Starting phenix.real_space_refine on Wed Jan 15 23:09:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yuu_39583/01_2025/8yuu_39583.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yuu_39583/01_2025/8yuu_39583.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yuu_39583/01_2025/8yuu_39583.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yuu_39583/01_2025/8yuu_39583.map" model { file = "/net/cci-nas-00/data/ceres_data/8yuu_39583/01_2025/8yuu_39583.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yuu_39583/01_2025/8yuu_39583.cif" } resolution = 2.7 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= 0.013 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 60 5.16 5 C 5762 2.51 5 N 1537 2.21 5 O 1678 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 9037 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2344 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 9, 'TRANS': 279} Chain breaks: 1 Chain: "A" Number of atoms: 1811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1811 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 2, 'TRANS': 222} Chain breaks: 1 Chain: "B" Number of atoms: 2607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2607 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "G" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 444 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "S" Number of atoms: 1795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1795 Classifications: {'peptide': 234} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 223} Chain breaks: 1 Chain: "R" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 36 Unusual residues: {'CLR': 1, 'HSM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.99, per 1000 atoms: 0.55 Number of scatterers: 9037 At special positions: 0 Unit cell: (106.47, 121.68, 115.596, 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 60 16.00 O 1678 8.00 N 1537 7.00 C 5762 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS R 107 " - pdb=" SG CYS R 188 " distance=2.03 Simple disulfide: pdb=" SG CYS R 384 " - pdb=" SG CYS R 388 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.04 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.48 Conformation dependent library (CDL) restraints added in 1.1 seconds 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2142 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 14 sheets defined 41.7% alpha, 24.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.10 Creating SS restraints... Processing helix chain 'R' and resid 33 through 62 removed outlier: 3.502A pdb=" N LEU R 37 " --> pdb=" O TRP R 33 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL R 49 " --> pdb=" O ILE R 45 " (cutoff:3.500A) Processing helix chain 'R' and resid 67 through 86 Processing helix chain 'R' and resid 86 through 98 Proline residue: R 93 - end of helix Processing helix chain 'R' and resid 106 through 138 removed outlier: 3.782A pdb=" N VAL R 136 " --> pdb=" O ARG R 132 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR R 137 " --> pdb=" O PHE R 133 " (cutoff:3.500A) Processing helix chain 'R' and resid 138 through 146 Processing helix chain 'R' and resid 149 through 173 removed outlier: 3.911A pdb=" N TYR R 167 " --> pdb=" O ALA R 163 " (cutoff:3.500A) Proline residue: R 169 - end of helix Processing helix chain 'R' and resid 174 through 179 Processing helix chain 'R' and resid 195 through 207 removed outlier: 3.713A pdb=" N LEU R 199 " --> pdb=" O ASN R 195 " (cutoff:3.500A) Processing helix chain 'R' and resid 207 through 235 Processing helix chain 'R' and resid 344 through 384 Proline residue: R 373 - end of helix Processing helix chain 'R' and resid 390 through 416 removed outlier: 3.542A pdb=" N TYR R 394 " --> pdb=" O PRO R 390 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU R 401 " --> pdb=" O SER R 397 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N TRP R 402 " --> pdb=" O PHE R 398 " (cutoff:3.500A) Proline residue: R 409 - end of helix Proline residue: R 413 - end of helix Processing helix chain 'R' and resid 416 through 427 Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.839A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 207 through 216 removed outlier: 3.729A pdb=" N LYS A 210 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 232 Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 256 through 260 removed outlier: 4.125A pdb=" N THR A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 279 removed outlier: 4.329A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 295 through 309 removed outlier: 3.640A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 3 through 25 removed outlier: 3.572A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'G' and resid 6 through 24 removed outlier: 3.592A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 removed outlier: 3.568A pdb=" N ASP G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 48' Processing helix chain 'G' and resid 55 through 59 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 62 through 65 Processing helix chain 'S' and resid 87 through 91 Processing helix chain 'S' and resid 220 through 224 removed outlier: 3.611A pdb=" N VAL S 224 " --> pdb=" O ALA S 221 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 3.604A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.428A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.568A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.034A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.804A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.973A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N MET B 217 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.423A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.672A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.045A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.045A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 140 through 141 Processing sheet with id=AB4, first strand: chain 'S' and resid 146 through 148 removed outlier: 4.944A pdb=" N LEU S 174 " --> pdb=" O TYR S 190 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N TYR S 190 " --> pdb=" O LEU S 174 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N TRP S 176 " --> pdb=" O LEU S 188 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ARG S 191 " --> pdb=" O ASN S 194 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'S' and resid 146 through 148 removed outlier: 4.023A pdb=" N THR S 238 " --> pdb=" O GLN S 231 " (cutoff:3.500A) 486 hydrogen bonds defined for protein. 1341 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: 2.75 Time building geometry restraints manager: 2.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2068 1.33 - 1.45: 2075 1.45 - 1.57: 5004 1.57 - 1.69: 5 1.69 - 1.82: 85 Bond restraints: 9237 Sorted by residual: bond pdb=" CA TYR A 296 " pdb=" C TYR A 296 " ideal model delta sigma weight residual 1.523 1.483 0.040 1.30e-02 5.92e+03 9.62e+00 bond pdb=" C23 CLR R 502 " pdb=" C24 CLR R 502 " ideal model delta sigma weight residual 1.525 1.578 -0.053 2.00e-02 2.50e+03 6.98e+00 bond pdb=" C16 CLR R 502 " pdb=" C17 CLR R 502 " ideal model delta sigma weight residual 1.554 1.607 -0.053 2.00e-02 2.50e+03 6.90e+00 bond pdb=" CA ALA R 53 " pdb=" C ALA R 53 " ideal model delta sigma weight residual 1.524 1.492 0.032 1.27e-02 6.20e+03 6.29e+00 bond pdb=" C GLN S 13 " pdb=" N PRO S 14 " ideal model delta sigma weight residual 1.332 1.364 -0.032 1.30e-02 5.92e+03 6.06e+00 ... (remaining 9232 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.11: 12137 2.11 - 4.21: 319 4.21 - 6.32: 48 6.32 - 8.43: 10 8.43 - 10.54: 6 Bond angle restraints: 12520 Sorted by residual: angle pdb=" N ASP B 76 " pdb=" CA ASP B 76 " pdb=" C ASP B 76 " ideal model delta sigma weight residual 112.92 102.38 10.54 1.23e+00 6.61e-01 7.34e+01 angle pdb=" N GLY S 114 " pdb=" CA GLY S 114 " pdb=" C GLY S 114 " ideal model delta sigma weight residual 112.18 122.53 -10.35 1.34e+00 5.57e-01 5.97e+01 angle pdb=" N LEU R 172 " pdb=" CA LEU R 172 " pdb=" C LEU R 172 " ideal model delta sigma weight residual 111.07 117.03 -5.96 1.07e+00 8.73e-01 3.10e+01 angle pdb=" N GLY B 282 " pdb=" CA GLY B 282 " pdb=" C GLY B 282 " ideal model delta sigma weight residual 115.27 107.68 7.59 1.41e+00 5.03e-01 2.90e+01 angle pdb=" N LYS B 78 " pdb=" CA LYS B 78 " pdb=" C LYS B 78 " ideal model delta sigma weight residual 109.50 117.94 -8.44 1.58e+00 4.01e-01 2.85e+01 ... (remaining 12515 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 5237 17.99 - 35.97: 229 35.97 - 53.96: 22 53.96 - 71.94: 5 71.94 - 89.93: 6 Dihedral angle restraints: 5499 sinusoidal: 2176 harmonic: 3323 Sorted by residual: dihedral pdb=" N SER S 193 " pdb=" C SER S 193 " pdb=" CA SER S 193 " pdb=" CB SER S 193 " ideal model delta harmonic sigma weight residual 122.80 131.92 -9.12 0 2.50e+00 1.60e-01 1.33e+01 dihedral pdb=" CA SER S 208 " pdb=" C SER S 208 " pdb=" N GLY S 209 " pdb=" CA GLY S 209 " ideal model delta harmonic sigma weight residual 180.00 162.52 17.48 0 5.00e+00 4.00e-02 1.22e+01 dihedral pdb=" C SER S 193 " pdb=" N SER S 193 " pdb=" CA SER S 193 " pdb=" CB SER S 193 " ideal model delta harmonic sigma weight residual -122.60 -131.11 8.51 0 2.50e+00 1.60e-01 1.16e+01 ... (remaining 5496 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 1187 0.075 - 0.150: 184 0.150 - 0.225: 24 0.225 - 0.300: 11 0.300 - 0.375: 2 Chirality restraints: 1408 Sorted by residual: chirality pdb=" CA SER S 193 " pdb=" N SER S 193 " pdb=" C SER S 193 " pdb=" CB SER S 193 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.51e+00 chirality pdb=" C13 CLR R 502 " pdb=" C12 CLR R 502 " pdb=" C14 CLR R 502 " pdb=" C17 CLR R 502 " both_signs ideal model delta sigma weight residual False -2.93 -3.24 0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" C17 CLR R 502 " pdb=" C13 CLR R 502 " pdb=" C16 CLR R 502 " pdb=" C20 CLR R 502 " both_signs ideal model delta sigma weight residual False 2.55 2.85 -0.30 2.00e-01 2.50e+01 2.23e+00 ... (remaining 1405 not shown) Planarity restraints: 1577 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN B 75 " 0.018 2.00e-02 2.50e+03 3.60e-02 1.30e+01 pdb=" C GLN B 75 " -0.062 2.00e-02 2.50e+03 pdb=" O GLN B 75 " 0.023 2.00e-02 2.50e+03 pdb=" N ASP B 76 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS S 35 " -0.012 2.00e-02 2.50e+03 2.45e-02 5.98e+00 pdb=" C HIS S 35 " 0.042 2.00e-02 2.50e+03 pdb=" O HIS S 35 " -0.016 2.00e-02 2.50e+03 pdb=" N TRP S 36 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR S 190 " 0.012 2.00e-02 2.50e+03 2.40e-02 5.76e+00 pdb=" C TYR S 190 " -0.042 2.00e-02 2.50e+03 pdb=" O TYR S 190 " 0.015 2.00e-02 2.50e+03 pdb=" N ARG S 191 " 0.014 2.00e-02 2.50e+03 ... (remaining 1574 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 77 2.64 - 3.21: 8124 3.21 - 3.77: 13503 3.77 - 4.34: 19935 4.34 - 4.90: 33421 Nonbonded interactions: 75060 Sorted by model distance: nonbonded pdb=" O THR B 86 " pdb=" OG1 THR B 87 " model vdw 2.076 3.040 nonbonded pdb=" O CYS A 3 " pdb=" OG1 THR A 4 " model vdw 2.173 3.040 nonbonded pdb=" O ASP B 154 " pdb=" OD1 ASP B 154 " model vdw 2.196 3.040 nonbonded pdb=" O GLY A 352 " pdb=" N PHE A 354 " model vdw 2.258 3.120 nonbonded pdb=" OD1 ASP R 62 " pdb=" OG SER R 64 " model vdw 2.315 3.040 ... (remaining 75055 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.390 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: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 22.850 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 9237 Z= 0.338 Angle : 0.834 10.537 12520 Z= 0.527 Chirality : 0.059 0.375 1408 Planarity : 0.004 0.053 1577 Dihedral : 10.474 89.929 3345 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.48 (0.26), residues: 1129 helix: 2.09 (0.26), residues: 418 sheet: 1.03 (0.30), residues: 286 loop : -0.12 (0.31), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 211 HIS 0.007 0.001 HIS B 91 PHE 0.017 0.002 PHE B 199 TYR 0.014 0.002 TYR S 103 ARG 0.005 0.001 ARG S 72 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 197 TYR cc_start: 0.6279 (m-80) cc_final: 0.6078 (m-10) REVERT: R 354 ARG cc_start: 0.6585 (ttt180) cc_final: 0.5941 (ttp-110) REVERT: A 47 ASN cc_start: 0.7235 (m-40) cc_final: 0.6777 (p0) REVERT: A 228 SER cc_start: 0.7781 (p) cc_final: 0.6761 (m) REVERT: A 306 GLN cc_start: 0.8032 (mm-40) cc_final: 0.7758 (mp10) REVERT: B 254 ASP cc_start: 0.7427 (t70) cc_final: 0.7188 (t70) outliers start: 0 outliers final: 0 residues processed: 188 average time/residue: 1.3890 time to fit residues: 277.2413 Evaluate side-chains 138 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.0670 chunk 84 optimal weight: 2.9990 chunk 46 optimal weight: 0.0570 chunk 28 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 87 optimal weight: 0.0770 chunk 33 optimal weight: 6.9990 chunk 52 optimal weight: 8.9990 chunk 64 optimal weight: 0.4980 chunk 100 optimal weight: 7.9990 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.174485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.114557 restraints weight = 9420.899| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 2.04 r_work: 0.3102 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 9237 Z= 0.153 Angle : 0.526 8.862 12520 Z= 0.285 Chirality : 0.041 0.171 1408 Planarity : 0.004 0.043 1577 Dihedral : 5.421 77.184 1314 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.25 % Allowed : 10.14 % Favored : 87.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.89 (0.25), residues: 1129 helix: 2.76 (0.25), residues: 419 sheet: 0.98 (0.29), residues: 278 loop : -0.05 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.002 0.001 HIS S 35 PHE 0.017 0.001 PHE R 192 TYR 0.010 0.001 TYR R 189 ARG 0.011 0.000 ARG R 99 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 140 time to evaluate : 1.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 376 LEU cc_start: 0.8007 (mm) cc_final: 0.7738 (mm) REVERT: A 47 ASN cc_start: 0.7036 (m-40) cc_final: 0.6369 (p0) REVERT: A 53 MET cc_start: 0.7092 (OUTLIER) cc_final: 0.6775 (mmm) REVERT: A 197 LYS cc_start: 0.8955 (mttt) cc_final: 0.8586 (mttm) REVERT: A 273 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.7962 (mm) REVERT: A 306 GLN cc_start: 0.8014 (mm-40) cc_final: 0.7679 (mp10) REVERT: B 44 GLN cc_start: 0.8484 (OUTLIER) cc_final: 0.8013 (mt0) REVERT: B 134 ARG cc_start: 0.8242 (mtm110) cc_final: 0.7944 (ptp90) REVERT: B 325 MET cc_start: 0.8910 (mmt) cc_final: 0.8349 (tpp) REVERT: G 46 LYS cc_start: 0.8341 (mttt) cc_final: 0.8020 (mmtm) REVERT: S 85 SER cc_start: 0.8881 (m) cc_final: 0.8384 (t) outliers start: 22 outliers final: 5 residues processed: 149 average time/residue: 1.4063 time to fit residues: 222.3485 Evaluate side-chains 137 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 129 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 56 MET Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 392 TYR Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain S residue 158 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 27 optimal weight: 2.9990 chunk 25 optimal weight: 9.9990 chunk 20 optimal weight: 0.6980 chunk 10 optimal weight: 6.9990 chunk 18 optimal weight: 0.5980 chunk 91 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 102 optimal weight: 20.0000 chunk 9 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 71 optimal weight: 8.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.174299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.114136 restraints weight = 9558.377| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 2.04 r_work: 0.3068 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9237 Z= 0.193 Angle : 0.535 8.383 12520 Z= 0.285 Chirality : 0.042 0.167 1408 Planarity : 0.004 0.038 1577 Dihedral : 5.347 73.312 1314 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.04 % Favored : 97.87 % Rotamer: Outliers : 2.97 % Allowed : 10.14 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.88 (0.25), residues: 1129 helix: 2.93 (0.25), residues: 413 sheet: 0.86 (0.29), residues: 279 loop : -0.12 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.005 0.001 HIS B 91 PHE 0.017 0.002 PHE R 192 TYR 0.011 0.001 TYR S 103 ARG 0.005 0.000 ARG R 154 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 130 time to evaluate : 0.996 Fit side-chains revert: symmetry clash REVERT: R 161 VAL cc_start: 0.7161 (t) cc_final: 0.6959 (m) REVERT: R 376 LEU cc_start: 0.8263 (mm) cc_final: 0.7977 (mm) REVERT: A 197 LYS cc_start: 0.8978 (mttt) cc_final: 0.8621 (mttm) REVERT: A 248 LYS cc_start: 0.8026 (mtmm) cc_final: 0.7804 (mtpt) REVERT: A 306 GLN cc_start: 0.8041 (mm-40) cc_final: 0.7682 (mp10) REVERT: B 44 GLN cc_start: 0.8428 (OUTLIER) cc_final: 0.7996 (mt0) REVERT: B 134 ARG cc_start: 0.8256 (mtm110) cc_final: 0.7951 (ptp90) REVERT: B 153 ASP cc_start: 0.7761 (t0) cc_final: 0.7536 (t70) REVERT: B 212 ASP cc_start: 0.8248 (t0) cc_final: 0.7926 (t0) REVERT: G 46 LYS cc_start: 0.8384 (mttt) cc_final: 0.8044 (mmtm) REVERT: S 85 SER cc_start: 0.8914 (m) cc_final: 0.8440 (t) outliers start: 29 outliers final: 13 residues processed: 143 average time/residue: 1.3840 time to fit residues: 210.1961 Evaluate side-chains 134 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 120 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 63 SER Chi-restraints excluded: chain R residue 159 VAL Chi-restraints excluded: chain R residue 233 LEU Chi-restraints excluded: chain R residue 392 TYR Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain S residue 23 SER Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 158 SER Chi-restraints excluded: chain S residue 245 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 42 optimal weight: 6.9990 chunk 5 optimal weight: 1.9990 chunk 62 optimal weight: 0.0970 chunk 36 optimal weight: 1.9990 chunk 2 optimal weight: 7.9990 chunk 47 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 65 optimal weight: 0.4980 chunk 50 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 109 optimal weight: 0.7980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 186 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.173104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.117021 restraints weight = 9507.320| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 2.09 r_work: 0.3083 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9237 Z= 0.170 Angle : 0.514 9.622 12520 Z= 0.271 Chirality : 0.041 0.163 1408 Planarity : 0.004 0.038 1577 Dihedral : 5.048 61.283 1314 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.13 % Favored : 97.79 % Rotamer: Outliers : 2.66 % Allowed : 12.09 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.90 (0.25), residues: 1129 helix: 3.03 (0.25), residues: 412 sheet: 0.80 (0.29), residues: 279 loop : -0.16 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.004 0.001 HIS B 91 PHE 0.018 0.001 PHE R 192 TYR 0.012 0.001 TYR S 190 ARG 0.004 0.000 ARG R 154 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 126 time to evaluate : 1.000 Fit side-chains revert: symmetry clash REVERT: A 24 ARG cc_start: 0.7979 (mtm-85) cc_final: 0.7532 (ttm-80) REVERT: A 197 LYS cc_start: 0.8974 (mttt) cc_final: 0.8601 (mttm) REVERT: A 248 LYS cc_start: 0.7995 (mtmm) cc_final: 0.7772 (mtpt) REVERT: A 306 GLN cc_start: 0.7952 (mm-40) cc_final: 0.7638 (mp10) REVERT: B 44 GLN cc_start: 0.8409 (OUTLIER) cc_final: 0.7990 (mt0) REVERT: B 134 ARG cc_start: 0.8274 (mtm110) cc_final: 0.7986 (ptp90) REVERT: B 153 ASP cc_start: 0.7816 (t0) cc_final: 0.7593 (t70) REVERT: B 212 ASP cc_start: 0.8218 (t0) cc_final: 0.7990 (t0) REVERT: B 217 MET cc_start: 0.7662 (ptt) cc_final: 0.7229 (ppp) REVERT: G 46 LYS cc_start: 0.8376 (mttt) cc_final: 0.8064 (mmtm) REVERT: S 85 SER cc_start: 0.8963 (m) cc_final: 0.8461 (t) outliers start: 26 outliers final: 13 residues processed: 141 average time/residue: 1.3751 time to fit residues: 206.0339 Evaluate side-chains 139 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 125 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 157 LEU Chi-restraints excluded: chain R residue 159 VAL Chi-restraints excluded: chain R residue 392 TYR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 23 SER Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 158 SER Chi-restraints excluded: chain S residue 245 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 30 optimal weight: 0.0870 chunk 104 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 45 optimal weight: 5.9990 chunk 5 optimal weight: 0.0570 chunk 51 optimal weight: 10.0000 chunk 74 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 overall best weight: 1.0280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 186 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.172456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.117342 restraints weight = 9456.348| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 1.93 r_work: 0.3088 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9237 Z= 0.161 Angle : 0.499 7.844 12520 Z= 0.264 Chirality : 0.041 0.161 1408 Planarity : 0.004 0.038 1577 Dihedral : 4.622 38.388 1314 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.13 % Favored : 97.79 % Rotamer: Outliers : 2.66 % Allowed : 12.50 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.92 (0.25), residues: 1129 helix: 3.08 (0.25), residues: 413 sheet: 0.73 (0.29), residues: 278 loop : -0.12 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS B 91 PHE 0.013 0.001 PHE A 189 TYR 0.013 0.001 TYR S 190 ARG 0.004 0.000 ARG R 154 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 134 time to evaluate : 1.025 Fit side-chains revert: symmetry clash REVERT: R 376 LEU cc_start: 0.8092 (mm) cc_final: 0.7813 (mm) REVERT: R 378 MET cc_start: 0.6424 (ttp) cc_final: 0.6175 (tpp) REVERT: A 24 ARG cc_start: 0.7839 (mtm-85) cc_final: 0.7378 (ttm-80) REVERT: A 197 LYS cc_start: 0.8969 (mttt) cc_final: 0.8584 (mttp) REVERT: A 248 LYS cc_start: 0.7873 (mtmm) cc_final: 0.7655 (mtpt) REVERT: A 306 GLN cc_start: 0.7864 (mm-40) cc_final: 0.7525 (mp10) REVERT: B 44 GLN cc_start: 0.8366 (OUTLIER) cc_final: 0.7936 (mt0) REVERT: B 134 ARG cc_start: 0.8227 (mtm110) cc_final: 0.7992 (ptp90) REVERT: B 153 ASP cc_start: 0.7800 (t0) cc_final: 0.7577 (t70) REVERT: B 212 ASP cc_start: 0.8159 (t0) cc_final: 0.7898 (t0) REVERT: G 46 LYS cc_start: 0.8330 (mttt) cc_final: 0.7974 (mmtt) REVERT: S 85 SER cc_start: 0.8964 (m) cc_final: 0.8438 (t) REVERT: S 183 GLN cc_start: 0.8576 (OUTLIER) cc_final: 0.8179 (mt0) outliers start: 26 outliers final: 12 residues processed: 148 average time/residue: 1.4162 time to fit residues: 222.8822 Evaluate side-chains 138 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 124 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 159 VAL Chi-restraints excluded: chain R residue 233 LEU Chi-restraints excluded: chain R residue 392 TYR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 23 SER Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 158 SER Chi-restraints excluded: chain S residue 183 GLN Chi-restraints excluded: chain S residue 245 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 77 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 93 optimal weight: 0.0870 chunk 102 optimal weight: 20.0000 chunk 40 optimal weight: 5.9990 chunk 51 optimal weight: 7.9990 chunk 53 optimal weight: 0.4980 chunk 55 optimal weight: 0.3980 chunk 78 optimal weight: 2.9990 chunk 90 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 overall best weight: 1.1962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 186 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.171657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.116375 restraints weight = 9441.361| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 1.97 r_work: 0.3071 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9237 Z= 0.175 Angle : 0.505 8.875 12520 Z= 0.267 Chirality : 0.041 0.164 1408 Planarity : 0.004 0.038 1577 Dihedral : 4.456 29.093 1314 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.95 % Favored : 97.96 % Rotamer: Outliers : 2.77 % Allowed : 13.73 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.90 (0.25), residues: 1129 helix: 3.09 (0.25), residues: 413 sheet: 0.69 (0.29), residues: 278 loop : -0.14 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.003 0.001 HIS B 91 PHE 0.020 0.001 PHE R 192 TYR 0.016 0.001 TYR S 190 ARG 0.003 0.000 ARG R 154 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 124 time to evaluate : 1.036 Fit side-chains revert: symmetry clash REVERT: R 378 MET cc_start: 0.6442 (ttp) cc_final: 0.6224 (tpp) REVERT: A 24 ARG cc_start: 0.7854 (mtm-85) cc_final: 0.7425 (ttm-80) REVERT: A 197 LYS cc_start: 0.8989 (mttt) cc_final: 0.8619 (mttp) REVERT: A 248 LYS cc_start: 0.7947 (mtmm) cc_final: 0.7730 (mtpt) REVERT: A 306 GLN cc_start: 0.7955 (mm-40) cc_final: 0.7621 (mp10) REVERT: B 44 GLN cc_start: 0.8399 (OUTLIER) cc_final: 0.7979 (mt0) REVERT: B 134 ARG cc_start: 0.8272 (mtm110) cc_final: 0.8034 (ptp90) REVERT: B 153 ASP cc_start: 0.7858 (t0) cc_final: 0.7641 (t70) REVERT: B 212 ASP cc_start: 0.8158 (t0) cc_final: 0.7920 (t0) REVERT: G 46 LYS cc_start: 0.8374 (mttt) cc_final: 0.8006 (mmtt) REVERT: S 85 SER cc_start: 0.9006 (m) cc_final: 0.8483 (t) outliers start: 27 outliers final: 16 residues processed: 140 average time/residue: 1.3582 time to fit residues: 202.1603 Evaluate side-chains 138 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 121 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 157 LEU Chi-restraints excluded: chain R residue 159 VAL Chi-restraints excluded: chain R residue 233 LEU Chi-restraints excluded: chain R residue 392 TYR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 23 SER Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 158 SER Chi-restraints excluded: chain S residue 245 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 49 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 83 optimal weight: 9.9990 chunk 77 optimal weight: 0.8980 chunk 50 optimal weight: 8.9990 chunk 21 optimal weight: 6.9990 chunk 70 optimal weight: 0.2980 chunk 29 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 186 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.171241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.115975 restraints weight = 9562.283| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 1.94 r_work: 0.3005 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 9237 Z= 0.157 Angle : 0.488 9.820 12520 Z= 0.258 Chirality : 0.041 0.158 1408 Planarity : 0.003 0.039 1577 Dihedral : 4.336 29.814 1314 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.95 % Favored : 97.96 % Rotamer: Outliers : 2.56 % Allowed : 14.04 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.92 (0.25), residues: 1129 helix: 3.16 (0.25), residues: 410 sheet: 0.67 (0.29), residues: 279 loop : -0.15 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 PHE 0.012 0.001 PHE A 189 TYR 0.015 0.001 TYR S 190 ARG 0.003 0.000 ARG R 154 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 124 time to evaluate : 1.048 Fit side-chains revert: symmetry clash REVERT: A 24 ARG cc_start: 0.7811 (mtm-85) cc_final: 0.7374 (ttm-80) REVERT: A 197 LYS cc_start: 0.8971 (mttt) cc_final: 0.8586 (mttp) REVERT: A 207 GLU cc_start: 0.7173 (tp30) cc_final: 0.6229 (mt-10) REVERT: A 208 ARG cc_start: 0.8149 (ttm110) cc_final: 0.7933 (ttm110) REVERT: A 248 LYS cc_start: 0.7910 (mtmm) cc_final: 0.7695 (mtpt) REVERT: A 306 GLN cc_start: 0.7897 (mm-40) cc_final: 0.7494 (mp10) REVERT: B 65 THR cc_start: 0.8927 (m) cc_final: 0.8593 (p) REVERT: B 134 ARG cc_start: 0.8256 (mtm110) cc_final: 0.8008 (ptp90) REVERT: B 153 ASP cc_start: 0.7845 (t0) cc_final: 0.7632 (t70) REVERT: B 212 ASP cc_start: 0.8106 (t0) cc_final: 0.7869 (t0) REVERT: B 219 ARG cc_start: 0.8483 (mtp180) cc_final: 0.8122 (mtp85) REVERT: G 46 LYS cc_start: 0.8378 (mttt) cc_final: 0.7988 (mmtt) REVERT: S 85 SER cc_start: 0.9005 (m) cc_final: 0.8486 (t) REVERT: S 183 GLN cc_start: 0.8534 (OUTLIER) cc_final: 0.8147 (mt0) outliers start: 25 outliers final: 17 residues processed: 138 average time/residue: 1.4055 time to fit residues: 205.7362 Evaluate side-chains 136 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 118 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 157 LEU Chi-restraints excluded: chain R residue 159 VAL Chi-restraints excluded: chain R residue 233 LEU Chi-restraints excluded: chain R residue 392 TYR Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 23 SER Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 158 SER Chi-restraints excluded: chain S residue 183 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 24 optimal weight: 0.5980 chunk 22 optimal weight: 0.6980 chunk 95 optimal weight: 0.9990 chunk 105 optimal weight: 0.5980 chunk 94 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 85 optimal weight: 8.9990 chunk 52 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 104 optimal weight: 0.9990 chunk 11 optimal weight: 7.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 186 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.174814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.114690 restraints weight = 9622.366| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 2.02 r_work: 0.3091 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 9237 Z= 0.134 Angle : 0.476 10.088 12520 Z= 0.251 Chirality : 0.040 0.157 1408 Planarity : 0.003 0.039 1577 Dihedral : 4.270 30.402 1314 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.95 % Favored : 97.96 % Rotamer: Outliers : 1.95 % Allowed : 15.27 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.99 (0.25), residues: 1129 helix: 3.21 (0.25), residues: 411 sheet: 0.77 (0.29), residues: 276 loop : -0.13 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 PHE 0.018 0.001 PHE R 192 TYR 0.014 0.001 TYR S 190 ARG 0.003 0.000 ARG R 154 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 126 time to evaluate : 1.101 Fit side-chains revert: symmetry clash REVERT: A 24 ARG cc_start: 0.7887 (mtm-85) cc_final: 0.7537 (ttm-80) REVERT: A 197 LYS cc_start: 0.8988 (mttt) cc_final: 0.8621 (mttp) REVERT: A 207 GLU cc_start: 0.7178 (tp30) cc_final: 0.6279 (mt-10) REVERT: A 208 ARG cc_start: 0.8169 (ttm110) cc_final: 0.7937 (ttm110) REVERT: A 248 LYS cc_start: 0.8091 (mtmm) cc_final: 0.7876 (mtpt) REVERT: A 306 GLN cc_start: 0.7876 (mm-40) cc_final: 0.7520 (mp10) REVERT: B 46 ARG cc_start: 0.8421 (mtp85) cc_final: 0.7744 (mtm-85) REVERT: B 65 THR cc_start: 0.8850 (OUTLIER) cc_final: 0.8554 (p) REVERT: B 134 ARG cc_start: 0.8299 (mtm110) cc_final: 0.7580 (ptt-90) REVERT: B 219 ARG cc_start: 0.8469 (mtp180) cc_final: 0.8141 (mtp85) REVERT: B 269 ILE cc_start: 0.7752 (mt) cc_final: 0.7509 (mt) REVERT: G 46 LYS cc_start: 0.8341 (mttt) cc_final: 0.7994 (mmtt) REVERT: S 85 SER cc_start: 0.9023 (m) cc_final: 0.8514 (t) REVERT: S 183 GLN cc_start: 0.8509 (OUTLIER) cc_final: 0.8130 (mt0) outliers start: 19 outliers final: 16 residues processed: 136 average time/residue: 1.3466 time to fit residues: 194.7801 Evaluate side-chains 141 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 123 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 157 LEU Chi-restraints excluded: chain R residue 159 VAL Chi-restraints excluded: chain R residue 233 LEU Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 23 SER Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 158 SER Chi-restraints excluded: chain S residue 183 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 1.9990 chunk 110 optimal weight: 0.7980 chunk 91 optimal weight: 4.9990 chunk 39 optimal weight: 8.9990 chunk 27 optimal weight: 0.8980 chunk 7 optimal weight: 6.9990 chunk 69 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 25 optimal weight: 10.0000 chunk 32 optimal weight: 8.9990 chunk 102 optimal weight: 20.0000 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 186 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.171924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.110915 restraints weight = 9470.110| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 2.02 r_work: 0.3065 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9237 Z= 0.190 Angle : 0.517 10.615 12520 Z= 0.272 Chirality : 0.042 0.162 1408 Planarity : 0.004 0.039 1577 Dihedral : 4.395 30.474 1314 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.13 % Favored : 97.79 % Rotamer: Outliers : 2.66 % Allowed : 14.65 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.93 (0.25), residues: 1129 helix: 3.14 (0.25), residues: 410 sheet: 0.76 (0.29), residues: 276 loop : -0.17 (0.30), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.004 0.001 HIS B 91 PHE 0.013 0.001 PHE R 192 TYR 0.016 0.001 TYR S 190 ARG 0.002 0.000 ARG R 154 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 123 time to evaluate : 1.128 Fit side-chains revert: symmetry clash REVERT: A 197 LYS cc_start: 0.8994 (mttt) cc_final: 0.8629 (mttp) REVERT: A 207 GLU cc_start: 0.7228 (tp30) cc_final: 0.6301 (mt-10) REVERT: A 208 ARG cc_start: 0.8206 (ttm110) cc_final: 0.8003 (ttm110) REVERT: A 248 LYS cc_start: 0.8096 (mtmm) cc_final: 0.7866 (mtpt) REVERT: A 306 GLN cc_start: 0.7969 (mm-40) cc_final: 0.7607 (mp10) REVERT: B 65 THR cc_start: 0.8880 (OUTLIER) cc_final: 0.8581 (p) REVERT: B 134 ARG cc_start: 0.8303 (mtm110) cc_final: 0.8075 (ptp90) REVERT: B 153 ASP cc_start: 0.7870 (t0) cc_final: 0.7657 (t70) REVERT: B 212 ASP cc_start: 0.8083 (t0) cc_final: 0.7752 (t0) REVERT: B 219 ARG cc_start: 0.8487 (mtp180) cc_final: 0.8066 (mtp85) REVERT: B 269 ILE cc_start: 0.7758 (mt) cc_final: 0.7529 (mt) REVERT: G 46 LYS cc_start: 0.8375 (mttt) cc_final: 0.8002 (mmtt) REVERT: S 85 SER cc_start: 0.9035 (m) cc_final: 0.8523 (t) REVERT: S 183 GLN cc_start: 0.8549 (OUTLIER) cc_final: 0.8153 (mt0) outliers start: 26 outliers final: 17 residues processed: 139 average time/residue: 1.3712 time to fit residues: 203.0165 Evaluate side-chains 139 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 120 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 63 SER Chi-restraints excluded: chain R residue 157 LEU Chi-restraints excluded: chain R residue 159 VAL Chi-restraints excluded: chain R residue 233 LEU Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 23 SER Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 158 SER Chi-restraints excluded: chain S residue 183 GLN Chi-restraints excluded: chain S residue 245 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 44 optimal weight: 4.9990 chunk 101 optimal weight: 9.9990 chunk 21 optimal weight: 8.9990 chunk 97 optimal weight: 8.9990 chunk 19 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 76 optimal weight: 3.9990 chunk 89 optimal weight: 0.9980 chunk 33 optimal weight: 0.0060 chunk 74 optimal weight: 1.9990 chunk 79 optimal weight: 0.5980 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 186 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.174304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.114135 restraints weight = 9581.657| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 2.02 r_work: 0.3109 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9237 Z= 0.134 Angle : 0.485 10.325 12520 Z= 0.255 Chirality : 0.040 0.155 1408 Planarity : 0.003 0.039 1577 Dihedral : 4.272 31.745 1314 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.74 % Allowed : 15.88 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 2.02 (0.25), residues: 1129 helix: 3.22 (0.25), residues: 411 sheet: 0.80 (0.29), residues: 276 loop : -0.13 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.002 0.001 HIS S 35 PHE 0.017 0.001 PHE R 192 TYR 0.013 0.001 TYR S 190 ARG 0.010 0.000 ARG A 313 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 122 time to evaluate : 1.099 Fit side-chains revert: symmetry clash REVERT: A 24 ARG cc_start: 0.7817 (ttm-80) cc_final: 0.7493 (ttm-80) REVERT: A 197 LYS cc_start: 0.8986 (mttt) cc_final: 0.8622 (mttp) REVERT: A 207 GLU cc_start: 0.7223 (tp30) cc_final: 0.6337 (mt-10) REVERT: A 208 ARG cc_start: 0.8173 (ttm110) cc_final: 0.7963 (ttm110) REVERT: A 248 LYS cc_start: 0.8047 (mtmm) cc_final: 0.7826 (mtpt) REVERT: A 277 LYS cc_start: 0.8556 (ttpt) cc_final: 0.8229 (ttpt) REVERT: A 306 GLN cc_start: 0.7852 (mm-40) cc_final: 0.7487 (mp10) REVERT: B 65 THR cc_start: 0.8825 (OUTLIER) cc_final: 0.8527 (p) REVERT: B 134 ARG cc_start: 0.8311 (mtm110) cc_final: 0.7574 (ptt-90) REVERT: B 212 ASP cc_start: 0.8071 (t0) cc_final: 0.7735 (t0) REVERT: B 219 ARG cc_start: 0.8468 (mtp180) cc_final: 0.8064 (mtp85) REVERT: B 269 ILE cc_start: 0.7775 (mt) cc_final: 0.7416 (mt) REVERT: G 46 LYS cc_start: 0.8352 (mttt) cc_final: 0.8001 (mmtt) REVERT: G 62 ARG cc_start: 0.7668 (ptp90) cc_final: 0.7448 (ptp90) REVERT: S 85 SER cc_start: 0.9022 (m) cc_final: 0.8541 (t) REVERT: S 183 GLN cc_start: 0.8521 (OUTLIER) cc_final: 0.8138 (mt0) outliers start: 17 outliers final: 11 residues processed: 130 average time/residue: 1.3890 time to fit residues: 192.1837 Evaluate side-chains 132 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 119 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 157 LEU Chi-restraints excluded: chain R residue 159 VAL Chi-restraints excluded: chain R residue 233 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 158 SER Chi-restraints excluded: chain S residue 183 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 7 optimal weight: 6.9990 chunk 11 optimal weight: 4.9990 chunk 12 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN S 186 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.169666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.113916 restraints weight = 9526.078| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.00 r_work: 0.3031 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 9237 Z= 0.281 Angle : 0.585 10.780 12520 Z= 0.308 Chirality : 0.044 0.196 1408 Planarity : 0.004 0.039 1577 Dihedral : 4.619 30.937 1314 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.84 % Allowed : 15.78 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.81 (0.25), residues: 1129 helix: 3.09 (0.25), residues: 404 sheet: 0.69 (0.29), residues: 277 loop : -0.24 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP S 47 HIS 0.005 0.001 HIS B 91 PHE 0.020 0.002 PHE R 192 TYR 0.020 0.002 TYR S 190 ARG 0.009 0.001 ARG A 313 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8542.39 seconds wall clock time: 151 minutes 36.52 seconds (9096.52 seconds total)