Starting phenix.real_space_refine on Sun Dec 29 06:39:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7bty_30191/12_2024/7bty_30191.cif Found real_map, /net/cci-nas-00/data/ceres_data/7bty_30191/12_2024/7bty_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7bty_30191/12_2024/7bty_30191.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7bty_30191/12_2024/7bty_30191.map" model { file = "/net/cci-nas-00/data/ceres_data/7bty_30191/12_2024/7bty_30191.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7bty_30191/12_2024/7bty_30191.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.018 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: {'GLN:plan1': 2, 'GLU:plan': 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: 6.14, per 1000 atoms: 0.60 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: 2.64 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 1.17 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: 2.92 Time building geometry restraints manager: 3.02 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: 0.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 25.100 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.270 ------------------------------------------------------------------------------- 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= 0.658 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.023 0.002 TRP A 323 HIS 0.012 0.002 HIS A 310 PHE 0.038 0.003 PHE B 68 TYR 0.029 0.003 TYR A 140 ARG 0.010 0.001 ARG B 120 *********************** 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 : 1.137 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: 0.2727 time to fit residues: 59.5532 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 : 1.294 ------------------------------------------------------------------------------- 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 104 optimal weight: 4.9990 chunk 93 optimal weight: 0.7980 chunk 52 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 59 optimal weight: 0.5980 chunk 72 optimal weight: 4.9990 chunk 112 optimal weight: 6.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 280 HIS A 303 ASN A 310 HIS A 369 GLN A 411 HIS ** A 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 466 HIS B 87 GLN B 94 ASN B 101 HIS 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10386 Z= 0.237 Angle : 0.694 9.451 14034 Z= 0.366 Chirality : 0.044 0.219 1573 Planarity : 0.006 0.103 1764 Dihedral : 7.579 68.594 1366 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.29 % Favored : 91.47 % Rotamer: Outliers : 1.76 % Allowed : 14.71 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.57 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.01 (0.21), residues: 1242 helix: -2.26 (0.22), residues: 369 sheet: -2.37 (0.24), residues: 383 loop : -3.03 (0.24), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 323 HIS 0.004 0.001 HIS A 310 PHE 0.021 0.002 PHE B 68 TYR 0.017 0.002 TYR C 260 ARG 0.004 0.000 ARG A 366 *********************** 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 160 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 140 time to evaluate : 1.186 Fit side-chains REVERT: A 157 ARG cc_start: 0.7676 (ptt90) cc_final: 0.7401 (ptt-90) REVERT: A 161 GLU cc_start: 0.7814 (tt0) cc_final: 0.7035 (mt-10) REVERT: A 266 MET cc_start: 0.8970 (mmt) cc_final: 0.8647 (mmm) REVERT: A 300 LYS cc_start: 0.8332 (tttt) cc_final: 0.8059 (tttm) REVERT: B 136 LYS cc_start: 0.8168 (mttp) cc_final: 0.7939 (mmtt) REVERT: B 168 ASP cc_start: 0.8552 (m-30) cc_final: 0.8269 (m-30) REVERT: B 189 MET cc_start: 0.9068 (mmm) cc_final: 0.8192 (mmt) REVERT: B 190 GLU cc_start: 0.7939 (tt0) cc_final: 0.7717 (tt0) REVERT: C 66 ASP cc_start: 0.4802 (p0) cc_final: 0.4601 (p0) REVERT: C 102 ILE cc_start: 0.8120 (mm) cc_final: 0.7911 (mm) REVERT: C 260 TYR cc_start: 0.7730 (t80) cc_final: 0.7358 (t80) REVERT: C 317 MET cc_start: 0.8237 (tpp) cc_final: 0.7927 (tpp) REVERT: L 38 ARG cc_start: 0.7334 (ttp-170) cc_final: 0.7031 (ttp-170) REVERT: L 146 MET cc_start: 0.7919 (ptp) cc_final: 0.7713 (ptm) REVERT: L 166 GLN cc_start: 0.8364 (mt0) cc_final: 0.7744 (tt0) REVERT: L 168 MET cc_start: 0.7466 (mtp) cc_final: 0.7093 (mtp) REVERT: L 253 ARG cc_start: 0.7590 (ptt-90) cc_final: 0.7280 (ptt-90) outliers start: 20 outliers final: 12 residues processed: 152 average time/residue: 0.2517 time to fit residues: 52.9912 Evaluate side-chains 132 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 120 time to evaluate : 1.205 ------------------------------------------------------------------------------- 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 B residue 212 LEU 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 L residue 139 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 62 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 93 optimal weight: 5.9990 chunk 76 optimal weight: 6.9990 chunk 31 optimal weight: 5.9990 chunk 112 optimal weight: 8.9990 chunk 121 optimal weight: 8.9990 chunk 100 optimal weight: 7.9990 chunk 111 optimal weight: 9.9990 chunk 38 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 ASN ** A 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 318 GLN ** C 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 258 ASN C 262 GLN L 212 HIS L 277 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.067 10386 Z= 0.594 Angle : 0.864 8.369 14034 Z= 0.446 Chirality : 0.052 0.207 1573 Planarity : 0.007 0.132 1764 Dihedral : 7.631 63.906 1361 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.32 % Allowed : 10.79 % Favored : 88.89 % Rotamer: Outliers : 3.70 % Allowed : 16.39 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.57 % Twisted General : 0.41 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.54 (0.22), residues: 1242 helix: -1.28 (0.26), residues: 355 sheet: -2.40 (0.24), residues: 397 loop : -2.95 (0.25), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 323 HIS 0.007 0.001 HIS A 422 PHE 0.031 0.003 PHE B 18 TYR 0.028 0.003 TYR A 140 ARG 0.007 0.001 ARG A 208 *********************** 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 166 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 124 time to evaluate : 1.133 Fit side-chains REVERT: A 266 MET cc_start: 0.8901 (mmt) cc_final: 0.8597 (mmm) REVERT: A 300 LYS cc_start: 0.8381 (tttt) cc_final: 0.8087 (tttm) REVERT: A 385 ASP cc_start: 0.8064 (m-30) cc_final: 0.7483 (m-30) REVERT: A 446 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8732 (tt) REVERT: B 136 LYS cc_start: 0.8195 (mttp) cc_final: 0.7915 (mmtt) REVERT: B 189 MET cc_start: 0.9103 (mmm) cc_final: 0.8359 (mmt) REVERT: B 190 GLU cc_start: 0.8068 (tt0) cc_final: 0.7788 (tt0) REVERT: C 11 LYS cc_start: 0.7453 (ptmt) cc_final: 0.7055 (ptmt) REVERT: C 40 MET cc_start: 0.8978 (ptt) cc_final: 0.8743 (ptm) REVERT: C 59 LYS cc_start: 0.7684 (mmtm) cc_final: 0.7195 (mttt) REVERT: C 66 ASP cc_start: 0.4883 (p0) cc_final: 0.4530 (p0) REVERT: C 102 ILE cc_start: 0.8297 (mm) cc_final: 0.8004 (mm) REVERT: C 111 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7499 (tm-30) REVERT: C 119 ASP cc_start: 0.7528 (t0) cc_final: 0.7256 (t0) REVERT: C 150 TYR cc_start: 0.7993 (m-80) cc_final: 0.7703 (m-80) REVERT: C 317 MET cc_start: 0.8208 (tpp) cc_final: 0.7943 (tpp) REVERT: L 13 TYR cc_start: 0.6668 (m-10) cc_final: 0.6161 (m-80) REVERT: L 38 ARG cc_start: 0.7448 (ttp-170) cc_final: 0.7173 (ttp-170) REVERT: L 146 MET cc_start: 0.8050 (ptp) cc_final: 0.7802 (ptm) REVERT: L 168 MET cc_start: 0.7512 (mtp) cc_final: 0.7042 (mtp) REVERT: L 254 TYR cc_start: 0.7434 (t80) cc_final: 0.6964 (t80) outliers start: 42 outliers final: 29 residues processed: 156 average time/residue: 0.2506 time to fit residues: 55.5396 Evaluate side-chains 149 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 118 time to evaluate : 1.146 ------------------------------------------------------------------------------- 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 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 144 VAL 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 97 GLU Chi-restraints excluded: chain C residue 111 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 C residue 277 GLN 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 111 optimal weight: 20.0000 chunk 84 optimal weight: 0.9990 chunk 58 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 53 optimal weight: 0.5980 chunk 75 optimal weight: 2.9990 chunk 113 optimal weight: 4.9990 chunk 119 optimal weight: 9.9990 chunk 59 optimal weight: 0.9990 chunk 107 optimal weight: 7.9990 chunk 32 optimal weight: 0.8980 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 112 ASN B 256 GLN C 50 ASN L 49 ASN L 68 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10386 Z= 0.185 Angle : 0.635 8.067 14034 Z= 0.332 Chirality : 0.042 0.170 1573 Planarity : 0.005 0.099 1764 Dihedral : 6.827 69.964 1361 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.53 % Favored : 91.22 % Rotamer: Outliers : 2.73 % Allowed : 17.36 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.57 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.97 (0.23), residues: 1242 helix: -0.63 (0.27), residues: 382 sheet: -1.93 (0.26), residues: 381 loop : -3.02 (0.25), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 323 HIS 0.005 0.001 HIS A 310 PHE 0.018 0.001 PHE B 18 TYR 0.018 0.001 TYR L 282 ARG 0.003 0.000 ARG A 366 *********************** 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 167 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 136 time to evaluate : 1.113 Fit side-chains REVERT: A 157 ARG cc_start: 0.7522 (ptt90) cc_final: 0.7261 (ptt-90) REVERT: A 266 MET cc_start: 0.8939 (mmt) cc_final: 0.8623 (mmm) REVERT: A 300 LYS cc_start: 0.8289 (tttt) cc_final: 0.8027 (tttm) REVERT: A 385 ASP cc_start: 0.8054 (m-30) cc_final: 0.7408 (m-30) REVERT: A 446 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8700 (tt) REVERT: B 136 LYS cc_start: 0.8093 (mttp) cc_final: 0.7806 (mmtt) REVERT: B 189 MET cc_start: 0.9029 (mmm) cc_final: 0.8196 (mmt) REVERT: B 312 GLU cc_start: 0.7882 (mt-10) cc_final: 0.7663 (mt-10) REVERT: C 11 LYS cc_start: 0.7400 (ptmt) cc_final: 0.7041 (ptmt) REVERT: C 40 MET cc_start: 0.8915 (ptt) cc_final: 0.8713 (ptm) REVERT: C 260 TYR cc_start: 0.7755 (t80) cc_final: 0.7430 (t80) REVERT: C 303 GLU cc_start: 0.7328 (OUTLIER) cc_final: 0.7058 (pt0) REVERT: C 317 MET cc_start: 0.8248 (tpp) cc_final: 0.7930 (tpp) REVERT: L 13 TYR cc_start: 0.6476 (m-10) cc_final: 0.5901 (m-80) REVERT: L 38 ARG cc_start: 0.7245 (ttp-170) cc_final: 0.6934 (ttp-170) REVERT: L 85 MET cc_start: 0.2029 (mmp) cc_final: 0.1526 (mtp) REVERT: L 146 MET cc_start: 0.8063 (ptp) cc_final: 0.7837 (ptm) REVERT: L 253 ARG cc_start: 0.7474 (ptt-90) cc_final: 0.7209 (ptt-90) REVERT: L 254 TYR cc_start: 0.7285 (t80) cc_final: 0.6822 (t80) REVERT: L 304 GLU cc_start: 0.6453 (OUTLIER) cc_final: 0.6193 (pt0) outliers start: 31 outliers final: 19 residues processed: 157 average time/residue: 0.2612 time to fit residues: 57.0373 Evaluate side-chains 138 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 116 time to evaluate : 1.323 ------------------------------------------------------------------------------- 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 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 110 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 203 THR Chi-restraints excluded: chain B residue 252 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 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 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 99 optimal weight: 9.9990 chunk 68 optimal weight: 3.9990 chunk 1 optimal weight: 0.0970 chunk 89 optimal weight: 8.9990 chunk 49 optimal weight: 2.9990 chunk 102 optimal weight: 0.7980 chunk 82 optimal weight: 20.0000 chunk 0 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 107 optimal weight: 8.9990 chunk 30 optimal weight: 7.9990 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 421 ASN ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 10386 Z= 0.339 Angle : 0.701 7.512 14034 Z= 0.363 Chirality : 0.045 0.161 1573 Planarity : 0.006 0.108 1764 Dihedral : 6.938 69.828 1361 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.90 % Favored : 89.77 % Rotamer: Outliers : 3.79 % Allowed : 17.80 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.57 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.80 (0.23), residues: 1242 helix: -0.34 (0.27), residues: 368 sheet: -1.91 (0.26), residues: 383 loop : -2.92 (0.26), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 323 HIS 0.003 0.001 HIS A 169 PHE 0.024 0.002 PHE L 485 TYR 0.020 0.002 TYR B 164 ARG 0.005 0.000 ARG A 211 *********************** 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: 43 poor density : 121 time to evaluate : 1.181 Fit side-chains REVERT: A 157 ARG cc_start: 0.7553 (ptt90) cc_final: 0.7220 (ptt180) REVERT: A 266 MET cc_start: 0.8921 (mmt) cc_final: 0.8638 (mmm) REVERT: A 299 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8782 (tt) REVERT: A 300 LYS cc_start: 0.8374 (tttt) cc_final: 0.8103 (tttm) REVERT: A 385 ASP cc_start: 0.8021 (m-30) cc_final: 0.7428 (m-30) REVERT: A 390 TYR cc_start: 0.8692 (p90) cc_final: 0.8330 (p90) REVERT: A 446 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8714 (tt) REVERT: B 136 LYS cc_start: 0.8141 (mttp) cc_final: 0.7841 (mmtt) REVERT: B 189 MET cc_start: 0.9100 (mmm) cc_final: 0.8261 (mmt) REVERT: B 312 GLU cc_start: 0.7930 (mt-10) cc_final: 0.7722 (mt-10) REVERT: C 40 MET cc_start: 0.8968 (ptt) cc_final: 0.8747 (ptm) REVERT: C 66 ASP cc_start: 0.5344 (p0) cc_final: 0.4921 (p0) REVERT: C 119 ASP cc_start: 0.7485 (t0) cc_final: 0.7162 (t0) REVERT: C 303 GLU cc_start: 0.7272 (OUTLIER) cc_final: 0.7002 (pt0) REVERT: C 317 MET cc_start: 0.8229 (tpp) cc_final: 0.7994 (tpp) REVERT: L 13 TYR cc_start: 0.6608 (m-10) cc_final: 0.6184 (m-80) REVERT: L 38 ARG cc_start: 0.7245 (ttp-170) cc_final: 0.6922 (ttp-170) REVERT: L 146 MET cc_start: 0.8089 (ptp) cc_final: 0.7859 (ptm) REVERT: L 148 TYR cc_start: 0.8182 (OUTLIER) cc_final: 0.7534 (p90) REVERT: L 166 GLN cc_start: 0.8383 (OUTLIER) cc_final: 0.7937 (mt0) REVERT: L 254 TYR cc_start: 0.7375 (t80) cc_final: 0.6882 (t80) outliers start: 43 outliers final: 30 residues processed: 150 average time/residue: 0.2380 time to fit residues: 49.9854 Evaluate side-chains 150 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 115 time to evaluate : 1.358 ------------------------------------------------------------------------------- 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 299 LEU Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 420 VAL 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 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 48 SER Chi-restraints excluded: chain L residue 49 ASN Chi-restraints excluded: chain L residue 148 TYR Chi-restraints excluded: chain L residue 166 GLN Chi-restraints excluded: chain L residue 169 LEU 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 40 optimal weight: 0.5980 chunk 107 optimal weight: 9.9990 chunk 23 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 119 optimal weight: 10.0000 chunk 99 optimal weight: 7.9990 chunk 55 optimal weight: 6.9990 chunk 9 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 chunk 62 optimal weight: 0.0770 overall best weight: 1.1344 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10386 Z= 0.212 Angle : 0.625 7.666 14034 Z= 0.326 Chirality : 0.042 0.162 1573 Planarity : 0.005 0.100 1764 Dihedral : 6.602 71.884 1361 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.70 % Favored : 91.06 % Rotamer: Outliers : 3.88 % Allowed : 18.24 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.57 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.57 (0.23), residues: 1242 helix: -0.12 (0.27), residues: 381 sheet: -1.67 (0.27), residues: 377 loop : -2.98 (0.25), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 301 HIS 0.004 0.001 HIS A 310 PHE 0.025 0.001 PHE L 485 TYR 0.015 0.001 TYR C 260 ARG 0.003 0.000 ARG A 211 *********************** 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 170 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 126 time to evaluate : 1.348 Fit side-chains REVERT: A 157 ARG cc_start: 0.7550 (ptt90) cc_final: 0.7260 (ptt180) REVERT: A 266 MET cc_start: 0.8930 (mmt) cc_final: 0.8637 (mmm) REVERT: A 300 LYS cc_start: 0.8355 (tttt) cc_final: 0.8071 (tttm) REVERT: A 385 ASP cc_start: 0.7950 (m-30) cc_final: 0.7304 (m-30) REVERT: A 390 TYR cc_start: 0.8569 (p90) cc_final: 0.8238 (p90) REVERT: A 446 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8705 (tt) REVERT: B 136 LYS cc_start: 0.8070 (mttp) cc_final: 0.7831 (mmtt) REVERT: B 189 MET cc_start: 0.9093 (mmm) cc_final: 0.8233 (mmt) REVERT: B 312 GLU cc_start: 0.7853 (mt-10) cc_final: 0.7608 (mt-10) REVERT: C 40 MET cc_start: 0.8919 (ptt) cc_final: 0.8713 (ptm) REVERT: C 66 ASP cc_start: 0.5292 (p0) cc_final: 0.4818 (p0) REVERT: C 104 ARG cc_start: 0.6783 (mmp-170) cc_final: 0.6430 (mmp-170) REVERT: C 111 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7518 (tm-30) REVERT: C 260 TYR cc_start: 0.7769 (t80) cc_final: 0.7531 (t80) REVERT: C 303 GLU cc_start: 0.7400 (OUTLIER) cc_final: 0.7161 (pt0) REVERT: C 317 MET cc_start: 0.8207 (tpp) cc_final: 0.7977 (tpp) REVERT: L 38 ARG cc_start: 0.7159 (ttp-170) cc_final: 0.6889 (ttp-170) REVERT: L 168 MET cc_start: 0.7355 (mtp) cc_final: 0.7107 (mtp) REVERT: L 254 TYR cc_start: 0.7365 (t80) cc_final: 0.6893 (t80) REVERT: L 304 GLU cc_start: 0.6547 (OUTLIER) cc_final: 0.6266 (pt0) REVERT: L 435 TRP cc_start: 0.7052 (OUTLIER) cc_final: 0.5589 (t60) outliers start: 44 outliers final: 33 residues processed: 156 average time/residue: 0.2618 time to fit residues: 57.0438 Evaluate side-chains 155 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 117 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 97 GLU Chi-restraints excluded: chain C residue 111 GLU 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 139 LYS 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 411 ILE 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 115 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 68 optimal weight: 0.0060 chunk 87 optimal weight: 0.5980 chunk 67 optimal weight: 8.9990 chunk 100 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 119 optimal weight: 9.9990 chunk 74 optimal weight: 0.6980 chunk 72 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 overall best weight: 1.0600 ------------------------------------------------------------------------------- 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 258 ASN L 195 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10386 Z= 0.201 Angle : 0.624 9.607 14034 Z= 0.321 Chirality : 0.043 0.249 1573 Planarity : 0.005 0.099 1764 Dihedral : 6.463 71.982 1361 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.86 % Favored : 90.90 % Rotamer: Outliers : 3.79 % Allowed : 18.15 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.57 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.39 (0.24), residues: 1242 helix: 0.09 (0.28), residues: 383 sheet: -1.52 (0.27), residues: 378 loop : -2.98 (0.25), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 323 HIS 0.003 0.001 HIS A 310 PHE 0.025 0.001 PHE L 485 TYR 0.015 0.001 TYR C 260 ARG 0.003 0.000 ARG A 211 *********************** 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 171 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 128 time to evaluate : 1.494 Fit side-chains REVERT: A 157 ARG cc_start: 0.7509 (ptt90) cc_final: 0.7152 (ptt180) REVERT: A 266 MET cc_start: 0.8940 (mmt) cc_final: 0.8645 (mmm) REVERT: A 300 LYS cc_start: 0.8408 (tttt) cc_final: 0.8137 (tttm) REVERT: A 385 ASP cc_start: 0.7927 (m-30) cc_final: 0.7381 (m-30) REVERT: A 390 TYR cc_start: 0.8554 (p90) cc_final: 0.8229 (p90) REVERT: B 136 LYS cc_start: 0.8012 (mttp) cc_final: 0.7688 (mmtt) REVERT: B 189 MET cc_start: 0.9091 (mmm) cc_final: 0.8198 (mmt) REVERT: B 312 GLU cc_start: 0.7888 (mt-10) cc_final: 0.7614 (mt-10) REVERT: C 40 MET cc_start: 0.8954 (ptt) cc_final: 0.8725 (ptm) REVERT: C 66 ASP cc_start: 0.5194 (p0) cc_final: 0.4721 (p0) REVERT: C 104 ARG cc_start: 0.6765 (mmp-170) cc_final: 0.6423 (mmp-170) REVERT: C 111 GLU cc_start: 0.7888 (OUTLIER) cc_final: 0.7467 (tm-30) REVERT: C 119 ASP cc_start: 0.7452 (t0) cc_final: 0.7136 (t0) REVERT: C 260 TYR cc_start: 0.7720 (t80) cc_final: 0.7490 (t80) REVERT: C 303 GLU cc_start: 0.7349 (OUTLIER) cc_final: 0.7122 (pt0) REVERT: C 317 MET cc_start: 0.8185 (tpp) cc_final: 0.7981 (tpp) REVERT: C 318 SER cc_start: 0.8098 (t) cc_final: 0.7861 (t) REVERT: L 38 ARG cc_start: 0.7148 (ttp-170) cc_final: 0.6892 (ttp-170) REVERT: L 85 MET cc_start: 0.2532 (mtp) cc_final: 0.1506 (mmt) REVERT: L 168 MET cc_start: 0.7135 (mtp) cc_final: 0.6893 (mtp) REVERT: L 231 LEU cc_start: 0.8175 (tt) cc_final: 0.7704 (pp) REVERT: L 253 ARG cc_start: 0.7553 (ptt-90) cc_final: 0.7296 (ptt-90) REVERT: L 254 TYR cc_start: 0.7466 (t80) cc_final: 0.6924 (t80) REVERT: L 435 TRP cc_start: 0.7041 (OUTLIER) cc_final: 0.5612 (t60) outliers start: 43 outliers final: 33 residues processed: 156 average time/residue: 0.2505 time to fit residues: 53.8169 Evaluate side-chains 158 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 122 time to evaluate : 1.204 ------------------------------------------------------------------------------- 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 332 SER 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 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 111 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 204 LEU 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 73 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 93 optimal weight: 7.9990 chunk 108 optimal weight: 6.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 10386 Z= 0.315 Angle : 0.686 10.903 14034 Z= 0.353 Chirality : 0.045 0.222 1573 Planarity : 0.005 0.106 1764 Dihedral : 6.690 71.457 1361 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.26 % Favored : 90.50 % Rotamer: Outliers : 4.23 % Allowed : 18.41 % Favored : 77.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.57 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.45 (0.24), residues: 1242 helix: 0.06 (0.28), residues: 376 sheet: -1.57 (0.27), residues: 380 loop : -3.00 (0.25), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 236 HIS 0.004 0.001 HIS A 169 PHE 0.036 0.002 PHE L 298 TYR 0.019 0.002 TYR B 164 ARG 0.004 0.000 ARG A 211 *********************** 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 173 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 125 time to evaluate : 1.283 Fit side-chains REVERT: A 157 ARG cc_start: 0.7549 (ptt90) cc_final: 0.7253 (ptt180) REVERT: A 161 GLU cc_start: 0.7657 (tt0) cc_final: 0.7154 (mt-10) REVERT: A 266 MET cc_start: 0.8921 (mmt) cc_final: 0.8643 (mmm) REVERT: A 300 LYS cc_start: 0.8362 (tttt) cc_final: 0.8092 (tttm) REVERT: A 341 LYS cc_start: 0.8781 (OUTLIER) cc_final: 0.8501 (ttmm) REVERT: A 385 ASP cc_start: 0.7932 (m-30) cc_final: 0.7329 (m-30) REVERT: A 390 TYR cc_start: 0.8670 (p90) cc_final: 0.8263 (p90) REVERT: B 136 LYS cc_start: 0.8146 (mttp) cc_final: 0.7799 (mmtt) REVERT: B 189 MET cc_start: 0.9093 (mmm) cc_final: 0.8250 (mmt) REVERT: B 312 GLU cc_start: 0.7931 (mt-10) cc_final: 0.7648 (mt-10) REVERT: C 40 MET cc_start: 0.8936 (ptt) cc_final: 0.8724 (ptm) REVERT: C 66 ASP cc_start: 0.5306 (p0) cc_final: 0.4790 (p0) REVERT: C 111 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7486 (tm-30) REVERT: C 119 ASP cc_start: 0.7498 (t0) cc_final: 0.7171 (t0) REVERT: C 303 GLU cc_start: 0.7341 (OUTLIER) cc_final: 0.7088 (pt0) REVERT: C 317 MET cc_start: 0.8386 (tpp) cc_final: 0.8153 (tpp) REVERT: L 38 ARG cc_start: 0.7168 (ttp-170) cc_final: 0.6889 (ttp-170) REVERT: L 49 ASN cc_start: 0.7268 (OUTLIER) cc_final: 0.6795 (m-40) REVERT: L 85 MET cc_start: 0.1976 (mtp) cc_final: 0.1041 (mmt) REVERT: L 168 MET cc_start: 0.7178 (mtp) cc_final: 0.6922 (mtp) REVERT: L 231 LEU cc_start: 0.8140 (tt) cc_final: 0.7681 (pp) REVERT: L 254 TYR cc_start: 0.7369 (t80) cc_final: 0.6954 (t80) REVERT: L 435 TRP cc_start: 0.6947 (OUTLIER) cc_final: 0.5479 (t60) outliers start: 48 outliers final: 33 residues processed: 158 average time/residue: 0.2502 time to fit residues: 54.7070 Evaluate side-chains 155 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 117 time to evaluate : 1.264 ------------------------------------------------------------------------------- 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 203 LEU Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 341 LYS 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 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 111 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 435 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 10.0000 chunk 104 optimal weight: 1.9990 chunk 111 optimal weight: 8.9990 chunk 67 optimal weight: 8.9990 chunk 48 optimal weight: 0.9990 chunk 87 optimal weight: 0.7980 chunk 34 optimal weight: 0.0670 chunk 100 optimal weight: 7.9990 chunk 105 optimal weight: 10.0000 chunk 110 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 overall best weight: 0.9722 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10386 Z= 0.193 Angle : 0.637 14.940 14034 Z= 0.322 Chirality : 0.042 0.207 1573 Planarity : 0.005 0.099 1764 Dihedral : 6.408 72.010 1361 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.37 % Favored : 91.38 % Rotamer: Outliers : 3.88 % Allowed : 18.77 % Favored : 77.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.57 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.24 (0.24), residues: 1242 helix: 0.29 (0.28), residues: 382 sheet: -1.42 (0.27), residues: 379 loop : -3.00 (0.25), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 301 HIS 0.004 0.001 HIS A 310 PHE 0.025 0.001 PHE L 485 TYR 0.014 0.001 TYR C 260 ARG 0.003 0.000 ARG B 120 *********************** 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 170 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 126 time to evaluate : 1.328 Fit side-chains REVERT: A 161 GLU cc_start: 0.7628 (tt0) cc_final: 0.7149 (mt-10) REVERT: A 266 MET cc_start: 0.8943 (mmt) cc_final: 0.8635 (mmm) REVERT: A 300 LYS cc_start: 0.8372 (tttt) cc_final: 0.8106 (tttm) REVERT: A 341 LYS cc_start: 0.8701 (OUTLIER) cc_final: 0.8497 (ttmm) REVERT: A 385 ASP cc_start: 0.7923 (m-30) cc_final: 0.7371 (m-30) REVERT: A 390 TYR cc_start: 0.8521 (p90) cc_final: 0.8151 (p90) REVERT: B 136 LYS cc_start: 0.8116 (mttp) cc_final: 0.7797 (mmtt) REVERT: B 150 MET cc_start: 0.8883 (mmm) cc_final: 0.8574 (mmp) REVERT: B 189 MET cc_start: 0.9087 (mmm) cc_final: 0.8160 (mmt) REVERT: B 312 GLU cc_start: 0.7899 (mt-10) cc_final: 0.7679 (mt-10) REVERT: C 40 MET cc_start: 0.8937 (ptt) cc_final: 0.8732 (ptm) REVERT: C 66 ASP cc_start: 0.5240 (p0) cc_final: 0.4754 (p0) REVERT: C 104 ARG cc_start: 0.6779 (mmp-170) cc_final: 0.6480 (mmp-170) REVERT: C 111 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7459 (tm-30) REVERT: C 119 ASP cc_start: 0.7389 (t0) cc_final: 0.7056 (t0) REVERT: C 150 TYR cc_start: 0.7865 (m-80) cc_final: 0.7563 (m-80) REVERT: C 260 TYR cc_start: 0.7692 (t80) cc_final: 0.7465 (t80) REVERT: C 303 GLU cc_start: 0.7387 (OUTLIER) cc_final: 0.7142 (pt0) REVERT: C 317 MET cc_start: 0.8156 (tpp) cc_final: 0.7909 (tpp) REVERT: L 38 ARG cc_start: 0.7155 (ttp-170) cc_final: 0.6900 (ttp-170) REVERT: L 49 ASN cc_start: 0.7225 (OUTLIER) cc_final: 0.6808 (m-40) REVERT: L 85 MET cc_start: 0.1766 (mtp) cc_final: 0.0918 (mmt) REVERT: L 168 MET cc_start: 0.7228 (mtp) cc_final: 0.6956 (mtp) REVERT: L 231 LEU cc_start: 0.8082 (tt) cc_final: 0.7678 (pp) REVERT: L 254 TYR cc_start: 0.7352 (t80) cc_final: 0.6891 (t80) REVERT: L 435 TRP cc_start: 0.6918 (OUTLIER) cc_final: 0.5502 (t60) outliers start: 44 outliers final: 35 residues processed: 152 average time/residue: 0.2578 time to fit residues: 54.3917 Evaluate side-chains 160 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 120 time to evaluate : 1.175 ------------------------------------------------------------------------------- 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 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 341 LYS 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 481 LEU Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 43 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 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 111 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 411 ILE Chi-restraints excluded: chain L residue 435 TRP Chi-restraints excluded: chain L residue 480 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 10.0000 chunk 71 optimal weight: 0.0070 chunk 55 optimal weight: 6.9990 chunk 81 optimal weight: 3.9990 chunk 123 optimal weight: 8.9990 chunk 113 optimal weight: 9.9990 chunk 98 optimal weight: 0.1980 chunk 10 optimal weight: 4.9990 chunk 75 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 overall best weight: 1.6404 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.2792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10386 Z= 0.268 Angle : 0.677 14.157 14034 Z= 0.342 Chirality : 0.044 0.198 1573 Planarity : 0.005 0.105 1764 Dihedral : 6.540 71.721 1361 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.02 % Favored : 90.66 % Rotamer: Outliers : 3.96 % Allowed : 18.85 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.57 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.25 (0.24), residues: 1242 helix: 0.36 (0.28), residues: 374 sheet: -1.48 (0.27), residues: 382 loop : -2.97 (0.25), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 301 HIS 0.003 0.001 HIS A 169 PHE 0.024 0.002 PHE L 485 TYR 0.016 0.002 TYR B 164 ARG 0.004 0.000 ARG B 120 ********************** 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 166 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 121 time to evaluate : 1.202 Fit side-chains REVERT: A 161 GLU cc_start: 0.7632 (tt0) cc_final: 0.7151 (mt-10) REVERT: A 266 MET cc_start: 0.8924 (mmt) cc_final: 0.8645 (mmm) REVERT: A 300 LYS cc_start: 0.8394 (tttt) cc_final: 0.8110 (tttm) REVERT: A 341 LYS cc_start: 0.8771 (OUTLIER) cc_final: 0.8488 (ttmm) REVERT: A 385 ASP cc_start: 0.7935 (m-30) cc_final: 0.7340 (m-30) REVERT: A 390 TYR cc_start: 0.8617 (p90) cc_final: 0.8228 (p90) REVERT: B 136 LYS cc_start: 0.8138 (mttp) cc_final: 0.7800 (mmtt) REVERT: B 189 MET cc_start: 0.9092 (mmm) cc_final: 0.8246 (mmt) REVERT: B 312 GLU cc_start: 0.7905 (mt-10) cc_final: 0.7636 (mt-10) REVERT: C 66 ASP cc_start: 0.5275 (p0) cc_final: 0.4789 (p0) REVERT: C 104 ARG cc_start: 0.6797 (mmp-170) cc_final: 0.6483 (mmp-170) REVERT: C 111 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7526 (tm-30) REVERT: C 119 ASP cc_start: 0.7434 (t0) cc_final: 0.7103 (t0) REVERT: C 150 TYR cc_start: 0.7794 (m-80) cc_final: 0.7489 (m-80) REVERT: C 303 GLU cc_start: 0.7447 (OUTLIER) cc_final: 0.7170 (pt0) REVERT: C 317 MET cc_start: 0.8351 (tpp) cc_final: 0.8127 (tpp) REVERT: L 38 ARG cc_start: 0.7168 (ttp-170) cc_final: 0.6906 (ttp-170) REVERT: L 49 ASN cc_start: 0.7176 (OUTLIER) cc_final: 0.6709 (m-40) REVERT: L 85 MET cc_start: 0.1821 (mtp) cc_final: 0.1007 (mmt) REVERT: L 168 MET cc_start: 0.7100 (mtp) cc_final: 0.6844 (mtp) REVERT: L 231 LEU cc_start: 0.8130 (tt) cc_final: 0.7693 (pp) REVERT: L 254 TYR cc_start: 0.7359 (t80) cc_final: 0.6783 (t80) REVERT: L 435 TRP cc_start: 0.7045 (OUTLIER) cc_final: 0.6809 (t60) outliers start: 45 outliers final: 37 residues processed: 150 average time/residue: 0.2457 time to fit residues: 51.5216 Evaluate side-chains 161 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 119 time to evaluate : 1.224 ------------------------------------------------------------------------------- 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 253 SER Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 341 LYS 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 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 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 111 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 166 GLN Chi-restraints excluded: chain L residue 204 LEU Chi-restraints excluded: chain L residue 435 TRP Chi-restraints excluded: chain L residue 480 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 5.9990 chunk 30 optimal weight: 6.9990 chunk 90 optimal weight: 6.9990 chunk 14 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 98 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 101 optimal weight: 6.9990 chunk 12 optimal weight: 0.6980 chunk 18 optimal weight: 3.9990 chunk 86 optimal weight: 0.1980 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 101 HIS B 318 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.177731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.147319 restraints weight = 10634.075| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 1.19 r_work: 0.3362 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10386 Z= 0.234 Angle : 0.657 14.181 14034 Z= 0.331 Chirality : 0.043 0.196 1573 Planarity : 0.005 0.102 1764 Dihedral : 6.460 71.956 1361 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.62 % Favored : 91.14 % Rotamer: Outliers : 3.88 % Allowed : 19.03 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.57 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.24), residues: 1242 helix: 0.49 (0.28), residues: 374 sheet: -1.43 (0.27), residues: 382 loop : -2.98 (0.24), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 301 HIS 0.003 0.001 HIS A 310 PHE 0.023 0.002 PHE L 485 TYR 0.015 0.002 TYR A 379 ARG 0.003 0.000 ARG B 120 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2073.17 seconds wall clock time: 39 minutes 12.58 seconds (2352.58 seconds total)