0) cc_final: 0.8026 (mp0) REVERT: R 280 PHE cc_start: 0.8647 (t80) cc_final: 0.7908 (m-80) REVERT: R 293 TYR cc_start: 0.8649 (m-10) cc_final: 0.8407 (m-80) REVERT: R 295 LEU cc_start: 0.8636 (mt) cc_final: 0.8402 (mt) REVERT: R 320 GLU cc_start: 0.8618 (mt-10) cc_final: 0.8269 (mt-10) REVERT: R 326 PHE cc_start: 0.8335 (m-10) cc_final: 0.7793 (t80) REVERT: L 7 MET cc_start: 0.7990 (tmm) cc_final: 0.7481 (tmm) REVERT: L 10 GLU cc_start: 0.8391 (mp0) cc_final: 0.8132 (pm20) REVERT: L 13 TYR cc_start: 0.8698 (t80) cc_final: 0.8344 (t80) REVERT: A 5 LEU cc_start: 0.8016 (mm) cc_final: 0.7390 (pt) REVERT: A 188 HIS cc_start: 0.8500 (OUTLIER) cc_final: 0.8198 (t-90) REVERT: A 213 HIS cc_start: 0.8731 (p90) cc_final: 0.7735 (p90) REVERT: A 223 PHE cc_start: 0.8824 (t80) cc_final: 0.8444 (t80) REVERT: A 224 CYS cc_start: 0.9222 (m) cc_final: 0.7822 (t) REVERT: A 256 ASN cc_start: 0.9160 (m-40) cc_final: 0.8838 (m110) REVERT: A 269 ASN cc_start: 0.9130 (m110) cc_final: 0.7910 (m-40) REVERT: A 304 GLN cc_start: 0.9458 (tt0) cc_final: 0.9099 (tm-30) REVERT: A 349 LYS cc_start: 0.9429 (mtmt) cc_final: 0.8732 (tmtt) REVERT: B 57 LYS cc_start: 0.9147 (pttp) cc_final: 0.8569 (ptpt) REVERT: B 192 LEU cc_start: 0.8578 (mt) cc_final: 0.8227 (pt) REVERT: B 252 LEU cc_start: 0.9745 (tt) cc_final: 0.9410 (mt) REVERT: B 254 ASP cc_start: 0.7646 (t70) cc_final: 0.7286 (t0) REVERT: B 283 ARG cc_start: 0.9194 (tpt90) cc_final: 0.8948 (tpt170) REVERT: B 289 TYR cc_start: 0.7821 (m-80) cc_final: 0.6289 (m-80) REVERT: C 21 MET cc_start: 0.9068 (mmm) cc_final: 0.8640 (mmm) REVERT: C 38 MET cc_start: 0.9269 (ptp) cc_final: 0.9028 (ptp) REVERT: D 73 ASP cc_start: 0.9163 (t70) cc_final: 0.8496 (t0) REVERT: D 78 THR cc_start: 0.8985 (m) cc_final: 0.8320 (p) REVERT: D 80 PHE cc_start: 0.8919 (m-80) cc_final: 0.8225 (m-10) REVERT: D 111 TRP cc_start: 0.8597 (m100) cc_final: 0.8162 (m-10) REVERT: D 159 ASN cc_start: 0.9192 (m110) cc_final: 0.8927 (m110) REVERT: D 164 TRP cc_start: 0.8354 (m100) cc_final: 0.7956 (m-10) REVERT: D 202 LEU cc_start: 0.9212 (tt) cc_final: 0.8765 (tt) outliers start: 4 outliers final: 1 residues processed: 280 average time/residue: 0.2350 time to fit residues: 87.5221 Evaluate side-chains 219 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 217 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 10 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 60 optimal weight: 8.9990 chunk 106 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 88 optimal weight: 0.9990 chunk 23 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 32 optimal weight: 10.0000 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 150 HIS R 181 GLN A 195 HIS B 32 GLN ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.077023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.061058 restraints weight = 40762.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.063293 restraints weight = 27121.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.064965 restraints weight = 19794.026| |-----------------------------------------------------------------------------| r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.4937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9272 Z= 0.132 Angle : 0.633 8.967 12566 Z= 0.330 Chirality : 0.044 0.169 1432 Planarity : 0.004 0.049 1579 Dihedral : 4.791 22.274 1251 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.25), residues: 1143 helix: 0.60 (0.25), residues: 401 sheet: -0.31 (0.33), residues: 252 loop : -1.10 (0.29), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 36 HIS 0.005 0.001 HIS R 258 PHE 0.030 0.002 PHE A 307 TYR 0.019 0.001 TYR R 369 ARG 0.009 0.000 ARG D 206 Details of bonding type rmsd hydrogen bonds : bond 0.03839 ( 449) hydrogen bonds : angle 5.09051 ( 1269) SS BOND : bond 0.00450 ( 6) SS BOND : angle 1.80938 ( 12) covalent geometry : bond 0.00287 ( 9266) covalent geometry : angle 0.63111 (12554) *********************** 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 296 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 296 time to evaluate : 1.042 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 94 ILE cc_start: 0.8222 (mt) cc_final: 0.7626 (mp) REVERT: R 119 ASN cc_start: 0.8659 (m-40) cc_final: 0.8195 (m110) REVERT: R 190 LEU cc_start: 0.9553 (mt) cc_final: 0.9345 (mt) REVERT: R 280 PHE cc_start: 0.8533 (t80) cc_final: 0.7839 (m-80) REVERT: R 293 TYR cc_start: 0.8655 (m-10) cc_final: 0.8363 (m-80) REVERT: R 295 LEU cc_start: 0.8575 (mt) cc_final: 0.8339 (mt) REVERT: R 316 LYS cc_start: 0.8515 (mtmt) cc_final: 0.8285 (mmtt) REVERT: R 320 GLU cc_start: 0.8612 (mt-10) cc_final: 0.8242 (mt-10) REVERT: R 326 PHE cc_start: 0.8126 (m-10) cc_final: 0.7731 (t80) REVERT: R 374 MET cc_start: 0.5056 (mmt) cc_final: 0.4586 (mmt) REVERT: R 381 ILE cc_start: 0.8877 (tp) cc_final: 0.8654 (tp) REVERT: L 7 MET cc_start: 0.7789 (tmm) cc_final: 0.7238 (tmm) REVERT: L 13 TYR cc_start: 0.8581 (t80) cc_final: 0.8293 (t80) REVERT: A 5 LEU cc_start: 0.8197 (mm) cc_final: 0.7566 (pt) REVERT: A 213 HIS cc_start: 0.8813 (p90) cc_final: 0.7798 (p90) REVERT: A 224 CYS cc_start: 0.9193 (m) cc_final: 0.8070 (t) REVERT: A 256 ASN cc_start: 0.9195 (m-40) cc_final: 0.8677 (m110) REVERT: A 304 GLN cc_start: 0.9450 (tt0) cc_final: 0.8592 (tm-30) REVERT: A 348 LEU cc_start: 0.9301 (mm) cc_final: 0.8971 (tp) REVERT: A 349 LYS cc_start: 0.9441 (mtmt) cc_final: 0.8820 (tptp) REVERT: B 49 ARG cc_start: 0.8943 (mmt180) cc_final: 0.8559 (mmt90) REVERT: B 57 LYS cc_start: 0.9128 (pttp) cc_final: 0.8590 (ptpt) REVERT: B 69 LEU cc_start: 0.9512 (mt) cc_final: 0.8668 (pp) REVERT: B 127 LYS cc_start: 0.9242 (mtpp) cc_final: 0.8935 (mttp) REVERT: B 192 LEU cc_start: 0.8478 (mt) cc_final: 0.8169 (pt) REVERT: B 219 ARG cc_start: 0.8340 (tpt170) cc_final: 0.8002 (tpt90) REVERT: B 222 PHE cc_start: 0.8117 (m-80) cc_final: 0.7880 (m-10) REVERT: B 254 ASP cc_start: 0.7711 (t70) cc_final: 0.7424 (t0) REVERT: B 264 TYR cc_start: 0.7357 (m-10) cc_final: 0.7052 (m-80) REVERT: B 283 ARG cc_start: 0.9083 (tpt90) cc_final: 0.8861 (tpt170) REVERT: B 289 TYR cc_start: 0.7502 (m-80) cc_final: 0.6321 (m-80) REVERT: C 38 MET cc_start: 0.9210 (ptp) cc_final: 0.8932 (ptp) REVERT: D 73 ASP cc_start: 0.9037 (t70) cc_final: 0.8631 (t0) REVERT: D 78 THR cc_start: 0.8979 (m) cc_final: 0.8209 (p) REVERT: D 80 PHE cc_start: 0.8829 (m-80) cc_final: 0.8427 (m-10) REVERT: D 81 LEU cc_start: 0.8643 (tp) cc_final: 0.8375 (tp) REVERT: D 111 TRP cc_start: 0.8258 (m100) cc_final: 0.7838 (m-10) REVERT: D 159 ASN cc_start: 0.9375 (m110) cc_final: 0.9001 (t0) REVERT: D 164 TRP cc_start: 0.8167 (m100) cc_final: 0.7388 (m-10) REVERT: D 165 PHE cc_start: 0.8510 (m-80) cc_final: 0.8046 (m-80) REVERT: D 202 LEU cc_start: 0.9189 (tt) cc_final: 0.8629 (tt) REVERT: D 218 MET cc_start: 0.8220 (tmm) cc_final: 0.7763 (tmm) REVERT: D 227 PHE cc_start: 0.8530 (m-80) cc_final: 0.8142 (m-80) outliers start: 0 outliers final: 0 residues processed: 296 average time/residue: 0.2181 time to fit residues: 87.1635 Evaluate side-chains 234 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 234 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 90 optimal weight: 20.0000 chunk 24 optimal weight: 3.9990 chunk 101 optimal weight: 6.9990 chunk 68 optimal weight: 7.9990 chunk 25 optimal weight: 5.9990 chunk 67 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 110 optimal weight: 0.0980 chunk 22 optimal weight: 5.9990 chunk 111 optimal weight: 0.9980 chunk 3 optimal weight: 7.9990 overall best weight: 3.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 150 HIS R 181 GLN A 188 HIS A 195 HIS A 294 ASN A 304 GLN B 32 GLN ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 219 GLN ** 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 = 0.3419 r_free = 0.3419 target = 0.074211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.058547 restraints weight = 41251.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.060624 restraints weight = 27449.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.062158 restraints weight = 20187.710| |-----------------------------------------------------------------------------| r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.5107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9272 Z= 0.184 Angle : 0.656 6.257 12566 Z= 0.348 Chirality : 0.045 0.224 1432 Planarity : 0.004 0.054 1579 Dihedral : 4.925 24.075 1251 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 16.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 0.40 % Allowed : 2.73 % Favored : 96.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.25), residues: 1143 helix: 0.57 (0.25), residues: 402 sheet: -0.28 (0.34), residues: 242 loop : -1.20 (0.28), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 211 HIS 0.011 0.002 HIS D 35 PHE 0.027 0.002 PHE D 68 TYR 0.020 0.002 TYR R 369 ARG 0.005 0.001 ARG D 206 Details of bonding type rmsd hydrogen bonds : bond 0.03847 ( 449) hydrogen bonds : angle 5.21255 ( 1269) SS BOND : bond 0.00480 ( 6) SS BOND : angle 1.54185 ( 12) covalent geometry : bond 0.00400 ( 9266) covalent geometry : angle 0.65473 (12554) *********************** 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 285 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 281 time to evaluate : 0.981 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 190 LEU cc_start: 0.9582 (mt) cc_final: 0.9380 (mt) REVERT: R 253 ARG cc_start: 0.7966 (tpp-160) cc_final: 0.7670 (mtt180) REVERT: R 280 PHE cc_start: 0.8556 (t80) cc_final: 0.7784 (m-80) REVERT: R 293 TYR cc_start: 0.8612 (m-10) cc_final: 0.8323 (m-80) REVERT: R 320 GLU cc_start: 0.8522 (mt-10) cc_final: 0.8155 (mt-10) REVERT: R 326 PHE cc_start: 0.8270 (m-10) cc_final: 0.7698 (t80) REVERT: R 374 MET cc_start: 0.5087 (mmt) cc_final: 0.4590 (mmt) REVERT: L 7 MET cc_start: 0.7914 (tmm) cc_final: 0.7365 (tmm) REVERT: L 13 TYR cc_start: 0.8656 (t80) cc_final: 0.8346 (t80) REVERT: A 5 LEU cc_start: 0.8364 (mm) cc_final: 0.7690 (pt) REVERT: A 188 HIS cc_start: 0.8367 (OUTLIER) cc_final: 0.8085 (t-90) REVERT: A 198 MET cc_start: 0.8562 (ttm) cc_final: 0.8342 (ttp) REVERT: A 213 HIS cc_start: 0.8813 (p90) cc_final: 0.8076 (p90) REVERT: A 224 CYS cc_start: 0.9167 (m) cc_final: 0.8098 (t) REVERT: A 253 ILE cc_start: 0.9637 (pt) cc_final: 0.9403 (pt) REVERT: A 256 ASN cc_start: 0.9224 (m-40) cc_final: 0.8802 (m110) REVERT: A 304 GLN cc_start: 0.9429 (tt0) cc_final: 0.8547 (tm-30) REVERT: A 348 LEU cc_start: 0.9367 (mm) cc_final: 0.9048 (tp) REVERT: B 57 LYS cc_start: 0.9151 (pttp) cc_final: 0.8632 (ptpt) REVERT: B 89 LYS cc_start: 0.9037 (mmtt) cc_final: 0.8654 (mmtm) REVERT: B 192 LEU cc_start: 0.8615 (mt) cc_final: 0.8246 (pt) REVERT: B 222 PHE cc_start: 0.8098 (m-80) cc_final: 0.7831 (m-10) REVERT: B 254 ASP cc_start: 0.7659 (t70) cc_final: 0.7449 (t0) REVERT: B 289 TYR cc_start: 0.7416 (m-80) cc_final: 0.6335 (m-80) REVERT: C 25 ILE cc_start: 0.7781 (pt) cc_final: 0.7347 (pt) REVERT: C 27 ARG cc_start: 0.8076 (ptp90) cc_final: 0.7764 (ptp90) REVERT: C 38 MET cc_start: 0.9155 (ptp) cc_final: 0.8887 (ptp) REVERT: D 35 HIS cc_start: 0.8866 (m-70) cc_final: 0.8394 (m-70) REVERT: D 73 ASP cc_start: 0.9055 (t70) cc_final: 0.8503 (t0) REVERT: D 78 THR cc_start: 0.8879 (m) cc_final: 0.8124 (p) REVERT: D 80 PHE cc_start: 0.8625 (m-80) cc_final: 0.8233 (m-10) REVERT: D 93 MET cc_start: 0.8010 (tpt) cc_final: 0.7786 (tpt) REVERT: D 111 TRP cc_start: 0.8247 (m100) cc_final: 0.7908 (m-10) REVERT: D 159 ASN cc_start: 0.9366 (m110) cc_final: 0.8965 (t0) REVERT: D 164 TRP cc_start: 0.8197 (m100) cc_final: 0.7387 (m-10) REVERT: D 202 LEU cc_start: 0.9201 (tt) cc_final: 0.8602 (tt) REVERT: D 218 MET cc_start: 0.8294 (tmm) cc_final: 0.7918 (tmm) REVERT: D 227 PHE cc_start: 0.8298 (m-80) cc_final: 0.7983 (m-80) outliers start: 4 outliers final: 1 residues processed: 283 average time/residue: 0.2237 time to fit residues: 85.0963 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 : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 80 optimal weight: 9.9990 chunk 82 optimal weight: 7.9990 chunk 8 optimal weight: 5.9990 chunk 13 optimal weight: 6.9990 chunk 32 optimal weight: 8.9990 chunk 86 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 chunk 71 optimal weight: 10.0000 chunk 103 optimal weight: 0.9990 chunk 93 optimal weight: 10.0000 chunk 46 optimal weight: 6.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 150 HIS ** R 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 HIS B 32 GLN ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 77 ASN ** D 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.072449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.057025 restraints weight = 43260.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.059046 restraints weight = 28957.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.060535 restraints weight = 21355.662| |-----------------------------------------------------------------------------| r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.5342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 9272 Z= 0.236 Angle : 0.721 6.564 12566 Z= 0.382 Chirality : 0.046 0.248 1432 Planarity : 0.005 0.058 1579 Dihedral : 5.247 26.643 1251 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 19.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 0.10 % Allowed : 2.22 % Favored : 97.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.25), residues: 1143 helix: 0.30 (0.25), residues: 402 sheet: -0.40 (0.34), residues: 248 loop : -1.22 (0.28), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP R 206 HIS 0.010 0.002 HIS D 35 PHE 0.016 0.002 PHE R 282 TYR 0.017 0.002 TYR B 124 ARG 0.006 0.001 ARG D 206 Details of bonding type rmsd hydrogen bonds : bond 0.04150 ( 449) hydrogen bonds : angle 5.37426 ( 1269) SS BOND : bond 0.00476 ( 6) SS BOND : angle 1.48247 ( 12) covalent geometry : bond 0.00503 ( 9266) covalent geometry : angle 0.71977 (12554) *********************** 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 269 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 268 time to evaluate : 1.105 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 280 PHE cc_start: 0.8593 (t80) cc_final: 0.7734 (m-80) REVERT: R 293 TYR cc_start: 0.8664 (m-10) cc_final: 0.8416 (m-10) REVERT: R 320 GLU cc_start: 0.8567 (mt-10) cc_final: 0.8198 (mt-10) REVERT: R 326 PHE cc_start: 0.8426 (m-10) cc_final: 0.7722 (t80) REVERT: R 374 MET cc_start: 0.5113 (mmt) cc_final: 0.4736 (mmt) REVERT: L 7 MET cc_start: 0.7963 (tmm) cc_final: 0.7404 (tmm) REVERT: L 13 TYR cc_start: 0.8762 (t80) cc_final: 0.8401 (t80) REVERT: A 213 HIS cc_start: 0.8739 (p90) cc_final: 0.8016 (p90) REVERT: A 243 MET cc_start: 0.9183 (ttp) cc_final: 0.8907 (tmm) REVERT: A 247 MET cc_start: 0.9263 (mtm) cc_final: 0.8403 (mtp) REVERT: A 269 ASN cc_start: 0.9006 (m110) cc_final: 0.8557 (m110) REVERT: A 274 PHE cc_start: 0.9096 (t80) cc_final: 0.8775 (t80) REVERT: A 275 GLU cc_start: 0.9248 (tm-30) cc_final: 0.8825 (tm-30) REVERT: A 304 GLN cc_start: 0.9464 (tt0) cc_final: 0.9067 (tm-30) REVERT: A 313 ARG cc_start: 0.8271 (mtt90) cc_final: 0.7941 (mpt180) REVERT: A 348 LEU cc_start: 0.9350 (mm) cc_final: 0.9098 (tp) REVERT: B 57 LYS cc_start: 0.9187 (pttp) cc_final: 0.8638 (ptpt) REVERT: B 101 MET cc_start: 0.8898 (mpp) cc_final: 0.8338 (mpp) REVERT: B 146 LEU cc_start: 0.8049 (mp) cc_final: 0.7787 (mp) REVERT: B 192 LEU cc_start: 0.8609 (mt) cc_final: 0.8213 (pt) REVERT: B 222 PHE cc_start: 0.8249 (m-80) cc_final: 0.7569 (m-80) REVERT: B 289 TYR cc_start: 0.7538 (m-80) cc_final: 0.6348 (m-80) REVERT: C 27 ARG cc_start: 0.8058 (ptp90) cc_final: 0.7663 (ptp90) REVERT: C 38 MET cc_start: 0.9122 (ptp) cc_final: 0.8863 (ptp) REVERT: D 73 ASP cc_start: 0.9106 (t70) cc_final: 0.8255 (t0) REVERT: D 78 THR cc_start: 0.8981 (m) cc_final: 0.8679 (p) REVERT: D 80 PHE cc_start: 0.8656 (m-80) cc_final: 0.8307 (m-80) REVERT: D 93 MET cc_start: 0.8026 (tpt) cc_final: 0.7727 (tpt) REVERT: D 111 TRP cc_start: 0.8305 (m100) cc_final: 0.7843 (m-10) REVERT: D 159 ASN cc_start: 0.9262 (m110) cc_final: 0.8728 (t0) REVERT: D 164 TRP cc_start: 0.8169 (m100) cc_final: 0.7422 (m-10) REVERT: D 165 PHE cc_start: 0.8552 (m-80) cc_final: 0.8338 (m-80) REVERT: D 202 LEU cc_start: 0.9208 (tt) cc_final: 0.8793 (tt) REVERT: D 218 MET cc_start: 0.8499 (tmm) cc_final: 0.8031 (tmm) REVERT: D 227 PHE cc_start: 0.8401 (m-80) cc_final: 0.8055 (m-80) outliers start: 1 outliers final: 0 residues processed: 268 average time/residue: 0.2138 time to fit residues: 77.3779 Evaluate side-chains 218 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 218 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 14 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 75 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 43 optimal weight: 8.9990 chunk 15 optimal weight: 0.3980 chunk 101 optimal weight: 0.4980 chunk 109 optimal weight: 0.9980 chunk 96 optimal weight: 5.9990 chunk 3 optimal weight: 6.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 150 HIS R 181 GLN A 188 HIS A 294 ASN A 306 GLN ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.075618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.059630 restraints weight = 41551.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.061794 restraints weight = 27475.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.063398 restraints weight = 20103.057| |-----------------------------------------------------------------------------| r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.5561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9272 Z= 0.139 Angle : 0.663 9.474 12566 Z= 0.342 Chirality : 0.044 0.163 1432 Planarity : 0.004 0.060 1579 Dihedral : 4.910 26.235 1251 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 0.30 % Allowed : 1.62 % Favored : 98.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.25), residues: 1143 helix: 0.50 (0.25), residues: 404 sheet: -0.52 (0.32), residues: 271 loop : -1.10 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 297 HIS 0.007 0.001 HIS B 142 PHE 0.012 0.001 PHE A 223 TYR 0.021 0.001 TYR R 369 ARG 0.015 0.000 ARG D 206 Details of bonding type rmsd hydrogen bonds : bond 0.03873 ( 449) hydrogen bonds : angle 5.17994 ( 1269) SS BOND : bond 0.00613 ( 6) SS BOND : angle 1.51806 ( 12) covalent geometry : bond 0.00305 ( 9266) covalent geometry : angle 0.66150 (12554) *********************** 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 293 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 290 time to evaluate : 1.099 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 94 ILE cc_start: 0.7179 (mt) cc_final: 0.6547 (mm) REVERT: R 119 ASN cc_start: 0.8777 (m-40) cc_final: 0.8428 (m-40) REVERT: R 245 MET cc_start: 0.8924 (mpp) cc_final: 0.8654 (mpp) REVERT: R 253 ARG cc_start: 0.7294 (mtt180) cc_final: 0.6779 (mtp180) REVERT: R 280 PHE cc_start: 0.8531 (t80) cc_final: 0.7752 (m-80) REVERT: R 282 PHE cc_start: 0.8724 (t80) cc_final: 0.8477 (t80) REVERT: R 293 TYR cc_start: 0.8717 (m-10) cc_final: 0.8482 (m-10) REVERT: R 295 LEU cc_start: 0.8471 (mt) cc_final: 0.8224 (mt) REVERT: R 320 GLU cc_start: 0.8594 (mt-10) cc_final: 0.8223 (mt-10) REVERT: R 326 PHE cc_start: 0.7899 (m-10) cc_final: 0.7689 (t80) REVERT: R 374 MET cc_start: 0.4700 (mmt) cc_final: 0.4302 (mmt) REVERT: R 381 ILE cc_start: 0.8888 (tp) cc_final: 0.8645 (tp) REVERT: L 7 MET cc_start: 0.7743 (tmm) cc_final: 0.7141 (tmm) REVERT: L 13 TYR cc_start: 0.8715 (t80) cc_final: 0.8499 (t80) REVERT: A 188 HIS cc_start: 0.8353 (OUTLIER) cc_final: 0.8096 (t-90) REVERT: A 213 HIS cc_start: 0.8821 (p90) cc_final: 0.8067 (p90) REVERT: A 224 CYS cc_start: 0.8957 (m) cc_final: 0.8204 (p) REVERT: A 243 MET cc_start: 0.9088 (ttp) cc_final: 0.8882 (tmm) REVERT: A 247 MET cc_start: 0.9266 (mtm) cc_final: 0.8143 (mtm) REVERT: A 248 LYS cc_start: 0.9469 (mtmm) cc_final: 0.9258 (mttt) REVERT: A 274 PHE cc_start: 0.9157 (t80) cc_final: 0.8786 (t80) REVERT: A 296 TYR cc_start: 0.8402 (t80) cc_final: 0.7697 (t80) REVERT: A 304 GLN cc_start: 0.9488 (tt0) cc_final: 0.8516 (tm-30) REVERT: A 313 ARG cc_start: 0.8190 (mtt90) cc_final: 0.7922 (mpt180) REVERT: A 348 LEU cc_start: 0.9335 (mm) cc_final: 0.8930 (tp) REVERT: A 349 LYS cc_start: 0.9474 (mtmt) cc_final: 0.9269 (mtpt) REVERT: B 57 LYS cc_start: 0.9151 (pttp) cc_final: 0.8632 (ptpt) REVERT: B 101 MET cc_start: 0.8960 (mpp) cc_final: 0.8533 (mpp) REVERT: B 146 LEU cc_start: 0.7935 (mp) cc_final: 0.7687 (mp) REVERT: B 192 LEU cc_start: 0.8501 (mt) cc_final: 0.8200 (pt) REVERT: B 222 PHE cc_start: 0.8139 (m-80) cc_final: 0.7927 (m-10) REVERT: B 283 ARG cc_start: 0.9109 (tpt170) cc_final: 0.8866 (tpt170) REVERT: B 289 TYR cc_start: 0.7346 (m-80) cc_final: 0.6274 (m-80) REVERT: B 292 PHE cc_start: 0.9205 (m-10) cc_final: 0.8610 (m-80) REVERT: C 25 ILE cc_start: 0.7737 (pt) cc_final: 0.6708 (pt) REVERT: C 27 ARG cc_start: 0.7938 (ptp90) cc_final: 0.7663 (ptp90) REVERT: D 29 PHE cc_start: 0.8910 (t80) cc_final: 0.8556 (t80) REVERT: D 73 ASP cc_start: 0.9057 (t70) cc_final: 0.8229 (t0) REVERT: D 93 MET cc_start: 0.8114 (tpt) cc_final: 0.7892 (tpt) REVERT: D 111 TRP cc_start: 0.8040 (m100) cc_final: 0.7554 (m-10) REVERT: D 159 ASN cc_start: 0.9338 (m110) cc_final: 0.8951 (t0) REVERT: D 164 TRP cc_start: 0.8058 (m100) cc_final: 0.7224 (m-10) REVERT: D 165 PHE cc_start: 0.8574 (m-80) cc_final: 0.8297 (m-80) REVERT: D 202 LEU cc_start: 0.9241 (tt) cc_final: 0.8722 (tt) REVERT: D 218 MET cc_start: 0.8342 (tmm) cc_final: 0.7851 (tmm) REVERT: D 227 PHE cc_start: 0.8352 (m-80) cc_final: 0.7877 (m-80) outliers start: 3 outliers final: 2 residues processed: 292 average time/residue: 0.2185 time to fit residues: 86.5448 Evaluate side-chains 223 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 220 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 101 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 chunk 52 optimal weight: 4.9990 chunk 79 optimal weight: 5.9990 chunk 86 optimal weight: 5.9990 chunk 0 optimal weight: 30.0000 chunk 26 optimal weight: 5.9990 chunk 110 optimal weight: 3.9990 chunk 64 optimal weight: 8.9990 chunk 8 optimal weight: 10.0000 chunk 75 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 150 HIS ** R 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 HIS B 32 GLN ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.072388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.057077 restraints weight = 42575.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.059038 restraints weight = 28652.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.060496 restraints weight = 21354.212| |-----------------------------------------------------------------------------| r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.5740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 9272 Z= 0.245 Angle : 0.736 8.112 12566 Z= 0.391 Chirality : 0.045 0.185 1432 Planarity : 0.006 0.121 1579 Dihedral : 5.207 27.582 1251 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 20.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 0.10 % Allowed : 0.71 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.24), residues: 1143 helix: 0.03 (0.25), residues: 412 sheet: -0.52 (0.33), residues: 243 loop : -1.31 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP R 206 HIS 0.011 0.002 HIS D 35 PHE 0.021 0.003 PHE D 29 TYR 0.026 0.002 TYR R 369 ARG 0.015 0.001 ARG D 206 Details of bonding type rmsd hydrogen bonds : bond 0.04234 ( 449) hydrogen bonds : angle 5.48990 ( 1269) SS BOND : bond 0.00565 ( 6) SS BOND : angle 1.57284 ( 12) covalent geometry : bond 0.00521 ( 9266) covalent geometry : angle 0.73454 (12554) *********************** 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 270 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 269 time to evaluate : 1.155 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 94 ILE cc_start: 0.6748 (mt) cc_final: 0.6181 (mm) REVERT: R 280 PHE cc_start: 0.8606 (t80) cc_final: 0.7662 (m-80) REVERT: R 293 TYR cc_start: 0.8716 (m-10) cc_final: 0.8442 (m-10) REVERT: R 320 GLU cc_start: 0.8507 (mt-10) cc_final: 0.8199 (mt-10) REVERT: R 326 PHE cc_start: 0.7956 (m-10) cc_final: 0.7629 (t80) REVERT: R 374 MET cc_start: 0.4952 (mmt) cc_final: 0.4651 (mmt) REVERT: R 381 ILE cc_start: 0.8959 (tp) cc_final: 0.8718 (tp) REVERT: L 7 MET cc_start: 0.7841 (tmm) cc_final: 0.7436 (tmm) REVERT: L 13 TYR cc_start: 0.8806 (t80) cc_final: 0.8454 (t80) REVERT: A 198 MET cc_start: 0.8531 (ttm) cc_final: 0.8195 (ttp) REVERT: A 200 ASP cc_start: 0.8329 (t0) cc_final: 0.8015 (t0) REVERT: A 213 HIS cc_start: 0.8727 (p90) cc_final: 0.8054 (p90) REVERT: A 243 MET cc_start: 0.9189 (ttp) cc_final: 0.8919 (tmm) REVERT: A 247 MET cc_start: 0.9109 (mtm) cc_final: 0.8203 (mtp) REVERT: A 269 ASN cc_start: 0.9032 (m110) cc_final: 0.8641 (m-40) REVERT: A 304 GLN cc_start: 0.9495 (tt0) cc_final: 0.9125 (tm-30) REVERT: A 348 LEU cc_start: 0.9376 (mm) cc_final: 0.9126 (tp) REVERT: A 349 LYS cc_start: 0.9487 (mtmt) cc_final: 0.8964 (tptt) REVERT: B 57 LYS cc_start: 0.9177 (pttp) cc_final: 0.8602 (ptpt) REVERT: B 101 MET cc_start: 0.8923 (mpp) cc_final: 0.8425 (mpp) REVERT: B 146 LEU cc_start: 0.8261 (mp) cc_final: 0.7978 (mp) REVERT: B 190 LEU cc_start: 0.8912 (tp) cc_final: 0.8246 (tp) REVERT: B 192 LEU cc_start: 0.8584 (mt) cc_final: 0.8236 (pt) REVERT: B 222 PHE cc_start: 0.8238 (m-80) cc_final: 0.7548 (m-80) REVERT: B 262 MET cc_start: 0.8507 (pmm) cc_final: 0.8174 (pmm) REVERT: B 289 TYR cc_start: 0.7490 (m-80) cc_final: 0.6360 (m-80) REVERT: D 29 PHE cc_start: 0.8879 (t80) cc_final: 0.8350 (t80) REVERT: D 73 ASP cc_start: 0.8988 (t70) cc_final: 0.8499 (t0) REVERT: D 74 ASP cc_start: 0.8847 (m-30) cc_final: 0.8514 (m-30) REVERT: D 81 LEU cc_start: 0.8823 (pp) cc_final: 0.8342 (pp) REVERT: D 93 MET cc_start: 0.8206 (tpt) cc_final: 0.7996 (tpt) REVERT: D 111 TRP cc_start: 0.8285 (m100) cc_final: 0.7815 (m-10) REVERT: D 159 ASN cc_start: 0.9209 (m110) cc_final: 0.8945 (m110) REVERT: D 164 TRP cc_start: 0.8090 (m100) cc_final: 0.7545 (m-10) REVERT: D 202 LEU cc_start: 0.9181 (tt) cc_final: 0.8689 (tt) REVERT: D 218 MET cc_start: 0.8526 (tmm) cc_final: 0.8090 (tmm) outliers start: 1 outliers final: 0 residues processed: 269 average time/residue: 0.2206 time to fit residues: 80.0600 Evaluate side-chains 206 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 206 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 87 optimal weight: 9.9990 chunk 65 optimal weight: 6.9990 chunk 80 optimal weight: 7.9990 chunk 48 optimal weight: 1.9990 chunk 12 optimal weight: 7.9990 chunk 64 optimal weight: 6.9990 chunk 44 optimal weight: 4.9990 chunk 78 optimal weight: 0.6980 chunk 88 optimal weight: 3.9990 chunk 46 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 150 HIS R 181 GLN A 188 HIS A 294 ASN B 32 GLN ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.073375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.057697 restraints weight = 42515.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.059778 restraints weight = 28158.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.061328 restraints weight = 20595.234| |-----------------------------------------------------------------------------| r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.5839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9272 Z= 0.191 Angle : 0.707 10.901 12566 Z= 0.376 Chirality : 0.045 0.190 1432 Planarity : 0.005 0.105 1579 Dihedral : 5.098 26.235 1251 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 17.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 0.30 % Allowed : 0.51 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.24), residues: 1143 helix: 0.17 (0.25), residues: 406 sheet: -0.47 (0.34), residues: 239 loop : -1.29 (0.27), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP R 206 HIS 0.009 0.002 HIS R 150 PHE 0.019 0.002 PHE A 336 TYR 0.026 0.002 TYR R 369 ARG 0.012 0.001 ARG D 206 Details of bonding type rmsd hydrogen bonds : bond 0.04022 ( 449) hydrogen bonds : angle 5.40322 ( 1269) SS BOND : bond 0.00467 ( 6) SS BOND : angle 1.44141 ( 12) covalent geometry : bond 0.00417 ( 9266) covalent geometry : angle 0.70627 (12554) ********************** 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 263 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 260 time to evaluate : 0.942 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: R 94 ILE cc_start: 0.6615 (mt) cc_final: 0.6089 (mm) REVERT: R 270 LYS cc_start: 0.9214 (tmtt) cc_final: 0.8912 (tttt) REVERT: R 280 PHE cc_start: 0.8596 (t80) cc_final: 0.7695 (m-80) REVERT: R 293 TYR cc_start: 0.8769 (m-10) cc_final: 0.8504 (m-80) REVERT: R 320 GLU cc_start: 0.8596 (mt-10) cc_final: 0.8247 (mt-10) REVERT: R 326 PHE cc_start: 0.7931 (m-10) cc_final: 0.7616 (t80) REVERT: R 374 MET cc_start: 0.4688 (mmt) cc_final: 0.4332 (mmt) REVERT: R 381 ILE cc_start: 0.8951 (tp) cc_final: 0.8724 (tp) REVERT: L 7 MET cc_start: 0.7829 (tmm) cc_final: 0.7410 (tmm) REVERT: L 13 TYR cc_start: 0.8796 (t80) cc_final: 0.8460 (t80) REVERT: A 200 ASP cc_start: 0.8308 (t0) cc_final: 0.8004 (t0) REVERT: A 213 HIS cc_start: 0.8763 (p90) cc_final: 0.8072 (p90) REVERT: A 224 CYS cc_start: 0.9020 (m) cc_final: 0.8282 (p) REVERT: A 243 MET cc_start: 0.9170 (ttp) cc_final: 0.8886 (tmm) REVERT: A 247 MET cc_start: 0.9076 (mtm) cc_final: 0.8205 (mtp) REVERT: A 304 GLN cc_start: 0.9493 (tt0) cc_final: 0.8708 (tm-30) REVERT: A 348 LEU cc_start: 0.9322 (mm) cc_final: 0.9044 (tp) REVERT: B 57 LYS cc_start: 0.9176 (pttp) cc_final: 0.8585 (ptpt) REVERT: B 101 MET cc_start: 0.8887 (mpp) cc_final: 0.8397 (mpp) REVERT: B 146 LEU cc_start: 0.8167 (mp) cc_final: 0.7853 (mp) REVERT: B 192 LEU cc_start: 0.8653 (mt) cc_final: 0.8269 (pt) REVERT: B 222 PHE cc_start: 0.8356 (m-80) cc_final: 0.7635 (m-80) REVERT: B 289 TYR cc_start: 0.7474 (m-80) cc_final: 0.6431 (m-80) REVERT: D 73 ASP cc_start: 0.8940 (t70) cc_final: 0.8309 (t0) REVERT: D 93 MET cc_start: 0.8211 (tpt) cc_final: 0.7984 (tpt) REVERT: D 111 TRP cc_start: 0.8241 (m100) cc_final: 0.7820 (m-10) REVERT: D 159 ASN cc_start: 0.9170 (m110) cc_final: 0.8914 (m110) REVERT: D 164 TRP cc_start: 0.8072 (m100) cc_final: 0.7430 (m-10) REVERT: D 202 LEU cc_start: 0.9182 (tt) cc_final: 0.8702 (tt) REVERT: D 218 MET cc_start: 0.8472 (tmm) cc_final: 0.8079 (tmm) REVERT: D 225 LEU cc_start: 0.7703 (mt) cc_final: 0.7471 (mt) outliers start: 3 outliers final: 1 residues processed: 261 average time/residue: 0.2059 time to fit residues: 73.0082 Evaluate side-chains 218 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 217 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 6 optimal weight: 7.9990 chunk 69 optimal weight: 10.0000 chunk 89 optimal weight: 2.9990 chunk 105 optimal weight: 10.0000 chunk 27 optimal weight: 1.9990 chunk 83 optimal weight: 7.9990 chunk 60 optimal weight: 6.9990 chunk 26 optimal weight: 7.9990 chunk 50 optimal weight: 10.0000 chunk 59 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 150 HIS ** R 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 HIS B 32 GLN ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.072718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.057334 restraints weight = 43272.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.059308 restraints weight = 28851.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.060812 restraints weight = 21347.232| |-----------------------------------------------------------------------------| r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.5967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 9272 Z= 0.212 Angle : 0.743 12.640 12566 Z= 0.390 Chirality : 0.045 0.199 1432 Planarity : 0.005 0.103 1579 Dihedral : 5.211 26.791 1251 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 18.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 0.10 % Allowed : 0.51 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.24), residues: 1143 helix: 0.06 (0.25), residues: 407 sheet: -0.61 (0.34), residues: 243 loop : -1.31 (0.28), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP R 336 HIS 0.009 0.002 HIS R 150 PHE 0.018 0.002 PHE R 282 TYR 0.057 0.002 TYR R 369 ARG 0.013 0.001 ARG D 206 Details of bonding type rmsd hydrogen bonds : bond 0.04236 ( 449) hydrogen bonds : angle 5.49690 ( 1269) SS BOND : bond 0.00472 ( 6) SS BOND : angle 1.40152 ( 12) covalent geometry : bond 0.00461 ( 9266) covalent geometry : angle 0.74188 (12554) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2954.81 seconds wall clock time: 52 minutes 53.19 seconds (3173.19 seconds total)