Starting phenix.real_space_refine on Thu Feb 13 12:46:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t6s_25726/02_2025/7t6s_25726.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t6s_25726/02_2025/7t6s_25726.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7t6s_25726/02_2025/7t6s_25726.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t6s_25726/02_2025/7t6s_25726.map" model { file = "/net/cci-nas-00/data/ceres_data/7t6s_25726/02_2025/7t6s_25726.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t6s_25726/02_2025/7t6s_25726.cif" } resolution = 3.0 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= 0.011 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: 5 Type Number sf(0) Gaussians S 63 5.16 5 Cl 1 4.86 5 C 5702 2.51 5 N 1504 2.21 5 O 1636 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 8906 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1753 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 214} Chain breaks: 2 Chain: "B" Number of atoms: 2584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2584 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 330} Chain: "C" Number of atoms: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 418 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 4, 'TRANS': 49} Chain: "E" Number of atoms: 1778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1778 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Chain: "R" Number of atoms: 2346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2346 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 13, 'TRANS': 284} Chain: "R" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'FUI': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.24, per 1000 atoms: 0.59 Number of scatterers: 8906 At special positions: 0 Unit cell: (117.72, 115.56, 103.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 1 17.00 S 63 16.00 O 1636 8.00 N 1504 7.00 C 5702 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.34 Conformation dependent library (CDL) restraints added in 1.0 seconds 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2110 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 14 sheets defined 38.3% alpha, 23.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'A' and resid 8 through 31 removed outlier: 3.544A pdb=" N ASP A 20 " --> pdb=" O SER A 16 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASN A 22 " --> pdb=" O MET A 18 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LEU A 23 " --> pdb=" O ILE A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 removed outlier: 3.506A pdb=" N LYS A 51 " --> pdb=" O SER A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.637A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.633A 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 242 through 255 Processing helix chain 'A' and resid 270 through 279 removed outlier: 3.831A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 295 through 309 removed outlier: 4.011A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 7 through 26 removed outlier: 3.532A pdb=" N ALA B 11 " --> pdb=" O LEU B 7 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLU B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA B 26 " --> pdb=" O ARG B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 10 through 24 Processing helix chain 'C' and resid 29 through 44 removed outlier: 3.944A pdb=" N LEU C 37 " --> pdb=" O ALA C 33 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TYR C 40 " --> pdb=" O ASP C 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 220 through 224 removed outlier: 3.730A pdb=" N VAL E 224 " --> pdb=" O ALA E 221 " (cutoff:3.500A) Processing helix chain 'R' and resid 23 through 26 Processing helix chain 'R' and resid 27 through 54 Processing helix chain 'R' and resid 58 through 77 removed outlier: 3.512A pdb=" N THR R 75 " --> pdb=" O ASP R 71 " (cutoff:3.500A) Processing helix chain 'R' and resid 78 through 87 removed outlier: 3.881A pdb=" N SER R 84 " --> pdb=" O PHE R 80 " (cutoff:3.500A) Processing helix chain 'R' and resid 94 through 129 removed outlier: 3.560A pdb=" N HIS R 102 " --> pdb=" O CYS R 98 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N ILE R 103 " --> pdb=" O LYS R 99 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE R 114 " --> pdb=" O PHE R 110 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL R 127 " --> pdb=" O ARG R 123 " (cutoff:3.500A) Processing helix chain 'R' and resid 131 through 136 Processing helix chain 'R' and resid 138 through 147 removed outlier: 3.951A pdb=" N VAL R 147 " --> pdb=" O MET R 143 " (cutoff:3.500A) Processing helix chain 'R' and resid 147 through 156 Processing helix chain 'R' and resid 157 through 163 Processing helix chain 'R' and resid 180 through 185 Processing helix chain 'R' and resid 186 through 208 removed outlier: 3.637A pdb=" N ARG R 205 " --> pdb=" O ARG R 201 " (cutoff:3.500A) Processing helix chain 'R' and resid 210 through 231 removed outlier: 3.850A pdb=" N ILE R 228 " --> pdb=" O ILE R 224 " (cutoff:3.500A) Processing helix chain 'R' and resid 237 through 267 removed outlier: 3.935A pdb=" N PHE R 250 " --> pdb=" O VAL R 246 " (cutoff:3.500A) Proline residue: R 256 - end of helix Processing helix chain 'R' and resid 267 through 273 Processing helix chain 'R' and resid 277 through 303 removed outlier: 4.242A pdb=" N ASP R 281 " --> pdb=" O TYR R 277 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ASN R 285 " --> pdb=" O ASP R 281 " (cutoff:3.500A) Proline residue: R 286 - end of helix removed outlier: 3.583A pdb=" N ASN R 294 " --> pdb=" O LEU R 290 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N SER R 295 " --> pdb=" O ALA R 291 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N CYS R 296 " --> pdb=" O PHE R 292 " (cutoff:3.500A) Proline residue: R 299 - end of helix Processing helix chain 'R' and resid 306 through 314 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 3.621A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.523A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.504A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.929A 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: 6.245A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.830A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.693A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.388A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 4.214A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'E' and resid 58 through 60 removed outlier: 6.650A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 58 through 60 removed outlier: 6.650A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 140 through 141 Processing sheet with id=AB4, first strand: chain 'E' and resid 146 through 148 removed outlier: 6.094A pdb=" N LEU E 178 " --> pdb=" O LEU E 187 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N LEU E 187 " --> pdb=" O LEU E 178 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASN E 194 " --> pdb=" O TYR E 190 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'R' and resid 164 through 168 447 hydrogen bonds defined for protein. 1248 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: 3.10 Time building geometry restraints manager: 2.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1430 1.30 - 1.43: 2465 1.43 - 1.56: 5111 1.56 - 1.68: 0 1.68 - 1.81: 93 Bond restraints: 9099 Sorted by residual: bond pdb=" C08 FUI R 401 " pdb=" N07 FUI R 401 " ideal model delta sigma weight residual 1.383 1.292 0.091 2.00e-02 2.50e+03 2.08e+01 bond pdb=" C PRO C 49 " pdb=" O PRO C 49 " ideal model delta sigma weight residual 1.237 1.185 0.052 1.16e-02 7.43e+03 2.04e+01 bond pdb=" C PHE R 110 " pdb=" O PHE R 110 " ideal model delta sigma weight residual 1.236 1.177 0.058 1.31e-02 5.83e+03 1.98e+01 bond pdb=" C PRO B 94 " pdb=" O PRO B 94 " ideal model delta sigma weight residual 1.235 1.201 0.034 7.90e-03 1.60e+04 1.86e+01 bond pdb=" C18 FUI R 401 " pdb=" N19 FUI R 401 " ideal model delta sigma weight residual 1.371 1.453 -0.082 2.00e-02 2.50e+03 1.68e+01 ... (remaining 9094 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.24: 11459 2.24 - 4.49: 801 4.49 - 6.73: 53 6.73 - 8.97: 11 8.97 - 11.21: 5 Bond angle restraints: 12329 Sorted by residual: angle pdb=" N LEU R 81 " pdb=" CA LEU R 81 " pdb=" C LEU R 81 " ideal model delta sigma weight residual 113.97 105.43 8.54 1.28e+00 6.10e-01 4.46e+01 angle pdb=" N GLY R 209 " pdb=" CA GLY R 209 " pdb=" C GLY R 209 " ideal model delta sigma weight residual 113.37 121.86 -8.49 1.34e+00 5.57e-01 4.02e+01 angle pdb=" N VAL B 315 " pdb=" CA VAL B 315 " pdb=" C VAL B 315 " ideal model delta sigma weight residual 109.58 101.51 8.07 1.29e+00 6.01e-01 3.91e+01 angle pdb=" N PHE R 110 " pdb=" CA PHE R 110 " pdb=" C PHE R 110 " ideal model delta sigma weight residual 113.18 106.19 6.99 1.21e+00 6.83e-01 3.33e+01 angle pdb=" N THR R 265 " pdb=" CA THR R 265 " pdb=" C THR R 265 " ideal model delta sigma weight residual 113.41 106.69 6.72 1.22e+00 6.72e-01 3.03e+01 ... (remaining 12324 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.57: 4880 17.57 - 35.14: 419 35.14 - 52.71: 60 52.71 - 70.28: 14 70.28 - 87.84: 10 Dihedral angle restraints: 5383 sinusoidal: 2109 harmonic: 3274 Sorted by residual: dihedral pdb=" CB CYS E 159 " pdb=" SG CYS E 159 " pdb=" SG CYS E 229 " pdb=" CB CYS E 229 " ideal model delta sinusoidal sigma weight residual 93.00 170.64 -77.64 1 1.00e+01 1.00e-02 7.55e+01 dihedral pdb=" C ASN R 108 " pdb=" N ASN R 108 " pdb=" CA ASN R 108 " pdb=" CB ASN R 108 " ideal model delta harmonic sigma weight residual -122.60 -139.29 16.69 0 2.50e+00 1.60e-01 4.46e+01 dihedral pdb=" N ASN R 108 " pdb=" C ASN R 108 " pdb=" CA ASN R 108 " pdb=" CB ASN R 108 " ideal model delta harmonic sigma weight residual 122.80 136.20 -13.40 0 2.50e+00 1.60e-01 2.87e+01 ... (remaining 5380 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.119: 1106 0.119 - 0.237: 271 0.237 - 0.356: 23 0.356 - 0.474: 2 0.474 - 0.593: 1 Chirality restraints: 1403 Sorted by residual: chirality pdb=" CA ASN R 108 " pdb=" N ASN R 108 " pdb=" C ASN R 108 " pdb=" CB ASN R 108 " both_signs ideal model delta sigma weight residual False 2.51 1.92 0.59 2.00e-01 2.50e+01 8.79e+00 chirality pdb=" CA TRP R 254 " pdb=" N TRP R 254 " pdb=" C TRP R 254 " pdb=" CB TRP R 254 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 3.93e+00 chirality pdb=" CA ARG E 191 " pdb=" N ARG E 191 " pdb=" C ARG E 191 " pdb=" CB ARG E 191 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.33e+00 ... (remaining 1400 not shown) Planarity restraints: 1549 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 54 " 0.017 2.00e-02 2.50e+03 3.55e-02 1.26e+01 pdb=" C LYS A 54 " -0.061 2.00e-02 2.50e+03 pdb=" O LYS A 54 " 0.023 2.00e-02 2.50e+03 pdb=" N ILE A 55 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG E 191 " 0.016 2.00e-02 2.50e+03 3.31e-02 1.10e+01 pdb=" C ARG E 191 " -0.057 2.00e-02 2.50e+03 pdb=" O ARG E 191 " 0.021 2.00e-02 2.50e+03 pdb=" N MET E 192 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS R 99 " 0.016 2.00e-02 2.50e+03 3.26e-02 1.06e+01 pdb=" C LYS R 99 " -0.056 2.00e-02 2.50e+03 pdb=" O LYS R 99 " 0.021 2.00e-02 2.50e+03 pdb=" N LEU R 100 " 0.020 2.00e-02 2.50e+03 ... (remaining 1546 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1247 2.76 - 3.29: 8725 3.29 - 3.83: 14689 3.83 - 4.36: 19426 4.36 - 4.90: 32229 Nonbonded interactions: 76316 Sorted by model distance: nonbonded pdb=" OG SER E 161 " pdb=" O LYS E 163 " model vdw 2.223 3.040 nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP C 48 " model vdw 2.257 3.040 nonbonded pdb=" NH1 ARG E 202 " pdb=" OD2 ASP E 223 " model vdw 2.281 3.120 nonbonded pdb=" OG SER B 147 " pdb=" O VAL B 187 " model vdw 2.285 3.040 nonbonded pdb=" O ARG B 68 " pdb=" OG SER B 84 " model vdw 2.293 3.040 ... (remaining 76311 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: 0.520 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: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.610 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 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 : 0.013 0.091 9099 Z= 0.840 Angle : 1.286 11.214 12329 Z= 0.916 Chirality : 0.096 0.593 1403 Planarity : 0.008 0.071 1549 Dihedral : 13.455 87.844 3267 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.10 % Allowed : 4.33 % Favored : 95.57 % Cbeta Deviations : 0.28 % Peptide Plane: Cis-proline : 2.94 % 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: -0.64 (0.24), residues: 1120 helix: -0.26 (0.25), residues: 392 sheet: 0.30 (0.31), residues: 268 loop : -0.87 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP R 150 HIS 0.009 0.002 HIS E 167 PHE 0.013 0.003 PHE R 80 TYR 0.014 0.003 TYR B 124 ARG 0.006 0.001 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 158 time to evaluate : 0.942 Fit side-chains revert: symmetry clash REVERT: A 245 GLU cc_start: 0.7245 (tt0) cc_final: 0.7002 (pt0) REVERT: B 271 CYS cc_start: 0.7631 (p) cc_final: 0.7298 (p) REVERT: R 103 ILE cc_start: 0.8741 (mt) cc_final: 0.8388 (mp) REVERT: R 314 ILE cc_start: 0.7705 (pt) cc_final: 0.7440 (mm) outliers start: 1 outliers final: 1 residues processed: 158 average time/residue: 1.1260 time to fit residues: 190.7967 Evaluate side-chains 126 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 125 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 27 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 4.9990 chunk 84 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 56 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 87 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 52 optimal weight: 0.9990 chunk 64 optimal weight: 5.9990 chunk 100 optimal weight: 5.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS B 268 ASN E 183 GLN E 186 GLN R 102 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.144466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.109450 restraints weight = 10220.221| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 1.86 r_work: 0.2924 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2784 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.1421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9099 Z= 0.197 Angle : 0.583 9.765 12329 Z= 0.307 Chirality : 0.043 0.146 1403 Planarity : 0.005 0.048 1549 Dihedral : 5.437 50.367 1250 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.34 % Allowed : 11.34 % Favored : 87.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.37 (0.24), residues: 1120 helix: 0.11 (0.25), residues: 405 sheet: 0.32 (0.31), residues: 273 loop : -0.82 (0.28), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 169 HIS 0.007 0.001 HIS E 167 PHE 0.013 0.001 PHE A 196 TYR 0.012 0.001 TYR E 190 ARG 0.003 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 142 time to evaluate : 0.865 Fit side-chains revert: symmetry clash REVERT: A 245 GLU cc_start: 0.8000 (tt0) cc_final: 0.7527 (pt0) REVERT: B 258 ASP cc_start: 0.8447 (t0) cc_final: 0.7981 (t0) REVERT: C 21 MET cc_start: 0.7691 (mmp) cc_final: 0.7425 (mmm) REVERT: E 166 LEU cc_start: 0.8375 (OUTLIER) cc_final: 0.8007 (tt) REVERT: E 219 LEU cc_start: 0.7879 (tt) cc_final: 0.7647 (tt) REVERT: R 103 ILE cc_start: 0.8471 (mt) cc_final: 0.8087 (mp) REVERT: R 197 MET cc_start: 0.5563 (OUTLIER) cc_final: 0.4418 (tpt) outliers start: 13 outliers final: 4 residues processed: 147 average time/residue: 1.0589 time to fit residues: 168.0124 Evaluate side-chains 133 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 127 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain R residue 197 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 0.2980 chunk 6 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 58 optimal weight: 5.9990 chunk 89 optimal weight: 6.9990 chunk 81 optimal weight: 4.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN E 82 GLN E 113 GLN E 183 GLN E 186 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.143506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.109119 restraints weight = 10340.689| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 1.97 r_work: 0.2891 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2752 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9099 Z= 0.220 Angle : 0.567 9.210 12329 Z= 0.294 Chirality : 0.042 0.138 1403 Planarity : 0.004 0.039 1549 Dihedral : 5.279 48.650 1248 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.27 % Allowed : 13.81 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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 (0.25), residues: 1120 helix: 0.37 (0.26), residues: 411 sheet: 0.14 (0.31), residues: 275 loop : -0.88 (0.28), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.006 0.001 HIS E 167 PHE 0.012 0.001 PHE A 189 TYR 0.015 0.001 TYR E 190 ARG 0.003 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 132 time to evaluate : 1.030 Fit side-chains revert: symmetry clash REVERT: A 245 GLU cc_start: 0.7954 (tt0) cc_final: 0.7593 (pt0) REVERT: A 306 GLN cc_start: 0.7448 (OUTLIER) cc_final: 0.6402 (mp10) REVERT: B 258 ASP cc_start: 0.8350 (t0) cc_final: 0.7888 (t0) REVERT: C 21 MET cc_start: 0.7721 (mmp) cc_final: 0.7498 (mmm) REVERT: E 166 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.7980 (tt) REVERT: R 25 LEU cc_start: 0.7446 (OUTLIER) cc_final: 0.7197 (mp) REVERT: R 103 ILE cc_start: 0.8413 (mt) cc_final: 0.7944 (mp) REVERT: R 197 MET cc_start: 0.5389 (OUTLIER) cc_final: 0.4257 (tpt) REVERT: R 312 ARG cc_start: 0.7552 (mmm160) cc_final: 0.7316 (mmm160) outliers start: 22 outliers final: 7 residues processed: 142 average time/residue: 1.1627 time to fit residues: 177.4684 Evaluate side-chains 137 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 126 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 GLN Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 87 MET Chi-restraints excluded: chain R residue 197 MET Chi-restraints excluded: chain R residue 314 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 43 optimal weight: 4.9990 chunk 95 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 37 optimal weight: 6.9990 chunk 34 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 79 optimal weight: 10.0000 chunk 17 optimal weight: 6.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN B 230 ASN B 239 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.142370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.108260 restraints weight = 10300.539| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 1.87 r_work: 0.2884 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2750 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 9099 Z= 0.318 Angle : 0.615 12.055 12329 Z= 0.316 Chirality : 0.045 0.208 1403 Planarity : 0.004 0.040 1549 Dihedral : 5.496 48.919 1248 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.51 % Allowed : 14.02 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.45 (0.24), residues: 1120 helix: 0.34 (0.26), residues: 410 sheet: -0.03 (0.31), residues: 274 loop : -0.98 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 82 HIS 0.006 0.001 HIS E 167 PHE 0.014 0.002 PHE A 189 TYR 0.014 0.002 TYR E 190 ARG 0.004 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 124 time to evaluate : 1.028 Fit side-chains revert: symmetry clash REVERT: A 245 GLU cc_start: 0.7918 (tt0) cc_final: 0.7556 (pt0) REVERT: B 258 ASP cc_start: 0.8407 (t0) cc_final: 0.7945 (t0) REVERT: E 89 GLU cc_start: 0.7800 (pm20) cc_final: 0.6936 (pp20) REVERT: E 166 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.8028 (tt) REVERT: R 25 LEU cc_start: 0.7450 (OUTLIER) cc_final: 0.7190 (mp) REVERT: R 87 MET cc_start: 0.7882 (mtm) cc_final: 0.7648 (mtp) REVERT: R 191 LEU cc_start: 0.7334 (OUTLIER) cc_final: 0.7009 (tm) REVERT: R 197 MET cc_start: 0.5389 (OUTLIER) cc_final: 0.4811 (tmt) REVERT: R 312 ARG cc_start: 0.7457 (OUTLIER) cc_final: 0.7256 (mmm160) outliers start: 34 outliers final: 13 residues processed: 143 average time/residue: 1.1229 time to fit residues: 172.7176 Evaluate side-chains 138 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 120 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 144 LYS Chi-restraints excluded: chain R residue 174 THR Chi-restraints excluded: chain R residue 191 LEU Chi-restraints excluded: chain R residue 197 MET Chi-restraints excluded: chain R residue 243 LEU Chi-restraints excluded: chain R residue 312 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 16 optimal weight: 2.9990 chunk 57 optimal weight: 0.3980 chunk 94 optimal weight: 5.9990 chunk 105 optimal weight: 0.7980 chunk 108 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 113 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.144156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.108677 restraints weight = 10184.910| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 1.84 r_work: 0.2908 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9099 Z= 0.177 Angle : 0.542 12.501 12329 Z= 0.278 Chirality : 0.042 0.165 1403 Planarity : 0.004 0.040 1549 Dihedral : 5.199 48.781 1248 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.99 % Allowed : 15.36 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.26 (0.25), residues: 1120 helix: 0.60 (0.26), residues: 411 sheet: 0.00 (0.31), residues: 273 loop : -0.92 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 169 HIS 0.005 0.001 HIS E 167 PHE 0.014 0.001 PHE A 189 TYR 0.010 0.001 TYR E 190 ARG 0.002 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 131 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 245 GLU cc_start: 0.7848 (tt0) cc_final: 0.7482 (pt0) REVERT: A 306 GLN cc_start: 0.7673 (OUTLIER) cc_final: 0.6567 (mp10) REVERT: B 258 ASP cc_start: 0.8388 (t0) cc_final: 0.7924 (t0) REVERT: C 21 MET cc_start: 0.7593 (mmp) cc_final: 0.7359 (mmm) REVERT: E 89 GLU cc_start: 0.7692 (pm20) cc_final: 0.6925 (pp20) REVERT: E 166 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.8002 (tt) REVERT: E 223 ASP cc_start: 0.7994 (m-30) cc_final: 0.7771 (m-30) REVERT: E 227 TYR cc_start: 0.8912 (m-80) cc_final: 0.8707 (m-80) REVERT: R 98 CYS cc_start: 0.7949 (t) cc_final: 0.7110 (t) REVERT: R 191 LEU cc_start: 0.7397 (OUTLIER) cc_final: 0.7077 (tt) REVERT: R 197 MET cc_start: 0.5588 (OUTLIER) cc_final: 0.4976 (tmt) outliers start: 29 outliers final: 14 residues processed: 147 average time/residue: 1.1316 time to fit residues: 179.4594 Evaluate side-chains 142 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 124 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 GLN Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain E residue 65 LYS Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 101 ILE Chi-restraints excluded: chain R residue 174 THR Chi-restraints excluded: chain R residue 191 LEU Chi-restraints excluded: chain R residue 197 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 43 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 chunk 29 optimal weight: 0.7980 chunk 47 optimal weight: 0.4980 chunk 4 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 105 optimal weight: 0.9990 chunk 24 optimal weight: 0.4980 chunk 92 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN B 220 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 294 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.145532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.112023 restraints weight = 10283.331| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 1.80 r_work: 0.2995 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9099 Z= 0.167 Angle : 0.524 12.477 12329 Z= 0.269 Chirality : 0.041 0.167 1403 Planarity : 0.004 0.040 1549 Dihedral : 5.032 48.839 1248 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.89 % Allowed : 16.39 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.12 (0.25), residues: 1120 helix: 0.76 (0.26), residues: 412 sheet: 0.05 (0.31), residues: 272 loop : -0.87 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 169 HIS 0.004 0.001 HIS E 167 PHE 0.017 0.001 PHE R 163 TYR 0.014 0.001 TYR R 274 ARG 0.002 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 134 time to evaluate : 1.042 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 245 GLU cc_start: 0.7854 (tt0) cc_final: 0.7634 (pt0) REVERT: A 306 GLN cc_start: 0.7582 (OUTLIER) cc_final: 0.6474 (mp10) REVERT: B 258 ASP cc_start: 0.8301 (t0) cc_final: 0.7792 (t0) REVERT: C 21 MET cc_start: 0.7733 (mmp) cc_final: 0.7483 (mmm) REVERT: E 82 GLN cc_start: 0.8490 (tp-100) cc_final: 0.8171 (tp-100) REVERT: E 89 GLU cc_start: 0.7665 (pm20) cc_final: 0.6920 (pp20) REVERT: E 166 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.7993 (tt) REVERT: E 223 ASP cc_start: 0.8008 (m-30) cc_final: 0.7771 (m-30) REVERT: R 98 CYS cc_start: 0.8034 (t) cc_final: 0.7111 (t) REVERT: R 103 ILE cc_start: 0.8352 (mt) cc_final: 0.7990 (mt) REVERT: R 191 LEU cc_start: 0.7424 (OUTLIER) cc_final: 0.7097 (tt) REVERT: R 197 MET cc_start: 0.5841 (OUTLIER) cc_final: 0.5204 (tmt) outliers start: 28 outliers final: 16 residues processed: 149 average time/residue: 1.1411 time to fit residues: 182.1550 Evaluate side-chains 145 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 125 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 GLN Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 101 ILE Chi-restraints excluded: chain R residue 174 THR Chi-restraints excluded: chain R residue 191 LEU Chi-restraints excluded: chain R residue 197 MET Chi-restraints excluded: chain R residue 203 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 40 optimal weight: 0.0370 chunk 49 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 110 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 84 optimal weight: 3.9990 overall best weight: 1.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN A 333 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 113 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.143739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.109114 restraints weight = 10266.835| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 1.86 r_work: 0.2957 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9099 Z= 0.232 Angle : 0.566 12.871 12329 Z= 0.287 Chirality : 0.043 0.169 1403 Planarity : 0.004 0.039 1549 Dihedral : 5.151 48.858 1248 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.89 % Allowed : 17.53 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.20 (0.25), residues: 1120 helix: 0.73 (0.26), residues: 412 sheet: -0.09 (0.31), residues: 274 loop : -0.90 (0.28), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.004 0.001 HIS E 167 PHE 0.017 0.001 PHE R 163 TYR 0.012 0.001 TYR E 190 ARG 0.003 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 127 time to evaluate : 1.025 Fit side-chains revert: symmetry clash REVERT: A 245 GLU cc_start: 0.7880 (tt0) cc_final: 0.7654 (pt0) REVERT: A 306 GLN cc_start: 0.7570 (OUTLIER) cc_final: 0.6518 (mp10) REVERT: B 217 MET cc_start: 0.8223 (ppp) cc_final: 0.7975 (pmm) REVERT: B 258 ASP cc_start: 0.8389 (t0) cc_final: 0.7907 (t0) REVERT: C 21 MET cc_start: 0.7724 (mmp) cc_final: 0.7472 (mmm) REVERT: C 46 LYS cc_start: 0.8238 (OUTLIER) cc_final: 0.7733 (mtpp) REVERT: E 82 GLN cc_start: 0.8424 (tp-100) cc_final: 0.8061 (tp-100) REVERT: E 89 GLU cc_start: 0.7718 (pm20) cc_final: 0.6935 (pp20) REVERT: E 166 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.8007 (tt) REVERT: R 103 ILE cc_start: 0.8501 (mt) cc_final: 0.8161 (mt) REVERT: R 191 LEU cc_start: 0.7414 (OUTLIER) cc_final: 0.7094 (tt) REVERT: R 197 MET cc_start: 0.5627 (OUTLIER) cc_final: 0.5047 (tmt) outliers start: 28 outliers final: 16 residues processed: 142 average time/residue: 1.1407 time to fit residues: 174.4032 Evaluate side-chains 143 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 122 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 GLN Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 101 ILE Chi-restraints excluded: chain R residue 174 THR Chi-restraints excluded: chain R residue 191 LEU Chi-restraints excluded: chain R residue 197 MET Chi-restraints excluded: chain R residue 303 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 66 optimal weight: 3.9990 chunk 46 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 22 optimal weight: 2.9990 chunk 79 optimal weight: 8.9990 chunk 30 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 96 optimal weight: 0.1980 chunk 6 optimal weight: 0.8980 chunk 60 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.140540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.106049 restraints weight = 10338.723| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 1.87 r_work: 0.2921 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2787 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 9099 Z= 0.343 Angle : 0.612 12.175 12329 Z= 0.315 Chirality : 0.045 0.208 1403 Planarity : 0.004 0.040 1549 Dihedral : 5.433 49.050 1248 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.09 % Allowed : 18.25 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.38 (0.25), residues: 1120 helix: 0.56 (0.26), residues: 411 sheet: -0.22 (0.31), residues: 268 loop : -0.94 (0.28), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 82 HIS 0.006 0.001 HIS B 62 PHE 0.017 0.002 PHE R 163 TYR 0.020 0.002 TYR A 296 ARG 0.003 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 126 time to evaluate : 1.071 Fit side-chains revert: symmetry clash REVERT: A 245 GLU cc_start: 0.7958 (tt0) cc_final: 0.7675 (pt0) REVERT: B 258 ASP cc_start: 0.8419 (t0) cc_final: 0.7937 (t0) REVERT: C 21 MET cc_start: 0.7724 (mmp) cc_final: 0.7491 (mmm) REVERT: C 46 LYS cc_start: 0.8266 (OUTLIER) cc_final: 0.7827 (mtpp) REVERT: E 166 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.8015 (tt) REVERT: R 103 ILE cc_start: 0.8557 (mt) cc_final: 0.8219 (mt) REVERT: R 191 LEU cc_start: 0.7195 (OUTLIER) cc_final: 0.6858 (tm) REVERT: R 197 MET cc_start: 0.5532 (OUTLIER) cc_final: 0.4917 (tmt) REVERT: R 270 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.6971 (mp0) outliers start: 30 outliers final: 18 residues processed: 145 average time/residue: 1.1224 time to fit residues: 174.9545 Evaluate side-chains 141 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 118 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 GLN Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 101 ILE Chi-restraints excluded: chain R residue 166 THR Chi-restraints excluded: chain R residue 174 THR Chi-restraints excluded: chain R residue 191 LEU Chi-restraints excluded: chain R residue 197 MET Chi-restraints excluded: chain R residue 270 GLU Chi-restraints excluded: chain R residue 303 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 64 optimal weight: 0.7980 chunk 65 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 54 optimal weight: 6.9990 chunk 98 optimal weight: 0.9990 chunk 88 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 82 optimal weight: 8.9990 chunk 45 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 113 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.144197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.109721 restraints weight = 10246.740| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 1.82 r_work: 0.2929 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9099 Z= 0.188 Angle : 0.539 13.235 12329 Z= 0.277 Chirality : 0.042 0.172 1403 Planarity : 0.004 0.040 1549 Dihedral : 5.158 48.813 1248 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.58 % Allowed : 18.87 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.20 (0.25), residues: 1120 helix: 0.74 (0.26), residues: 410 sheet: -0.07 (0.31), residues: 271 loop : -0.91 (0.29), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 169 HIS 0.004 0.001 HIS E 167 PHE 0.018 0.001 PHE R 163 TYR 0.010 0.001 TYR E 190 ARG 0.002 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 129 time to evaluate : 0.987 Fit side-chains revert: symmetry clash REVERT: A 245 GLU cc_start: 0.7898 (tt0) cc_final: 0.7547 (pt0) REVERT: B 217 MET cc_start: 0.8064 (pmm) cc_final: 0.7850 (ppp) REVERT: B 258 ASP cc_start: 0.8372 (t0) cc_final: 0.7902 (t0) REVERT: C 21 MET cc_start: 0.7708 (mmp) cc_final: 0.7483 (mmm) REVERT: C 46 LYS cc_start: 0.8226 (OUTLIER) cc_final: 0.7747 (mtpp) REVERT: E 87 ARG cc_start: 0.8204 (mtp180) cc_final: 0.7944 (mtp180) REVERT: E 89 GLU cc_start: 0.7696 (pm20) cc_final: 0.6970 (pp20) REVERT: E 166 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.7986 (tt) REVERT: R 87 MET cc_start: 0.7438 (ptp) cc_final: 0.6780 (ptp) REVERT: R 103 ILE cc_start: 0.8468 (mt) cc_final: 0.8124 (mt) REVERT: R 191 LEU cc_start: 0.7414 (OUTLIER) cc_final: 0.7107 (tt) REVERT: R 197 MET cc_start: 0.5448 (OUTLIER) cc_final: 0.4855 (tmt) outliers start: 25 outliers final: 17 residues processed: 144 average time/residue: 1.1583 time to fit residues: 178.8731 Evaluate side-chains 148 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 127 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 193 SER Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 101 ILE Chi-restraints excluded: chain R residue 174 THR Chi-restraints excluded: chain R residue 191 LEU Chi-restraints excluded: chain R residue 197 MET Chi-restraints excluded: chain R residue 303 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 101 optimal weight: 0.6980 chunk 100 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 6 optimal weight: 0.0980 chunk 38 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.146071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.112216 restraints weight = 10260.147| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 1.79 r_work: 0.2972 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9099 Z= 0.168 Angle : 0.525 13.099 12329 Z= 0.270 Chirality : 0.041 0.170 1403 Planarity : 0.004 0.040 1549 Dihedral : 5.006 48.903 1248 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.16 % Allowed : 19.48 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.10 (0.25), residues: 1120 helix: 0.87 (0.26), residues: 410 sheet: -0.05 (0.31), residues: 271 loop : -0.88 (0.29), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 169 HIS 0.004 0.001 HIS E 167 PHE 0.018 0.001 PHE R 163 TYR 0.012 0.001 TYR B 111 ARG 0.001 0.000 ARG B 137 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 134 time to evaluate : 0.978 Fit side-chains REVERT: A 245 GLU cc_start: 0.7944 (tt0) cc_final: 0.7710 (pt0) REVERT: B 217 MET cc_start: 0.8144 (pmm) cc_final: 0.7672 (ppp) REVERT: B 258 ASP cc_start: 0.8299 (t0) cc_final: 0.7874 (t0) REVERT: C 15 LEU cc_start: 0.6016 (OUTLIER) cc_final: 0.5364 (mp) REVERT: C 21 MET cc_start: 0.7716 (mmp) cc_final: 0.7501 (mmm) REVERT: C 46 LYS cc_start: 0.8206 (OUTLIER) cc_final: 0.7600 (mtpp) REVERT: E 82 GLN cc_start: 0.8517 (tp-100) cc_final: 0.8161 (tp-100) REVERT: E 89 GLU cc_start: 0.7626 (pm20) cc_final: 0.6929 (pp20) REVERT: E 90 ASP cc_start: 0.8420 (m-30) cc_final: 0.8181 (m-30) REVERT: E 166 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.7963 (tt) REVERT: R 103 ILE cc_start: 0.8488 (mt) cc_final: 0.8132 (mt) REVERT: R 191 LEU cc_start: 0.7435 (OUTLIER) cc_final: 0.7110 (tt) REVERT: R 197 MET cc_start: 0.5818 (OUTLIER) cc_final: 0.5185 (tmt) REVERT: R 312 ARG cc_start: 0.7351 (mmm160) cc_final: 0.6923 (tpt90) outliers start: 21 outliers final: 13 residues processed: 146 average time/residue: 1.1215 time to fit residues: 176.1265 Evaluate side-chains 146 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 128 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 193 SER Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 174 THR Chi-restraints excluded: chain R residue 191 LEU Chi-restraints excluded: chain R residue 197 MET Chi-restraints excluded: chain R residue 303 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 7 optimal weight: 7.9990 chunk 103 optimal weight: 0.9980 chunk 101 optimal weight: 0.7980 chunk 23 optimal weight: 7.9990 chunk 27 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 9 optimal weight: 0.0010 overall best weight: 0.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN E 113 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.145921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.111714 restraints weight = 10261.057| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 1.82 r_work: 0.3012 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9099 Z= 0.174 Angle : 0.538 12.959 12329 Z= 0.273 Chirality : 0.042 0.171 1403 Planarity : 0.004 0.041 1549 Dihedral : 4.963 48.699 1248 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.16 % Allowed : 19.69 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.05 (0.25), residues: 1120 helix: 0.97 (0.26), residues: 410 sheet: -0.06 (0.31), residues: 271 loop : -0.90 (0.29), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 169 HIS 0.004 0.001 HIS E 167 PHE 0.020 0.001 PHE R 163 TYR 0.023 0.001 TYR A 296 ARG 0.002 0.000 ARG B 314 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6846.22 seconds wall clock time: 121 minutes 44.13 seconds (7304.13 seconds total)