Starting phenix.real_space_refine on Fri Feb 14 02:05:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vl9_32021/02_2025/7vl9_32021.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vl9_32021/02_2025/7vl9_32021.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7vl9_32021/02_2025/7vl9_32021.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vl9_32021/02_2025/7vl9_32021.map" model { file = "/net/cci-nas-00/data/ceres_data/7vl9_32021/02_2025/7vl9_32021.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vl9_32021/02_2025/7vl9_32021.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.014 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 68 5.16 5 C 6152 2.51 5 N 1616 2.21 5 O 1769 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 9605 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1756 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 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: "L" Number of atoms: 496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 496 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 5, 'TRANS': 59} Chain: "R" Number of atoms: 2493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2493 Classifications: {'peptide': 302} Link IDs: {'PTRANS': 10, 'TRANS': 291} Chain: "S" Number of atoms: 1781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1781 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.70, per 1000 atoms: 0.59 Number of scatterers: 9605 At special positions: 0 Unit cell: (110.313, 134.946, 126.378, 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 68 16.00 O 1769 8.00 N 1616 7.00 C 6152 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS L 32 " - pdb=" SG CYS L 56 " distance=2.03 Simple disulfide: pdb=" SG CYS L 33 " - pdb=" SG CYS L 72 " distance=2.03 Simple disulfide: pdb=" SG CYS L 43 " - pdb=" SG CYS L 83 " distance=2.03 Simple disulfide: pdb=" SG CYS R 24 " - pdb=" SG CYS R 273 " distance=2.04 Simple disulfide: pdb=" SG CYS R 106 " - pdb=" SG CYS R 183 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.04 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.41 Conformation dependent library (CDL) restraints added in 1.2 seconds 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2274 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 15 sheets defined 39.2% alpha, 23.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.527A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.374A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 256 through 260 removed outlier: 4.013A pdb=" N THR A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 281 removed outlier: 4.256A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.883A 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 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.520A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'G' and resid 6 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 55 through 59 Processing helix chain 'L' and resid 42 through 44 No H-bonds generated for 'chain 'L' and resid 42 through 44' Processing helix chain 'L' and resid 77 through 87 removed outlier: 4.128A pdb=" N GLN L 81 " --> pdb=" O GLY L 77 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N ASP L 82 " --> pdb=" O PRO L 78 " (cutoff:3.500A) Processing helix chain 'R' and resid 26 through 59 Proline residue: R 38 - end of helix removed outlier: 3.775A pdb=" N VAL R 46 " --> pdb=" O SER R 42 " (cutoff:3.500A) Processing helix chain 'R' and resid 67 through 97 removed outlier: 4.112A pdb=" N THR R 86 " --> pdb=" O LEU R 82 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LEU R 87 " --> pdb=" O PHE R 83 " (cutoff:3.500A) Proline residue: R 88 - end of helix Processing helix chain 'R' and resid 102 through 137 Processing helix chain 'R' and resid 139 through 143 Processing helix chain 'R' and resid 146 through 165 Processing helix chain 'R' and resid 165 through 172 removed outlier: 3.569A pdb=" N SER R 172 " --> pdb=" O GLY R 168 " (cutoff:3.500A) Processing helix chain 'R' and resid 191 through 206 removed outlier: 3.647A pdb=" N LEU R 203 " --> pdb=" O GLN R 199 " (cutoff:3.500A) Processing helix chain 'R' and resid 208 through 228 removed outlier: 3.876A pdb=" N GLY R 221 " --> pdb=" O ILE R 217 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG R 228 " --> pdb=" O LYS R 224 " (cutoff:3.500A) Processing helix chain 'R' and resid 231 through 264 Proline residue: R 254 - end of helix Processing helix chain 'R' and resid 264 through 269 Processing helix chain 'R' and resid 274 through 302 removed outlier: 4.281A pdb=" N HIS R 278 " --> pdb=" O GLU R 274 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE R 289 " --> pdb=" O VAL R 285 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N CYS R 294 " --> pdb=" O ALA R 290 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N CYS R 295 " --> pdb=" O TYR R 291 " (cutoff:3.500A) Proline residue: R 298 - end of helix Processing helix chain 'R' and resid 305 through 318 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 8.710A pdb=" N ALA A 220 " --> pdb=" O GLU A 33 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.754A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.684A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.584A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.019A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 3.583A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLN B 175 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.091A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.662A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.696A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 46 through 51 Processing sheet with id=AB1, first strand: chain 'R' and resid 173 through 177 Processing sheet with id=AB2, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB3, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.027A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.027A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'S' and resid 140 through 141 Processing sheet with id=AB6, first strand: chain 'S' and resid 146 through 148 removed outlier: 6.624A pdb=" N TRP S 176 " --> pdb=" O LEU S 188 " (cutoff:3.500A) 495 hydrogen bonds defined for protein. 1383 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: 2.99 Time building geometry restraints manager: 2.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1715 1.32 - 1.45: 2785 1.45 - 1.58: 5219 1.58 - 1.71: 2 1.71 - 1.84: 96 Bond restraints: 9817 Sorted by residual: bond pdb=" CA ILE S 100 " pdb=" C ILE S 100 " ideal model delta sigma weight residual 1.522 1.458 0.063 1.22e-02 6.72e+03 2.70e+01 bond pdb=" CA GLN S 82 " pdb=" C GLN S 82 " ideal model delta sigma weight residual 1.522 1.463 0.059 1.20e-02 6.94e+03 2.44e+01 bond pdb=" CA LYS L 66 " pdb=" C LYS L 66 " ideal model delta sigma weight residual 1.524 1.464 0.060 1.32e-02 5.74e+03 2.08e+01 bond pdb=" CA LEU R 192 " pdb=" C LEU R 192 " ideal model delta sigma weight residual 1.524 1.466 0.058 1.27e-02 6.20e+03 2.07e+01 bond pdb=" CA THR B 47 " pdb=" C THR B 47 " ideal model delta sigma weight residual 1.524 1.472 0.052 1.33e-02 5.65e+03 1.51e+01 ... (remaining 9812 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.27: 12817 2.27 - 4.54: 390 4.54 - 6.81: 59 6.81 - 9.09: 20 9.09 - 11.36: 4 Bond angle restraints: 13290 Sorted by residual: angle pdb=" N ASP B 205 " pdb=" CA ASP B 205 " pdb=" C ASP B 205 " ideal model delta sigma weight residual 112.88 103.30 9.58 1.29e+00 6.01e-01 5.52e+01 angle pdb=" N GLY L 68 " pdb=" CA GLY L 68 " pdb=" C GLY L 68 " ideal model delta sigma weight residual 115.21 124.60 -9.39 1.30e+00 5.92e-01 5.22e+01 angle pdb=" N LEU R 197 " pdb=" CA LEU R 197 " pdb=" C LEU R 197 " ideal model delta sigma weight residual 111.07 103.83 7.24 1.07e+00 8.73e-01 4.57e+01 angle pdb=" N LYS L 66 " pdb=" CA LYS L 66 " pdb=" C LYS L 66 " ideal model delta sigma weight residual 111.69 103.45 8.24 1.23e+00 6.61e-01 4.48e+01 angle pdb=" N ASP B 163 " pdb=" CA ASP B 163 " pdb=" C ASP B 163 " ideal model delta sigma weight residual 112.59 104.44 8.15 1.22e+00 6.72e-01 4.46e+01 ... (remaining 13285 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 5389 17.96 - 35.91: 403 35.91 - 53.87: 67 53.87 - 71.82: 19 71.82 - 89.78: 7 Dihedral angle restraints: 5885 sinusoidal: 2359 harmonic: 3526 Sorted by residual: dihedral pdb=" CB CYS S 159 " pdb=" SG CYS S 159 " pdb=" SG CYS S 229 " pdb=" CB CYS S 229 " ideal model delta sinusoidal sigma weight residual 93.00 3.86 89.14 1 1.00e+01 1.00e-02 9.46e+01 dihedral pdb=" CB CYS R 106 " pdb=" SG CYS R 106 " pdb=" SG CYS R 183 " pdb=" CB CYS R 183 " ideal model delta sinusoidal sigma weight residual -86.00 -168.72 82.72 1 1.00e+01 1.00e-02 8.38e+01 dihedral pdb=" CB CYS L 32 " pdb=" SG CYS L 32 " pdb=" SG CYS L 56 " pdb=" CB CYS L 56 " ideal model delta sinusoidal sigma weight residual 93.00 147.84 -54.84 1 1.00e+01 1.00e-02 4.07e+01 ... (remaining 5882 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 1316 0.089 - 0.178: 159 0.178 - 0.267: 15 0.267 - 0.356: 5 0.356 - 0.445: 6 Chirality restraints: 1501 Sorted by residual: chirality pdb=" CA SER B 334 " pdb=" N SER B 334 " pdb=" C SER B 334 " pdb=" CB SER B 334 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.45 2.00e-01 2.50e+01 4.96e+00 chirality pdb=" CA ASN S 77 " pdb=" N ASN S 77 " pdb=" C ASN S 77 " pdb=" CB ASN S 77 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.40 2.00e-01 2.50e+01 3.91e+00 chirality pdb=" CA THR B 164 " pdb=" N THR B 164 " pdb=" C THR B 164 " pdb=" CB THR B 164 " both_signs ideal model delta sigma weight residual False 2.53 2.15 0.38 2.00e-01 2.50e+01 3.53e+00 ... (remaining 1498 not shown) Planarity restraints: 1667 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR S 190 " -0.013 2.00e-02 2.50e+03 2.57e-02 6.62e+00 pdb=" C TYR S 190 " 0.045 2.00e-02 2.50e+03 pdb=" O TYR S 190 " -0.016 2.00e-02 2.50e+03 pdb=" N ARG S 191 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 63 " -0.015 2.00e-02 2.50e+03 1.38e-02 4.78e+00 pdb=" CG TRP B 63 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 TRP B 63 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP B 63 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP B 63 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 63 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 63 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 63 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 63 " -0.009 2.00e-02 2.50e+03 pdb=" CH2 TRP B 63 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER S 106 " 0.036 5.00e-02 4.00e+02 5.40e-02 4.67e+00 pdb=" N PRO S 107 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO S 107 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO S 107 " 0.030 5.00e-02 4.00e+02 ... (remaining 1664 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 495 2.72 - 3.27: 9495 3.27 - 3.81: 15710 3.81 - 4.36: 19997 4.36 - 4.90: 34316 Nonbonded interactions: 80013 Sorted by model distance: nonbonded pdb=" O PHE R 178 " pdb=" OG1 THR R 179 " model vdw 2.176 3.040 nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR S 175 " model vdw 2.213 3.040 nonbonded pdb=" O MET S 192 " pdb=" OG SER S 193 " model vdw 2.216 3.040 nonbonded pdb=" O GLY B 224 " pdb=" NH1 ARG B 251 " model vdw 2.222 3.120 nonbonded pdb=" OE2 GLU L 51 " pdb=" NE2 GLN R 175 " model vdw 2.251 3.120 ... (remaining 80008 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: 0.620 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: 0.000 Extract box with map and model: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 24.150 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 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 : 0.007 0.063 9817 Z= 0.444 Angle : 0.955 11.358 13290 Z= 0.573 Chirality : 0.064 0.445 1501 Planarity : 0.005 0.054 1667 Dihedral : 13.152 89.775 3590 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.10 % Allowed : 1.43 % Favored : 98.48 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 2.78 % 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: 0.32 (0.24), residues: 1196 helix: 1.01 (0.25), residues: 414 sheet: 0.80 (0.30), residues: 279 loop : -0.76 (0.26), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP B 63 HIS 0.008 0.002 HIS B 91 PHE 0.030 0.003 PHE S 212 TYR 0.034 0.003 TYR S 175 ARG 0.030 0.001 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 176 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 23 LYS cc_start: 0.8022 (tptp) cc_final: 0.7581 (OUTLIER) REVERT: B 129 ARG cc_start: 0.7324 (ttt180) cc_final: 0.7023 (tpt90) REVERT: B 245 SER cc_start: 0.8329 (p) cc_final: 0.8105 (p) REVERT: S 80 PHE cc_start: 0.8260 (m-80) cc_final: 0.8013 (m-80) REVERT: S 83 MET cc_start: 0.8889 (mtm) cc_final: 0.8687 (mtp) outliers start: 1 outliers final: 1 residues processed: 176 average time/residue: 1.3159 time to fit residues: 246.7975 Evaluate side-chains 133 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 60 optimal weight: 9.9990 chunk 47 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 68 optimal weight: 0.9980 chunk 107 optimal weight: 6.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 88 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 18 GLN R 61 GLN R 75 ASN ** R 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 82 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.198109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 91)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.142793 restraints weight = 9797.282| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 1.54 r_work: 0.3356 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3236 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 9817 Z= 0.217 Angle : 0.604 7.506 13290 Z= 0.326 Chirality : 0.044 0.165 1501 Planarity : 0.005 0.048 1667 Dihedral : 6.528 59.032 1377 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.19 % Allowed : 8.19 % Favored : 89.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.79 (0.24), residues: 1196 helix: 1.65 (0.25), residues: 423 sheet: 0.73 (0.30), residues: 282 loop : -0.57 (0.27), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 82 HIS 0.005 0.001 HIS S 35 PHE 0.022 0.002 PHE R 32 TYR 0.019 0.002 TYR S 175 ARG 0.007 0.001 ARG R 307 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 139 time to evaluate : 1.080 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 ASN cc_start: 0.8294 (m-40) cc_final: 0.7977 (m110) REVERT: B 23 LYS cc_start: 0.7718 (tptp) cc_final: 0.7067 (mmpt) REVERT: B 101 MET cc_start: 0.8761 (OUTLIER) cc_final: 0.8512 (mpp) REVERT: B 129 ARG cc_start: 0.7865 (ttt180) cc_final: 0.7424 (tpt90) REVERT: B 155 ASN cc_start: 0.8586 (t0) cc_final: 0.8294 (t0) REVERT: B 219 ARG cc_start: 0.8055 (mpt90) cc_final: 0.7762 (mmm160) REVERT: S 76 LYS cc_start: 0.8015 (mtpp) cc_final: 0.7463 (mtpt) outliers start: 23 outliers final: 11 residues processed: 147 average time/residue: 1.3009 time to fit residues: 204.2522 Evaluate side-chains 137 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 125 time to evaluate : 1.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain L residue 46 MET Chi-restraints excluded: chain R residue 155 ILE Chi-restraints excluded: chain R residue 174 THR Chi-restraints excluded: chain R residue 257 LEU Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 204 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 115 optimal weight: 10.0000 chunk 37 optimal weight: 0.9990 chunk 86 optimal weight: 8.9990 chunk 78 optimal weight: 1.9990 chunk 59 optimal weight: 7.9990 chunk 80 optimal weight: 8.9990 chunk 56 optimal weight: 4.9990 chunk 64 optimal weight: 9.9990 chunk 16 optimal weight: 4.9990 chunk 117 optimal weight: 0.0970 chunk 18 optimal weight: 0.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN B 268 ASN ** R 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.195049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.139074 restraints weight = 9994.961| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 1.57 r_work: 0.3313 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.101 9817 Z= 0.312 Angle : 0.631 9.189 13290 Z= 0.341 Chirality : 0.045 0.181 1501 Planarity : 0.005 0.052 1667 Dihedral : 6.420 58.379 1377 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.76 % Allowed : 10.00 % Favored : 87.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.87 (0.24), residues: 1196 helix: 1.93 (0.25), residues: 422 sheet: 0.57 (0.29), residues: 276 loop : -0.58 (0.27), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 82 HIS 0.005 0.001 HIS S 35 PHE 0.020 0.002 PHE A 196 TYR 0.024 0.002 TYR S 190 ARG 0.009 0.001 ARG R 307 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 126 time to evaluate : 1.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ASN cc_start: 0.8441 (m-40) cc_final: 0.8012 (m110) REVERT: B 101 MET cc_start: 0.8876 (OUTLIER) cc_final: 0.8376 (mtm) REVERT: B 217 MET cc_start: 0.8511 (OUTLIER) cc_final: 0.8270 (pmt) REVERT: R 311 TYR cc_start: 0.5751 (t80) cc_final: 0.5513 (t80) REVERT: S 76 LYS cc_start: 0.8052 (mtpp) cc_final: 0.7482 (mtpt) REVERT: S 90 ASP cc_start: 0.8681 (m-30) cc_final: 0.8464 (m-30) outliers start: 29 outliers final: 16 residues processed: 138 average time/residue: 1.3318 time to fit residues: 196.3378 Evaluate side-chains 140 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 122 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain L residue 46 MET Chi-restraints excluded: chain R residue 87 LEU Chi-restraints excluded: chain R residue 155 ILE Chi-restraints excluded: chain R residue 174 THR Chi-restraints excluded: chain R residue 217 ILE Chi-restraints excluded: chain R residue 257 LEU Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 204 SER Chi-restraints excluded: chain S residue 213 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 67 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 107 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 103 optimal weight: 7.9990 chunk 99 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 83 optimal weight: 0.9990 chunk 40 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN S 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.194982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.143070 restraints weight = 10053.543| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 1.64 r_work: 0.3338 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 9817 Z= 0.246 Angle : 0.570 8.641 13290 Z= 0.310 Chirality : 0.043 0.173 1501 Planarity : 0.005 0.054 1667 Dihedral : 5.887 52.920 1377 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.10 % Allowed : 12.67 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.97 (0.24), residues: 1196 helix: 2.11 (0.25), residues: 421 sheet: 0.55 (0.30), residues: 276 loop : -0.56 (0.27), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 82 HIS 0.004 0.001 HIS S 35 PHE 0.017 0.002 PHE A 196 TYR 0.021 0.002 TYR S 190 ARG 0.009 0.001 ARG R 307 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 125 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 ASN cc_start: 0.8383 (m-40) cc_final: 0.8081 (m-40) REVERT: A 32 ARG cc_start: 0.7995 (mtt-85) cc_final: 0.7618 (mmt90) REVERT: B 44 GLN cc_start: 0.8271 (OUTLIER) cc_final: 0.7668 (mp10) REVERT: B 101 MET cc_start: 0.8772 (OUTLIER) cc_final: 0.8520 (mpp) REVERT: B 155 ASN cc_start: 0.8664 (t0) cc_final: 0.8302 (t0) REVERT: B 217 MET cc_start: 0.8518 (OUTLIER) cc_final: 0.8145 (pp-130) REVERT: G 58 GLU cc_start: 0.7661 (pt0) cc_final: 0.7459 (pt0) REVERT: L 46 MET cc_start: 0.6713 (OUTLIER) cc_final: 0.5813 (ptt) REVERT: S 76 LYS cc_start: 0.8039 (mtpp) cc_final: 0.7493 (mtpt) REVERT: S 90 ASP cc_start: 0.8703 (m-30) cc_final: 0.8489 (m-30) outliers start: 22 outliers final: 11 residues processed: 136 average time/residue: 1.3273 time to fit residues: 192.8044 Evaluate side-chains 131 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 116 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain L residue 46 MET Chi-restraints excluded: chain R residue 155 ILE Chi-restraints excluded: chain R residue 257 LEU Chi-restraints excluded: chain R residue 300 ILE Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 204 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 117 optimal weight: 3.9990 chunk 60 optimal weight: 30.0000 chunk 54 optimal weight: 9.9990 chunk 91 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 81 optimal weight: 9.9990 chunk 40 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 333 GLN B 175 GLN ** R 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.192719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.139917 restraints weight = 9955.894| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 1.63 r_work: 0.3302 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.113 9817 Z= 0.385 Angle : 0.659 11.132 13290 Z= 0.355 Chirality : 0.047 0.196 1501 Planarity : 0.005 0.057 1667 Dihedral : 6.108 55.710 1377 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.62 % Allowed : 11.81 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.83 (0.24), residues: 1196 helix: 2.03 (0.25), residues: 420 sheet: 0.42 (0.29), residues: 278 loop : -0.64 (0.27), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP B 63 HIS 0.006 0.001 HIS S 35 PHE 0.021 0.002 PHE A 196 TYR 0.028 0.002 TYR S 190 ARG 0.006 0.001 ARG R 307 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 118 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 ASN cc_start: 0.8470 (m-40) cc_final: 0.8103 (m-40) REVERT: A 32 ARG cc_start: 0.8164 (mtt-85) cc_final: 0.7863 (mmt90) REVERT: A 275 GLU cc_start: 0.8743 (OUTLIER) cc_final: 0.8456 (tp30) REVERT: A 318 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7707 (tt0) REVERT: B 44 GLN cc_start: 0.8306 (OUTLIER) cc_final: 0.7714 (mp10) REVERT: G 58 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7402 (pt0) REVERT: L 46 MET cc_start: 0.6755 (OUTLIER) cc_final: 0.5774 (ptt) REVERT: R 311 TYR cc_start: 0.6039 (t80) cc_final: 0.5730 (t80) REVERT: S 76 LYS cc_start: 0.8091 (mtpp) cc_final: 0.7525 (mtpt) REVERT: S 90 ASP cc_start: 0.8760 (m-30) cc_final: 0.8556 (m-30) outliers start: 38 outliers final: 16 residues processed: 136 average time/residue: 1.3384 time to fit residues: 194.6037 Evaluate side-chains 136 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 115 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain L residue 46 MET Chi-restraints excluded: chain R residue 155 ILE Chi-restraints excluded: chain R residue 217 ILE Chi-restraints excluded: chain R residue 257 LEU Chi-restraints excluded: chain R residue 296 VAL Chi-restraints excluded: chain R residue 300 ILE Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 204 SER Chi-restraints excluded: chain S residue 213 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 92 optimal weight: 3.9990 chunk 105 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 91 optimal weight: 6.9990 chunk 64 optimal weight: 10.0000 chunk 59 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 chunk 103 optimal weight: 5.9990 chunk 7 optimal weight: 0.4980 chunk 72 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN B 175 GLN S 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.192848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.139953 restraints weight = 10043.589| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 1.64 r_work: 0.3304 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.130 9817 Z= 0.357 Angle : 0.646 10.292 13290 Z= 0.345 Chirality : 0.046 0.184 1501 Planarity : 0.005 0.056 1667 Dihedral : 5.548 44.299 1377 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.24 % Allowed : 12.95 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.81 (0.24), residues: 1196 helix: 2.05 (0.25), residues: 421 sheet: 0.45 (0.29), residues: 279 loop : -0.73 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.005 0.001 HIS S 35 PHE 0.020 0.002 PHE A 196 TYR 0.022 0.002 TYR S 190 ARG 0.006 0.001 ARG A 15 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 118 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 ASN cc_start: 0.8461 (m-40) cc_final: 0.8098 (m-40) REVERT: A 32 ARG cc_start: 0.8213 (mtt-85) cc_final: 0.7887 (mmt90) REVERT: A 275 GLU cc_start: 0.8713 (OUTLIER) cc_final: 0.8444 (tp30) REVERT: A 318 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7716 (tt0) REVERT: B 44 GLN cc_start: 0.8306 (OUTLIER) cc_final: 0.7714 (mp10) REVERT: G 58 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.6993 (tt0) REVERT: L 46 MET cc_start: 0.6767 (OUTLIER) cc_final: 0.5779 (ptt) REVERT: R 311 TYR cc_start: 0.6077 (t80) cc_final: 0.5684 (t80) REVERT: S 18 ARG cc_start: 0.8297 (tpt170) cc_final: 0.7876 (tpt90) REVERT: S 20 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8365 (mt) REVERT: S 76 LYS cc_start: 0.8074 (mtpp) cc_final: 0.7499 (mtpt) outliers start: 34 outliers final: 16 residues processed: 135 average time/residue: 1.2988 time to fit residues: 187.5849 Evaluate side-chains 139 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 117 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain L residue 46 MET Chi-restraints excluded: chain R residue 155 ILE Chi-restraints excluded: chain R residue 257 LEU Chi-restraints excluded: chain R residue 296 VAL Chi-restraints excluded: chain R residue 300 ILE Chi-restraints excluded: chain S residue 20 LEU Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 204 SER Chi-restraints excluded: chain S residue 213 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 48 optimal weight: 0.5980 chunk 79 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 chunk 98 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 108 optimal weight: 4.9990 chunk 112 optimal weight: 1.9990 chunk 65 optimal weight: 30.0000 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 70 GLN R 25 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.195324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.148931 restraints weight = 10101.365| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 1.71 r_work: 0.3321 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 9817 Z= 0.199 Angle : 0.546 7.967 13290 Z= 0.293 Chirality : 0.042 0.164 1501 Planarity : 0.004 0.057 1667 Dihedral : 5.095 36.885 1377 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.67 % Allowed : 14.19 % Favored : 83.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.98 (0.24), residues: 1196 helix: 2.20 (0.25), residues: 425 sheet: 0.56 (0.30), residues: 277 loop : -0.67 (0.28), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 82 HIS 0.003 0.001 HIS B 183 PHE 0.021 0.002 PHE R 45 TYR 0.021 0.001 TYR S 190 ARG 0.004 0.000 ARG R 307 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 122 time to evaluate : 1.010 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 ASN cc_start: 0.8398 (m-40) cc_final: 0.8090 (m-40) REVERT: A 32 ARG cc_start: 0.8207 (mtt-85) cc_final: 0.7893 (mmt90) REVERT: A 275 GLU cc_start: 0.8733 (OUTLIER) cc_final: 0.8471 (tp30) REVERT: B 155 ASN cc_start: 0.8692 (t0) cc_final: 0.8444 (t0) REVERT: B 234 PHE cc_start: 0.9253 (OUTLIER) cc_final: 0.7703 (m-80) REVERT: G 58 GLU cc_start: 0.7609 (OUTLIER) cc_final: 0.6970 (tt0) REVERT: L 46 MET cc_start: 0.6695 (OUTLIER) cc_final: 0.5852 (ptt) REVERT: R 311 TYR cc_start: 0.6101 (t80) cc_final: 0.5742 (t80) REVERT: S 76 LYS cc_start: 0.8165 (mtpp) cc_final: 0.7617 (mtpt) outliers start: 28 outliers final: 12 residues processed: 138 average time/residue: 1.3396 time to fit residues: 197.6672 Evaluate side-chains 132 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 116 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain L residue 46 MET Chi-restraints excluded: chain R residue 155 ILE Chi-restraints excluded: chain R residue 296 VAL Chi-restraints excluded: chain R residue 300 ILE Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 204 SER Chi-restraints excluded: chain S residue 233 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 98 optimal weight: 0.8980 chunk 50 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 81 optimal weight: 10.0000 chunk 77 optimal weight: 0.6980 chunk 56 optimal weight: 8.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 112 optimal weight: 5.9990 chunk 106 optimal weight: 0.8980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.193949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.141521 restraints weight = 10166.926| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 1.67 r_work: 0.3319 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 9817 Z= 0.264 Angle : 0.587 9.490 13290 Z= 0.314 Chirality : 0.044 0.179 1501 Planarity : 0.004 0.058 1667 Dihedral : 5.193 38.316 1377 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.19 % Allowed : 14.95 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 1.02 (0.24), residues: 1196 helix: 2.31 (0.25), residues: 419 sheet: 0.52 (0.29), residues: 277 loop : -0.63 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.004 0.001 HIS S 35 PHE 0.020 0.002 PHE R 45 TYR 0.024 0.002 TYR S 190 ARG 0.004 0.000 ARG A 15 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 113 time to evaluate : 1.070 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 ASN cc_start: 0.8437 (m-40) cc_final: 0.8071 (m-40) REVERT: A 32 ARG cc_start: 0.8189 (mtt-85) cc_final: 0.7854 (mmt90) REVERT: A 275 GLU cc_start: 0.8716 (OUTLIER) cc_final: 0.8436 (tp30) REVERT: B 234 PHE cc_start: 0.9260 (OUTLIER) cc_final: 0.7684 (m-80) REVERT: G 58 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.7066 (tt0) REVERT: L 46 MET cc_start: 0.6668 (OUTLIER) cc_final: 0.5696 (ptt) REVERT: R 311 TYR cc_start: 0.6036 (t80) cc_final: 0.5625 (t80) REVERT: S 18 ARG cc_start: 0.8262 (tpt170) cc_final: 0.7843 (tpt90) REVERT: S 76 LYS cc_start: 0.8062 (mtpp) cc_final: 0.7505 (mtpt) outliers start: 23 outliers final: 15 residues processed: 127 average time/residue: 1.4625 time to fit residues: 197.2562 Evaluate side-chains 130 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 111 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain L residue 46 MET Chi-restraints excluded: chain R residue 155 ILE Chi-restraints excluded: chain R residue 296 VAL Chi-restraints excluded: chain R residue 300 ILE Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 204 SER Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain S residue 233 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 79 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 46 optimal weight: 0.4980 chunk 111 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 84 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 chunk 97 optimal weight: 7.9990 chunk 7 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.196206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.144662 restraints weight = 10004.364| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 1.59 r_work: 0.3351 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 9817 Z= 0.185 Angle : 0.536 7.655 13290 Z= 0.287 Chirality : 0.042 0.163 1501 Planarity : 0.004 0.060 1667 Dihedral : 4.974 35.598 1377 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.00 % Allowed : 15.81 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 1.10 (0.24), residues: 1196 helix: 2.34 (0.25), residues: 426 sheet: 0.49 (0.29), residues: 282 loop : -0.55 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 82 HIS 0.004 0.001 HIS S 35 PHE 0.020 0.001 PHE R 45 TYR 0.019 0.001 TYR S 190 ARG 0.013 0.001 ARG R 307 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 116 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 ASN cc_start: 0.8329 (m-40) cc_final: 0.8025 (m-40) REVERT: A 32 ARG cc_start: 0.8160 (mtt-85) cc_final: 0.7836 (mmt90) REVERT: A 275 GLU cc_start: 0.8697 (OUTLIER) cc_final: 0.8419 (tp30) REVERT: B 155 ASN cc_start: 0.8688 (t0) cc_final: 0.8405 (t0) REVERT: B 234 PHE cc_start: 0.9234 (OUTLIER) cc_final: 0.7717 (m-80) REVERT: G 58 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.7077 (tt0) REVERT: L 46 MET cc_start: 0.6678 (OUTLIER) cc_final: 0.5815 (ptt) REVERT: R 311 TYR cc_start: 0.6132 (t80) cc_final: 0.5740 (t80) REVERT: S 76 LYS cc_start: 0.8154 (mtpp) cc_final: 0.7623 (mtpt) outliers start: 21 outliers final: 14 residues processed: 126 average time/residue: 1.3729 time to fit residues: 184.7387 Evaluate side-chains 129 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 111 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain L residue 46 MET Chi-restraints excluded: chain R residue 155 ILE Chi-restraints excluded: chain R residue 296 VAL Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 204 SER Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain S residue 233 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 0 optimal weight: 5.9990 chunk 89 optimal weight: 0.6980 chunk 62 optimal weight: 3.9990 chunk 84 optimal weight: 0.0050 chunk 10 optimal weight: 0.9990 chunk 54 optimal weight: 8.9990 chunk 35 optimal weight: 0.9990 chunk 112 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 113 optimal weight: 0.7980 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN S 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.196691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.145540 restraints weight = 10169.700| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 1.69 r_work: 0.3362 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 9817 Z= 0.162 Angle : 0.517 7.314 13290 Z= 0.276 Chirality : 0.041 0.159 1501 Planarity : 0.004 0.062 1667 Dihedral : 4.861 35.393 1377 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.52 % Allowed : 16.29 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 1.23 (0.25), residues: 1196 helix: 2.43 (0.25), residues: 428 sheet: 0.53 (0.30), residues: 283 loop : -0.46 (0.29), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 82 HIS 0.003 0.001 HIS S 35 PHE 0.019 0.001 PHE R 45 TYR 0.019 0.001 TYR S 190 ARG 0.012 0.000 ARG R 307 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 125 time to evaluate : 1.130 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 ASN cc_start: 0.8300 (m-40) cc_final: 0.8018 (m-40) REVERT: A 32 ARG cc_start: 0.8132 (mtt-85) cc_final: 0.7805 (mmt90) REVERT: A 275 GLU cc_start: 0.8686 (OUTLIER) cc_final: 0.8399 (tp30) REVERT: B 155 ASN cc_start: 0.8650 (t0) cc_final: 0.8396 (t0) REVERT: B 234 PHE cc_start: 0.9221 (OUTLIER) cc_final: 0.7674 (m-80) REVERT: G 58 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.7123 (tt0) REVERT: L 46 MET cc_start: 0.6733 (OUTLIER) cc_final: 0.5835 (ptt) REVERT: R 311 TYR cc_start: 0.6120 (t80) cc_final: 0.5752 (t80) REVERT: S 76 LYS cc_start: 0.8161 (mtpp) cc_final: 0.7638 (mtpt) outliers start: 16 outliers final: 10 residues processed: 132 average time/residue: 1.4784 time to fit residues: 207.7846 Evaluate side-chains 134 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 120 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain L residue 46 MET Chi-restraints excluded: chain R residue 155 ILE Chi-restraints excluded: chain R residue 296 VAL Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 204 SER Chi-restraints excluded: chain S residue 233 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 75 optimal weight: 0.6980 chunk 9 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 69 optimal weight: 0.0370 chunk 24 optimal weight: 0.0980 chunk 100 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 overall best weight: 0.9260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN S 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.195695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.143349 restraints weight = 10076.793| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 1.61 r_work: 0.3357 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 9817 Z= 0.192 Angle : 0.537 7.567 13290 Z= 0.287 Chirality : 0.042 0.167 1501 Planarity : 0.004 0.062 1667 Dihedral : 4.922 35.729 1377 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.10 % Allowed : 16.48 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 1196 helix: 2.43 (0.25), residues: 427 sheet: 0.47 (0.29), residues: 292 loop : -0.40 (0.29), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 82 HIS 0.004 0.001 HIS S 35 PHE 0.019 0.001 PHE R 45 TYR 0.021 0.001 TYR S 190 ARG 0.012 0.001 ARG R 307 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9473.68 seconds wall clock time: 167 minutes 15.95 seconds (10035.95 seconds total)