Starting phenix.real_space_refine on Wed Sep 17 13:17:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yuu_39583/09_2025/8yuu_39583.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yuu_39583/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8yuu_39583/09_2025/8yuu_39583.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yuu_39583/09_2025/8yuu_39583.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8yuu_39583/09_2025/8yuu_39583.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yuu_39583/09_2025/8yuu_39583.map" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.013 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 2.27, per 1000 atoms: 0.25 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: 0.93 Conformation dependent library (CDL) restraints added in 383.0 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 0.29 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: 1.41 Time building geometry restraints manager: 1.19 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: 0.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 10.260 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.620 ------------------------------------------------------------------------------- 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 9241 Z= 0.317 Angle : 0.834 10.537 12528 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 : 10.25 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 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 ARG 0.005 0.001 ARG S 72 TYR 0.014 0.002 TYR S 103 PHE 0.017 0.002 PHE B 199 TRP 0.014 0.002 TRP B 211 HIS 0.007 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00525 ( 9237) covalent geometry : angle 0.83350 (12520) SS BOND : bond 0.00710 ( 4) SS BOND : angle 1.24206 ( 8) hydrogen bonds : bond 0.15596 ( 478) hydrogen bonds : angle 6.27415 ( 1341) *********************** 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 : 0.354 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: 0.6847 time to fit residues: 136.2222 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 : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 9.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 9.9990 chunk 100 optimal weight: 7.9990 chunk 106 optimal weight: 7.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 70 ASN B 220 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.172469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.111656 restraints weight = 9485.965| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 2.01 r_work: 0.3087 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 9241 Z= 0.161 Angle : 0.571 8.351 12528 Z= 0.308 Chirality : 0.043 0.178 1408 Planarity : 0.004 0.041 1577 Dihedral : 5.718 83.674 1314 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.77 % Allowed : 9.84 % Favored : 87.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.77 (0.25), residues: 1129 helix: 2.66 (0.25), residues: 417 sheet: 0.91 (0.29), residues: 278 loop : -0.10 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG R 99 TYR 0.012 0.002 TYR R 189 PHE 0.018 0.002 PHE R 192 TRP 0.012 0.001 TRP B 82 HIS 0.005 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00367 ( 9237) covalent geometry : angle 0.57030 (12520) SS BOND : bond 0.00694 ( 4) SS BOND : angle 0.93679 ( 8) hydrogen bonds : bond 0.05206 ( 478) hydrogen bonds : angle 4.64856 ( 1341) *********************** 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: 27 poor density : 135 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 354 ARG cc_start: 0.6719 (ttt180) cc_final: 0.5852 (ttm110) REVERT: R 376 LEU cc_start: 0.7999 (mm) cc_final: 0.7739 (mm) REVERT: A 47 ASN cc_start: 0.6998 (m-40) cc_final: 0.6322 (p0) REVERT: A 53 MET cc_start: 0.7077 (OUTLIER) cc_final: 0.6817 (mmm) REVERT: A 197 LYS cc_start: 0.8992 (mttt) cc_final: 0.8637 (mttm) REVERT: A 273 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.7993 (mm) REVERT: A 306 GLN cc_start: 0.8091 (mm-40) cc_final: 0.7788 (mp10) REVERT: A 318 GLU cc_start: 0.8660 (tt0) cc_final: 0.8459 (tt0) REVERT: B 44 GLN cc_start: 0.8469 (OUTLIER) cc_final: 0.8004 (mt0) REVERT: B 134 ARG cc_start: 0.8287 (mtm110) cc_final: 0.7975 (ptp90) REVERT: B 254 ASP cc_start: 0.8205 (t70) cc_final: 0.7851 (t70) REVERT: B 325 MET cc_start: 0.8943 (mmt) cc_final: 0.8548 (tpp) REVERT: G 46 LYS cc_start: 0.8362 (mttt) cc_final: 0.8028 (mmtm) REVERT: S 85 SER cc_start: 0.8904 (m) cc_final: 0.8420 (t) outliers start: 27 outliers final: 11 residues processed: 146 average time/residue: 0.7519 time to fit residues: 115.8275 Evaluate side-chains 141 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 127 time to evaluate : 0.362 ------------------------------------------------------------------------------- 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 159 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 B residue 65 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 262 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 107 optimal weight: 5.9990 chunk 82 optimal weight: 0.0370 chunk 2 optimal weight: 7.9990 chunk 69 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 101 optimal weight: 0.0980 chunk 84 optimal weight: 10.0000 chunk 52 optimal weight: 9.9990 chunk 71 optimal weight: 0.8980 overall best weight: 0.5858 ------------------------------------------------------------------------------- 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 = 0.3955 r_free = 0.3955 target = 0.174682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.114708 restraints weight = 9568.487| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 2.02 r_work: 0.3090 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 9241 Z= 0.104 Angle : 0.491 8.500 12528 Z= 0.262 Chirality : 0.041 0.159 1408 Planarity : 0.003 0.039 1577 Dihedral : 5.388 79.371 1314 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.95 % Favored : 97.96 % Rotamer: Outliers : 2.05 % Allowed : 10.76 % Favored : 87.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.97 (0.25), residues: 1129 helix: 3.05 (0.25), residues: 414 sheet: 0.88 (0.29), residues: 277 loop : -0.11 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 99 TYR 0.010 0.001 TYR R 392 PHE 0.016 0.001 PHE R 192 TRP 0.017 0.001 TRP B 82 HIS 0.002 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00216 ( 9237) covalent geometry : angle 0.49114 (12520) SS BOND : bond 0.00475 ( 4) SS BOND : angle 0.74080 ( 8) hydrogen bonds : bond 0.04018 ( 478) hydrogen bonds : angle 4.29003 ( 1341) *********************** 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 155 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 135 time to evaluate : 0.436 Fit side-chains revert: symmetry clash REVERT: R 414 LEU cc_start: 0.8035 (tt) cc_final: 0.7815 (tm) REVERT: A 197 LYS cc_start: 0.8968 (mttt) cc_final: 0.8590 (mttm) REVERT: A 207 GLU cc_start: 0.6917 (tp30) cc_final: 0.6109 (mt-10) REVERT: A 248 LYS cc_start: 0.7971 (mttm) cc_final: 0.7757 (mtpt) REVERT: A 306 GLN cc_start: 0.7943 (mm-40) cc_final: 0.7591 (mp10) REVERT: A 318 GLU cc_start: 0.8587 (tt0) cc_final: 0.8357 (tt0) REVERT: B 44 GLN cc_start: 0.8451 (OUTLIER) cc_final: 0.7986 (mt0) REVERT: B 134 ARG cc_start: 0.8264 (mtm110) cc_final: 0.8010 (ptp90) REVERT: B 153 ASP cc_start: 0.7628 (t0) cc_final: 0.7387 (t70) REVERT: B 212 ASP cc_start: 0.8194 (t0) cc_final: 0.7865 (t0) REVERT: G 46 LYS cc_start: 0.8347 (mttt) cc_final: 0.8048 (mmtm) REVERT: S 85 SER cc_start: 0.8887 (m) cc_final: 0.8405 (t) outliers start: 20 outliers final: 5 residues processed: 143 average time/residue: 0.7088 time to fit residues: 107.4038 Evaluate side-chains 136 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 130 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 159 VAL Chi-restraints excluded: chain R residue 392 TYR Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain S residue 23 SER Chi-restraints excluded: chain S residue 63 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 3 optimal weight: 0.0020 chunk 87 optimal weight: 0.0970 chunk 1 optimal weight: 0.9990 chunk 14 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 50 optimal weight: 5.9990 chunk 18 optimal weight: 0.9980 chunk 47 optimal weight: 9.9990 chunk 37 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 70 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.176331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.121462 restraints weight = 9547.901| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 2.02 r_work: 0.3090 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 9241 Z= 0.101 Angle : 0.484 7.170 12528 Z= 0.257 Chirality : 0.040 0.158 1408 Planarity : 0.003 0.039 1577 Dihedral : 5.054 67.935 1314 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.30 % Favored : 97.61 % Rotamer: Outliers : 2.25 % Allowed : 12.09 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.04 (0.25), residues: 1129 helix: 3.17 (0.25), residues: 412 sheet: 0.81 (0.29), residues: 280 loop : -0.05 (0.31), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 219 TYR 0.010 0.001 TYR R 189 PHE 0.017 0.001 PHE R 192 TRP 0.014 0.001 TRP B 82 HIS 0.002 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00212 ( 9237) covalent geometry : angle 0.48377 (12520) SS BOND : bond 0.00433 ( 4) SS BOND : angle 0.69556 ( 8) hydrogen bonds : bond 0.03771 ( 478) hydrogen bonds : angle 4.13928 ( 1341) *********************** 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 156 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 134 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 414 LEU cc_start: 0.8017 (tt) cc_final: 0.7774 (tm) REVERT: A 197 LYS cc_start: 0.8922 (mttt) cc_final: 0.8507 (mttm) REVERT: A 248 LYS cc_start: 0.7883 (mttm) cc_final: 0.7675 (mtpt) REVERT: A 273 LEU cc_start: 0.8369 (mp) cc_final: 0.8152 (mm) REVERT: A 306 GLN cc_start: 0.7845 (mm-40) cc_final: 0.7538 (mp10) REVERT: A 318 GLU cc_start: 0.8590 (tt0) cc_final: 0.8341 (tt0) REVERT: B 44 GLN cc_start: 0.8402 (OUTLIER) cc_final: 0.7963 (mt0) REVERT: B 134 ARG cc_start: 0.8239 (mtm110) cc_final: 0.8024 (ptp90) REVERT: B 219 ARG cc_start: 0.8291 (mtp85) cc_final: 0.7951 (mmm160) REVERT: G 46 LYS cc_start: 0.8314 (mttt) cc_final: 0.8025 (mmtm) REVERT: S 85 SER cc_start: 0.8900 (m) cc_final: 0.8419 (t) outliers start: 22 outliers final: 8 residues processed: 148 average time/residue: 0.7044 time to fit residues: 110.4227 Evaluate side-chains 136 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 127 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 146 LEU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain S residue 23 SER Chi-restraints excluded: chain S residue 158 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 69 optimal weight: 0.0170 chunk 79 optimal weight: 1.9990 chunk 72 optimal weight: 9.9990 chunk 27 optimal weight: 1.9990 chunk 98 optimal weight: 0.8980 chunk 43 optimal weight: 7.9990 chunk 11 optimal weight: 7.9990 chunk 3 optimal weight: 0.9990 chunk 100 optimal weight: 5.9990 chunk 96 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 overall best weight: 0.9822 ------------------------------------------------------------------------------- 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 = 0.3928 r_free = 0.3928 target = 0.172276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.112813 restraints weight = 9449.355| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 2.21 r_work: 0.3071 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9241 Z= 0.115 Angle : 0.501 8.838 12528 Z= 0.264 Chirality : 0.041 0.162 1408 Planarity : 0.003 0.040 1577 Dihedral : 4.728 49.177 1314 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.04 % Favored : 97.87 % Rotamer: Outliers : 2.77 % Allowed : 12.40 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.97 (0.25), residues: 1129 helix: 3.12 (0.25), residues: 413 sheet: 0.76 (0.29), residues: 280 loop : -0.10 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 154 TYR 0.012 0.001 TYR S 190 PHE 0.014 0.001 PHE B 199 TRP 0.012 0.001 TRP B 82 HIS 0.003 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 9237) covalent geometry : angle 0.50052 (12520) SS BOND : bond 0.00553 ( 4) SS BOND : angle 0.72260 ( 8) hydrogen bonds : bond 0.03902 ( 478) hydrogen bonds : angle 4.10587 ( 1341) *********************** 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 158 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 131 time to evaluate : 0.361 Fit side-chains revert: symmetry clash REVERT: R 378 MET cc_start: 0.6507 (ttp) cc_final: 0.6205 (tpp) REVERT: A 197 LYS cc_start: 0.8956 (mttt) cc_final: 0.8572 (mttp) REVERT: A 207 GLU cc_start: 0.7039 (tp30) cc_final: 0.6354 (mt-10) REVERT: A 248 LYS cc_start: 0.7977 (mttm) cc_final: 0.7772 (mtpt) REVERT: A 306 GLN cc_start: 0.7907 (mm-40) cc_final: 0.7586 (mp10) REVERT: A 318 GLU cc_start: 0.8619 (tt0) cc_final: 0.8369 (tt0) REVERT: B 44 GLN cc_start: 0.8419 (OUTLIER) cc_final: 0.7999 (mt0) REVERT: B 134 ARG cc_start: 0.8284 (mtm110) cc_final: 0.8028 (ptp90) REVERT: B 212 ASP cc_start: 0.8146 (t0) cc_final: 0.7763 (t0) REVERT: B 217 MET cc_start: 0.7738 (OUTLIER) cc_final: 0.6978 (ppp) REVERT: B 219 ARG cc_start: 0.8375 (mtp85) cc_final: 0.7630 (mmm160) REVERT: G 46 LYS cc_start: 0.8351 (mttt) cc_final: 0.7995 (mmtt) REVERT: S 34 MET cc_start: 0.9159 (mmp) cc_final: 0.8939 (mmm) REVERT: S 85 SER cc_start: 0.8999 (m) cc_final: 0.8476 (t) outliers start: 27 outliers final: 12 residues processed: 145 average time/residue: 0.6489 time to fit residues: 99.9141 Evaluate side-chains 142 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 128 time to evaluate : 0.397 ------------------------------------------------------------------------------- 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 392 TYR Chi-restraints excluded: chain A residue 272 ASP 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 217 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 67 optimal weight: 6.9990 chunk 100 optimal weight: 4.9990 chunk 94 optimal weight: 0.0570 chunk 96 optimal weight: 3.9990 chunk 8 optimal weight: 7.9990 chunk 24 optimal weight: 8.9990 chunk 50 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 83 optimal weight: 9.9990 chunk 109 optimal weight: 3.9990 chunk 104 optimal weight: 0.9980 overall best weight: 1.3902 ------------------------------------------------------------------------------- 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 = 0.3921 r_free = 0.3921 target = 0.171467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.117408 restraints weight = 9535.062| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 1.91 r_work: 0.3046 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9241 Z= 0.136 Angle : 0.525 9.140 12528 Z= 0.277 Chirality : 0.042 0.158 1408 Planarity : 0.004 0.041 1577 Dihedral : 4.612 33.313 1314 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.30 % Favored : 97.61 % Rotamer: Outliers : 2.77 % Allowed : 13.32 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.89 (0.25), residues: 1129 helix: 3.06 (0.25), residues: 413 sheet: 0.67 (0.29), residues: 279 loop : -0.12 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 154 TYR 0.016 0.001 TYR S 190 PHE 0.020 0.001 PHE R 192 TRP 0.010 0.001 TRP B 82 HIS 0.004 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 9237) covalent geometry : angle 0.52514 (12520) SS BOND : bond 0.00659 ( 4) SS BOND : angle 0.75518 ( 8) hydrogen bonds : bond 0.04157 ( 478) hydrogen bonds : angle 4.13542 ( 1341) *********************** 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 157 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 130 time to evaluate : 0.356 Fit side-chains revert: symmetry clash REVERT: A 197 LYS cc_start: 0.8959 (mttt) cc_final: 0.8561 (mttp) REVERT: A 207 GLU cc_start: 0.6995 (tp30) cc_final: 0.6264 (mt-10) REVERT: A 248 LYS cc_start: 0.7837 (mttm) cc_final: 0.7620 (mtpt) REVERT: A 306 GLN cc_start: 0.7808 (mm-40) cc_final: 0.7460 (mp10) REVERT: A 318 GLU cc_start: 0.8599 (tt0) cc_final: 0.8295 (tt0) REVERT: B 44 GLN cc_start: 0.8368 (OUTLIER) cc_final: 0.7940 (mt0) REVERT: B 134 ARG cc_start: 0.8211 (mtm110) cc_final: 0.7908 (ptp90) REVERT: B 153 ASP cc_start: 0.7858 (t0) cc_final: 0.7630 (t70) REVERT: B 212 ASP cc_start: 0.8152 (t0) cc_final: 0.7926 (t0) REVERT: B 217 MET cc_start: 0.7681 (OUTLIER) cc_final: 0.6999 (ppp) REVERT: B 219 ARG cc_start: 0.8401 (mtp85) cc_final: 0.7620 (mmm160) REVERT: G 46 LYS cc_start: 0.8363 (mttt) cc_final: 0.7975 (mmtt) REVERT: S 85 SER cc_start: 0.8973 (m) cc_final: 0.8429 (t) outliers start: 27 outliers final: 15 residues processed: 146 average time/residue: 0.7170 time to fit residues: 110.8773 Evaluate side-chains 144 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 127 time to evaluate : 0.368 ------------------------------------------------------------------------------- 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 74 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 217 MET 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 14 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 67 optimal weight: 6.9990 chunk 38 optimal weight: 10.0000 chunk 12 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 overall best weight: 1.5986 ------------------------------------------------------------------------------- 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 = 0.3942 r_free = 0.3942 target = 0.173287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.112463 restraints weight = 9526.099| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 2.03 r_work: 0.3074 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9241 Z= 0.147 Angle : 0.540 10.069 12528 Z= 0.283 Chirality : 0.042 0.163 1408 Planarity : 0.004 0.041 1577 Dihedral : 4.550 29.252 1314 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.30 % Favored : 97.61 % Rotamer: Outliers : 2.77 % Allowed : 13.83 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.83 (0.25), residues: 1129 helix: 3.03 (0.25), residues: 412 sheet: 0.70 (0.29), residues: 278 loop : -0.20 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 143 TYR 0.018 0.001 TYR S 190 PHE 0.014 0.001 PHE R 192 TRP 0.010 0.001 TRP S 47 HIS 0.004 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 9237) covalent geometry : angle 0.53983 (12520) SS BOND : bond 0.00695 ( 4) SS BOND : angle 0.71042 ( 8) hydrogen bonds : bond 0.04270 ( 478) hydrogen bonds : angle 4.17538 ( 1341) *********************** 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: 27 poor density : 122 time to evaluate : 0.365 Fit side-chains revert: symmetry clash REVERT: A 197 LYS cc_start: 0.8995 (mttt) cc_final: 0.8643 (mttp) REVERT: A 207 GLU cc_start: 0.7257 (tp30) cc_final: 0.6523 (mt-10) REVERT: A 248 LYS cc_start: 0.7970 (mttm) cc_final: 0.7751 (mtpt) REVERT: A 306 GLN cc_start: 0.7975 (mm-40) cc_final: 0.7635 (mp10) REVERT: B 44 GLN cc_start: 0.8415 (OUTLIER) cc_final: 0.8004 (mt0) REVERT: B 134 ARG cc_start: 0.8316 (mtm110) cc_final: 0.8050 (ptp90) REVERT: B 212 ASP cc_start: 0.8234 (t0) cc_final: 0.7959 (t0) REVERT: G 46 LYS cc_start: 0.8404 (mttt) cc_final: 0.8043 (mmtt) REVERT: S 85 SER cc_start: 0.9013 (m) cc_final: 0.8505 (t) REVERT: S 183 GLN cc_start: 0.8646 (OUTLIER) cc_final: 0.8301 (mt0) outliers start: 27 outliers final: 14 residues processed: 136 average time/residue: 0.7271 time to fit residues: 104.7171 Evaluate side-chains 131 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 115 time to evaluate : 0.365 ------------------------------------------------------------------------------- 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 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 183 GLN Chi-restraints excluded: chain S residue 245 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 59 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 chunk 63 optimal weight: 0.9990 chunk 90 optimal weight: 0.6980 chunk 66 optimal weight: 0.9990 chunk 104 optimal weight: 0.9990 chunk 88 optimal weight: 10.0000 chunk 5 optimal weight: 0.0010 chunk 70 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 73 optimal weight: 0.9990 overall best weight: 0.6786 ------------------------------------------------------------------------------- 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 = 0.3966 r_free = 0.3966 target = 0.175583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.116205 restraints weight = 9578.304| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 2.03 r_work: 0.3070 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9241 Z= 0.099 Angle : 0.485 9.981 12528 Z= 0.254 Chirality : 0.040 0.152 1408 Planarity : 0.003 0.042 1577 Dihedral : 4.287 30.170 1314 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.04 % Favored : 97.87 % Rotamer: Outliers : 1.84 % Allowed : 14.96 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.96 (0.25), residues: 1129 helix: 3.17 (0.25), residues: 410 sheet: 0.79 (0.29), residues: 276 loop : -0.17 (0.30), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 154 TYR 0.013 0.001 TYR S 190 PHE 0.018 0.001 PHE R 192 TRP 0.016 0.001 TRP B 82 HIS 0.002 0.000 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00209 ( 9237) covalent geometry : angle 0.48459 (12520) SS BOND : bond 0.00415 ( 4) SS BOND : angle 0.55138 ( 8) hydrogen bonds : bond 0.03617 ( 478) hydrogen bonds : angle 4.03346 ( 1341) *********************** 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 149 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 131 time to evaluate : 0.361 Fit side-chains revert: symmetry clash REVERT: A 197 LYS cc_start: 0.8988 (mttt) cc_final: 0.8624 (mttp) REVERT: A 207 GLU cc_start: 0.7163 (tp30) cc_final: 0.6420 (mt-10) REVERT: A 248 LYS cc_start: 0.7945 (mttm) cc_final: 0.7742 (mtpt) REVERT: A 306 GLN cc_start: 0.7831 (mm-40) cc_final: 0.7527 (mp10) REVERT: A 318 GLU cc_start: 0.8450 (tt0) cc_final: 0.8249 (tt0) REVERT: B 65 THR cc_start: 0.8861 (m) cc_final: 0.8589 (p) REVERT: B 134 ARG cc_start: 0.8300 (mtm110) cc_final: 0.7548 (ptt-90) REVERT: B 212 ASP cc_start: 0.8135 (t0) cc_final: 0.7924 (t0) REVERT: G 46 LYS cc_start: 0.8351 (mttt) cc_final: 0.8009 (mmtt) REVERT: S 85 SER cc_start: 0.9028 (m) cc_final: 0.8517 (t) outliers start: 18 outliers final: 12 residues processed: 140 average time/residue: 0.7165 time to fit residues: 106.3677 Evaluate side-chains 141 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 129 time to evaluate : 0.366 ------------------------------------------------------------------------------- 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 392 TYR Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 262 MET 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 49 optimal weight: 3.9990 chunk 44 optimal weight: 8.9990 chunk 78 optimal weight: 0.0570 chunk 21 optimal weight: 6.9990 chunk 9 optimal weight: 4.9990 chunk 54 optimal weight: 0.5980 chunk 97 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 87 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 overall best weight: 1.7304 ------------------------------------------------------------------------------- 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 = 0.3937 r_free = 0.3937 target = 0.172820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.112082 restraints weight = 9500.445| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 2.01 r_work: 0.3033 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9241 Z= 0.155 Angle : 0.558 10.487 12528 Z= 0.290 Chirality : 0.043 0.175 1408 Planarity : 0.004 0.041 1577 Dihedral : 4.537 29.866 1314 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.21 % Favored : 97.70 % Rotamer: Outliers : 1.54 % Allowed : 15.68 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.84 (0.25), residues: 1129 helix: 3.03 (0.25), residues: 409 sheet: 0.75 (0.30), residues: 277 loop : -0.21 (0.30), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 314 TYR 0.018 0.002 TYR S 190 PHE 0.014 0.002 PHE R 192 TRP 0.010 0.001 TRP S 47 HIS 0.004 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 9237) covalent geometry : angle 0.55759 (12520) SS BOND : bond 0.00736 ( 4) SS BOND : angle 0.68218 ( 8) hydrogen bonds : bond 0.04333 ( 478) hydrogen bonds : angle 4.18662 ( 1341) *********************** 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 139 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 124 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 197 LYS cc_start: 0.8987 (mttt) cc_final: 0.8620 (mttp) REVERT: A 208 ARG cc_start: 0.8342 (ttp80) cc_final: 0.8014 (ttm110) REVERT: A 248 LYS cc_start: 0.7951 (mttm) cc_final: 0.7736 (mtpt) REVERT: A 306 GLN cc_start: 0.7931 (mm-40) cc_final: 0.7622 (mp10) REVERT: B 65 THR cc_start: 0.8980 (m) cc_final: 0.8648 (p) REVERT: B 134 ARG cc_start: 0.8320 (mtm110) cc_final: 0.7519 (ptt-90) REVERT: B 153 ASP cc_start: 0.7917 (t0) cc_final: 0.7707 (t70) REVERT: B 212 ASP cc_start: 0.8157 (t0) cc_final: 0.7891 (t0) REVERT: B 217 MET cc_start: 0.7544 (ppp) cc_final: 0.7230 (pp-130) REVERT: G 46 LYS cc_start: 0.8410 (mttt) cc_final: 0.8025 (mmtt) REVERT: S 85 SER cc_start: 0.8989 (m) cc_final: 0.8505 (t) outliers start: 15 outliers final: 11 residues processed: 133 average time/residue: 0.7286 time to fit residues: 102.5207 Evaluate side-chains 133 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 122 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 63 SER Chi-restraints excluded: chain R residue 159 VAL 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 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 245 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 94 optimal weight: 0.5980 chunk 45 optimal weight: 3.9990 chunk 69 optimal weight: 9.9990 chunk 102 optimal weight: 20.0000 chunk 89 optimal weight: 1.9990 chunk 108 optimal weight: 10.0000 chunk 17 optimal weight: 0.9980 chunk 109 optimal weight: 3.9990 chunk 106 optimal weight: 0.6980 chunk 98 optimal weight: 0.4980 chunk 71 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 = 0.3928 r_free = 0.3928 target = 0.172106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.116711 restraints weight = 9480.487| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.15 r_work: 0.3103 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9241 Z= 0.113 Angle : 0.510 10.559 12528 Z= 0.266 Chirality : 0.041 0.159 1408 Planarity : 0.003 0.042 1577 Dihedral : 4.419 30.674 1314 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.39 % Favored : 97.52 % Rotamer: Outliers : 1.33 % Allowed : 16.09 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.89 (0.25), residues: 1129 helix: 3.14 (0.25), residues: 409 sheet: 0.75 (0.29), residues: 276 loop : -0.23 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 154 TYR 0.015 0.001 TYR S 190 PHE 0.013 0.001 PHE R 192 TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 9237) covalent geometry : angle 0.50993 (12520) SS BOND : bond 0.00563 ( 4) SS BOND : angle 0.68108 ( 8) hydrogen bonds : bond 0.03831 ( 478) hydrogen bonds : angle 4.12201 ( 1341) ********************** 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 136 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 123 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 197 LYS cc_start: 0.8999 (mttt) cc_final: 0.8647 (mttp) REVERT: A 208 ARG cc_start: 0.8324 (ttp80) cc_final: 0.8011 (ttm110) REVERT: A 248 LYS cc_start: 0.7958 (mttm) cc_final: 0.7750 (mtpt) REVERT: A 277 LYS cc_start: 0.8570 (ttpt) cc_final: 0.8177 (ttpt) REVERT: A 306 GLN cc_start: 0.7890 (mm-40) cc_final: 0.7506 (mp10) REVERT: B 65 THR cc_start: 0.8861 (m) cc_final: 0.8583 (p) REVERT: B 134 ARG cc_start: 0.8340 (mtm110) cc_final: 0.7558 (ptt-90) REVERT: B 153 ASP cc_start: 0.7840 (t0) cc_final: 0.7617 (t70) REVERT: B 212 ASP cc_start: 0.8171 (t0) cc_final: 0.7922 (t0) REVERT: B 217 MET cc_start: 0.7460 (ppp) cc_final: 0.7212 (pp-130) REVERT: G 46 LYS cc_start: 0.8383 (mttt) cc_final: 0.8019 (mmtt) REVERT: S 34 MET cc_start: 0.9092 (mmt) cc_final: 0.8768 (mmm) REVERT: S 85 SER cc_start: 0.9015 (m) cc_final: 0.8505 (t) outliers start: 13 outliers final: 10 residues processed: 129 average time/residue: 0.7449 time to fit residues: 101.7617 Evaluate side-chains 133 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 123 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 63 SER Chi-restraints excluded: chain R residue 159 VAL Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 262 MET 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 58 optimal weight: 2.9990 chunk 15 optimal weight: 7.9990 chunk 26 optimal weight: 1.9990 chunk 62 optimal weight: 0.4980 chunk 48 optimal weight: 5.9990 chunk 105 optimal weight: 0.9980 chunk 79 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 86 optimal weight: 7.9990 chunk 4 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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 = 0.3907 r_free = 0.3907 target = 0.170230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.115670 restraints weight = 9461.678| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 2.00 r_work: 0.2969 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9241 Z= 0.141 Angle : 0.544 10.785 12528 Z= 0.284 Chirality : 0.042 0.169 1408 Planarity : 0.004 0.042 1577 Dihedral : 4.531 31.030 1314 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.23 % Allowed : 16.09 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.81 (0.25), residues: 1129 helix: 3.06 (0.25), residues: 409 sheet: 0.69 (0.29), residues: 277 loop : -0.24 (0.30), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 219 TYR 0.018 0.001 TYR S 190 PHE 0.014 0.001 PHE R 192 TRP 0.010 0.001 TRP B 82 HIS 0.004 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 9237) covalent geometry : angle 0.54411 (12520) SS BOND : bond 0.00708 ( 4) SS BOND : angle 0.76237 ( 8) hydrogen bonds : bond 0.04181 ( 478) hydrogen bonds : angle 4.19141 ( 1341) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4651.59 seconds wall clock time: 79 minutes 55.78 seconds (4795.78 seconds total)