Starting phenix.real_space_refine on Sun Jul 27 19:35:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vl9_32021/07_2025/7vl9_32021.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vl9_32021/07_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_32021/07_2025/7vl9_32021.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vl9_32021/07_2025/7vl9_32021.map" model { file = "/net/cci-nas-00/data/ceres_data/7vl9_32021/07_2025/7vl9_32021.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vl9_32021/07_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-5711/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: 6.04, per 1000 atoms: 0.63 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: 2.62 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: 2.68 Time building geometry restraints manager: 3.09 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: 0.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 25.230 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.440 ------------------------------------------------------------------------------- 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 9824 Z= 0.402 Angle : 0.961 11.358 13304 Z= 0.575 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 Details of bonding type rmsd hydrogen bonds : bond 0.14637 ( 491) hydrogen bonds : angle 6.18019 ( 1383) SS BOND : bond 0.00496 ( 7) SS BOND : angle 3.40066 ( 14) covalent geometry : bond 0.00671 ( 9817) covalent geometry : angle 0.95545 (13290) *********************** 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 : 1.109 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: 1.2500 time to fit residues: 234.8980 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 : 0.975 ------------------------------------------------------------------------------- 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 = 83)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.143054 restraints weight = 9797.282| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 1.54 r_work: 0.3361 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3241 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3241 ------------------------------------------------------------------------------- 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 9824 Z= 0.153 Angle : 0.608 7.506 13304 Z= 0.327 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 Details of bonding type rmsd hydrogen bonds : bond 0.04615 ( 491) hydrogen bonds : angle 4.87954 ( 1383) SS BOND : bond 0.00405 ( 7) SS BOND : angle 2.14928 ( 14) covalent geometry : bond 0.00344 ( 9817) covalent geometry : angle 0.60402 (13290) *********************** 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 : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 ASN cc_start: 0.8293 (m-40) cc_final: 0.7976 (m110) REVERT: B 23 LYS cc_start: 0.7725 (tptp) cc_final: 0.7076 (mmpt) REVERT: B 101 MET cc_start: 0.8761 (OUTLIER) cc_final: 0.8514 (mpp) REVERT: B 129 ARG cc_start: 0.7866 (ttt180) cc_final: 0.7426 (tpt90) REVERT: B 155 ASN cc_start: 0.8587 (t0) cc_final: 0.8298 (t0) REVERT: B 219 ARG cc_start: 0.8052 (mpt90) cc_final: 0.7764 (mmm160) REVERT: S 76 LYS cc_start: 0.8016 (mtpp) cc_final: 0.7464 (mtpt) outliers start: 23 outliers final: 11 residues processed: 147 average time/residue: 1.2987 time to fit residues: 203.9140 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 : 1.050 ------------------------------------------------------------------------------- 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: 0.0030 chunk 37 optimal weight: 1.9990 chunk 86 optimal weight: 7.9990 chunk 78 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 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: 0.7980 overall best weight: 0.9792 ------------------------------------------------------------------------------- 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 S 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.197654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.142505 restraints weight = 10040.699| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 1.56 r_work: 0.3348 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3225 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 9824 Z= 0.143 Angle : 0.560 7.505 13304 Z= 0.303 Chirality : 0.043 0.167 1501 Planarity : 0.005 0.054 1667 Dihedral : 6.037 56.307 1377 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.48 % Allowed : 10.10 % Favored : 87.43 % 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: 1.00 (0.24), residues: 1196 helix: 2.03 (0.25), residues: 426 sheet: 0.64 (0.30), residues: 277 loop : -0.53 (0.27), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 82 HIS 0.004 0.001 HIS B 183 PHE 0.021 0.002 PHE R 32 TYR 0.020 0.002 TYR S 190 ARG 0.008 0.001 ARG R 307 Details of bonding type rmsd hydrogen bonds : bond 0.04235 ( 491) hydrogen bonds : angle 4.60391 ( 1383) SS BOND : bond 0.00357 ( 7) SS BOND : angle 1.43164 ( 14) covalent geometry : bond 0.00326 ( 9817) covalent geometry : angle 0.55819 (13290) *********************** 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 160 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 134 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ASN cc_start: 0.8331 (m-40) cc_final: 0.7947 (m110) REVERT: B 23 LYS cc_start: 0.7961 (tptp) cc_final: 0.7756 (tptp) REVERT: B 101 MET cc_start: 0.8792 (OUTLIER) cc_final: 0.8502 (mpp) REVERT: B 155 ASN cc_start: 0.8602 (t0) cc_final: 0.8322 (t0) REVERT: S 76 LYS cc_start: 0.7977 (mtpp) cc_final: 0.7426 (mtpt) REVERT: S 90 ASP cc_start: 0.8651 (m-30) cc_final: 0.8421 (m-30) outliers start: 26 outliers final: 13 residues processed: 144 average time/residue: 1.2561 time to fit residues: 193.1107 Evaluate side-chains 138 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 124 time to evaluate : 0.966 ------------------------------------------------------------------------------- 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 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 155 VAL Chi-restraints excluded: chain S residue 204 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 67 optimal weight: 3.9990 chunk 12 optimal weight: 0.3980 chunk 107 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 77 optimal weight: 6.9990 chunk 103 optimal weight: 7.9990 chunk 99 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 83 optimal weight: 5.9990 chunk 40 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- 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 = 0.4206 r_free = 0.4206 target = 0.195471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 92)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.139397 restraints weight = 9847.091| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 1.62 r_work: 0.3317 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 9824 Z= 0.177 Angle : 0.582 9.005 13304 Z= 0.316 Chirality : 0.044 0.177 1501 Planarity : 0.005 0.058 1667 Dihedral : 5.897 48.880 1377 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.67 % Allowed : 11.62 % Favored : 85.71 % 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: 1.04 (0.24), residues: 1196 helix: 2.14 (0.25), residues: 422 sheet: 0.64 (0.30), residues: 273 loop : -0.53 (0.27), residues: 501 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 0.018 0.002 PHE A 196 TYR 0.024 0.002 TYR S 190 ARG 0.009 0.001 ARG R 307 Details of bonding type rmsd hydrogen bonds : bond 0.04405 ( 491) hydrogen bonds : angle 4.58046 ( 1383) SS BOND : bond 0.00383 ( 7) SS BOND : angle 1.38483 ( 14) covalent geometry : bond 0.00413 ( 9817) covalent geometry : angle 0.58095 (13290) *********************** 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 151 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 123 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 ASN cc_start: 0.8388 (m-40) cc_final: 0.8055 (m-40) REVERT: B 23 LYS cc_start: 0.7883 (tptp) cc_final: 0.7683 (tptp) REVERT: B 44 GLN cc_start: 0.8384 (OUTLIER) cc_final: 0.7736 (mp10) REVERT: B 101 MET cc_start: 0.8844 (OUTLIER) cc_final: 0.8385 (mtm) REVERT: B 217 MET cc_start: 0.8459 (pmm) cc_final: 0.8115 (pp-130) REVERT: G 58 GLU cc_start: 0.7670 (pt0) cc_final: 0.7390 (pt0) REVERT: L 46 MET cc_start: 0.6704 (OUTLIER) cc_final: 0.5768 (ptt) REVERT: S 76 LYS cc_start: 0.7994 (mtpp) cc_final: 0.7470 (mtpt) REVERT: S 90 ASP cc_start: 0.8648 (m-30) cc_final: 0.8397 (m-30) outliers start: 28 outliers final: 13 residues processed: 137 average time/residue: 1.2868 time to fit residues: 188.1865 Evaluate side-chains 131 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 115 time to evaluate : 0.976 ------------------------------------------------------------------------------- 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 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 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 Chi-restraints excluded: chain S residue 213 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 117 optimal weight: 0.8980 chunk 60 optimal weight: 40.0000 chunk 54 optimal weight: 9.9990 chunk 91 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 81 optimal weight: 6.9990 chunk 40 optimal weight: 0.8980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 268 ASN S 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.196253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.141075 restraints weight = 9808.070| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 1.58 r_work: 0.3325 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 9824 Z= 0.153 Angle : 0.549 8.237 13304 Z= 0.298 Chirality : 0.042 0.168 1501 Planarity : 0.004 0.060 1667 Dihedral : 5.614 48.810 1377 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.95 % Allowed : 12.00 % Favored : 85.05 % 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: 1.06 (0.24), residues: 1196 helix: 2.21 (0.25), residues: 426 sheet: 0.53 (0.30), residues: 277 loop : -0.51 (0.28), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.003 0.001 HIS B 183 PHE 0.018 0.002 PHE R 45 TYR 0.021 0.001 TYR S 190 ARG 0.006 0.001 ARG R 307 Details of bonding type rmsd hydrogen bonds : bond 0.04099 ( 491) hydrogen bonds : angle 4.46725 ( 1383) SS BOND : bond 0.00382 ( 7) SS BOND : angle 1.28588 ( 14) covalent geometry : bond 0.00351 ( 9817) covalent geometry : angle 0.54756 (13290) *********************** 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 151 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 120 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 ASN cc_start: 0.8381 (m-40) cc_final: 0.8042 (m-40) REVERT: A 275 GLU cc_start: 0.8778 (OUTLIER) cc_final: 0.8510 (tp30) REVERT: B 23 LYS cc_start: 0.7875 (tptp) cc_final: 0.7672 (tptp) REVERT: B 101 MET cc_start: 0.8804 (OUTLIER) cc_final: 0.8548 (mpp) REVERT: B 217 MET cc_start: 0.8439 (pmm) cc_final: 0.8215 (pmt) REVERT: G 58 GLU cc_start: 0.7635 (OUTLIER) cc_final: 0.6970 (tt0) REVERT: L 46 MET cc_start: 0.6697 (OUTLIER) cc_final: 0.5791 (ptt) REVERT: R 311 TYR cc_start: 0.5784 (t80) cc_final: 0.5576 (t80) REVERT: S 76 LYS cc_start: 0.7985 (mtpp) cc_final: 0.7466 (mtpt) REVERT: S 90 ASP cc_start: 0.8616 (m-30) cc_final: 0.8383 (m-30) outliers start: 31 outliers final: 11 residues processed: 135 average time/residue: 1.2914 time to fit residues: 186.2592 Evaluate side-chains 130 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 115 time to evaluate : 1.003 ------------------------------------------------------------------------------- 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 96 ARG Chi-restraints excluded: chain B residue 101 MET 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 296 VAL 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: 1.9990 chunk 105 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 chunk 64 optimal weight: 3.9990 chunk 59 optimal weight: 0.0000 chunk 61 optimal weight: 7.9990 chunk 103 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 chunk 72 optimal weight: 0.0370 chunk 81 optimal weight: 3.9990 overall best weight: 1.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 181 HIS S 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.196059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.137142 restraints weight = 9908.021| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 1.74 r_work: 0.3326 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 9824 Z= 0.155 Angle : 0.553 8.930 13304 Z= 0.299 Chirality : 0.042 0.171 1501 Planarity : 0.004 0.059 1667 Dihedral : 5.684 53.706 1377 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.29 % Allowed : 12.76 % Favored : 84.95 % 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: 1.18 (0.24), residues: 1196 helix: 2.38 (0.25), residues: 419 sheet: 0.60 (0.30), residues: 275 loop : -0.48 (0.28), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.003 0.001 HIS B 183 PHE 0.018 0.002 PHE R 45 TYR 0.022 0.002 TYR S 190 ARG 0.006 0.001 ARG A 32 Details of bonding type rmsd hydrogen bonds : bond 0.04091 ( 491) hydrogen bonds : angle 4.44417 ( 1383) SS BOND : bond 0.00375 ( 7) SS BOND : angle 1.26818 ( 14) covalent geometry : bond 0.00358 ( 9817) covalent geometry : angle 0.55163 (13290) *********************** 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 148 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 124 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 ASN cc_start: 0.8355 (m-40) cc_final: 0.8008 (m-40) REVERT: A 275 GLU cc_start: 0.8700 (OUTLIER) cc_final: 0.8442 (tp30) REVERT: A 318 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7658 (tt0) REVERT: B 23 LYS cc_start: 0.7985 (tptp) cc_final: 0.7298 (tmmt) REVERT: B 101 MET cc_start: 0.8781 (OUTLIER) cc_final: 0.8359 (mtm) REVERT: B 258 ASP cc_start: 0.8525 (t0) cc_final: 0.8303 (t0) REVERT: G 58 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.7078 (tt0) REVERT: L 46 MET cc_start: 0.6652 (OUTLIER) cc_final: 0.5715 (ptt) REVERT: R 311 TYR cc_start: 0.5691 (t80) cc_final: 0.5396 (t80) REVERT: S 76 LYS cc_start: 0.7962 (mtpp) cc_final: 0.7430 (mtpt) REVERT: S 90 ASP cc_start: 0.8613 (m-30) cc_final: 0.8356 (m-30) outliers start: 24 outliers final: 12 residues processed: 137 average time/residue: 1.4425 time to fit residues: 210.3301 Evaluate side-chains 138 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 121 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 96 ARG Chi-restraints excluded: chain B residue 101 MET 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 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: 0.0980 chunk 79 optimal weight: 0.8980 chunk 73 optimal weight: 4.9990 chunk 98 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 chunk 95 optimal weight: 0.8980 chunk 71 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 108 optimal weight: 0.6980 chunk 112 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN L 70 GLN R 25 GLN S 82 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.198066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.142394 restraints weight = 9964.293| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 1.57 r_work: 0.3357 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9824 Z= 0.118 Angle : 0.507 7.218 13304 Z= 0.274 Chirality : 0.041 0.156 1501 Planarity : 0.004 0.060 1667 Dihedral : 5.535 57.084 1377 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.38 % Allowed : 13.14 % Favored : 84.48 % 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: 1.24 (0.25), residues: 1196 helix: 2.41 (0.25), residues: 426 sheet: 0.61 (0.30), residues: 278 loop : -0.46 (0.28), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 PHE 0.019 0.001 PHE R 45 TYR 0.018 0.001 TYR S 190 ARG 0.011 0.001 ARG R 307 Details of bonding type rmsd hydrogen bonds : bond 0.03657 ( 491) hydrogen bonds : angle 4.31533 ( 1383) SS BOND : bond 0.00302 ( 7) SS BOND : angle 1.10420 ( 14) covalent geometry : bond 0.00262 ( 9817) covalent geometry : angle 0.50611 (13290) *********************** 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 148 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 123 time to evaluate : 1.024 Fit side-chains revert: symmetry clash REVERT: A 22 ASN cc_start: 0.8286 (m-40) cc_final: 0.7969 (m-40) REVERT: A 275 GLU cc_start: 0.8696 (OUTLIER) cc_final: 0.8437 (tp30) REVERT: B 101 MET cc_start: 0.8737 (OUTLIER) cc_final: 0.8464 (mpp) REVERT: B 217 MET cc_start: 0.8338 (OUTLIER) cc_final: 0.8058 (pmt) REVERT: B 258 ASP cc_start: 0.8517 (t0) cc_final: 0.8294 (t0) REVERT: G 58 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7090 (tt0) REVERT: L 46 MET cc_start: 0.6639 (OUTLIER) cc_final: 0.5735 (ptt) REVERT: R 181 HIS cc_start: 0.7677 (OUTLIER) cc_final: 0.7140 (t-90) REVERT: R 311 TYR cc_start: 0.5852 (t80) cc_final: 0.5640 (t80) REVERT: S 76 LYS cc_start: 0.8003 (mtpp) cc_final: 0.7455 (mtpt) REVERT: S 90 ASP cc_start: 0.8592 (m-30) cc_final: 0.8372 (m-30) outliers start: 25 outliers final: 7 residues processed: 133 average time/residue: 1.3473 time to fit residues: 190.8951 Evaluate side-chains 131 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 118 time to evaluate : 1.068 ------------------------------------------------------------------------------- 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 101 MET Chi-restraints excluded: chain B residue 217 MET 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 181 HIS Chi-restraints excluded: chain R residue 257 LEU Chi-restraints excluded: chain R residue 296 VAL Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 204 SER 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: 5.9990 chunk 11 optimal weight: 0.8980 chunk 95 optimal weight: 0.3980 chunk 81 optimal weight: 10.0000 chunk 77 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 112 optimal weight: 0.4980 chunk 106 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 ASN B 175 GLN B 259 GLN S 82 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.198800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.140904 restraints weight = 10021.047| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 1.67 r_work: 0.3367 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9824 Z= 0.121 Angle : 0.511 6.981 13304 Z= 0.276 Chirality : 0.041 0.162 1501 Planarity : 0.004 0.062 1667 Dihedral : 5.436 54.400 1377 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.19 % Allowed : 13.62 % Favored : 84.19 % 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: 1.30 (0.25), residues: 1196 helix: 2.49 (0.25), residues: 426 sheet: 0.62 (0.30), residues: 278 loop : -0.44 (0.28), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.004 0.001 HIS S 35 PHE 0.018 0.001 PHE R 45 TYR 0.020 0.001 TYR S 190 ARG 0.010 0.001 ARG R 307 Details of bonding type rmsd hydrogen bonds : bond 0.03653 ( 491) hydrogen bonds : angle 4.26092 ( 1383) SS BOND : bond 0.00310 ( 7) SS BOND : angle 1.06337 ( 14) covalent geometry : bond 0.00270 ( 9817) covalent geometry : angle 0.51053 (13290) *********************** 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 144 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 121 time to evaluate : 1.113 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 ASN cc_start: 0.8288 (m-40) cc_final: 0.7972 (m-40) REVERT: A 275 GLU cc_start: 0.8673 (OUTLIER) cc_final: 0.8398 (tp30) REVERT: B 23 LYS cc_start: 0.7672 (tptp) cc_final: 0.7413 (tptp) REVERT: B 101 MET cc_start: 0.8760 (OUTLIER) cc_final: 0.8452 (mpp) REVERT: B 234 PHE cc_start: 0.9242 (OUTLIER) cc_final: 0.7645 (m-80) REVERT: B 258 ASP cc_start: 0.8532 (t0) cc_final: 0.8290 (t0) REVERT: G 58 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.7092 (tt0) REVERT: L 46 MET cc_start: 0.6615 (OUTLIER) cc_final: 0.5668 (ptt) REVERT: R 181 HIS cc_start: 0.7530 (OUTLIER) cc_final: 0.7029 (t-90) REVERT: R 311 TYR cc_start: 0.5932 (t80) cc_final: 0.5673 (t80) REVERT: S 76 LYS cc_start: 0.7959 (mtpp) cc_final: 0.7427 (mtpt) REVERT: S 90 ASP cc_start: 0.8578 (m-30) cc_final: 0.8362 (m-30) outliers start: 23 outliers final: 9 residues processed: 131 average time/residue: 1.3932 time to fit residues: 194.1308 Evaluate side-chains 132 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 117 time to evaluate : 0.903 ------------------------------------------------------------------------------- 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 101 MET Chi-restraints excluded: chain B residue 234 PHE 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 181 HIS 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 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: 0.4980 chunk 46 optimal weight: 2.9990 chunk 111 optimal weight: 0.6980 chunk 57 optimal weight: 0.6980 chunk 84 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 45 optimal weight: 5.9990 chunk 97 optimal weight: 0.9990 chunk 7 optimal weight: 0.0050 chunk 72 optimal weight: 0.9990 overall best weight: 0.5594 ------------------------------------------------------------------------------- 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 = 0.4241 r_free = 0.4241 target = 0.199273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 91)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.143714 restraints weight = 9940.770| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 1.56 r_work: 0.3375 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 9824 Z= 0.108 Angle : 0.491 6.503 13304 Z= 0.266 Chirality : 0.041 0.156 1501 Planarity : 0.004 0.062 1667 Dihedral : 5.214 51.750 1377 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.81 % Allowed : 14.86 % Favored : 83.33 % 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: 1.40 (0.25), residues: 1196 helix: 2.55 (0.25), residues: 427 sheet: 0.80 (0.30), residues: 274 loop : -0.45 (0.29), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 PHE 0.018 0.001 PHE R 45 TYR 0.017 0.001 TYR S 190 ARG 0.013 0.000 ARG R 307 Details of bonding type rmsd hydrogen bonds : bond 0.03438 ( 491) hydrogen bonds : angle 4.20454 ( 1383) SS BOND : bond 0.00265 ( 7) SS BOND : angle 0.97080 ( 14) covalent geometry : bond 0.00235 ( 9817) covalent geometry : angle 0.49056 (13290) *********************** 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 140 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 121 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 ASN cc_start: 0.8242 (m-40) cc_final: 0.7964 (m-40) REVERT: A 275 GLU cc_start: 0.8673 (OUTLIER) cc_final: 0.8398 (tp30) REVERT: B 23 LYS cc_start: 0.7564 (tptp) cc_final: 0.7308 (tptp) REVERT: B 101 MET cc_start: 0.8698 (OUTLIER) cc_final: 0.8448 (mpp) REVERT: B 215 GLU cc_start: 0.7466 (OUTLIER) cc_final: 0.7009 (mp0) REVERT: B 234 PHE cc_start: 0.9226 (OUTLIER) cc_final: 0.7612 (m-80) REVERT: B 258 ASP cc_start: 0.8516 (t0) cc_final: 0.8268 (t0) REVERT: G 58 GLU cc_start: 0.7641 (OUTLIER) cc_final: 0.7125 (tt0) REVERT: L 46 MET cc_start: 0.6667 (OUTLIER) cc_final: 0.5853 (ptt) REVERT: R 181 HIS cc_start: 0.7548 (OUTLIER) cc_final: 0.7038 (t-90) REVERT: R 311 TYR cc_start: 0.5875 (t80) cc_final: 0.5637 (t80) REVERT: S 90 ASP cc_start: 0.8564 (m-30) cc_final: 0.8353 (m-30) outliers start: 19 outliers final: 10 residues processed: 131 average time/residue: 1.3981 time to fit residues: 194.7733 Evaluate side-chains 135 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 118 time to evaluate : 1.045 ------------------------------------------------------------------------------- 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 101 MET Chi-restraints excluded: chain B residue 215 GLU 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 181 HIS 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 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: 0.0970 chunk 62 optimal weight: 0.9990 chunk 84 optimal weight: 0.3980 chunk 10 optimal weight: 0.9990 chunk 54 optimal weight: 6.9990 chunk 35 optimal weight: 1.9990 chunk 112 optimal weight: 5.9990 chunk 75 optimal weight: 0.8980 chunk 33 optimal weight: 0.0770 chunk 113 optimal weight: 7.9990 overall best weight: 0.4938 ------------------------------------------------------------------------------- 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 = 0.4247 r_free = 0.4247 target = 0.199879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.141041 restraints weight = 10078.781| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 1.77 r_work: 0.3392 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3273 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 9824 Z= 0.104 Angle : 0.487 6.488 13304 Z= 0.263 Chirality : 0.040 0.155 1501 Planarity : 0.004 0.062 1667 Dihedral : 5.032 47.678 1377 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.52 % Allowed : 15.81 % Favored : 82.67 % 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: 1.45 (0.25), residues: 1196 helix: 2.62 (0.25), residues: 426 sheet: 0.83 (0.30), residues: 276 loop : -0.46 (0.29), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 PHE 0.019 0.001 PHE R 45 TYR 0.017 0.001 TYR S 190 ARG 0.013 0.000 ARG R 307 Details of bonding type rmsd hydrogen bonds : bond 0.03339 ( 491) hydrogen bonds : angle 4.13568 ( 1383) SS BOND : bond 0.00256 ( 7) SS BOND : angle 0.95278 ( 14) covalent geometry : bond 0.00224 ( 9817) covalent geometry : angle 0.48602 (13290) ********************** 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 139 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 123 time to evaluate : 1.036 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 275 GLU cc_start: 0.8667 (OUTLIER) cc_final: 0.8385 (tp30) REVERT: B 23 LYS cc_start: 0.7529 (tptp) cc_final: 0.7259 (tptp) REVERT: B 45 MET cc_start: 0.8598 (mtt) cc_final: 0.8385 (mmm) REVERT: B 101 MET cc_start: 0.8697 (OUTLIER) cc_final: 0.8451 (mpp) REVERT: B 234 PHE cc_start: 0.9212 (OUTLIER) cc_final: 0.7627 (m-80) REVERT: B 258 ASP cc_start: 0.8456 (t0) cc_final: 0.8187 (t0) REVERT: G 58 GLU cc_start: 0.7622 (OUTLIER) cc_final: 0.7108 (tt0) REVERT: L 46 MET cc_start: 0.6477 (OUTLIER) cc_final: 0.5621 (ptt) REVERT: R 181 HIS cc_start: 0.7278 (OUTLIER) cc_final: 0.6816 (t-90) REVERT: R 311 TYR cc_start: 0.5847 (t80) cc_final: 0.5618 (t80) REVERT: S 90 ASP cc_start: 0.8510 (m-30) cc_final: 0.8215 (m-30) outliers start: 16 outliers final: 8 residues processed: 129 average time/residue: 1.3702 time to fit residues: 188.1957 Evaluate side-chains 135 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 121 time to evaluate : 0.999 ------------------------------------------------------------------------------- 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 101 MET 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 181 HIS 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 204 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 75 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 4 optimal weight: 0.3980 chunk 69 optimal weight: 0.0060 chunk 24 optimal weight: 0.3980 chunk 100 optimal weight: 0.9990 chunk 41 optimal weight: 6.9990 chunk 62 optimal weight: 0.8980 chunk 40 optimal weight: 4.9990 chunk 49 optimal weight: 0.5980 chunk 67 optimal weight: 0.6980 overall best weight: 0.4196 ------------------------------------------------------------------------------- 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 = 0.4253 r_free = 0.4253 target = 0.200457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 91)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.141975 restraints weight = 10000.817| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 1.79 r_work: 0.3410 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3294 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9824 Z= 0.099 Angle : 0.480 6.545 13304 Z= 0.259 Chirality : 0.040 0.155 1501 Planarity : 0.004 0.062 1667 Dihedral : 4.873 44.753 1377 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.71 % Allowed : 15.81 % Favored : 82.48 % 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: 1.48 (0.25), residues: 1196 helix: 2.67 (0.25), residues: 426 sheet: 0.92 (0.30), residues: 265 loop : -0.47 (0.28), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 PHE 0.019 0.001 PHE R 45 TYR 0.016 0.001 TYR S 190 ARG 0.013 0.000 ARG R 307 Details of bonding type rmsd hydrogen bonds : bond 0.03224 ( 491) hydrogen bonds : angle 4.09417 ( 1383) SS BOND : bond 0.00251 ( 7) SS BOND : angle 0.89514 ( 14) covalent geometry : bond 0.00214 ( 9817) covalent geometry : angle 0.47956 (13290) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10186.42 seconds wall clock time: 173 minutes 28.09 seconds (10408.09 seconds total)