Starting phenix.real_space_refine on Wed Mar 4 02:00:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7bty_30191/03_2026/7bty_30191.cif Found real_map, /net/cci-nas-00/data/ceres_data/7bty_30191/03_2026/7bty_30191.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7bty_30191/03_2026/7bty_30191.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7bty_30191/03_2026/7bty_30191.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7bty_30191/03_2026/7bty_30191.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7bty_30191/03_2026/7bty_30191.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.018 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 44 5.16 5 C 6512 2.51 5 N 1724 2.21 5 O 1888 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 77 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10168 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2775 Classifications: {'peptide': 348} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 335} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 2399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2399 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 8, 'TRANS': 290} Chain breaks: 2 Chain: "C" Number of atoms: 2439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2439 Classifications: {'peptide': 307} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 6, 'TRANS': 300} Chain breaks: 2 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 16 Chain: "L" Number of atoms: 2555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2555 Classifications: {'peptide': 314} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 304} Chain breaks: 4 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 2.35, per 1000 atoms: 0.23 Number of scatterers: 10168 At special positions: 0 Unit cell: (100.845, 104.58, 108.315, 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 44 16.00 O 1888 8.00 N 1724 7.00 C 6512 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.77 Conformation dependent library (CDL) restraints added in 442.4 milliseconds 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2400 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 12 sheets defined 32.3% alpha, 25.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 197 through 202 removed outlier: 3.586A pdb=" N LYS A 201 " --> pdb=" O TRP A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 270 removed outlier: 3.512A pdb=" N ALA A 270 " --> pdb=" O MET A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 435 removed outlier: 3.978A pdb=" N ILE A 431 " --> pdb=" O LEU A 427 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY A 432 " --> pdb=" O GLY A 428 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLN A 433 " --> pdb=" O ASN A 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 40 removed outlier: 3.510A pdb=" N GLN B 38 " --> pdb=" O ALA B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 94 Processing helix chain 'B' and resid 119 through 123 removed outlier: 3.546A pdb=" N ASN B 123 " --> pdb=" O ARG B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 152 Processing helix chain 'B' and resid 158 through 168 Processing helix chain 'B' and resid 169 through 181 Processing helix chain 'B' and resid 184 through 192 removed outlier: 3.817A pdb=" N MET B 189 " --> pdb=" O ASP B 185 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU B 191 " --> pdb=" O GLN B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 216 removed outlier: 3.621A pdb=" N GLU B 208 " --> pdb=" O PRO B 204 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLN B 213 " --> pdb=" O ASN B 209 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS B 214 " --> pdb=" O SER B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 225 removed outlier: 3.621A pdb=" N SER B 223 " --> pdb=" O SER B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 234 Processing helix chain 'B' and resid 234 through 240 Processing helix chain 'B' and resid 247 through 272 removed outlier: 3.702A pdb=" N GLN B 256 " --> pdb=" O VAL B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 275 No H-bonds generated for 'chain 'B' and resid 273 through 275' Processing helix chain 'B' and resid 285 through 297 removed outlier: 3.631A pdb=" N CYS B 295 " --> pdb=" O SER B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 312 Processing helix chain 'B' and resid 313 through 325 removed outlier: 3.540A pdb=" N GLN B 318 " --> pdb=" O LYS B 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 31 removed outlier: 3.559A pdb=" N ILE C 23 " --> pdb=" O SER C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 40 removed outlier: 3.711A pdb=" N SER C 39 " --> pdb=" O GLU C 35 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N MET C 40 " --> pdb=" O GLU C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 55 removed outlier: 3.780A pdb=" N LEU C 54 " --> pdb=" O ASN C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 84 Processing helix chain 'C' and resid 104 through 106 No H-bonds generated for 'chain 'C' and resid 104 through 106' Processing helix chain 'C' and resid 107 through 121 Processing helix chain 'C' and resid 122 through 132 removed outlier: 3.597A pdb=" N PHE C 131 " --> pdb=" O ASP C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 140 removed outlier: 3.591A pdb=" N ASN C 138 " --> pdb=" O THR C 134 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU C 139 " --> pdb=" O LYS C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 169 Processing helix chain 'C' and resid 203 through 206 removed outlier: 3.649A pdb=" N HIS C 206 " --> pdb=" O LYS C 203 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 203 through 206' Processing helix chain 'C' and resid 207 through 227 removed outlier: 3.788A pdb=" N LYS C 213 " --> pdb=" O LYS C 209 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N LEU C 216 " --> pdb=" O GLY C 212 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN C 217 " --> pdb=" O LYS C 213 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL C 219 " --> pdb=" O GLU C 215 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS C 220 " --> pdb=" O LEU C 216 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLN C 224 " --> pdb=" O LYS C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 241 removed outlier: 3.583A pdb=" N SER C 234 " --> pdb=" O GLN C 230 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS C 241 " --> pdb=" O LEU C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 265 removed outlier: 3.766A pdb=" N VAL C 261 " --> pdb=" O ALA C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 280 removed outlier: 4.018A pdb=" N ILE C 271 " --> pdb=" O ASP C 267 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU C 276 " --> pdb=" O ARG C 272 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N THR C 278 " --> pdb=" O LYS C 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 296 removed outlier: 3.927A pdb=" N LEU C 284 " --> pdb=" O GLY C 280 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N SER C 286 " --> pdb=" O GLU C 282 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N HIS C 296 " --> pdb=" O ASP C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 324 removed outlier: 3.576A pdb=" N TYR C 320 " --> pdb=" O VAL C 316 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU C 322 " --> pdb=" O SER C 318 " (cutoff:3.500A) Processing helix chain 'L' and resid 4 through 17 removed outlier: 4.122A pdb=" N ARG L 10 " --> pdb=" O ASP L 6 " (cutoff:3.500A) Processing helix chain 'L' and resid 19 through 23 Processing helix chain 'L' and resid 29 through 34 Processing helix chain 'L' and resid 81 through 87 removed outlier: 4.033A pdb=" N ARG L 86 " --> pdb=" O LYS L 83 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ASN L 87 " --> pdb=" O PHE L 84 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 126 through 129 removed outlier: 3.603A pdb=" N TYR A 140 " --> pdb=" O GLY A 128 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N ALA A 139 " --> pdb=" O ARG A 164 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ARG A 164 " --> pdb=" O ALA A 139 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASN A 175 " --> pdb=" O ASN A 159 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY A 165 " --> pdb=" O HIS A 169 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N HIS A 169 " --> pdb=" O GLY A 165 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N SER A 170 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N PHE A 194 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N SER A 184 " --> pdb=" O LEU A 180 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLY A 416 " --> pdb=" O TYR A 390 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 464 through 466 removed outlier: 7.305A pdb=" N ALA A 465 " --> pdb=" O TYR B 23 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 41 through 42 Processing sheet with id=AA4, first strand: chain 'B' and resid 67 through 69 Processing sheet with id=AA5, first strand: chain 'C' and resid 5 through 7 removed outlier: 4.459A pdb=" N THR C 69 " --> pdb=" O LEU C 65 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 46 through 47 removed outlier: 6.683A pdb=" N ILE C 46 " --> pdb=" O ARG C 305 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'L' and resid 44 through 52 removed outlier: 3.624A pdb=" N ASN L 57 " --> pdb=" O ASN L 49 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N THR L 55 " --> pdb=" O SER L 51 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASP L 60 " --> pdb=" O ASN L 68 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU L 179 " --> pdb=" O SER L 174 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLN L 195 " --> pdb=" O ARG L 188 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 209 through 210 removed outlier: 4.085A pdb=" N VAL L 210 " --> pdb=" O ALA L 235 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N THR L 251 " --> pdb=" O GLY L 234 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLU L 236 " --> pdb=" O SER L 249 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER L 249 " --> pdb=" O GLU L 236 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 230 through 231 removed outlier: 3.715A pdb=" N TYR L 255 " --> pdb=" O SER L 230 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 282 through 284 Processing sheet with id=AB2, first strand: chain 'L' and resid 413 through 421 removed outlier: 3.764A pdb=" N THR L 413 " --> pdb=" O LYS L 434 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER L 421 " --> pdb=" O THR L 426 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR L 426 " --> pdb=" O SER L 421 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLU L 445 " --> pdb=" O LYS L 484 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N LYS L 484 " --> pdb=" O GLU L 445 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL L 447 " --> pdb=" O PRO L 482 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 413 through 421 removed outlier: 3.764A pdb=" N THR L 413 " --> pdb=" O LYS L 434 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER L 421 " --> pdb=" O THR L 426 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR L 426 " --> pdb=" O SER L 421 " (cutoff:3.500A) 458 hydrogen bonds defined for protein. 1287 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: 1.68 Time building geometry restraints manager: 1.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.98 - 1.15: 2 1.15 - 1.32: 1686 1.32 - 1.49: 4442 1.49 - 1.66: 4191 1.66 - 1.83: 65 Bond restraints: 10386 Sorted by residual: bond pdb=" C GLN A 433 " pdb=" O GLN A 433 " ideal model delta sigma weight residual 1.233 0.979 0.254 1.46e-02 4.69e+03 3.03e+02 bond pdb=" CA GLN A 433 " pdb=" C GLN A 433 " ideal model delta sigma weight residual 1.520 1.322 0.197 1.40e-02 5.10e+03 1.99e+02 bond pdb=" CA GLN A 433 " pdb=" CB GLN A 433 " ideal model delta sigma weight residual 1.537 1.402 0.134 1.67e-02 3.59e+03 6.46e+01 bond pdb=" C GLN A 433 " pdb=" N LEU A 434 " ideal model delta sigma weight residual 1.333 1.232 0.101 1.49e-02 4.50e+03 4.57e+01 bond pdb=" CD GLN A 433 " pdb=" NE2 GLN A 433 " ideal model delta sigma weight residual 1.328 1.186 0.142 2.10e-02 2.27e+03 4.56e+01 ... (remaining 10381 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.54: 13797 3.54 - 7.08: 197 7.08 - 10.62: 34 10.62 - 14.16: 5 14.16 - 17.70: 1 Bond angle restraints: 14034 Sorted by residual: angle pdb=" C ALA B 127 " pdb=" N LEU B 128 " pdb=" CA LEU B 128 " ideal model delta sigma weight residual 122.37 113.15 9.22 9.30e-01 1.16e+00 9.84e+01 angle pdb=" N GLU C 98 " pdb=" CA GLU C 98 " pdb=" C GLU C 98 " ideal model delta sigma weight residual 110.80 128.50 -17.70 2.13e+00 2.20e-01 6.90e+01 angle pdb=" C THR C 87 " pdb=" N SER C 88 " pdb=" CA SER C 88 " ideal model delta sigma weight residual 121.70 135.52 -13.82 1.80e+00 3.09e-01 5.90e+01 angle pdb=" C TYR L 147 " pdb=" N TYR L 148 " pdb=" CA TYR L 148 " ideal model delta sigma weight residual 123.21 114.20 9.01 1.19e+00 7.06e-01 5.74e+01 angle pdb=" CA THR C 87 " pdb=" C THR C 87 " pdb=" N SER C 88 " ideal model delta sigma weight residual 116.84 104.59 12.25 1.71e+00 3.42e-01 5.13e+01 ... (remaining 14029 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.20: 5332 17.20 - 34.39: 682 34.39 - 51.59: 147 51.59 - 68.79: 13 68.79 - 85.98: 12 Dihedral angle restraints: 6186 sinusoidal: 2480 harmonic: 3706 Sorted by residual: dihedral pdb=" CA LEU B 128 " pdb=" C LEU B 128 " pdb=" N PRO B 129 " pdb=" CA PRO B 129 " ideal model delta harmonic sigma weight residual 180.00 115.98 64.02 0 5.00e+00 4.00e-02 1.64e+02 dihedral pdb=" N GLU C 98 " pdb=" C GLU C 98 " pdb=" CA GLU C 98 " pdb=" CB GLU C 98 " ideal model delta harmonic sigma weight residual 122.80 150.43 -27.63 0 2.50e+00 1.60e-01 1.22e+02 dihedral pdb=" C GLU C 98 " pdb=" N GLU C 98 " pdb=" CA GLU C 98 " pdb=" CB GLU C 98 " ideal model delta harmonic sigma weight residual -122.60 -149.54 26.94 0 2.50e+00 1.60e-01 1.16e+02 ... (remaining 6183 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.265: 1570 0.265 - 0.529: 2 0.529 - 0.794: 0 0.794 - 1.058: 0 1.058 - 1.323: 1 Chirality restraints: 1573 Sorted by residual: chirality pdb=" CA GLU C 98 " pdb=" N GLU C 98 " pdb=" C GLU C 98 " pdb=" CB GLU C 98 " both_signs ideal model delta sigma weight residual False 2.51 1.19 1.32 2.00e-01 2.50e+01 4.37e+01 chirality pdb=" CA GLN A 433 " pdb=" N GLN A 433 " pdb=" C GLN A 433 " pdb=" CB GLN A 433 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.65e+00 chirality pdb=" CA GLU C 97 " pdb=" N GLU C 97 " pdb=" C GLU C 97 " pdb=" CB GLU C 97 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.29 2.00e-01 2.50e+01 2.03e+00 ... (remaining 1570 not shown) Planarity restraints: 1764 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR C 87 " 0.046 2.00e-02 2.50e+03 1.00e-01 1.01e+02 pdb=" C THR C 87 " -0.173 2.00e-02 2.50e+03 pdb=" O THR C 87 " 0.071 2.00e-02 2.50e+03 pdb=" N SER C 88 " 0.056 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU C 60 " 0.093 5.00e-02 4.00e+02 1.39e-01 3.07e+01 pdb=" N PRO C 61 " -0.240 5.00e-02 4.00e+02 pdb=" CA PRO C 61 " 0.075 5.00e-02 4.00e+02 pdb=" CD PRO C 61 " 0.072 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 432 " 0.024 2.00e-02 2.50e+03 4.83e-02 2.33e+01 pdb=" C GLY A 432 " -0.083 2.00e-02 2.50e+03 pdb=" O GLY A 432 " 0.031 2.00e-02 2.50e+03 pdb=" N GLN A 433 " 0.029 2.00e-02 2.50e+03 ... (remaining 1761 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2304 2.78 - 3.31: 8310 3.31 - 3.84: 16242 3.84 - 4.37: 20023 4.37 - 4.90: 35344 Nonbonded interactions: 82223 Sorted by model distance: nonbonded pdb=" O GLN C 230 " pdb=" OG SER C 234 " model vdw 2.247 3.040 nonbonded pdb=" OG SER B 184 " pdb=" OE2 GLU B 301 " model vdw 2.254 3.040 nonbonded pdb=" O THR B 165 " pdb=" OG1 THR B 169 " model vdw 2.266 3.040 nonbonded pdb=" OG1 THR A 265 " pdb=" OD2 ASP A 377 " model vdw 2.279 3.040 nonbonded pdb=" OG SER A 344 " pdb=" O SER A 348 " model vdw 2.279 3.040 ... (remaining 82218 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: 0.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 10.290 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 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:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 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 : 0.010 0.254 10386 Z= 0.498 Angle : 1.151 17.699 14034 Z= 0.638 Chirality : 0.069 1.323 1573 Planarity : 0.009 0.139 1764 Dihedral : 15.857 85.983 3786 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.64 % Allowed : 10.23 % Favored : 89.13 % Rotamer: Outliers : 0.70 % Allowed : 11.89 % Favored : 87.40 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.57 % Twisted General : 0.66 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.57 (0.18), residues: 1242 helix: -4.33 (0.13), residues: 362 sheet: -3.05 (0.22), residues: 396 loop : -3.44 (0.22), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 120 TYR 0.029 0.003 TYR A 140 PHE 0.038 0.003 PHE B 68 TRP 0.023 0.002 TRP A 323 HIS 0.012 0.002 HIS A 310 Details of bonding type rmsd covalent geometry : bond 0.01049 (10386) covalent geometry : angle 1.15100 (14034) hydrogen bonds : bond 0.27295 ( 443) hydrogen bonds : angle 10.57915 ( 1287) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 156 time to evaluate : 0.391 Fit side-chains REVERT: A 300 LYS cc_start: 0.8372 (tttt) cc_final: 0.8104 (tttm) REVERT: A 385 ASP cc_start: 0.8050 (m-30) cc_final: 0.7394 (m-30) REVERT: B 136 LYS cc_start: 0.8181 (mttp) cc_final: 0.7906 (mmtt) REVERT: B 189 MET cc_start: 0.9165 (mmm) cc_final: 0.8276 (mmt) REVERT: B 236 GLU cc_start: 0.8080 (mm-30) cc_final: 0.7442 (pm20) REVERT: C 11 LYS cc_start: 0.7420 (ptmt) cc_final: 0.7157 (ptmt) REVERT: C 40 MET cc_start: 0.9016 (ptt) cc_final: 0.8773 (ptm) REVERT: C 102 ILE cc_start: 0.8568 (mm) cc_final: 0.8175 (mm) REVERT: C 111 GLU cc_start: 0.8116 (tm-30) cc_final: 0.7903 (tp30) REVERT: C 121 GLU cc_start: 0.7505 (mm-30) cc_final: 0.7115 (mm-30) REVERT: C 150 TYR cc_start: 0.8141 (m-80) cc_final: 0.7840 (m-80) REVERT: C 317 MET cc_start: 0.8282 (tpp) cc_final: 0.7934 (tpp) REVERT: L 5 MET cc_start: 0.6691 (ttp) cc_final: 0.6314 (ttp) REVERT: L 146 MET cc_start: 0.8010 (ptp) cc_final: 0.7545 (ptm) REVERT: L 168 MET cc_start: 0.7353 (mtp) cc_final: 0.7125 (mtp) REVERT: L 254 TYR cc_start: 0.7447 (t80) cc_final: 0.6703 (t80) outliers start: 8 outliers final: 3 residues processed: 163 average time/residue: 0.1280 time to fit residues: 28.1190 Evaluate side-chains 122 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 119 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 274 ASP Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 98 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 108 optimal weight: 9.9990 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 9.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 123 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN A 207 GLN A 269 GLN A 273 GLN A 303 ASN A 310 HIS A 314 GLN A 369 GLN A 411 HIS ** A 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 466 HIS B 87 GLN B 94 ASN B 112 ASN B 178 GLN B 321 GLN C 7 HIS C 129 GLN C 133 ASN C 224 GLN C 227 ASN C 285 ASN L 57 ASN L 195 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.173305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.124266 restraints weight = 10640.419| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 1.79 r_work: 0.3134 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10386 Z= 0.138 Angle : 0.664 9.285 14034 Z= 0.351 Chirality : 0.043 0.217 1573 Planarity : 0.006 0.100 1764 Dihedral : 7.405 70.464 1366 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.73 % Favored : 91.95 % Rotamer: Outliers : 1.50 % Allowed : 14.54 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.57 % Twisted General : 0.25 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.97 (0.21), residues: 1242 helix: -2.25 (0.22), residues: 368 sheet: -2.32 (0.24), residues: 385 loop : -3.01 (0.24), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 366 TYR 0.015 0.002 TYR L 296 PHE 0.020 0.001 PHE A 237 TRP 0.014 0.001 TRP A 323 HIS 0.003 0.001 HIS A 466 Details of bonding type rmsd covalent geometry : bond 0.00301 (10386) covalent geometry : angle 0.66370 (14034) hydrogen bonds : bond 0.03855 ( 443) hydrogen bonds : angle 5.60841 ( 1287) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 151 time to evaluate : 0.396 Fit side-chains REVERT: A 157 ARG cc_start: 0.8085 (ptt90) cc_final: 0.7865 (ptt-90) REVERT: A 161 GLU cc_start: 0.8557 (tt0) cc_final: 0.7582 (mt-10) REVERT: A 260 TYR cc_start: 0.8013 (m-80) cc_final: 0.7805 (m-80) REVERT: A 266 MET cc_start: 0.9331 (mmt) cc_final: 0.9082 (mmm) REVERT: A 277 ILE cc_start: 0.8961 (tt) cc_final: 0.8719 (pt) REVERT: A 291 MET cc_start: 0.7684 (mmm) cc_final: 0.7401 (tpp) REVERT: A 300 LYS cc_start: 0.8760 (tttt) cc_final: 0.8509 (tttm) REVERT: B 136 LYS cc_start: 0.8340 (mttp) cc_final: 0.7933 (mmtt) REVERT: B 189 MET cc_start: 0.9221 (mmm) cc_final: 0.8539 (mmt) REVERT: B 190 GLU cc_start: 0.8863 (tt0) cc_final: 0.8659 (tt0) REVERT: C 66 ASP cc_start: 0.4735 (p0) cc_final: 0.4498 (p0) REVERT: C 102 ILE cc_start: 0.7840 (mm) cc_final: 0.7587 (mm) REVERT: C 260 TYR cc_start: 0.8110 (t80) cc_final: 0.7774 (t80) REVERT: C 317 MET cc_start: 0.8051 (tpp) cc_final: 0.7723 (tpp) REVERT: L 13 TYR cc_start: 0.6670 (m-10) cc_final: 0.5885 (m-80) REVERT: L 38 ARG cc_start: 0.7478 (ttp-170) cc_final: 0.7145 (ttp-170) REVERT: L 166 GLN cc_start: 0.8759 (mt0) cc_final: 0.8187 (tt0) REVERT: L 169 LEU cc_start: 0.8625 (mt) cc_final: 0.8378 (tt) REVERT: L 253 ARG cc_start: 0.7826 (ptt-90) cc_final: 0.7520 (ptt-90) outliers start: 17 outliers final: 9 residues processed: 161 average time/residue: 0.1084 time to fit residues: 24.2702 Evaluate side-chains 127 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 118 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 TRP Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain L residue 139 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 81 optimal weight: 6.9990 chunk 77 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 76 optimal weight: 0.6980 chunk 89 optimal weight: 10.0000 chunk 100 optimal weight: 8.9990 chunk 109 optimal weight: 9.9990 chunk 91 optimal weight: 5.9990 chunk 114 optimal weight: 9.9990 chunk 74 optimal weight: 5.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 HIS A 421 ASN ** A 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 101 HIS B 318 GLN C 50 ASN C 133 ASN C 258 ASN C 262 GLN L 68 ASN L 212 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.166843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.117313 restraints weight = 10854.439| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 1.86 r_work: 0.3034 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.058 10386 Z= 0.336 Angle : 0.816 7.532 14034 Z= 0.421 Chirality : 0.049 0.189 1573 Planarity : 0.007 0.131 1764 Dihedral : 7.447 65.129 1361 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.32 % Allowed : 10.39 % Favored : 89.29 % Rotamer: Outliers : 3.17 % Allowed : 16.48 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.57 % Twisted General : 0.33 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.45 (0.22), residues: 1242 helix: -1.19 (0.26), residues: 355 sheet: -2.31 (0.24), residues: 397 loop : -2.95 (0.25), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 208 TYR 0.025 0.003 TYR A 140 PHE 0.028 0.003 PHE B 18 TRP 0.011 0.002 TRP A 323 HIS 0.006 0.002 HIS A 422 Details of bonding type rmsd covalent geometry : bond 0.00795 (10386) covalent geometry : angle 0.81649 (14034) hydrogen bonds : bond 0.04486 ( 443) hydrogen bonds : angle 5.44979 ( 1287) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 125 time to evaluate : 0.347 Fit side-chains REVERT: A 157 ARG cc_start: 0.8095 (ptt90) cc_final: 0.7703 (ptt180) REVERT: A 266 MET cc_start: 0.9322 (mmt) cc_final: 0.9097 (mmm) REVERT: A 300 LYS cc_start: 0.8726 (tttt) cc_final: 0.8482 (tttm) REVERT: A 385 ASP cc_start: 0.8595 (m-30) cc_final: 0.8085 (m-30) REVERT: A 390 TYR cc_start: 0.9003 (p90) cc_final: 0.8638 (p90) REVERT: A 446 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8906 (tt) REVERT: B 136 LYS cc_start: 0.8345 (mttp) cc_final: 0.7907 (mmtt) REVERT: B 168 ASP cc_start: 0.8998 (m-30) cc_final: 0.8785 (m-30) REVERT: B 189 MET cc_start: 0.9237 (mmm) cc_final: 0.8625 (mmt) REVERT: B 190 GLU cc_start: 0.8977 (tt0) cc_final: 0.8758 (tt0) REVERT: B 236 GLU cc_start: 0.8579 (mm-30) cc_final: 0.7742 (pm20) REVERT: C 40 MET cc_start: 0.8968 (ptt) cc_final: 0.8713 (ptm) REVERT: C 66 ASP cc_start: 0.4993 (p0) cc_final: 0.4708 (p0) REVERT: C 102 ILE cc_start: 0.8002 (mm) cc_final: 0.7690 (mm) REVERT: C 111 GLU cc_start: 0.8665 (tp30) cc_final: 0.8452 (tp30) REVERT: C 119 ASP cc_start: 0.8374 (t0) cc_final: 0.8127 (t0) REVERT: C 317 MET cc_start: 0.8017 (tpp) cc_final: 0.7749 (tpp) REVERT: L 13 TYR cc_start: 0.6690 (m-10) cc_final: 0.6021 (m-80) REVERT: L 38 ARG cc_start: 0.7658 (ttp-170) cc_final: 0.7444 (ttp-170) REVERT: L 168 MET cc_start: 0.8198 (mtp) cc_final: 0.7830 (mtp) REVERT: L 169 LEU cc_start: 0.8854 (mt) cc_final: 0.8350 (tt) REVERT: L 253 ARG cc_start: 0.7934 (ptt-90) cc_final: 0.7644 (ptt-90) REVERT: L 254 TYR cc_start: 0.7569 (t80) cc_final: 0.7170 (t80) outliers start: 36 outliers final: 25 residues processed: 154 average time/residue: 0.1076 time to fit residues: 23.0376 Evaluate side-chains 149 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 123 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 TRP Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 120 ARG Chi-restraints excluded: chain B residue 123 ASN Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 274 ASP Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain L residue 5 MET Chi-restraints excluded: chain L residue 139 LYS Chi-restraints excluded: chain L residue 204 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 123 optimal weight: 0.9980 chunk 52 optimal weight: 0.6980 chunk 61 optimal weight: 0.6980 chunk 6 optimal weight: 3.9990 chunk 89 optimal weight: 6.9990 chunk 34 optimal weight: 0.2980 chunk 96 optimal weight: 0.9990 chunk 71 optimal weight: 5.9990 chunk 83 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 256 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.173328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.127527 restraints weight = 10740.770| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 1.83 r_work: 0.3128 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10386 Z= 0.124 Angle : 0.625 8.643 14034 Z= 0.326 Chirality : 0.042 0.169 1573 Planarity : 0.005 0.097 1764 Dihedral : 6.709 70.396 1361 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.29 % Favored : 91.47 % Rotamer: Outliers : 2.73 % Allowed : 17.44 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.57 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.90 (0.23), residues: 1242 helix: -0.52 (0.27), residues: 379 sheet: -1.87 (0.26), residues: 388 loop : -3.04 (0.25), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 366 TYR 0.015 0.001 TYR C 260 PHE 0.020 0.001 PHE L 485 TRP 0.013 0.001 TRP A 323 HIS 0.004 0.001 HIS A 310 Details of bonding type rmsd covalent geometry : bond 0.00273 (10386) covalent geometry : angle 0.62521 (14034) hydrogen bonds : bond 0.03156 ( 443) hydrogen bonds : angle 4.93436 ( 1287) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 138 time to evaluate : 0.401 Fit side-chains REVERT: A 157 ARG cc_start: 0.7821 (ptt90) cc_final: 0.7591 (ptt180) REVERT: A 260 TYR cc_start: 0.8010 (m-80) cc_final: 0.7726 (m-80) REVERT: A 266 MET cc_start: 0.9188 (mmt) cc_final: 0.8909 (mmm) REVERT: A 300 LYS cc_start: 0.8532 (tttt) cc_final: 0.8327 (tttm) REVERT: A 385 ASP cc_start: 0.8274 (m-30) cc_final: 0.7725 (m-30) REVERT: A 446 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8796 (tt) REVERT: B 136 LYS cc_start: 0.8273 (mttp) cc_final: 0.7905 (mmtt) REVERT: B 178 GLN cc_start: 0.8822 (mt0) cc_final: 0.8541 (tt0) REVERT: B 189 MET cc_start: 0.9130 (mmm) cc_final: 0.8313 (mmt) REVERT: B 312 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7819 (mt-10) REVERT: C 11 LYS cc_start: 0.7415 (ptmt) cc_final: 0.7011 (ptmt) REVERT: C 40 MET cc_start: 0.8904 (ptt) cc_final: 0.8699 (ptm) REVERT: C 102 ILE cc_start: 0.7904 (mm) cc_final: 0.7672 (mm) REVERT: C 260 TYR cc_start: 0.8021 (t80) cc_final: 0.7716 (t80) REVERT: C 303 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.7318 (pt0) REVERT: C 317 MET cc_start: 0.8149 (tpp) cc_final: 0.7875 (tpp) REVERT: L 13 TYR cc_start: 0.6420 (m-10) cc_final: 0.5664 (m-80) REVERT: L 38 ARG cc_start: 0.7416 (ttp-170) cc_final: 0.7097 (ttp-170) REVERT: L 85 MET cc_start: 0.2270 (mmp) cc_final: 0.1487 (mtp) REVERT: L 166 GLN cc_start: 0.8712 (mt0) cc_final: 0.8186 (tt0) REVERT: L 169 LEU cc_start: 0.8710 (mt) cc_final: 0.8345 (tt) REVERT: L 253 ARG cc_start: 0.7608 (ptt-90) cc_final: 0.7321 (ptt-90) REVERT: L 254 TYR cc_start: 0.7400 (t80) cc_final: 0.7047 (t80) REVERT: L 304 GLU cc_start: 0.6475 (OUTLIER) cc_final: 0.6211 (pt0) outliers start: 31 outliers final: 20 residues processed: 157 average time/residue: 0.1166 time to fit residues: 25.2601 Evaluate side-chains 147 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 124 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 TRP Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 120 ARG Chi-restraints excluded: chain B residue 123 ASN Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 303 GLU Chi-restraints excluded: chain L residue 5 MET Chi-restraints excluded: chain L residue 139 LYS Chi-restraints excluded: chain L residue 204 LEU Chi-restraints excluded: chain L residue 304 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 29 optimal weight: 6.9990 chunk 7 optimal weight: 0.0980 chunk 83 optimal weight: 0.9990 chunk 121 optimal weight: 7.9990 chunk 97 optimal weight: 4.9990 chunk 90 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 102 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 122 optimal weight: 7.9990 chunk 118 optimal weight: 4.9990 overall best weight: 2.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 318 GLN C 133 ASN L 49 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.169424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 91)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.121411 restraints weight = 10777.529| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 1.79 r_work: 0.3032 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 10386 Z= 0.242 Angle : 0.708 7.459 14034 Z= 0.367 Chirality : 0.045 0.161 1573 Planarity : 0.006 0.107 1764 Dihedral : 6.925 70.216 1361 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.98 % Favored : 89.69 % Rotamer: Outliers : 3.61 % Allowed : 17.53 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.57 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.77 (0.23), residues: 1242 helix: -0.36 (0.27), residues: 368 sheet: -1.84 (0.26), residues: 383 loop : -2.92 (0.26), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 211 TYR 0.021 0.002 TYR B 164 PHE 0.023 0.002 PHE L 485 TRP 0.010 0.001 TRP A 323 HIS 0.004 0.001 HIS A 169 Details of bonding type rmsd covalent geometry : bond 0.00568 (10386) covalent geometry : angle 0.70848 (14034) hydrogen bonds : bond 0.03680 ( 443) hydrogen bonds : angle 5.02124 ( 1287) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 123 time to evaluate : 0.317 Fit side-chains REVERT: A 157 ARG cc_start: 0.7880 (ptt90) cc_final: 0.7577 (ptt180) REVERT: A 260 TYR cc_start: 0.8125 (m-80) cc_final: 0.7764 (m-80) REVERT: A 266 MET cc_start: 0.9212 (mmt) cc_final: 0.8970 (mmm) REVERT: A 300 LYS cc_start: 0.8597 (tttt) cc_final: 0.8371 (tttm) REVERT: A 385 ASP cc_start: 0.8380 (m-30) cc_final: 0.7824 (m-30) REVERT: A 390 TYR cc_start: 0.8843 (p90) cc_final: 0.8470 (p90) REVERT: A 446 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8800 (tt) REVERT: B 136 LYS cc_start: 0.8332 (mttp) cc_final: 0.7920 (mmtt) REVERT: B 189 MET cc_start: 0.9176 (mmm) cc_final: 0.8434 (mmt) REVERT: B 236 GLU cc_start: 0.8420 (mm-30) cc_final: 0.7717 (pm20) REVERT: C 40 MET cc_start: 0.8954 (ptt) cc_final: 0.8725 (ptm) REVERT: C 57 ASP cc_start: 0.8723 (p0) cc_final: 0.8516 (p0) REVERT: C 102 ILE cc_start: 0.7962 (mm) cc_final: 0.7714 (mm) REVERT: C 119 ASP cc_start: 0.8126 (t0) cc_final: 0.7840 (t0) REVERT: C 303 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.7365 (pt0) REVERT: C 317 MET cc_start: 0.8138 (tpp) cc_final: 0.7841 (tpp) REVERT: L 13 TYR cc_start: 0.6513 (m-10) cc_final: 0.5991 (m-80) REVERT: L 38 ARG cc_start: 0.7387 (ttp-170) cc_final: 0.7054 (ttp-170) REVERT: L 85 MET cc_start: 0.1552 (mmp) cc_final: 0.1014 (mtp) REVERT: L 169 LEU cc_start: 0.8766 (mt) cc_final: 0.8267 (tt) REVERT: L 253 ARG cc_start: 0.7769 (ptt-90) cc_final: 0.7480 (ptt-90) REVERT: L 254 TYR cc_start: 0.7521 (t80) cc_final: 0.7105 (t80) outliers start: 41 outliers final: 30 residues processed: 152 average time/residue: 0.1110 time to fit residues: 23.5639 Evaluate side-chains 152 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 120 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 TRP Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 440 THR Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 120 ARG Chi-restraints excluded: chain B residue 123 ASN Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 303 GLU Chi-restraints excluded: chain L residue 5 MET Chi-restraints excluded: chain L residue 49 ASN Chi-restraints excluded: chain L residue 148 TYR Chi-restraints excluded: chain L residue 204 LEU Chi-restraints excluded: chain L residue 304 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 6 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 59 optimal weight: 0.9990 chunk 101 optimal weight: 9.9990 chunk 86 optimal weight: 0.6980 chunk 105 optimal weight: 10.0000 chunk 94 optimal weight: 7.9990 chunk 26 optimal weight: 10.0000 chunk 47 optimal weight: 0.5980 chunk 89 optimal weight: 7.9990 chunk 97 optimal weight: 4.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 49 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.171078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 102)---------------| | r_work = 0.3291 r_free = 0.3291 target = 0.122463 restraints weight = 10813.657| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 1.82 r_work: 0.3082 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 10386 Z= 0.213 Angle : 0.683 7.271 14034 Z= 0.355 Chirality : 0.045 0.158 1573 Planarity : 0.005 0.103 1764 Dihedral : 6.837 71.483 1361 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.66 % Favored : 90.10 % Rotamer: Outliers : 4.14 % Allowed : 18.06 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.57 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.71 (0.23), residues: 1242 helix: -0.25 (0.27), residues: 374 sheet: -1.82 (0.26), residues: 384 loop : -2.94 (0.26), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 120 TYR 0.020 0.002 TYR B 164 PHE 0.024 0.002 PHE L 485 TRP 0.011 0.001 TRP A 301 HIS 0.004 0.001 HIS A 310 Details of bonding type rmsd covalent geometry : bond 0.00497 (10386) covalent geometry : angle 0.68306 (14034) hydrogen bonds : bond 0.03489 ( 443) hydrogen bonds : angle 4.96117 ( 1287) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 125 time to evaluate : 0.391 Fit side-chains REVERT: A 157 ARG cc_start: 0.7861 (ptt90) cc_final: 0.7581 (ptt-90) REVERT: A 161 GLU cc_start: 0.8210 (tt0) cc_final: 0.7378 (mt-10) REVERT: A 260 TYR cc_start: 0.8096 (m-80) cc_final: 0.7748 (m-80) REVERT: A 266 MET cc_start: 0.9182 (mmt) cc_final: 0.8936 (mmm) REVERT: A 385 ASP cc_start: 0.8325 (m-30) cc_final: 0.7768 (m-30) REVERT: A 390 TYR cc_start: 0.8785 (p90) cc_final: 0.8439 (p90) REVERT: A 446 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8826 (tt) REVERT: B 136 LYS cc_start: 0.8343 (mttp) cc_final: 0.8010 (mmtt) REVERT: B 189 MET cc_start: 0.9160 (mmm) cc_final: 0.8383 (mmt) REVERT: C 40 MET cc_start: 0.8934 (ptt) cc_final: 0.8720 (ptm) REVERT: C 102 ILE cc_start: 0.8024 (mm) cc_final: 0.7790 (mm) REVERT: C 119 ASP cc_start: 0.8039 (t0) cc_final: 0.7733 (t0) REVERT: C 150 TYR cc_start: 0.7615 (m-80) cc_final: 0.7315 (m-80) REVERT: C 303 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.7486 (pt0) REVERT: C 317 MET cc_start: 0.8197 (tpp) cc_final: 0.7913 (tpp) REVERT: L 13 TYR cc_start: 0.6508 (m-10) cc_final: 0.6047 (m-80) REVERT: L 38 ARG cc_start: 0.7370 (ttp-170) cc_final: 0.7045 (ttp-170) REVERT: L 85 MET cc_start: 0.1110 (mmp) cc_final: 0.0743 (mtp) REVERT: L 169 LEU cc_start: 0.8749 (mt) cc_final: 0.8249 (tt) REVERT: L 254 TYR cc_start: 0.7586 (t80) cc_final: 0.7105 (t80) REVERT: L 435 TRP cc_start: 0.7223 (OUTLIER) cc_final: 0.5689 (t60) outliers start: 47 outliers final: 37 residues processed: 158 average time/residue: 0.1098 time to fit residues: 24.3170 Evaluate side-chains 158 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 118 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 197 TRP Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 440 THR Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 120 ARG Chi-restraints excluded: chain B residue 123 ASN Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 303 GLU Chi-restraints excluded: chain L residue 5 MET Chi-restraints excluded: chain L residue 49 ASN Chi-restraints excluded: chain L residue 148 TYR Chi-restraints excluded: chain L residue 187 GLN Chi-restraints excluded: chain L residue 204 LEU Chi-restraints excluded: chain L residue 300 LEU Chi-restraints excluded: chain L residue 304 GLU Chi-restraints excluded: chain L residue 435 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 123 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 100 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 115 optimal weight: 10.0000 chunk 118 optimal weight: 5.9990 chunk 41 optimal weight: 0.7980 chunk 64 optimal weight: 0.8980 chunk 112 optimal weight: 10.0000 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 GLN ** A 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 318 GLN ** C 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.169502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.119954 restraints weight = 10721.859| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 1.80 r_work: 0.3070 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 10386 Z= 0.219 Angle : 0.686 7.178 14034 Z= 0.357 Chirality : 0.045 0.277 1573 Planarity : 0.005 0.104 1764 Dihedral : 6.843 71.442 1361 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.90 % Favored : 89.86 % Rotamer: Outliers : 4.05 % Allowed : 18.24 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.57 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.65 (0.23), residues: 1242 helix: -0.17 (0.28), residues: 368 sheet: -1.80 (0.26), residues: 385 loop : -2.90 (0.26), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 120 TYR 0.020 0.002 TYR B 164 PHE 0.024 0.002 PHE L 485 TRP 0.010 0.001 TRP A 301 HIS 0.004 0.001 HIS A 310 Details of bonding type rmsd covalent geometry : bond 0.00513 (10386) covalent geometry : angle 0.68628 (14034) hydrogen bonds : bond 0.03520 ( 443) hydrogen bonds : angle 4.94855 ( 1287) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 121 time to evaluate : 0.420 Fit side-chains REVERT: A 157 ARG cc_start: 0.8022 (ptt90) cc_final: 0.7722 (ptt-90) REVERT: A 260 TYR cc_start: 0.8183 (m-80) cc_final: 0.7841 (m-80) REVERT: A 266 MET cc_start: 0.9312 (mmt) cc_final: 0.9089 (mmm) REVERT: A 385 ASP cc_start: 0.8563 (m-30) cc_final: 0.8018 (m-30) REVERT: A 390 TYR cc_start: 0.8897 (p90) cc_final: 0.8533 (p90) REVERT: A 446 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8868 (tt) REVERT: B 136 LYS cc_start: 0.8377 (mttp) cc_final: 0.7897 (mmtt) REVERT: B 189 MET cc_start: 0.9217 (mmm) cc_final: 0.8535 (mmt) REVERT: C 40 MET cc_start: 0.8984 (ptt) cc_final: 0.8760 (ptm) REVERT: C 102 ILE cc_start: 0.7898 (mm) cc_final: 0.7630 (mm) REVERT: C 119 ASP cc_start: 0.8313 (t0) cc_final: 0.8026 (t0) REVERT: C 150 TYR cc_start: 0.7441 (m-80) cc_final: 0.7151 (m-80) REVERT: C 303 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7627 (pt0) REVERT: C 317 MET cc_start: 0.8048 (tpp) cc_final: 0.7783 (tpp) REVERT: L 13 TYR cc_start: 0.6483 (m-10) cc_final: 0.6044 (m-80) REVERT: L 38 ARG cc_start: 0.7443 (ttp-170) cc_final: 0.7096 (ttp-170) REVERT: L 85 MET cc_start: 0.1408 (mmp) cc_final: 0.0827 (mtp) REVERT: L 166 GLN cc_start: 0.8819 (OUTLIER) cc_final: 0.8422 (mt0) REVERT: L 169 LEU cc_start: 0.8881 (mt) cc_final: 0.8411 (tt) REVERT: L 254 TYR cc_start: 0.7589 (t80) cc_final: 0.7118 (t80) REVERT: L 435 TRP cc_start: 0.7318 (OUTLIER) cc_final: 0.5731 (t60) outliers start: 46 outliers final: 37 residues processed: 154 average time/residue: 0.1097 time to fit residues: 23.7828 Evaluate side-chains 156 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 115 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 197 TRP Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 440 THR Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 120 ARG Chi-restraints excluded: chain B residue 123 ASN Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 303 GLU Chi-restraints excluded: chain L residue 5 MET Chi-restraints excluded: chain L residue 148 TYR Chi-restraints excluded: chain L residue 166 GLN Chi-restraints excluded: chain L residue 187 GLN Chi-restraints excluded: chain L residue 300 LEU Chi-restraints excluded: chain L residue 304 GLU Chi-restraints excluded: chain L residue 411 ILE Chi-restraints excluded: chain L residue 435 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 17 optimal weight: 1.9990 chunk 113 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 56 optimal weight: 4.9990 chunk 80 optimal weight: 20.0000 chunk 90 optimal weight: 7.9990 chunk 71 optimal weight: 2.9990 chunk 92 optimal weight: 9.9990 chunk 78 optimal weight: 0.8980 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 195 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.169166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.119565 restraints weight = 10738.149| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 1.90 r_work: 0.3049 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 10386 Z= 0.239 Angle : 0.717 10.901 14034 Z= 0.368 Chirality : 0.046 0.251 1573 Planarity : 0.006 0.105 1764 Dihedral : 6.900 71.547 1361 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.58 % Favored : 90.10 % Rotamer: Outliers : 4.23 % Allowed : 18.06 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.57 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.69 (0.23), residues: 1242 helix: -0.18 (0.27), residues: 368 sheet: -1.81 (0.26), residues: 383 loop : -2.95 (0.25), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 120 TYR 0.021 0.002 TYR B 164 PHE 0.025 0.002 PHE L 485 TRP 0.011 0.001 TRP A 301 HIS 0.004 0.001 HIS A 169 Details of bonding type rmsd covalent geometry : bond 0.00561 (10386) covalent geometry : angle 0.71707 (14034) hydrogen bonds : bond 0.03606 ( 443) hydrogen bonds : angle 4.95920 ( 1287) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 112 time to evaluate : 0.470 Fit side-chains REVERT: A 157 ARG cc_start: 0.7852 (ptt90) cc_final: 0.7514 (ptt180) REVERT: A 260 TYR cc_start: 0.8009 (m-80) cc_final: 0.7628 (m-80) REVERT: A 266 MET cc_start: 0.9181 (mmt) cc_final: 0.8937 (mmm) REVERT: A 385 ASP cc_start: 0.8392 (m-30) cc_final: 0.7856 (m-30) REVERT: A 390 TYR cc_start: 0.8841 (p90) cc_final: 0.8454 (p90) REVERT: A 446 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8825 (tt) REVERT: B 136 LYS cc_start: 0.8316 (mttp) cc_final: 0.7905 (mmtt) REVERT: B 189 MET cc_start: 0.9167 (mmm) cc_final: 0.8414 (mmt) REVERT: C 40 MET cc_start: 0.8955 (ptt) cc_final: 0.8749 (ptm) REVERT: C 102 ILE cc_start: 0.8043 (mm) cc_final: 0.7788 (mm) REVERT: C 119 ASP cc_start: 0.8057 (t0) cc_final: 0.7751 (t0) REVERT: C 150 TYR cc_start: 0.7615 (m-80) cc_final: 0.7343 (m-80) REVERT: C 303 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.7459 (pt0) REVERT: C 317 MET cc_start: 0.8320 (tpp) cc_final: 0.8092 (tpp) REVERT: L 38 ARG cc_start: 0.7379 (ttp-170) cc_final: 0.7029 (ttp-170) REVERT: L 85 MET cc_start: 0.1349 (mmp) cc_final: 0.1002 (mtp) REVERT: L 166 GLN cc_start: 0.8723 (OUTLIER) cc_final: 0.8383 (mt0) REVERT: L 169 LEU cc_start: 0.8752 (mt) cc_final: 0.8256 (tt) REVERT: L 254 TYR cc_start: 0.7565 (t80) cc_final: 0.7034 (t80) REVERT: L 435 TRP cc_start: 0.7099 (OUTLIER) cc_final: 0.6817 (t60) outliers start: 48 outliers final: 40 residues processed: 148 average time/residue: 0.1080 time to fit residues: 22.6682 Evaluate side-chains 150 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 106 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 197 TRP Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 440 THR Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 120 ARG Chi-restraints excluded: chain B residue 123 ASN Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 303 GLU Chi-restraints excluded: chain L residue 5 MET Chi-restraints excluded: chain L residue 148 TYR Chi-restraints excluded: chain L residue 166 GLN Chi-restraints excluded: chain L residue 204 LEU Chi-restraints excluded: chain L residue 300 LEU Chi-restraints excluded: chain L residue 304 GLU Chi-restraints excluded: chain L residue 435 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 28 optimal weight: 3.9990 chunk 91 optimal weight: 9.9990 chunk 107 optimal weight: 9.9990 chunk 0 optimal weight: 7.9990 chunk 72 optimal weight: 3.9990 chunk 90 optimal weight: 6.9990 chunk 111 optimal weight: 20.0000 chunk 64 optimal weight: 0.0470 chunk 46 optimal weight: 4.9990 chunk 101 optimal weight: 10.0000 chunk 98 optimal weight: 2.9990 overall best weight: 3.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 318 GLN ** C 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 195 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.167328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.120776 restraints weight = 10780.224| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 1.88 r_work: 0.3052 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2904 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 10386 Z= 0.308 Angle : 0.777 10.783 14034 Z= 0.398 Chirality : 0.049 0.233 1573 Planarity : 0.006 0.110 1764 Dihedral : 7.147 70.741 1361 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.32 % Allowed : 10.63 % Favored : 89.05 % Rotamer: Outliers : 4.14 % Allowed : 18.94 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.57 % Twisted General : 0.25 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.93 (0.23), residues: 1242 helix: -0.34 (0.27), residues: 368 sheet: -2.05 (0.25), residues: 398 loop : -3.04 (0.25), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 120 TYR 0.024 0.002 TYR B 164 PHE 0.025 0.002 PHE L 485 TRP 0.011 0.002 TRP L 435 HIS 0.005 0.001 HIS A 169 Details of bonding type rmsd covalent geometry : bond 0.00728 (10386) covalent geometry : angle 0.77738 (14034) hydrogen bonds : bond 0.03939 ( 443) hydrogen bonds : angle 5.07418 ( 1287) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 113 time to evaluate : 0.426 Fit side-chains REVERT: A 157 ARG cc_start: 0.8038 (ptt90) cc_final: 0.7656 (ptt180) REVERT: A 266 MET cc_start: 0.9290 (mmt) cc_final: 0.9059 (mmm) REVERT: A 385 ASP cc_start: 0.8557 (m-30) cc_final: 0.8028 (m-30) REVERT: A 446 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8841 (tt) REVERT: B 136 LYS cc_start: 0.8332 (mttp) cc_final: 0.7892 (mmtt) REVERT: B 189 MET cc_start: 0.9212 (mmm) cc_final: 0.8549 (mmt) REVERT: C 40 MET cc_start: 0.9003 (ptt) cc_final: 0.8793 (ptm) REVERT: C 102 ILE cc_start: 0.8016 (mm) cc_final: 0.7731 (mm) REVERT: C 119 ASP cc_start: 0.8330 (t0) cc_final: 0.8043 (t0) REVERT: C 150 TYR cc_start: 0.7561 (m-80) cc_final: 0.7330 (m-80) REVERT: C 303 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7587 (pt0) REVERT: L 38 ARG cc_start: 0.7590 (ttp-170) cc_final: 0.7379 (ttp-170) REVERT: L 49 ASN cc_start: 0.7584 (OUTLIER) cc_final: 0.7173 (m-40) REVERT: L 85 MET cc_start: 0.1841 (mmp) cc_final: 0.1211 (mtp) REVERT: L 166 GLN cc_start: 0.8871 (OUTLIER) cc_final: 0.8630 (mt0) REVERT: L 168 MET cc_start: 0.8277 (mtp) cc_final: 0.8001 (mtm) REVERT: L 254 TYR cc_start: 0.7681 (t80) cc_final: 0.7008 (t80) REVERT: L 435 TRP cc_start: 0.7425 (OUTLIER) cc_final: 0.7149 (t60) outliers start: 47 outliers final: 36 residues processed: 148 average time/residue: 0.1073 time to fit residues: 22.5143 Evaluate side-chains 148 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 107 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 197 TRP Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 440 THR Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 120 ARG Chi-restraints excluded: chain B residue 123 ASN Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 303 GLU Chi-restraints excluded: chain L residue 5 MET Chi-restraints excluded: chain L residue 49 ASN Chi-restraints excluded: chain L residue 166 GLN Chi-restraints excluded: chain L residue 204 LEU Chi-restraints excluded: chain L residue 241 LEU Chi-restraints excluded: chain L residue 300 LEU Chi-restraints excluded: chain L residue 304 GLU Chi-restraints excluded: chain L residue 435 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 44 optimal weight: 0.7980 chunk 17 optimal weight: 0.3980 chunk 117 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 chunk 115 optimal weight: 20.0000 chunk 69 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 58 optimal weight: 0.2980 chunk 15 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 258 ASN L 49 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.172893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 93)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.125204 restraints weight = 10644.240| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 1.89 r_work: 0.3095 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.2775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10386 Z= 0.129 Angle : 0.650 15.384 14034 Z= 0.329 Chirality : 0.043 0.227 1573 Planarity : 0.005 0.097 1764 Dihedral : 6.142 55.201 1358 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.62 % Favored : 91.14 % Rotamer: Outliers : 3.35 % Allowed : 19.74 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.57 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.55 (0.23), residues: 1242 helix: 0.04 (0.27), residues: 382 sheet: -1.75 (0.27), residues: 379 loop : -3.03 (0.25), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 120 TYR 0.014 0.001 TYR A 140 PHE 0.032 0.002 PHE L 292 TRP 0.012 0.001 TRP A 323 HIS 0.004 0.001 HIS A 310 Details of bonding type rmsd covalent geometry : bond 0.00292 (10386) covalent geometry : angle 0.65019 (14034) hydrogen bonds : bond 0.03034 ( 443) hydrogen bonds : angle 4.70669 ( 1287) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 123 time to evaluate : 0.434 Fit side-chains REVERT: A 260 TYR cc_start: 0.8062 (m-80) cc_final: 0.7678 (m-80) REVERT: A 266 MET cc_start: 0.9201 (mmt) cc_final: 0.8935 (mmm) REVERT: A 385 ASP cc_start: 0.8263 (m-30) cc_final: 0.7647 (m-30) REVERT: B 136 LYS cc_start: 0.8314 (mttp) cc_final: 0.7857 (mmtt) REVERT: B 178 GLN cc_start: 0.8886 (mt0) cc_final: 0.8575 (tt0) REVERT: B 189 MET cc_start: 0.9168 (mmm) cc_final: 0.8406 (mmt) REVERT: C 66 ASP cc_start: 0.5126 (p0) cc_final: 0.4788 (p0) REVERT: C 102 ILE cc_start: 0.8036 (mm) cc_final: 0.7784 (mm) REVERT: C 303 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7657 (pt0) REVERT: C 318 SER cc_start: 0.7903 (t) cc_final: 0.7691 (t) REVERT: L 13 TYR cc_start: 0.6416 (m-10) cc_final: 0.5934 (m-80) REVERT: L 38 ARG cc_start: 0.7358 (ttp-170) cc_final: 0.7022 (ttp-170) REVERT: L 231 LEU cc_start: 0.8209 (tt) cc_final: 0.7669 (pp) REVERT: L 254 TYR cc_start: 0.7399 (t80) cc_final: 0.6766 (t80) REVERT: L 435 TRP cc_start: 0.7164 (OUTLIER) cc_final: 0.6920 (t60) outliers start: 38 outliers final: 31 residues processed: 146 average time/residue: 0.1115 time to fit residues: 22.9419 Evaluate side-chains 150 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 117 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 197 TRP Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 440 THR Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 120 ARG Chi-restraints excluded: chain B residue 123 ASN Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 303 GLU Chi-restraints excluded: chain L residue 5 MET Chi-restraints excluded: chain L residue 49 ASN Chi-restraints excluded: chain L residue 204 LEU Chi-restraints excluded: chain L residue 435 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 49 optimal weight: 0.6980 chunk 33 optimal weight: 0.0270 chunk 28 optimal weight: 0.9980 chunk 87 optimal weight: 0.6980 chunk 14 optimal weight: 6.9990 chunk 79 optimal weight: 9.9990 chunk 12 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 102 optimal weight: 0.6980 chunk 44 optimal weight: 0.8980 chunk 97 optimal weight: 5.9990 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.180693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.153793 restraints weight = 10734.526| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 1.60 r_work: 0.3163 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.2933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 10386 Z= 0.112 Angle : 0.640 15.135 14034 Z= 0.321 Chirality : 0.042 0.215 1573 Planarity : 0.005 0.098 1764 Dihedral : 5.933 52.230 1358 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.62 % Favored : 91.14 % Rotamer: Outliers : 2.38 % Allowed : 20.79 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.57 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.24 (0.24), residues: 1242 helix: 0.37 (0.28), residues: 383 sheet: -1.61 (0.26), residues: 390 loop : -2.90 (0.25), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 263 TYR 0.017 0.001 TYR B 135 PHE 0.037 0.002 PHE L 298 TRP 0.011 0.001 TRP A 323 HIS 0.003 0.000 HIS A 310 Details of bonding type rmsd covalent geometry : bond 0.00245 (10386) covalent geometry : angle 0.64048 (14034) hydrogen bonds : bond 0.02883 ( 443) hydrogen bonds : angle 4.57041 ( 1287) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2614.01 seconds wall clock time: 45 minutes 33.28 seconds (2733.28 seconds total)