Starting phenix.real_space_refine on Thu Mar 13 15:15:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wig_32529/03_2025/7wig_32529.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wig_32529/03_2025/7wig_32529.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wig_32529/03_2025/7wig_32529.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wig_32529/03_2025/7wig_32529.map" model { file = "/net/cci-nas-00/data/ceres_data/7wig_32529/03_2025/7wig_32529.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wig_32529/03_2025/7wig_32529.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= 0.002 sd= 0.033 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 67 5.16 5 C 5697 2.51 5 N 1507 2.21 5 O 1660 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8931 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2234 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 11, 'TRANS': 271} 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: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'9FI': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.24, per 1000 atoms: 0.59 Number of scatterers: 8931 At special positions: 0 Unit cell: (106.47, 126.75, 111.54, 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 67 16.00 O 1660 8.00 N 1507 7.00 C 5697 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 115 " - pdb=" SG CYS R 193 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.28 Conformation dependent library (CDL) restraints added in 1.0 seconds 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2126 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 14 sheets defined 38.5% alpha, 23.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'R' and resid 41 through 69 Processing helix chain 'R' and resid 77 through 96 Processing helix chain 'R' and resid 97 through 105 removed outlier: 3.961A pdb=" N MET R 101 " --> pdb=" O PRO R 97 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLN R 102 " --> pdb=" O PHE R 98 " (cutoff:3.500A) Processing helix chain 'R' and resid 112 through 145 removed outlier: 3.891A pdb=" N PHE R 127 " --> pdb=" O GLY R 123 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE R 130 " --> pdb=" O GLN R 126 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N PHE R 131 " --> pdb=" O PHE R 127 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N CYS R 132 " --> pdb=" O THR R 128 " (cutoff:3.500A) Processing helix chain 'R' and resid 148 through 154 removed outlier: 4.103A pdb=" N LYS R 152 " --> pdb=" O ILE R 148 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N TRP R 153 " --> pdb=" O LYS R 149 " (cutoff:3.500A) Processing helix chain 'R' and resid 155 through 174 removed outlier: 3.888A pdb=" N ILE R 174 " --> pdb=" O SER R 170 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 180 Processing helix chain 'R' and resid 202 through 243 removed outlier: 5.273A pdb=" N VAL R 219 " --> pdb=" O LEU R 215 " (cutoff:3.500A) Proline residue: R 220 - end of helix Processing helix chain 'R' and resid 246 through 282 removed outlier: 3.759A pdb=" N SER R 250 " --> pdb=" O LYS R 246 " (cutoff:3.500A) Proline residue: R 271 - end of helix Processing helix chain 'R' and resid 287 through 314 removed outlier: 3.752A pdb=" N SER R 305 " --> pdb=" O THR R 301 " (cutoff:3.500A) Proline residue: R 309 - end of helix Processing helix chain 'R' and resid 316 through 327 removed outlier: 3.841A pdb=" N SER R 322 " --> pdb=" O ASN R 318 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ASN R 325 " --> pdb=" O LYS R 321 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N VAL R 326 " --> pdb=" O SER R 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.550A pdb=" N GLU A 28 " --> pdb=" O ARG A 24 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS A 29 " --> pdb=" O GLU A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 52 removed outlier: 3.733A pdb=" N VAL A 50 " --> pdb=" O LYS A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 3.536A pdb=" N LYS A 210 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE A 215 " --> pdb=" O ILE A 212 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 279 removed outlier: 4.085A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.569A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 330 through 352 Processing helix chain 'B' and resid 3 through 26 removed outlier: 3.511A pdb=" N ALA B 26 " --> pdb=" O ARG B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.550A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 24 removed outlier: 3.617A 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 'S' and resid 28 through 32 removed outlier: 3.610A pdb=" N PHE S 32 " --> pdb=" O PHE S 29 " (cutoff:3.500A) Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.766A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing helix chain 'S' and resid 220 through 224 removed outlier: 3.537A pdb=" N VAL S 224 " --> pdb=" O ALA S 221 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 181 through 183 Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 190 removed outlier: 3.620A pdb=" N PHE A 189 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51 removed outlier: 3.736A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.583A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.740A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.641A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.671A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.705A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.725A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.103A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N ALA S 40 " --> pdb=" O LEU S 45 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N LEU S 45 " --> pdb=" O ALA S 40 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.103A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 140 through 141 Processing sheet with id=AB5, first strand: chain 'S' and resid 146 through 148 removed outlier: 3.777A pdb=" N GLU S 246 " --> pdb=" O VAL S 147 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE S 189 " --> pdb=" O TRP S 176 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N LEU S 178 " --> pdb=" O LEU S 187 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N LEU S 187 " --> pdb=" O LEU S 178 " (cutoff:3.500A) 446 hydrogen bonds defined for protein. 1278 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.41 Time building geometry restraints manager: 2.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1444 1.30 - 1.43: 2413 1.43 - 1.56: 5163 1.56 - 1.69: 1 1.69 - 1.82: 98 Bond restraints: 9119 Sorted by residual: bond pdb=" C19 9FI R 401 " pdb=" N1 9FI R 401 " ideal model delta sigma weight residual 1.369 1.492 -0.123 2.00e-02 2.50e+03 3.78e+01 bond pdb=" C11 9FI R 401 " pdb=" N1 9FI R 401 " ideal model delta sigma weight residual 1.455 1.571 -0.116 2.00e-02 2.50e+03 3.37e+01 bond pdb=" C20 9FI R 401 " pdb=" N3 9FI R 401 " ideal model delta sigma weight residual 1.444 1.334 0.110 2.00e-02 2.50e+03 3.00e+01 bond pdb=" C12 9FI R 401 " pdb=" N1 9FI R 401 " ideal model delta sigma weight residual 1.456 1.347 0.109 2.00e-02 2.50e+03 2.97e+01 bond pdb=" C PHE R 127 " pdb=" O PHE R 127 " ideal model delta sigma weight residual 1.235 1.168 0.067 1.33e-02 5.65e+03 2.53e+01 ... (remaining 9114 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.87: 12308 4.87 - 9.75: 37 9.75 - 14.62: 3 14.62 - 19.50: 1 19.50 - 24.37: 1 Bond angle restraints: 12350 Sorted by residual: angle pdb=" C22 9FI R 401 " pdb=" C20 9FI R 401 " pdb=" N3 9FI R 401 " ideal model delta sigma weight residual 110.53 86.16 24.37 3.00e+00 1.11e-01 6.60e+01 angle pdb=" N ILE R 124 " pdb=" CA ILE R 124 " pdb=" C ILE R 124 " ideal model delta sigma weight residual 111.81 105.17 6.64 8.60e-01 1.35e+00 5.96e+01 angle pdb=" C6 9FI R 401 " pdb=" C12 9FI R 401 " pdb=" N1 9FI R 401 " ideal model delta sigma weight residual 111.52 127.12 -15.60 3.00e+00 1.11e-01 2.70e+01 angle pdb=" N ALA R 307 " pdb=" CA ALA R 307 " pdb=" C ALA R 307 " ideal model delta sigma weight residual 111.36 116.61 -5.25 1.09e+00 8.42e-01 2.32e+01 angle pdb=" C TYR R 302 " pdb=" N ALA R 303 " pdb=" CA ALA R 303 " ideal model delta sigma weight residual 120.28 126.19 -5.91 1.34e+00 5.57e-01 1.94e+01 ... (remaining 12345 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.36: 4880 16.36 - 32.72: 432 32.72 - 49.07: 94 49.07 - 65.43: 16 65.43 - 81.79: 7 Dihedral angle restraints: 5429 sinusoidal: 2132 harmonic: 3297 Sorted by residual: dihedral pdb=" CA LEU R 105 " pdb=" C LEU R 105 " pdb=" N VAL R 106 " pdb=" CA VAL R 106 " ideal model delta harmonic sigma weight residual -180.00 -161.70 -18.30 0 5.00e+00 4.00e-02 1.34e+01 dihedral pdb=" CA GLU B 130 " pdb=" C GLU B 130 " pdb=" N GLY B 131 " pdb=" CA GLY B 131 " ideal model delta harmonic sigma weight residual 180.00 162.01 17.99 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" CA TYR S 190 " pdb=" C TYR S 190 " pdb=" N ARG S 191 " pdb=" CA ARG S 191 " ideal model delta harmonic sigma weight residual 180.00 163.54 16.46 0 5.00e+00 4.00e-02 1.08e+01 ... (remaining 5426 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1231 0.069 - 0.138: 158 0.138 - 0.207: 6 0.207 - 0.275: 7 0.275 - 0.344: 2 Chirality restraints: 1404 Sorted by residual: chirality pdb=" CA ASN R 125 " pdb=" N ASN R 125 " pdb=" C ASN R 125 " pdb=" CB ASN R 125 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.96e+00 chirality pdb=" CA THR R 128 " pdb=" N THR R 128 " pdb=" C THR R 128 " pdb=" CB THR R 128 " both_signs ideal model delta sigma weight residual False 2.53 2.25 0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" CB ILE R 174 " pdb=" CA ILE R 174 " pdb=" CG1 ILE R 174 " pdb=" CG2 ILE R 174 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.85e+00 ... (remaining 1401 not shown) Planarity restraints: 1550 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE R 127 " 0.035 2.00e-02 2.50e+03 2.61e-02 1.19e+01 pdb=" CG PHE R 127 " -0.051 2.00e-02 2.50e+03 pdb=" CD1 PHE R 127 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE R 127 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE R 127 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE R 127 " -0.009 2.00e-02 2.50e+03 pdb=" CZ PHE R 127 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C19 9FI R 401 " 0.005 2.00e-02 2.50e+03 2.77e-02 9.56e+00 pdb=" C20 9FI R 401 " -0.036 2.00e-02 2.50e+03 pdb=" N1 9FI R 401 " -0.023 2.00e-02 2.50e+03 pdb=" N3 9FI R 401 " 0.043 2.00e-02 2.50e+03 pdb=" O1 9FI R 401 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY R 123 " -0.015 2.00e-02 2.50e+03 2.94e-02 8.67e+00 pdb=" C GLY R 123 " 0.051 2.00e-02 2.50e+03 pdb=" O GLY R 123 " -0.018 2.00e-02 2.50e+03 pdb=" N ILE R 124 " -0.018 2.00e-02 2.50e+03 ... (remaining 1547 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 527 2.73 - 3.27: 8601 3.27 - 3.82: 14610 3.82 - 4.36: 17149 4.36 - 4.90: 30796 Nonbonded interactions: 71683 Sorted by model distance: nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.192 3.040 nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR S 175 " model vdw 2.244 3.040 nonbonded pdb=" OG SER G 57 " pdb=" OE1 GLU G 58 " model vdw 2.252 3.040 nonbonded pdb=" O HIS R 146 " pdb=" OG SER R 150 " model vdw 2.302 3.040 nonbonded pdb=" NH1 ARG B 48 " pdb=" O ARG G 62 " model vdw 2.307 3.120 ... (remaining 71678 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: 0.490 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: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.450 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 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 : 0.006 0.123 9119 Z= 0.433 Angle : 0.746 24.373 12350 Z= 0.383 Chirality : 0.048 0.344 1404 Planarity : 0.004 0.064 1550 Dihedral : 13.302 81.791 3294 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.11 (0.26), residues: 1123 helix: 1.86 (0.27), residues: 398 sheet: 0.93 (0.32), residues: 282 loop : -0.39 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 108 HIS 0.003 0.001 HIS A 188 PHE 0.051 0.001 PHE R 127 TYR 0.016 0.001 TYR R 211 ARG 0.007 0.000 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 1.036 Fit side-chains revert: symmetry clash REVERT: A 28 GLU cc_start: 0.7294 (mp0) cc_final: 0.6651 (mp0) REVERT: B 135 VAL cc_start: 0.8506 (t) cc_final: 0.8177 (p) REVERT: B 217 MET cc_start: 0.6505 (ppp) cc_final: 0.6131 (ppp) outliers start: 0 outliers final: 1 residues processed: 187 average time/residue: 1.2095 time to fit residues: 241.2839 Evaluate side-chains 176 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 175 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 28 optimal weight: 0.5980 chunk 56 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 87 optimal weight: 0.0970 chunk 33 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 125 ASN A 188 HIS A 195 HIS B 176 GLN B 220 GLN B 239 ASN B 259 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.137570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.117452 restraints weight = 12257.069| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 1.89 r_work: 0.3415 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3270 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.1089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9119 Z= 0.227 Angle : 0.561 7.838 12350 Z= 0.296 Chirality : 0.044 0.255 1404 Planarity : 0.004 0.041 1550 Dihedral : 5.418 64.483 1266 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.23 % Allowed : 9.42 % Favored : 89.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.25 (0.25), residues: 1123 helix: 2.03 (0.26), residues: 401 sheet: 0.93 (0.31), residues: 277 loop : -0.32 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 169 HIS 0.004 0.001 HIS S 35 PHE 0.022 0.001 PHE R 92 TYR 0.030 0.001 TYR S 190 ARG 0.007 0.000 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 183 time to evaluate : 1.010 Fit side-chains revert: symmetry clash REVERT: R 119 MET cc_start: 0.6891 (mmm) cc_final: 0.6670 (mpp) REVERT: A 20 ASP cc_start: 0.7966 (m-30) cc_final: 0.7765 (m-30) REVERT: A 28 GLU cc_start: 0.7772 (mp0) cc_final: 0.6902 (mp0) REVERT: A 255 ASN cc_start: 0.8508 (m-40) cc_final: 0.8276 (m-40) REVERT: B 135 VAL cc_start: 0.8641 (t) cc_final: 0.8315 (p) REVERT: S 140 MET cc_start: 0.8444 (OUTLIER) cc_final: 0.8134 (mtp) outliers start: 12 outliers final: 2 residues processed: 185 average time/residue: 1.1870 time to fit residues: 234.3655 Evaluate side-chains 182 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 179 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 140 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 58 optimal weight: 0.8980 chunk 88 optimal weight: 6.9990 chunk 6 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 53 optimal weight: 0.0980 chunk 32 optimal weight: 6.9990 chunk 60 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 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 75 GLN B 220 GLN B 259 GLN B 340 ASN S 142 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.137713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.117744 restraints weight = 12400.802| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 1.89 r_work: 0.3417 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.1303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9119 Z= 0.184 Angle : 0.523 7.708 12350 Z= 0.275 Chirality : 0.043 0.206 1404 Planarity : 0.003 0.039 1550 Dihedral : 4.968 66.297 1264 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.25 % Allowed : 10.95 % Favored : 86.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.42 (0.26), residues: 1123 helix: 2.27 (0.26), residues: 401 sheet: 0.95 (0.31), residues: 278 loop : -0.26 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 211 HIS 0.003 0.001 HIS S 35 PHE 0.017 0.001 PHE R 92 TYR 0.026 0.001 TYR S 190 ARG 0.004 0.000 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 179 time to evaluate : 1.008 Fit side-chains REVERT: A 20 ASP cc_start: 0.7977 (m-30) cc_final: 0.7766 (m-30) REVERT: A 28 GLU cc_start: 0.7739 (mp0) cc_final: 0.6998 (mp0) REVERT: A 53 MET cc_start: 0.5398 (mmm) cc_final: 0.5195 (mmp) REVERT: A 255 ASN cc_start: 0.8487 (m-40) cc_final: 0.8264 (m-40) REVERT: B 135 VAL cc_start: 0.8641 (t) cc_final: 0.8336 (p) REVERT: B 217 MET cc_start: 0.7774 (OUTLIER) cc_final: 0.7188 (ptp) REVERT: B 219 ARG cc_start: 0.7632 (mpt180) cc_final: 0.7086 (mpt180) REVERT: S 140 MET cc_start: 0.8407 (OUTLIER) cc_final: 0.8142 (mtp) REVERT: S 141 THR cc_start: 0.8557 (OUTLIER) cc_final: 0.8326 (p) outliers start: 22 outliers final: 5 residues processed: 184 average time/residue: 1.3663 time to fit residues: 267.6747 Evaluate side-chains 186 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 178 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 101 MET Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain S residue 140 MET Chi-restraints excluded: chain S residue 141 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 79 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 14 optimal weight: 0.6980 chunk 102 optimal weight: 6.9990 chunk 50 optimal weight: 7.9990 chunk 11 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 107 optimal weight: 0.9980 chunk 2 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 220 GLN B 259 GLN B 340 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.132988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.113248 restraints weight = 12187.317| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 1.85 r_work: 0.3348 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.068 9119 Z= 0.504 Angle : 0.681 10.682 12350 Z= 0.357 Chirality : 0.050 0.280 1404 Planarity : 0.005 0.047 1550 Dihedral : 5.610 73.935 1264 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.56 % Allowed : 12.38 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.07 (0.25), residues: 1123 helix: 1.88 (0.26), residues: 402 sheet: 0.90 (0.31), residues: 282 loop : -0.50 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP R 108 HIS 0.007 0.002 HIS S 35 PHE 0.024 0.002 PHE R 92 TYR 0.031 0.003 TYR S 190 ARG 0.005 0.001 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 184 time to evaluate : 0.925 Fit side-chains revert: symmetry clash REVERT: R 53 VAL cc_start: 0.5780 (OUTLIER) cc_final: 0.5500 (t) REVERT: R 61 ASN cc_start: 0.7802 (m-40) cc_final: 0.7600 (m-40) REVERT: R 119 MET cc_start: 0.7007 (mmm) cc_final: 0.6775 (mpp) REVERT: R 172 LEU cc_start: 0.7073 (tt) cc_final: 0.6845 (tp) REVERT: A 20 ASP cc_start: 0.7954 (m-30) cc_final: 0.7752 (m-30) REVERT: A 275 GLU cc_start: 0.7632 (mm-30) cc_final: 0.7380 (mm-30) REVERT: B 135 VAL cc_start: 0.8821 (t) cc_final: 0.8584 (p) REVERT: B 212 ASP cc_start: 0.7696 (p0) cc_final: 0.7401 (p0) REVERT: B 217 MET cc_start: 0.7862 (OUTLIER) cc_final: 0.7309 (ptp) REVERT: B 219 ARG cc_start: 0.7717 (mpt180) cc_final: 0.7073 (mpt180) REVERT: S 140 MET cc_start: 0.8529 (OUTLIER) cc_final: 0.8150 (mtp) outliers start: 25 outliers final: 11 residues processed: 189 average time/residue: 1.2594 time to fit residues: 253.6076 Evaluate side-chains 193 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 179 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 53 VAL Chi-restraints excluded: chain R residue 101 MET Chi-restraints excluded: chain R residue 209 ILE Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain S residue 140 MET Chi-restraints excluded: chain S residue 141 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 106 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 87 optimal weight: 0.0970 chunk 60 optimal weight: 0.5980 chunk 79 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 chunk 91 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 132 ASN B 220 GLN B 259 GLN B 340 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.136179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.116410 restraints weight = 12174.441| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 1.87 r_work: 0.3395 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9119 Z= 0.179 Angle : 0.528 8.646 12350 Z= 0.278 Chirality : 0.042 0.208 1404 Planarity : 0.003 0.041 1550 Dihedral : 5.093 74.178 1264 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.97 % Allowed : 13.82 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.39 (0.26), residues: 1123 helix: 2.30 (0.27), residues: 401 sheet: 1.06 (0.31), residues: 275 loop : -0.45 (0.30), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.003 0.001 HIS S 35 PHE 0.008 0.001 PHE B 151 TYR 0.021 0.001 TYR S 190 ARG 0.006 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 177 time to evaluate : 1.029 Fit side-chains REVERT: R 119 MET cc_start: 0.6949 (mmm) cc_final: 0.6708 (mpp) REVERT: A 275 GLU cc_start: 0.7631 (mm-30) cc_final: 0.7388 (mm-30) REVERT: B 135 VAL cc_start: 0.8700 (t) cc_final: 0.8456 (p) REVERT: B 212 ASP cc_start: 0.7693 (p0) cc_final: 0.7424 (p0) REVERT: B 217 MET cc_start: 0.7842 (OUTLIER) cc_final: 0.7308 (ptp) REVERT: B 219 ARG cc_start: 0.7701 (mpt180) cc_final: 0.7018 (mpt180) REVERT: S 140 MET cc_start: 0.8388 (OUTLIER) cc_final: 0.8097 (mtp) outliers start: 29 outliers final: 12 residues processed: 186 average time/residue: 1.2688 time to fit residues: 251.7217 Evaluate side-chains 189 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 175 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 101 MET Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 140 MET Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 234 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 109 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 chunk 6 optimal weight: 4.9990 chunk 78 optimal weight: 0.9990 chunk 97 optimal weight: 0.5980 chunk 65 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 71 optimal weight: 0.1980 chunk 90 optimal weight: 4.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 269 ASN B 220 GLN B 340 ASN S 142 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.136648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.116871 restraints weight = 12201.540| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 1.88 r_work: 0.3405 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3260 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9119 Z= 0.172 Angle : 0.525 8.266 12350 Z= 0.276 Chirality : 0.042 0.199 1404 Planarity : 0.003 0.041 1550 Dihedral : 4.891 69.169 1264 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.35 % Allowed : 14.74 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.46 (0.26), residues: 1123 helix: 2.41 (0.27), residues: 401 sheet: 1.00 (0.31), residues: 278 loop : -0.39 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 108 HIS 0.002 0.001 HIS S 35 PHE 0.008 0.001 PHE B 151 TYR 0.021 0.001 TYR S 190 ARG 0.006 0.000 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 173 time to evaluate : 0.952 Fit side-chains REVERT: R 53 VAL cc_start: 0.5710 (OUTLIER) cc_final: 0.5454 (t) REVERT: A 275 GLU cc_start: 0.7650 (mm-30) cc_final: 0.7392 (mm-30) REVERT: B 129 ARG cc_start: 0.8051 (ttt90) cc_final: 0.7799 (mmm-85) REVERT: B 135 VAL cc_start: 0.8643 (t) cc_final: 0.8387 (p) REVERT: B 212 ASP cc_start: 0.7637 (p0) cc_final: 0.7353 (p0) REVERT: B 217 MET cc_start: 0.7795 (OUTLIER) cc_final: 0.7242 (ptp) REVERT: B 219 ARG cc_start: 0.7746 (mpt180) cc_final: 0.7095 (mpt180) REVERT: S 140 MET cc_start: 0.8376 (OUTLIER) cc_final: 0.8139 (mtp) outliers start: 23 outliers final: 15 residues processed: 181 average time/residue: 1.2474 time to fit residues: 241.0221 Evaluate side-chains 188 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 170 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 41 THR Chi-restraints excluded: chain R residue 53 VAL Chi-restraints excluded: chain R residue 101 MET Chi-restraints excluded: chain R residue 301 THR Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 140 MET Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 234 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 43 optimal weight: 5.9990 chunk 56 optimal weight: 0.7980 chunk 57 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 chunk 72 optimal weight: 0.0670 chunk 39 optimal weight: 3.9990 chunk 79 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN B 340 ASN S 142 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.136670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.116763 restraints weight = 12350.684| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 1.89 r_work: 0.3406 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9119 Z= 0.178 Angle : 0.529 11.450 12350 Z= 0.274 Chirality : 0.042 0.199 1404 Planarity : 0.003 0.040 1550 Dihedral : 4.722 60.615 1264 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.76 % Allowed : 14.74 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.54 (0.26), residues: 1123 helix: 2.49 (0.27), residues: 401 sheet: 1.04 (0.31), residues: 279 loop : -0.35 (0.30), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 108 HIS 0.003 0.001 HIS A 188 PHE 0.008 0.001 PHE B 234 TYR 0.021 0.001 TYR S 190 ARG 0.006 0.000 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 176 time to evaluate : 0.923 Fit side-chains REVERT: R 53 VAL cc_start: 0.5700 (OUTLIER) cc_final: 0.5444 (t) REVERT: A 275 GLU cc_start: 0.7677 (mm-30) cc_final: 0.7423 (mm-30) REVERT: B 135 VAL cc_start: 0.8611 (t) cc_final: 0.8366 (p) REVERT: B 212 ASP cc_start: 0.7610 (p0) cc_final: 0.7315 (p0) REVERT: B 217 MET cc_start: 0.7814 (OUTLIER) cc_final: 0.7259 (ptp) REVERT: B 219 ARG cc_start: 0.7732 (tpt170) cc_final: 0.6983 (mpt180) REVERT: S 140 MET cc_start: 0.8376 (OUTLIER) cc_final: 0.8094 (mtp) outliers start: 27 outliers final: 18 residues processed: 187 average time/residue: 1.1839 time to fit residues: 236.0677 Evaluate side-chains 196 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 175 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 41 THR Chi-restraints excluded: chain R residue 53 VAL Chi-restraints excluded: chain R residue 101 MET Chi-restraints excluded: chain R residue 164 MET Chi-restraints excluded: chain R residue 301 THR Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 140 MET Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 234 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 51 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 chunk 83 optimal weight: 7.9990 chunk 40 optimal weight: 4.9990 chunk 96 optimal weight: 0.9980 chunk 32 optimal weight: 20.0000 chunk 88 optimal weight: 4.9990 chunk 78 optimal weight: 0.6980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN B 340 ASN S 142 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.134377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.114497 restraints weight = 12329.087| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 1.89 r_work: 0.3366 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 9119 Z= 0.356 Angle : 0.621 11.964 12350 Z= 0.321 Chirality : 0.046 0.244 1404 Planarity : 0.004 0.044 1550 Dihedral : 5.122 71.964 1264 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.46 % Allowed : 16.07 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.31 (0.26), residues: 1123 helix: 2.23 (0.26), residues: 402 sheet: 1.07 (0.31), residues: 271 loop : -0.50 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP R 108 HIS 0.006 0.001 HIS A 188 PHE 0.013 0.002 PHE R 275 TYR 0.024 0.002 TYR S 190 ARG 0.006 0.000 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 181 time to evaluate : 0.903 Fit side-chains revert: symmetry clash REVERT: R 53 VAL cc_start: 0.5746 (OUTLIER) cc_final: 0.5532 (t) REVERT: A 275 GLU cc_start: 0.7692 (mm-30) cc_final: 0.7415 (mm-30) REVERT: B 135 VAL cc_start: 0.8682 (t) cc_final: 0.8466 (p) REVERT: S 140 MET cc_start: 0.8457 (OUTLIER) cc_final: 0.8207 (mtp) outliers start: 24 outliers final: 15 residues processed: 189 average time/residue: 1.2340 time to fit residues: 249.3901 Evaluate side-chains 197 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 180 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 41 THR Chi-restraints excluded: chain R residue 53 VAL Chi-restraints excluded: chain R residue 101 MET Chi-restraints excluded: chain R residue 301 THR Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain S residue 140 MET Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 234 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 33 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 6 optimal weight: 6.9990 chunk 59 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 10 optimal weight: 4.9990 chunk 48 optimal weight: 0.6980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 132 ASN B 220 GLN B 259 GLN S 142 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.135821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.116110 restraints weight = 12345.854| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 1.88 r_work: 0.3392 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9119 Z= 0.211 Angle : 0.555 10.875 12350 Z= 0.287 Chirality : 0.043 0.211 1404 Planarity : 0.004 0.041 1550 Dihedral : 4.977 74.244 1264 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.35 % Allowed : 15.97 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.44 (0.26), residues: 1123 helix: 2.44 (0.27), residues: 401 sheet: 1.02 (0.32), residues: 273 loop : -0.47 (0.30), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 108 HIS 0.003 0.001 HIS A 188 PHE 0.010 0.001 PHE B 234 TYR 0.020 0.001 TYR S 190 ARG 0.006 0.000 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 171 time to evaluate : 1.011 Fit side-chains REVERT: R 53 VAL cc_start: 0.5715 (OUTLIER) cc_final: 0.5476 (t) REVERT: A 25 GLU cc_start: 0.8060 (tt0) cc_final: 0.7746 (tt0) REVERT: A 275 GLU cc_start: 0.7687 (mm-30) cc_final: 0.7378 (mm-30) REVERT: B 135 VAL cc_start: 0.8635 (t) cc_final: 0.8408 (p) REVERT: B 212 ASP cc_start: 0.7706 (p0) cc_final: 0.7277 (p0) REVERT: B 217 MET cc_start: 0.8067 (OUTLIER) cc_final: 0.7756 (ptp) REVERT: B 219 ARG cc_start: 0.7720 (tpt170) cc_final: 0.7153 (mpt180) REVERT: B 254 ASP cc_start: 0.7904 (t70) cc_final: 0.7618 (p0) REVERT: S 140 MET cc_start: 0.8384 (OUTLIER) cc_final: 0.8132 (mtp) outliers start: 23 outliers final: 14 residues processed: 179 average time/residue: 1.1842 time to fit residues: 226.5142 Evaluate side-chains 188 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 171 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 41 THR Chi-restraints excluded: chain R residue 53 VAL Chi-restraints excluded: chain R residue 101 MET Chi-restraints excluded: chain R residue 301 THR Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain S residue 140 MET Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 234 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 35 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 20 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 49 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.136050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.116333 restraints weight = 12303.639| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 1.88 r_work: 0.3394 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3248 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9119 Z= 0.209 Angle : 0.555 12.677 12350 Z= 0.287 Chirality : 0.043 0.207 1404 Planarity : 0.003 0.042 1550 Dihedral : 4.948 77.016 1264 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.74 % Allowed : 16.68 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.46 (0.26), residues: 1123 helix: 2.47 (0.27), residues: 404 sheet: 0.98 (0.31), residues: 274 loop : -0.45 (0.30), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 108 HIS 0.004 0.001 HIS A 188 PHE 0.011 0.001 PHE R 92 TYR 0.019 0.001 TYR S 190 ARG 0.005 0.000 ARG B 251 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 174 time to evaluate : 1.109 Fit side-chains REVERT: R 53 VAL cc_start: 0.5716 (OUTLIER) cc_final: 0.5473 (t) REVERT: R 178 MET cc_start: 0.5372 (mmm) cc_final: 0.5100 (mmm) REVERT: A 25 GLU cc_start: 0.8062 (tt0) cc_final: 0.7739 (tt0) REVERT: A 275 GLU cc_start: 0.7714 (mm-30) cc_final: 0.7383 (mm-30) REVERT: B 135 VAL cc_start: 0.8617 (t) cc_final: 0.8383 (p) REVERT: B 212 ASP cc_start: 0.7682 (p0) cc_final: 0.7412 (p0) REVERT: B 217 MET cc_start: 0.8041 (ptp) cc_final: 0.7595 (ptp) REVERT: B 219 ARG cc_start: 0.7712 (tpt170) cc_final: 0.7151 (mpt180) REVERT: B 254 ASP cc_start: 0.7886 (t70) cc_final: 0.7636 (p0) REVERT: S 140 MET cc_start: 0.8367 (OUTLIER) cc_final: 0.8083 (mtp) outliers start: 17 outliers final: 14 residues processed: 181 average time/residue: 1.1836 time to fit residues: 229.3533 Evaluate side-chains 190 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 174 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 41 THR Chi-restraints excluded: chain R residue 53 VAL Chi-restraints excluded: chain R residue 101 MET Chi-restraints excluded: chain R residue 301 THR Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain S residue 140 MET Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 234 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 30 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 43 optimal weight: 0.2980 chunk 98 optimal weight: 0.5980 chunk 8 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 88 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.138579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.118154 restraints weight = 12202.694| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 1.93 r_work: 0.3421 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3273 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9119 Z= 0.180 Angle : 0.546 11.736 12350 Z= 0.281 Chirality : 0.042 0.197 1404 Planarity : 0.003 0.041 1550 Dihedral : 4.876 78.434 1264 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.84 % Allowed : 16.68 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.54 (0.26), residues: 1123 helix: 2.54 (0.27), residues: 404 sheet: 1.06 (0.31), residues: 273 loop : -0.44 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 108 HIS 0.003 0.001 HIS A 188 PHE 0.011 0.001 PHE R 92 TYR 0.019 0.001 TYR S 190 ARG 0.005 0.000 ARG B 251 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7952.88 seconds wall clock time: 138 minutes 59.09 seconds (8339.09 seconds total)