Starting phenix.real_space_refine on Fri Jul 19 20:00:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yuu_39583/07_2024/8yuu_39583.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yuu_39583/07_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_39583/07_2024/8yuu_39583.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yuu_39583/07_2024/8yuu_39583.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yuu_39583/07_2024/8yuu_39583.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yuu_39583/07_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-5388/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: 5.52, per 1000 atoms: 0.61 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: 3.67 Conformation dependent library (CDL) restraints added in 1.7 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: 1.23 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: 2.65 Time building geometry restraints manager: 4.01 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 2.440 nonbonded pdb=" O CYS A 3 " pdb=" OG1 THR A 4 " model vdw 2.173 2.440 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 2.520 nonbonded pdb=" OD1 ASP R 62 " pdb=" OG SER R 64 " model vdw 2.315 2.440 ... (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 ========== 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: 0.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 28.200 Find NCS groups from input model: 0.120 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: 0.010 Load rotamer database and sin/cos tables:13.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.270 ------------------------------------------------------------------------------- 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 : 0.957 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: 1.2979 time to fit residues: 259.3813 Evaluate side-chains 138 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 1.026 ------------------------------------------------------------------------------- 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: 0.6980 chunk 84 optimal weight: 2.9990 chunk 46 optimal weight: 0.1980 chunk 28 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 44 optimal weight: 9.9990 chunk 87 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 52 optimal weight: 10.0000 chunk 64 optimal weight: 0.6980 chunk 100 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 B 340 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 9237 Z= 0.159 Angle : 0.520 9.027 12520 Z= 0.281 Chirality : 0.041 0.172 1408 Planarity : 0.004 0.040 1577 Dihedral : 5.437 78.050 1314 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.30 % Favored : 97.61 % Rotamer: Outliers : 2.36 % Allowed : 10.14 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.25), residues: 1129 helix: 2.78 (0.25), residues: 419 sheet: 1.01 (0.29), residues: 278 loop : -0.05 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.002 0.001 HIS B 91 PHE 0.017 0.001 PHE R 192 TYR 0.011 0.001 TYR S 175 ARG 0.012 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 166 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 143 time to evaluate : 1.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 354 ARG cc_start: 0.6561 (ttt180) cc_final: 0.5931 (ttp-110) REVERT: R 376 LEU cc_start: 0.8054 (mm) cc_final: 0.7798 (mm) REVERT: A 47 ASN cc_start: 0.6985 (m-40) cc_final: 0.6606 (p0) REVERT: A 53 MET cc_start: 0.7069 (OUTLIER) cc_final: 0.6791 (mmm) REVERT: A 197 LYS cc_start: 0.8681 (mttt) cc_final: 0.8355 (mttm) REVERT: A 273 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8120 (mm) REVERT: A 306 GLN cc_start: 0.7990 (mm-40) cc_final: 0.7689 (mp10) REVERT: B 44 GLN cc_start: 0.8049 (OUTLIER) cc_final: 0.7408 (mt0) REVERT: B 153 ASP cc_start: 0.6989 (t0) cc_final: 0.6745 (t70) REVERT: B 217 MET cc_start: 0.7237 (ptt) cc_final: 0.7015 (ptt) REVERT: B 325 MET cc_start: 0.8351 (mmt) cc_final: 0.8105 (tpp) REVERT: S 85 SER cc_start: 0.8850 (m) cc_final: 0.8501 (t) outliers start: 23 outliers final: 7 residues processed: 153 average time/residue: 1.3096 time to fit residues: 213.2560 Evaluate side-chains 140 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 130 time to evaluate : 1.040 ------------------------------------------------------------------------------- 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 B residue 65 THR 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 56 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 83 optimal weight: 8.9990 chunk 68 optimal weight: 6.9990 chunk 27 optimal weight: 0.7980 chunk 100 optimal weight: 10.0000 chunk 109 optimal weight: 5.9990 chunk 89 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 99 optimal weight: 6.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN B 220 GLN B 340 ASN G 59 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.1917 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= 0.213 Angle : 0.532 8.442 12520 Z= 0.283 Chirality : 0.042 0.167 1408 Planarity : 0.004 0.037 1577 Dihedral : 5.452 75.613 1314 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.75 % Favored : 97.17 % Rotamer: Outliers : 2.56 % Allowed : 11.07 % Favored : 86.37 % 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: 1.95 (0.25), residues: 1129 helix: 3.00 (0.25), residues: 411 sheet: 0.95 (0.29), residues: 278 loop : -0.13 (0.30), residues: 440 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 0.018 0.002 PHE R 192 TYR 0.012 0.001 TYR S 103 ARG 0.007 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 156 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 131 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 376 LEU cc_start: 0.8312 (mm) cc_final: 0.8020 (mm) REVERT: A 24 ARG cc_start: 0.7771 (mtm-85) cc_final: 0.7436 (ttm-80) REVERT: A 197 LYS cc_start: 0.8736 (mttt) cc_final: 0.8406 (mttm) REVERT: A 306 GLN cc_start: 0.8052 (mm-40) cc_final: 0.7726 (mp10) REVERT: B 44 GLN cc_start: 0.8024 (OUTLIER) cc_final: 0.7461 (mt0) REVERT: B 217 MET cc_start: 0.7319 (ptt) cc_final: 0.7074 (ptt) REVERT: B 259 GLN cc_start: 0.8479 (mt0) cc_final: 0.8250 (mt0) REVERT: B 325 MET cc_start: 0.8439 (mmt) cc_final: 0.8002 (tpp) REVERT: S 85 SER cc_start: 0.8885 (m) cc_final: 0.8552 (t) outliers start: 25 outliers final: 15 residues processed: 141 average time/residue: 1.3049 time to fit residues: 195.6243 Evaluate side-chains 143 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 127 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 159 VAL Chi-restraints excluded: chain R residue 233 LEU Chi-restraints excluded: chain R residue 392 TYR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 228 ASP 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 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: 2.9990 chunk 52 optimal weight: 10.0000 chunk 11 optimal weight: 8.9990 chunk 48 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 chunk 101 optimal weight: 5.9990 chunk 107 optimal weight: 0.9990 chunk 96 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 89 optimal weight: 2.9990 chunk 60 optimal weight: 0.2980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 59 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.2159 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= 0.144 Angle : 0.476 8.191 12520 Z= 0.254 Chirality : 0.040 0.158 1408 Planarity : 0.003 0.037 1577 Dihedral : 4.999 62.321 1314 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.13 % Favored : 97.79 % Rotamer: Outliers : 2.36 % Allowed : 12.70 % Favored : 84.94 % 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: 2.04 (0.25), residues: 1129 helix: 3.13 (0.25), residues: 413 sheet: 0.90 (0.29), residues: 278 loop : -0.08 (0.30), residues: 438 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 0.018 0.001 PHE R 192 TYR 0.011 0.001 TYR S 190 ARG 0.004 0.000 ARG R 154 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 133 time to evaluate : 1.128 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 ARG cc_start: 0.7711 (mtm-85) cc_final: 0.7443 (ttm-80) REVERT: A 197 LYS cc_start: 0.8697 (mttt) cc_final: 0.8373 (mttm) REVERT: A 248 LYS cc_start: 0.8068 (mtmm) cc_final: 0.7837 (mtpt) REVERT: A 306 GLN cc_start: 0.7867 (mm-40) cc_final: 0.7615 (mp10) REVERT: B 44 GLN cc_start: 0.7989 (OUTLIER) cc_final: 0.7452 (mt0) REVERT: B 217 MET cc_start: 0.7239 (ptt) cc_final: 0.6985 (ptt) REVERT: B 325 MET cc_start: 0.8321 (mmt) cc_final: 0.8065 (tpt) REVERT: S 85 SER cc_start: 0.8910 (m) cc_final: 0.8551 (t) outliers start: 23 outliers final: 11 residues processed: 144 average time/residue: 1.3055 time to fit residues: 199.8886 Evaluate side-chains 136 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 124 time to evaluate : 1.014 ------------------------------------------------------------------------------- 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 272 ASP 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 228 ASP 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 4.9990 chunk 79 optimal weight: 6.9990 chunk 44 optimal weight: 6.9990 chunk 91 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 chunk 0 optimal weight: 30.0000 chunk 54 optimal weight: 3.9990 chunk 96 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 21 optimal weight: 5.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 9237 Z= 0.296 Angle : 0.576 8.958 12520 Z= 0.305 Chirality : 0.044 0.181 1408 Planarity : 0.004 0.044 1577 Dihedral : 5.294 60.335 1314 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.57 % Favored : 97.34 % Rotamer: Outliers : 3.69 % Allowed : 12.19 % Favored : 84.12 % 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: 1.78 (0.25), residues: 1129 helix: 2.92 (0.25), residues: 411 sheet: 0.75 (0.29), residues: 268 loop : -0.19 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP S 47 HIS 0.006 0.001 HIS B 91 PHE 0.015 0.002 PHE R 192 TYR 0.020 0.002 TYR S 190 ARG 0.004 0.001 ARG R 143 *********************** 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 163 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 127 time to evaluate : 0.943 Fit side-chains revert: symmetry clash REVERT: R 56 MET cc_start: 0.7530 (OUTLIER) cc_final: 0.6772 (mtp) REVERT: R 354 ARG cc_start: 0.6649 (ttt180) cc_final: 0.5943 (ttp-110) REVERT: R 376 LEU cc_start: 0.8312 (OUTLIER) cc_final: 0.7983 (mm) REVERT: A 24 ARG cc_start: 0.7771 (mtm-85) cc_final: 0.7452 (ttm-80) REVERT: A 197 LYS cc_start: 0.8713 (mttt) cc_final: 0.8389 (mttm) REVERT: A 248 LYS cc_start: 0.8079 (mtmm) cc_final: 0.7837 (mtpt) REVERT: A 306 GLN cc_start: 0.8036 (mm-40) cc_final: 0.7755 (mp10) REVERT: B 44 GLN cc_start: 0.7998 (OUTLIER) cc_final: 0.7474 (mt0) REVERT: B 217 MET cc_start: 0.7323 (ptt) cc_final: 0.7060 (ptt) REVERT: S 85 SER cc_start: 0.8926 (m) cc_final: 0.8575 (t) outliers start: 36 outliers final: 17 residues processed: 148 average time/residue: 1.2293 time to fit residues: 194.1861 Evaluate side-chains 142 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 122 time to evaluate : 1.032 ------------------------------------------------------------------------------- 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 157 LEU Chi-restraints excluded: chain R residue 159 VAL Chi-restraints excluded: chain R residue 376 LEU Chi-restraints excluded: chain R residue 392 TYR Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 272 ASP 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 179 THR Chi-restraints excluded: chain B residue 228 ASP 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 62 ASP Chi-restraints excluded: chain S residue 158 SER Chi-restraints excluded: chain S residue 245 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 chunk 49 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN B 340 ASN G 59 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2289 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= 0.164 Angle : 0.491 7.825 12520 Z= 0.262 Chirality : 0.041 0.159 1408 Planarity : 0.003 0.042 1577 Dihedral : 4.879 46.849 1314 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.86 % Favored : 98.05 % Rotamer: Outliers : 2.46 % Allowed : 14.55 % Favored : 82.99 % 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: 3.06 (0.25), residues: 411 sheet: 0.79 (0.30), residues: 266 loop : -0.16 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS B 91 PHE 0.019 0.001 PHE R 192 TYR 0.015 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 149 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 125 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 162 LEU cc_start: 0.7331 (OUTLIER) cc_final: 0.6749 (mm) REVERT: A 24 ARG cc_start: 0.7688 (mtm-85) cc_final: 0.7435 (ttm-80) REVERT: A 197 LYS cc_start: 0.8697 (mttt) cc_final: 0.8370 (mttm) REVERT: A 248 LYS cc_start: 0.8071 (mtmm) cc_final: 0.7836 (mtpt) REVERT: A 306 GLN cc_start: 0.7925 (mm-40) cc_final: 0.7651 (mp10) REVERT: B 217 MET cc_start: 0.7210 (ptt) cc_final: 0.6923 (ptt) REVERT: S 85 SER cc_start: 0.8915 (m) cc_final: 0.8570 (t) outliers start: 24 outliers final: 16 residues processed: 137 average time/residue: 1.3142 time to fit residues: 191.5402 Evaluate side-chains 141 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 124 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 157 LEU Chi-restraints excluded: chain R residue 159 VAL Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 233 LEU Chi-restraints excluded: chain R residue 392 TYR Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 228 ASP 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 62 ASP 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: 5.9990 chunk 60 optimal weight: 0.0040 chunk 90 optimal weight: 7.9990 chunk 59 optimal weight: 0.7980 chunk 106 optimal weight: 0.6980 chunk 66 optimal weight: 0.8980 chunk 65 optimal weight: 0.8980 chunk 49 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 59 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.2478 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= 0.126 Angle : 0.462 8.935 12520 Z= 0.244 Chirality : 0.040 0.152 1408 Planarity : 0.003 0.042 1577 Dihedral : 4.387 29.745 1314 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.04 % Favored : 97.87 % Rotamer: Outliers : 2.46 % Allowed : 14.86 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.25), residues: 1129 helix: 3.19 (0.25), residues: 413 sheet: 0.81 (0.30), residues: 267 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 0.012 0.001 PHE A 189 TYR 0.011 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: 24 poor density : 129 time to evaluate : 1.101 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 376 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.7870 (mm) REVERT: A 24 ARG cc_start: 0.7639 (mtm-85) cc_final: 0.7398 (ttm-80) REVERT: A 197 LYS cc_start: 0.8700 (mttt) cc_final: 0.8369 (mttm) REVERT: A 207 GLU cc_start: 0.7019 (tp30) cc_final: 0.6610 (mt-10) REVERT: A 248 LYS cc_start: 0.8039 (mtmm) cc_final: 0.7811 (mtpt) REVERT: A 306 GLN cc_start: 0.7850 (mm-40) cc_final: 0.7517 (mp10) REVERT: B 217 MET cc_start: 0.7183 (ptt) cc_final: 0.6903 (ptt) REVERT: S 85 SER cc_start: 0.8913 (m) cc_final: 0.8585 (t) outliers start: 24 outliers final: 16 residues processed: 143 average time/residue: 1.2257 time to fit residues: 187.1783 Evaluate side-chains 149 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 132 time to evaluate : 0.999 ------------------------------------------------------------------------------- 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 376 LEU Chi-restraints excluded: chain R residue 392 TYR Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 228 ASP 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 62 ASP Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 158 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 0.9980 chunk 20 optimal weight: 10.0000 chunk 68 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 52 optimal weight: 7.9990 chunk 9 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 chunk 97 optimal weight: 6.9990 chunk 102 optimal weight: 8.9990 chunk 93 optimal weight: 0.3980 chunk 99 optimal weight: 0.7980 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN B 340 ASN G 59 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9237 Z= 0.236 Angle : 0.539 10.598 12520 Z= 0.284 Chirality : 0.042 0.172 1408 Planarity : 0.004 0.042 1577 Dihedral : 4.563 29.196 1314 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.66 % Favored : 97.25 % Rotamer: Outliers : 2.77 % Allowed : 15.16 % 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: 1.84 (0.25), residues: 1129 helix: 3.03 (0.25), residues: 411 sheet: 0.80 (0.29), residues: 266 loop : -0.22 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP S 47 HIS 0.004 0.001 HIS B 91 PHE 0.020 0.002 PHE R 192 TYR 0.018 0.002 TYR S 190 ARG 0.003 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 151 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 124 time to evaluate : 1.056 Fit side-chains revert: symmetry clash REVERT: R 376 LEU cc_start: 0.8263 (OUTLIER) cc_final: 0.7897 (mm) REVERT: A 197 LYS cc_start: 0.8691 (mttt) cc_final: 0.8371 (mttm) REVERT: A 208 ARG cc_start: 0.8203 (ttm110) cc_final: 0.7943 (ttm110) REVERT: A 248 LYS cc_start: 0.8131 (mtmm) cc_final: 0.7895 (mtpt) REVERT: A 306 GLN cc_start: 0.7927 (mm-40) cc_final: 0.7694 (mp10) REVERT: A 341 ASP cc_start: 0.8157 (OUTLIER) cc_final: 0.7870 (t70) REVERT: B 217 MET cc_start: 0.7233 (ptt) cc_final: 0.6944 (ptt) REVERT: S 85 SER cc_start: 0.8911 (m) cc_final: 0.8597 (t) outliers start: 27 outliers final: 15 residues processed: 141 average time/residue: 1.3589 time to fit residues: 203.8062 Evaluate side-chains 136 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 119 time to evaluate : 1.029 ------------------------------------------------------------------------------- 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 376 LEU Chi-restraints excluded: chain R residue 392 TYR Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 340 ASN 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 9.9990 chunk 60 optimal weight: 0.9990 chunk 43 optimal weight: 0.1980 chunk 78 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 chunk 94 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 chunk 65 optimal weight: 0.7980 chunk 105 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 59 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 9237 Z= 0.134 Angle : 0.484 10.795 12520 Z= 0.255 Chirality : 0.040 0.152 1408 Planarity : 0.004 0.043 1577 Dihedral : 4.418 31.864 1314 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.21 % Favored : 97.70 % Rotamer: Outliers : 1.64 % Allowed : 16.60 % Favored : 81.76 % 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: 1.95 (0.25), residues: 1129 helix: 3.18 (0.25), residues: 411 sheet: 0.79 (0.30), residues: 266 loop : -0.19 (0.30), residues: 452 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 0.012 0.001 PHE R 192 TYR 0.014 0.001 TYR S 190 ARG 0.010 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 140 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 124 time to evaluate : 0.954 Fit side-chains revert: symmetry clash REVERT: R 162 LEU cc_start: 0.7343 (OUTLIER) cc_final: 0.6729 (mm) REVERT: R 376 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.7868 (mm) REVERT: A 24 ARG cc_start: 0.7687 (ttm-80) cc_final: 0.7392 (ttm-80) REVERT: A 197 LYS cc_start: 0.8691 (mttt) cc_final: 0.8368 (mttm) REVERT: A 208 ARG cc_start: 0.8156 (ttm110) cc_final: 0.7883 (ttm110) REVERT: A 248 LYS cc_start: 0.8102 (mtmm) cc_final: 0.7869 (mtpt) REVERT: A 306 GLN cc_start: 0.7897 (mm-40) cc_final: 0.7557 (mp10) REVERT: S 85 SER cc_start: 0.8905 (m) cc_final: 0.8600 (t) outliers start: 16 outliers final: 12 residues processed: 132 average time/residue: 1.3249 time to fit residues: 186.0741 Evaluate side-chains 141 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 127 time to evaluate : 1.016 ------------------------------------------------------------------------------- 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 162 LEU Chi-restraints excluded: chain R residue 376 LEU Chi-restraints excluded: chain R residue 392 TYR Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 228 ASP 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 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 50 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 110 optimal weight: 0.0470 chunk 101 optimal weight: 20.0000 chunk 88 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 68 optimal weight: 6.9990 chunk 53 optimal weight: 0.6980 chunk 69 optimal weight: 0.0070 chunk 93 optimal weight: 0.0970 chunk 26 optimal weight: 6.9990 overall best weight: 0.3694 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN G 5 ASN G 59 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.2757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9237 Z= 0.107 Angle : 0.455 10.283 12520 Z= 0.237 Chirality : 0.039 0.145 1408 Planarity : 0.003 0.042 1577 Dihedral : 4.155 32.095 1314 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.21 % Favored : 97.70 % Rotamer: Outliers : 1.33 % Allowed : 17.32 % Favored : 81.35 % 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: 2.12 (0.26), residues: 1129 helix: 3.30 (0.25), residues: 411 sheet: 0.89 (0.30), residues: 266 loop : -0.07 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 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 147 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 134 time to evaluate : 1.031 Fit side-chains revert: symmetry clash REVERT: R 162 LEU cc_start: 0.7284 (OUTLIER) cc_final: 0.6694 (mm) REVERT: R 369 LEU cc_start: 0.7770 (tp) cc_final: 0.7487 (tm) REVERT: R 376 LEU cc_start: 0.8131 (OUTLIER) cc_final: 0.7772 (mm) REVERT: A 24 ARG cc_start: 0.7688 (ttm-80) cc_final: 0.7393 (ttm-80) REVERT: A 197 LYS cc_start: 0.8699 (mttt) cc_final: 0.8339 (mttm) REVERT: A 208 ARG cc_start: 0.8142 (ttm110) cc_final: 0.7864 (ttm110) REVERT: A 306 GLN cc_start: 0.7728 (mm-40) cc_final: 0.7457 (mp10) REVERT: B 219 ARG cc_start: 0.8258 (mtp180) cc_final: 0.7805 (mmm160) REVERT: S 85 SER cc_start: 0.8906 (m) cc_final: 0.8589 (t) outliers start: 13 outliers final: 6 residues processed: 141 average time/residue: 1.2711 time to fit residues: 190.9494 Evaluate side-chains 133 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 125 time to evaluate : 1.018 ------------------------------------------------------------------------------- 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 162 LEU Chi-restraints excluded: chain R residue 376 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 228 ASP 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 81 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 24 optimal weight: 8.9990 chunk 88 optimal weight: 0.0470 chunk 36 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 16 optimal weight: 0.6980 chunk 77 optimal weight: 0.6980 chunk 5 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 overall best weight: 0.8680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 5 ASN G 59 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.175124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.115264 restraints weight = 9433.136| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 2.01 r_work: 0.3129 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.2734 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= 0.145 Angle : 0.491 10.298 12520 Z= 0.259 Chirality : 0.040 0.151 1408 Planarity : 0.004 0.042 1577 Dihedral : 4.248 32.488 1314 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.86 % Favored : 98.05 % Rotamer: Outliers : 1.13 % Allowed : 17.73 % Favored : 81.15 % 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 (0.25), residues: 1129 helix: 3.26 (0.25), residues: 411 sheet: 0.89 (0.30), residues: 266 loop : -0.09 (0.30), residues: 452 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 0.013 0.001 PHE R 192 TYR 0.013 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: 3979.18 seconds wall clock time: 70 minutes 7.76 seconds (4207.76 seconds total)