Starting phenix.real_space_refine on Sat Jun 7 20:47:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wig_32529/06_2025/7wig_32529.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wig_32529/06_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_32529/06_2025/7wig_32529.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wig_32529/06_2025/7wig_32529.map" model { file = "/net/cci-nas-00/data/ceres_data/7wig_32529/06_2025/7wig_32529.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wig_32529/06_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-5710/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: 5.29, 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: 2.25 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: 1.00 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: 2.96 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: 0.580 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: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.540 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.170 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:16.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.710 ------------------------------------------------------------------------------- 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 9122 Z= 0.354 Angle : 0.746 24.373 12356 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 Details of bonding type rmsd hydrogen bonds : bond 0.18215 ( 442) hydrogen bonds : angle 6.46646 ( 1278) SS BOND : bond 0.00294 ( 3) SS BOND : angle 0.79614 ( 6) covalent geometry : bond 0.00633 ( 9119) covalent geometry : angle 0.74647 (12350) *********************** 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 : 0.992 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: 1.2005 time to fit residues: 239.5633 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 : 0.948 ------------------------------------------------------------------------------- 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 9122 Z= 0.150 Angle : 0.561 7.838 12356 Z= 0.297 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 Details of bonding type rmsd hydrogen bonds : bond 0.04547 ( 442) hydrogen bonds : angle 4.66100 ( 1278) SS BOND : bond 0.00683 ( 3) SS BOND : angle 1.04384 ( 6) covalent geometry : bond 0.00347 ( 9119) covalent geometry : angle 0.56069 (12350) *********************** 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 : 1.002 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: 1.1678 time to fit residues: 230.5232 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 : 0.909 ------------------------------------------------------------------------------- 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 9122 Z= 0.123 Angle : 0.524 7.708 12356 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 Details of bonding type rmsd hydrogen bonds : bond 0.04022 ( 442) hydrogen bonds : angle 4.41389 ( 1278) SS BOND : bond 0.00603 ( 3) SS BOND : angle 1.09571 ( 6) covalent geometry : bond 0.00279 ( 9119) covalent geometry : angle 0.52314 (12350) *********************** 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 : 0.918 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: 1.1915 time to fit residues: 233.7583 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 : 1.034 ------------------------------------------------------------------------------- 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 9122 Z= 0.320 Angle : 0.682 10.682 12356 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 Details of bonding type rmsd hydrogen bonds : bond 0.05907 ( 442) hydrogen bonds : angle 4.75497 ( 1278) SS BOND : bond 0.01155 ( 3) SS BOND : angle 1.95451 ( 6) covalent geometry : bond 0.00773 ( 9119) covalent geometry : angle 0.68078 (12350) *********************** 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 : 0.971 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: 1.2043 time to fit residues: 243.6223 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 : 1.125 ------------------------------------------------------------------------------- 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 9122 Z= 0.122 Angle : 0.529 8.646 12356 Z= 0.279 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 Details of bonding type rmsd hydrogen bonds : bond 0.04097 ( 442) hydrogen bonds : angle 4.43147 ( 1278) SS BOND : bond 0.00561 ( 3) SS BOND : angle 1.20450 ( 6) covalent geometry : bond 0.00274 ( 9119) covalent geometry : angle 0.52847 (12350) *********************** 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 : 0.996 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: 1.2389 time to fit residues: 246.1058 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 : 0.909 ------------------------------------------------------------------------------- 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: 0.5980 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: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3794 r_free = 0.3794 target = 0.136781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.117013 restraints weight = 12201.788| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 1.87 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: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9122 Z= 0.114 Angle : 0.523 8.206 12356 Z= 0.275 Chirality : 0.042 0.197 1404 Planarity : 0.003 0.041 1550 Dihedral : 4.876 68.645 1264 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.61 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: 1.47 (0.26), residues: 1123 helix: 2.42 (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 B 169 HIS 0.002 0.001 HIS S 35 PHE 0.007 0.001 PHE B 151 TYR 0.021 0.001 TYR S 190 ARG 0.006 0.000 ARG B 251 Details of bonding type rmsd hydrogen bonds : bond 0.03836 ( 442) hydrogen bonds : angle 4.31859 ( 1278) SS BOND : bond 0.00543 ( 3) SS BOND : angle 1.14891 ( 6) covalent geometry : bond 0.00255 ( 9119) covalent geometry : angle 0.52259 (12350) *********************** 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 197 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 174 time to evaluate : 1.604 Fit side-chains REVERT: R 53 VAL cc_start: 0.5714 (OUTLIER) cc_final: 0.5452 (t) REVERT: A 275 GLU cc_start: 0.7661 (mm-30) cc_final: 0.7409 (mm-30) REVERT: B 129 ARG cc_start: 0.8076 (ttt90) cc_final: 0.7827 (mmm-85) REVERT: B 135 VAL cc_start: 0.8636 (t) cc_final: 0.8379 (p) REVERT: B 212 ASP cc_start: 0.7640 (p0) cc_final: 0.7354 (p0) REVERT: B 217 MET cc_start: 0.7801 (OUTLIER) cc_final: 0.7249 (ptp) REVERT: B 219 ARG cc_start: 0.7762 (mpt180) cc_final: 0.7112 (mpt180) REVERT: S 140 MET cc_start: 0.8367 (OUTLIER) cc_final: 0.8135 (mtp) outliers start: 23 outliers final: 15 residues processed: 182 average time/residue: 1.4686 time to fit residues: 286.1891 Evaluate side-chains 189 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 171 time to evaluate : 0.983 ------------------------------------------------------------------------------- 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: 1.9990 chunk 56 optimal weight: 0.9980 chunk 57 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 chunk 18 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 72 optimal weight: 0.0980 chunk 39 optimal weight: 3.9990 chunk 79 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 33 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: 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 = 0.3794 r_free = 0.3794 target = 0.136910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.117062 restraints weight = 12365.517| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 1.90 r_work: 0.3408 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3263 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 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 9122 Z= 0.116 Angle : 0.524 11.381 12356 Z= 0.272 Chirality : 0.042 0.196 1404 Planarity : 0.003 0.040 1550 Dihedral : 4.693 59.550 1264 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.56 % Allowed : 15.05 % Favored : 82.40 % 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: 2.50 (0.27), residues: 401 sheet: 0.99 (0.31), residues: 281 loop : -0.34 (0.31), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 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 Details of bonding type rmsd hydrogen bonds : bond 0.03721 ( 442) hydrogen bonds : angle 4.27357 ( 1278) SS BOND : bond 0.00551 ( 3) SS BOND : angle 1.15623 ( 6) covalent geometry : bond 0.00262 ( 9119) covalent geometry : angle 0.52353 (12350) *********************** 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 200 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 175 time to evaluate : 1.073 Fit side-chains REVERT: R 53 VAL cc_start: 0.5695 (OUTLIER) cc_final: 0.5434 (t) REVERT: A 275 GLU cc_start: 0.7668 (mm-30) cc_final: 0.7417 (mm-30) REVERT: B 135 VAL cc_start: 0.8613 (t) cc_final: 0.8365 (p) REVERT: B 212 ASP cc_start: 0.7619 (p0) cc_final: 0.7331 (p0) REVERT: B 217 MET cc_start: 0.7816 (OUTLIER) cc_final: 0.7263 (ptp) REVERT: B 219 ARG cc_start: 0.7736 (tpt170) cc_final: 0.6993 (mpt180) REVERT: S 140 MET cc_start: 0.8372 (OUTLIER) cc_final: 0.8130 (mtp) outliers start: 25 outliers final: 16 residues processed: 185 average time/residue: 1.2076 time to fit residues: 238.2357 Evaluate side-chains 193 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 174 time to evaluate : 1.013 ------------------------------------------------------------------------------- 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 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: 0.7980 chunk 61 optimal weight: 0.7980 chunk 110 optimal weight: 2.9990 chunk 83 optimal weight: 6.9990 chunk 40 optimal weight: 4.9990 chunk 96 optimal weight: 0.0870 chunk 32 optimal weight: 20.0000 chunk 88 optimal weight: 4.9990 chunk 78 optimal weight: 0.7980 overall best weight: 0.8960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN S 142 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.136349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.116513 restraints weight = 12352.342| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 1.90 r_work: 0.3400 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9122 Z= 0.139 Angle : 0.547 11.385 12356 Z= 0.283 Chirality : 0.043 0.208 1404 Planarity : 0.003 0.041 1550 Dihedral : 4.605 47.558 1264 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.05 % Allowed : 16.17 % Favored : 81.78 % 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: 1.53 (0.26), residues: 1123 helix: 2.49 (0.26), residues: 401 sheet: 1.10 (0.31), residues: 271 loop : -0.39 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 339 HIS 0.004 0.001 HIS A 188 PHE 0.010 0.001 PHE B 234 TYR 0.021 0.001 TYR S 190 ARG 0.006 0.000 ARG B 251 Details of bonding type rmsd hydrogen bonds : bond 0.03950 ( 442) hydrogen bonds : angle 4.31726 ( 1278) SS BOND : bond 0.00636 ( 3) SS BOND : angle 1.25660 ( 6) covalent geometry : bond 0.00324 ( 9119) covalent geometry : angle 0.54639 (12350) *********************** 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 196 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 176 time to evaluate : 0.937 Fit side-chains REVERT: R 53 VAL cc_start: 0.5690 (OUTLIER) cc_final: 0.5450 (t) REVERT: A 275 GLU cc_start: 0.7681 (mm-30) cc_final: 0.7430 (mm-30) REVERT: B 135 VAL cc_start: 0.8608 (t) cc_final: 0.8365 (p) REVERT: B 212 ASP cc_start: 0.7602 (p0) cc_final: 0.7317 (p0) REVERT: B 217 MET cc_start: 0.7829 (OUTLIER) cc_final: 0.7275 (ptp) REVERT: B 219 ARG cc_start: 0.7728 (tpt170) cc_final: 0.6964 (mpt180) REVERT: S 140 MET cc_start: 0.8383 (OUTLIER) cc_final: 0.8058 (mtp) REVERT: S 141 THR cc_start: 0.8505 (OUTLIER) cc_final: 0.8248 (p) outliers start: 20 outliers final: 13 residues processed: 182 average time/residue: 1.1736 time to fit residues: 228.4901 Evaluate side-chains 192 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 175 time to evaluate : 1.037 ------------------------------------------------------------------------------- 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 240 MET 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 33 optimal weight: 2.9990 chunk 42 optimal weight: 0.0870 chunk 31 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 6 optimal weight: 6.9990 chunk 59 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 10 optimal weight: 6.9990 chunk 48 optimal weight: 1.9990 overall best weight: 0.9762 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.137794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.117400 restraints weight = 12161.152| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 1.93 r_work: 0.3409 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3260 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9122 Z= 0.147 Angle : 0.559 10.883 12356 Z= 0.288 Chirality : 0.043 0.216 1404 Planarity : 0.004 0.041 1550 Dihedral : 4.571 37.654 1264 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.35 % Allowed : 15.86 % Favored : 81.78 % 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: 1.53 (0.26), residues: 1123 helix: 2.47 (0.27), residues: 402 sheet: 1.14 (0.31), residues: 271 loop : -0.42 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 108 HIS 0.005 0.001 HIS A 188 PHE 0.010 0.001 PHE B 234 TYR 0.021 0.001 TYR S 190 ARG 0.006 0.000 ARG B 251 Details of bonding type rmsd hydrogen bonds : bond 0.04093 ( 442) hydrogen bonds : angle 4.34005 ( 1278) SS BOND : bond 0.00667 ( 3) SS BOND : angle 1.28209 ( 6) covalent geometry : bond 0.00346 ( 9119) covalent geometry : angle 0.55880 (12350) *********************** 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 198 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 175 time to evaluate : 0.988 Fit side-chains revert: symmetry clash REVERT: R 53 VAL cc_start: 0.5717 (OUTLIER) cc_final: 0.5484 (t) REVERT: A 275 GLU cc_start: 0.7675 (mm-30) cc_final: 0.7380 (mm-30) REVERT: B 135 VAL cc_start: 0.8620 (t) cc_final: 0.8387 (p) outliers start: 23 outliers final: 14 residues processed: 184 average time/residue: 1.1999 time to fit residues: 235.8989 Evaluate side-chains 190 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 175 time to evaluate : 1.247 ------------------------------------------------------------------------------- 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 263 THR Chi-restraints excluded: chain B residue 270 ILE 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: 4.9990 chunk 23 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 chunk 7 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 77 optimal weight: 0.8980 chunk 45 optimal weight: 0.6980 chunk 82 optimal weight: 0.7980 chunk 49 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS B 220 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.138746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.118365 restraints weight = 12157.182| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 1.93 r_work: 0.3422 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3273 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9122 Z= 0.122 Angle : 0.541 11.561 12356 Z= 0.279 Chirality : 0.042 0.200 1404 Planarity : 0.003 0.041 1550 Dihedral : 4.463 31.878 1264 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.84 % Allowed : 16.17 % Favored : 81.99 % 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: 1.58 (0.26), residues: 1123 helix: 2.53 (0.27), residues: 402 sheet: 1.12 (0.31), residues: 274 loop : -0.37 (0.30), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 108 HIS 0.004 0.001 HIS A 188 PHE 0.010 0.001 PHE R 92 TYR 0.019 0.001 TYR S 190 ARG 0.006 0.000 ARG B 251 Details of bonding type rmsd hydrogen bonds : bond 0.03762 ( 442) hydrogen bonds : angle 4.28556 ( 1278) SS BOND : bond 0.00513 ( 3) SS BOND : angle 1.10941 ( 6) covalent geometry : bond 0.00279 ( 9119) covalent geometry : angle 0.54021 (12350) ********************** 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 193 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 175 time to evaluate : 1.142 Fit side-chains REVERT: R 53 VAL cc_start: 0.5706 (OUTLIER) cc_final: 0.5470 (t) REVERT: R 178 MET cc_start: 0.5317 (mmm) cc_final: 0.5094 (mmm) REVERT: A 25 GLU cc_start: 0.7964 (tt0) cc_final: 0.7650 (tt0) REVERT: A 275 GLU cc_start: 0.7687 (mm-30) cc_final: 0.7368 (mm-30) REVERT: B 135 VAL cc_start: 0.8583 (t) cc_final: 0.8348 (p) REVERT: B 219 ARG cc_start: 0.7746 (tpt170) cc_final: 0.7275 (mpt180) REVERT: B 254 ASP cc_start: 0.7947 (t70) cc_final: 0.7631 (p0) outliers start: 18 outliers final: 14 residues processed: 181 average time/residue: 1.2651 time to fit residues: 245.0036 Evaluate side-chains 190 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 175 time to evaluate : 1.046 ------------------------------------------------------------------------------- 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 229 LEU 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 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 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: 4.9990 chunk 10 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 chunk 39 optimal weight: 0.1980 chunk 36 optimal weight: 0.6980 chunk 43 optimal weight: 7.9990 chunk 98 optimal weight: 0.3980 chunk 8 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 88 optimal weight: 0.8980 chunk 77 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3820 r_free = 0.3820 target = 0.139236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.118812 restraints weight = 12254.656| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 1.94 r_work: 0.3426 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3277 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9122 Z= 0.113 Angle : 0.541 10.913 12356 Z= 0.277 Chirality : 0.042 0.194 1404 Planarity : 0.003 0.040 1550 Dihedral : 4.370 28.157 1264 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.74 % Allowed : 16.27 % Favored : 81.99 % 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: 1.62 (0.26), residues: 1123 helix: 2.55 (0.27), residues: 402 sheet: 1.16 (0.31), residues: 272 loop : -0.36 (0.30), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 269 HIS 0.003 0.001 HIS S 35 PHE 0.010 0.001 PHE R 92 TYR 0.019 0.001 TYR S 190 ARG 0.005 0.000 ARG B 251 Details of bonding type rmsd hydrogen bonds : bond 0.03619 ( 442) hydrogen bonds : angle 4.29110 ( 1278) SS BOND : bond 0.00476 ( 3) SS BOND : angle 1.03615 ( 6) covalent geometry : bond 0.00256 ( 9119) covalent geometry : angle 0.54044 (12350) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8130.82 seconds wall clock time: 143 minutes 19.83 seconds (8599.83 seconds total)