Starting phenix.real_space_refine on Sat Aug 3 20:11:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yuu_39583/08_2024/8yuu_39583.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yuu_39583/08_2024/8yuu_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yuu_39583/08_2024/8yuu_39583.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yuu_39583/08_2024/8yuu_39583.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yuu_39583/08_2024/8yuu_39583.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yuu_39583/08_2024/8yuu_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 Residue "R PHE 398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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: 5.38, per 1000 atoms: 0.60 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 - 3.50 Amino acid : False - 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: 3.74 Conformation dependent library (CDL) restraints added in 1.5 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: 1.09 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: 2.89 Time building geometry restraints manager: 4.12 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: 96.83 - 104.27: 103 104.27 - 111.72: 4301 111.72 - 119.16: 3157 119.16 - 126.60: 4814 126.60 - 134.05: 145 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: 0.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 28.110 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:13.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.180 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 188 time to evaluate : 0.914 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: 1.2507 time to fit residues: 249.7310 Evaluate side-chains 138 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 0.967 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 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 fitting. rotamer outliers: 22 poor density : 140 time to evaluate : 1.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 376 LEU cc_start: 0.8049 (mm) cc_final: 0.7798 (mm) REVERT: A 47 ASN cc_start: 0.6991 (m-40) cc_final: 0.6608 (p0) REVERT: A 53 MET cc_start: 0.7066 (OUTLIER) cc_final: 0.6812 (mmm) REVERT: A 197 LYS cc_start: 0.8676 (mttt) cc_final: 0.8351 (mttm) REVERT: A 273 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8126 (mm) REVERT: A 306 GLN cc_start: 0.7977 (mm-40) cc_final: 0.7675 (mp10) REVERT: B 44 GLN cc_start: 0.8095 (OUTLIER) cc_final: 0.7456 (mt0) REVERT: B 217 MET cc_start: 0.7205 (ptt) cc_final: 0.6973 (ptt) REVERT: B 259 GLN cc_start: 0.8488 (mt0) cc_final: 0.8267 (mt0) REVERT: B 325 MET cc_start: 0.8399 (mmt) cc_final: 0.7809 (tpp) REVERT: S 85 SER cc_start: 0.8829 (m) cc_final: 0.8470 (t) outliers start: 22 outliers final: 5 residues processed: 149 average time/residue: 1.3313 time to fit residues: 210.7109 Evaluate side-chains 137 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 129 time to evaluate : 0.822 ------------------------------------------------------------------------------- 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 56 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 83 optimal weight: 0.9980 chunk 68 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 100 optimal weight: 0.4980 chunk 109 optimal weight: 7.9990 chunk 89 optimal weight: 6.9990 chunk 34 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 99 optimal weight: 6.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9237 Z= 0.210 Angle : 0.547 8.377 12520 Z= 0.291 Chirality : 0.043 0.169 1408 Planarity : 0.004 0.038 1577 Dihedral : 5.460 76.515 1314 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.95 % Favored : 97.96 % Rotamer: Outliers : 3.18 % Allowed : 10.14 % Favored : 86.68 % 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: 1.87 (0.25), residues: 1129 helix: 2.94 (0.25), residues: 412 sheet: 0.86 (0.29), residues: 279 loop : -0.14 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.006 0.001 HIS B 91 PHE 0.017 0.002 PHE R 192 TYR 0.012 0.002 TYR S 103 ARG 0.006 0.000 ARG R 99 *********************** 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 fitting. rotamer outliers: 31 poor density : 128 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 56 MET cc_start: 0.8072 (OUTLIER) cc_final: 0.7657 (mtp) REVERT: R 376 LEU cc_start: 0.8316 (mm) cc_final: 0.8024 (mm) REVERT: A 197 LYS cc_start: 0.8716 (mttt) cc_final: 0.8392 (mttm) REVERT: A 306 GLN cc_start: 0.8034 (mm-40) cc_final: 0.7713 (mp10) REVERT: B 44 GLN cc_start: 0.8030 (OUTLIER) cc_final: 0.7462 (mt0) REVERT: B 217 MET cc_start: 0.7316 (ptt) cc_final: 0.7101 (ptt) REVERT: B 325 MET cc_start: 0.8310 (mmt) cc_final: 0.8046 (tpt) REVERT: S 85 SER cc_start: 0.8863 (m) cc_final: 0.8523 (t) outliers start: 31 outliers final: 14 residues processed: 142 average time/residue: 1.2697 time to fit residues: 192.1984 Evaluate side-chains 136 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 120 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 56 MET Chi-restraints excluded: chain R residue 63 SER Chi-restraints excluded: chain R residue 95 VAL 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 4.9990 chunk 52 optimal weight: 5.9990 chunk 11 optimal weight: 7.9990 chunk 48 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 101 optimal weight: 5.9990 chunk 107 optimal weight: 4.9990 chunk 96 optimal weight: 0.6980 chunk 28 optimal weight: 0.9990 chunk 89 optimal weight: 4.9990 chunk 60 optimal weight: 0.4980 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.2157 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= 0.165 Angle : 0.509 8.341 12520 Z= 0.271 Chirality : 0.041 0.162 1408 Planarity : 0.004 0.040 1577 Dihedral : 5.189 67.707 1314 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.04 % Favored : 97.87 % Rotamer: Outliers : 2.77 % Allowed : 11.89 % Favored : 85.35 % 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: 3.04 (0.25), residues: 412 sheet: 0.78 (0.29), residues: 279 loop : -0.18 (0.30), residues: 438 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 0.013 0.001 TYR S 190 ARG 0.003 0.000 ARG R 99 *********************** 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 154 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 127 time to evaluate : 0.937 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 ARG cc_start: 0.7748 (mtm-85) cc_final: 0.7427 (ttm-80) REVERT: A 197 LYS cc_start: 0.8723 (mttt) cc_final: 0.8385 (mttm) REVERT: A 248 LYS cc_start: 0.8059 (mtmm) cc_final: 0.7824 (mtpt) REVERT: A 306 GLN cc_start: 0.7886 (mm-40) cc_final: 0.7633 (mp10) REVERT: B 44 GLN cc_start: 0.8006 (OUTLIER) cc_final: 0.7467 (mt0) REVERT: B 217 MET cc_start: 0.7265 (ptt) cc_final: 0.7008 (ptt) REVERT: B 325 MET cc_start: 0.8326 (mmt) cc_final: 0.8068 (tpt) REVERT: S 85 SER cc_start: 0.8888 (m) cc_final: 0.8540 (t) outliers start: 27 outliers final: 13 residues processed: 141 average time/residue: 1.2936 time to fit residues: 194.1981 Evaluate side-chains 138 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 124 time to evaluate : 0.995 ------------------------------------------------------------------------------- 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 18 MET 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 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 1 optimal weight: 1.9990 chunk 79 optimal weight: 6.9990 chunk 44 optimal weight: 6.9990 chunk 91 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 54 optimal weight: 0.0020 chunk 96 optimal weight: 0.6980 chunk 27 optimal weight: 5.9990 chunk 36 optimal weight: 0.8980 chunk 21 optimal weight: 7.9990 overall best weight: 0.9192 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 9237 Z= 0.154 Angle : 0.498 8.566 12520 Z= 0.264 Chirality : 0.041 0.160 1408 Planarity : 0.003 0.040 1577 Dihedral : 4.782 49.270 1314 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.04 % Favored : 97.87 % Rotamer: Outliers : 2.56 % Allowed : 13.11 % Favored : 84.32 % 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: 3.07 (0.25), residues: 412 sheet: 0.75 (0.29), residues: 279 loop : -0.20 (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 S 35 PHE 0.013 0.001 PHE R 192 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 159 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 134 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 ARG cc_start: 0.7700 (mtm-85) cc_final: 0.7386 (ttm-80) REVERT: A 197 LYS cc_start: 0.8707 (mttt) cc_final: 0.8341 (mttm) REVERT: A 248 LYS cc_start: 0.8037 (mtmm) cc_final: 0.7802 (mtpt) REVERT: A 306 GLN cc_start: 0.7860 (mm-40) cc_final: 0.7598 (mp10) REVERT: B 44 GLN cc_start: 0.8004 (OUTLIER) cc_final: 0.7464 (mt0) REVERT: B 153 ASP cc_start: 0.7279 (t0) cc_final: 0.7050 (t70) REVERT: B 217 MET cc_start: 0.7270 (ptt) cc_final: 0.6986 (ptt) REVERT: B 325 MET cc_start: 0.8333 (mmt) cc_final: 0.8093 (tpt) REVERT: S 85 SER cc_start: 0.8903 (m) cc_final: 0.8543 (t) REVERT: S 183 GLN cc_start: 0.8563 (OUTLIER) cc_final: 0.8107 (mt0) outliers start: 25 outliers final: 13 residues processed: 149 average time/residue: 1.2817 time to fit residues: 203.0567 Evaluate side-chains 134 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 119 time to evaluate : 0.953 ------------------------------------------------------------------------------- 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 324 THR Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain G residue 21 MET 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 89 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 8 optimal weight: 6.9990 chunk 35 optimal weight: 8.9990 chunk 56 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9237 Z= 0.198 Angle : 0.525 8.626 12520 Z= 0.277 Chirality : 0.042 0.164 1408 Planarity : 0.004 0.041 1577 Dihedral : 4.680 35.586 1314 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.86 % Favored : 98.05 % Rotamer: Outliers : 2.56 % Allowed : 13.73 % Favored : 83.71 % 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: 1.84 (0.25), residues: 1129 helix: 3.04 (0.25), residues: 413 sheet: 0.69 (0.29), residues: 278 loop : -0.18 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.004 0.001 HIS B 91 PHE 0.020 0.001 PHE R 192 TYR 0.017 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 147 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 122 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 ARG cc_start: 0.7716 (mtm-85) cc_final: 0.7419 (ttm-80) REVERT: A 197 LYS cc_start: 0.8740 (mttt) cc_final: 0.8412 (mttp) REVERT: A 248 LYS cc_start: 0.8055 (mtmm) cc_final: 0.7821 (mtpt) REVERT: A 306 GLN cc_start: 0.7909 (mm-40) cc_final: 0.7646 (mp10) REVERT: B 44 GLN cc_start: 0.8015 (OUTLIER) cc_final: 0.7480 (mt0) REVERT: B 153 ASP cc_start: 0.7293 (t0) cc_final: 0.7090 (t70) REVERT: B 217 MET cc_start: 0.7274 (ptt) cc_final: 0.6991 (ptt) REVERT: S 85 SER cc_start: 0.8912 (m) cc_final: 0.8553 (t) outliers start: 25 outliers final: 16 residues processed: 137 average time/residue: 1.2359 time to fit residues: 180.4916 Evaluate side-chains 139 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 122 time to evaluate : 0.979 ------------------------------------------------------------------------------- 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 R residue 392 TYR Chi-restraints excluded: chain A residue 247 MET 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 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 78 optimal weight: 0.0980 chunk 60 optimal weight: 4.9990 chunk 90 optimal weight: 5.9990 chunk 59 optimal weight: 0.9980 chunk 106 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 42 optimal weight: 4.9990 chunk 63 optimal weight: 0.7980 chunk 32 optimal weight: 6.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 186 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 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 : 0.003 0.043 9237 Z= 0.168 Angle : 0.505 9.604 12520 Z= 0.266 Chirality : 0.041 0.160 1408 Planarity : 0.004 0.042 1577 Dihedral : 4.463 29.211 1314 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.68 % Favored : 98.23 % Rotamer: Outliers : 3.07 % Allowed : 13.83 % Favored : 83.09 % 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: 3.11 (0.25), residues: 412 sheet: 0.72 (0.29), residues: 276 loop : -0.17 (0.30), residues: 441 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 R 192 TYR 0.016 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 153 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 123 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 ARG cc_start: 0.7675 (mtm-85) cc_final: 0.7383 (ttm-80) REVERT: A 197 LYS cc_start: 0.8737 (mttt) cc_final: 0.8410 (mttp) REVERT: A 207 GLU cc_start: 0.7046 (tp30) cc_final: 0.6703 (mt-10) REVERT: A 208 ARG cc_start: 0.8152 (ttm110) cc_final: 0.7903 (ttm110) REVERT: A 248 LYS cc_start: 0.8066 (mtmm) cc_final: 0.7827 (mtpt) REVERT: A 306 GLN cc_start: 0.7899 (mm-40) cc_final: 0.7629 (mp10) REVERT: B 153 ASP cc_start: 0.7356 (t0) cc_final: 0.7122 (t70) REVERT: B 217 MET cc_start: 0.7247 (ptt) cc_final: 0.6956 (ptt) REVERT: S 85 SER cc_start: 0.8913 (m) cc_final: 0.8561 (t) REVERT: S 183 GLN cc_start: 0.8527 (OUTLIER) cc_final: 0.8078 (mt0) outliers start: 30 outliers final: 17 residues processed: 139 average time/residue: 1.2908 time to fit residues: 190.6193 Evaluate side-chains 137 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 119 time to evaluate : 0.894 ------------------------------------------------------------------------------- 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 A residue 18 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 262 MET Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain G residue 21 MET 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 21 optimal weight: 9.9990 chunk 20 optimal weight: 6.9990 chunk 68 optimal weight: 7.9990 chunk 72 optimal weight: 2.9990 chunk 52 optimal weight: 7.9990 chunk 9 optimal weight: 4.9990 chunk 84 optimal weight: 6.9990 chunk 97 optimal weight: 1.9990 chunk 102 optimal weight: 9.9990 chunk 93 optimal weight: 0.3980 chunk 99 optimal weight: 0.9980 overall best weight: 2.2786 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 9237 Z= 0.284 Angle : 0.579 10.505 12520 Z= 0.306 Chirality : 0.044 0.198 1408 Planarity : 0.004 0.045 1577 Dihedral : 4.688 28.521 1314 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.30 % Favored : 97.61 % Rotamer: Outliers : 2.77 % Allowed : 14.34 % Favored : 82.89 % 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: 1.74 (0.25), residues: 1129 helix: 2.92 (0.25), residues: 412 sheet: 0.67 (0.29), residues: 278 loop : -0.23 (0.30), residues: 439 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 0.021 0.002 PHE R 192 TYR 0.021 0.002 TYR S 190 ARG 0.004 0.000 ARG R 143 *********************** 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 148 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 121 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 354 ARG cc_start: 0.6587 (ttt180) cc_final: 0.5815 (ttm110) REVERT: A 24 ARG cc_start: 0.7739 (mtm-85) cc_final: 0.7417 (ttm-80) REVERT: A 197 LYS cc_start: 0.8718 (mttt) cc_final: 0.8409 (mttp) REVERT: A 208 ARG cc_start: 0.8236 (ttm110) cc_final: 0.7962 (ttm110) REVERT: A 248 LYS cc_start: 0.8179 (mtmm) cc_final: 0.7932 (mtpt) REVERT: A 306 GLN cc_start: 0.7979 (mm-40) cc_final: 0.7735 (mp10) REVERT: B 217 MET cc_start: 0.7299 (ptt) cc_final: 0.7008 (ptt) REVERT: S 85 SER cc_start: 0.8929 (m) cc_final: 0.8577 (t) REVERT: S 183 GLN cc_start: 0.8599 (OUTLIER) cc_final: 0.8160 (mt0) outliers start: 27 outliers final: 18 residues processed: 138 average time/residue: 1.3149 time to fit residues: 193.3080 Evaluate side-chains 137 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 118 time to evaluate : 0.955 ------------------------------------------------------------------------------- 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 247 MET Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 120 ILE 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 G residue 21 MET 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 20.0000 chunk 60 optimal weight: 3.9990 chunk 43 optimal weight: 8.9990 chunk 78 optimal weight: 0.9980 chunk 30 optimal weight: 0.0870 chunk 90 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 105 optimal weight: 0.7980 chunk 64 optimal weight: 3.9990 overall best weight: 0.7760 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.2515 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= 0.141 Angle : 0.490 10.427 12520 Z= 0.259 Chirality : 0.041 0.155 1408 Planarity : 0.004 0.043 1577 Dihedral : 4.417 29.700 1314 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.95 % Favored : 97.96 % Rotamer: Outliers : 1.64 % Allowed : 15.78 % 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 (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: 3.10 (0.25), residues: 412 sheet: 0.71 (0.29), residues: 276 loop : -0.15 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 PHE 0.013 0.001 PHE R 192 TYR 0.014 0.001 TYR S 190 ARG 0.009 0.000 ARG A 313 *********************** 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 138 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 122 time to evaluate : 1.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ARG cc_start: 0.7648 (mtm-85) cc_final: 0.7413 (ttm-80) REVERT: A 197 LYS cc_start: 0.8739 (mttt) cc_final: 0.8416 (mttp) REVERT: A 207 GLU cc_start: 0.7046 (tp30) cc_final: 0.6641 (mt-10) REVERT: A 208 ARG cc_start: 0.8181 (ttm110) cc_final: 0.7932 (ttm110) REVERT: A 248 LYS cc_start: 0.8164 (mtmm) cc_final: 0.7923 (mtpt) REVERT: A 306 GLN cc_start: 0.7919 (mm-40) cc_final: 0.7661 (mp10) REVERT: B 217 MET cc_start: 0.7223 (ptt) cc_final: 0.6935 (ptt) REVERT: S 85 SER cc_start: 0.8922 (m) cc_final: 0.8571 (t) REVERT: S 183 GLN cc_start: 0.8529 (OUTLIER) cc_final: 0.8074 (mt0) outliers start: 16 outliers final: 10 residues processed: 130 average time/residue: 1.3150 time to fit residues: 181.6173 Evaluate side-chains 128 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 117 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 63 SER Chi-restraints excluded: chain R residue 392 TYR Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 324 THR 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 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 50 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 110 optimal weight: 0.3980 chunk 101 optimal weight: 0.0870 chunk 88 optimal weight: 9.9990 chunk 9 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 69 optimal weight: 0.8980 chunk 93 optimal weight: 0.0010 chunk 26 optimal weight: 0.9980 overall best weight: 0.4564 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9237 Z= 0.116 Angle : 0.472 10.366 12520 Z= 0.248 Chirality : 0.040 0.158 1408 Planarity : 0.003 0.043 1577 Dihedral : 4.228 31.728 1314 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.23 % Allowed : 16.29 % Favored : 82.48 % 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: 2.06 (0.26), residues: 1129 helix: 3.32 (0.25), residues: 405 sheet: 0.80 (0.29), residues: 276 loop : -0.09 (0.31), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.002 0.000 HIS S 35 PHE 0.012 0.001 PHE R 192 TYR 0.010 0.001 TYR R 189 ARG 0.009 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 140 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 128 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ARG cc_start: 0.7616 (mtm-85) cc_final: 0.7389 (ttm-80) REVERT: A 197 LYS cc_start: 0.8715 (mttt) cc_final: 0.8350 (mttm) REVERT: A 207 GLU cc_start: 0.7057 (tp30) cc_final: 0.6696 (mt-10) REVERT: A 208 ARG cc_start: 0.8178 (ttm110) cc_final: 0.7915 (ttm110) REVERT: A 241 ASN cc_start: 0.6706 (t0) cc_final: 0.6421 (t0) REVERT: A 248 LYS cc_start: 0.8157 (mtmm) cc_final: 0.7919 (mtpt) REVERT: A 277 LYS cc_start: 0.8616 (ttpt) cc_final: 0.8209 (ttpt) REVERT: A 306 GLN cc_start: 0.7768 (mm-40) cc_final: 0.7487 (mp10) REVERT: B 217 MET cc_start: 0.7190 (ptt) cc_final: 0.6873 (ptt) REVERT: S 85 SER cc_start: 0.8923 (m) cc_final: 0.8575 (t) REVERT: S 183 GLN cc_start: 0.8404 (OUTLIER) cc_final: 0.8027 (mt0) outliers start: 12 outliers final: 10 residues processed: 135 average time/residue: 1.2674 time to fit residues: 182.0744 Evaluate side-chains 138 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 127 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 159 VAL Chi-restraints excluded: chain A residue 247 MET 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 G residue 21 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 81 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 88 optimal weight: 9.9990 chunk 36 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 chunk 11 optimal weight: 7.9990 chunk 16 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 chunk 5 optimal weight: 0.0970 chunk 63 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3959 r_free = 0.3959 target = 0.175190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.115228 restraints weight = 9439.533| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 2.00 r_work: 0.3111 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.2752 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= 0.140 Angle : 0.494 10.253 12520 Z= 0.259 Chirality : 0.041 0.151 1408 Planarity : 0.004 0.042 1577 Dihedral : 4.256 32.402 1314 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.23 % Allowed : 16.70 % Favored : 82.07 % 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: 2.08 (0.26), residues: 1129 helix: 3.35 (0.25), residues: 404 sheet: 0.80 (0.29), residues: 276 loop : -0.10 (0.30), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.002 0.001 HIS S 35 PHE 0.013 0.001 PHE R 192 TYR 0.014 0.001 TYR S 190 ARG 0.009 0.000 ARG A 313 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3902.47 seconds wall clock time: 68 minutes 44.46 seconds (4124.46 seconds total)