Starting phenix.real_space_refine on Fri Feb 14 09:04:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7bty_30191/02_2025/7bty_30191.cif Found real_map, /net/cci-nas-00/data/ceres_data/7bty_30191/02_2025/7bty_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_30191/02_2025/7bty_30191.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7bty_30191/02_2025/7bty_30191.map" model { file = "/net/cci-nas-00/data/ceres_data/7bty_30191/02_2025/7bty_30191.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7bty_30191/02_2025/7bty_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 5.95, per 1000 atoms: 0.59 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: 2.57 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: 1.13 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: 3.28 Time building geometry restraints manager: 2.89 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: 0.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 25.230 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.390 ------------------------------------------------------------------------------- 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 : 1.096 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: 0.2831 time to fit residues: 61.9442 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 : 1.220 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.171685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.122543 restraints weight = 10636.912| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 1.77 r_work: 0.3110 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 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 : 1.114 Fit side-chains REVERT: A 157 ARG cc_start: 0.8116 (ptt90) cc_final: 0.7862 (ptt-90) REVERT: A 161 GLU cc_start: 0.8540 (tt0) cc_final: 0.7534 (mt-10) REVERT: A 266 MET cc_start: 0.9324 (mmt) cc_final: 0.9082 (mmm) REVERT: A 291 MET cc_start: 0.7776 (mmm) cc_final: 0.7465 (tpp) REVERT: A 300 LYS cc_start: 0.8675 (tttt) cc_final: 0.8463 (tttm) REVERT: B 135 TYR cc_start: 0.8344 (t80) cc_final: 0.8125 (t80) REVERT: B 136 LYS cc_start: 0.8350 (mttp) cc_final: 0.7972 (mmtt) REVERT: B 168 ASP cc_start: 0.8856 (m-30) cc_final: 0.8606 (m-30) REVERT: B 189 MET cc_start: 0.9189 (mmm) cc_final: 0.8499 (mmt) REVERT: B 190 GLU cc_start: 0.8871 (tt0) cc_final: 0.8664 (tt0) REVERT: C 102 ILE cc_start: 0.7896 (mm) cc_final: 0.7655 (mm) REVERT: C 260 TYR cc_start: 0.8213 (t80) cc_final: 0.7856 (t80) REVERT: C 317 MET cc_start: 0.8077 (tpp) cc_final: 0.7768 (tpp) REVERT: L 38 ARG cc_start: 0.7492 (ttp-170) cc_final: 0.7155 (ttp-170) REVERT: L 146 MET cc_start: 0.8450 (ptp) cc_final: 0.8249 (ptm) REVERT: L 166 GLN cc_start: 0.8772 (mt0) cc_final: 0.8182 (tt0) REVERT: L 168 MET cc_start: 0.8194 (mtp) cc_final: 0.7888 (mtp) REVERT: L 253 ARG cc_start: 0.7890 (ptt-90) cc_final: 0.7609 (ptt-90) outliers start: 20 outliers final: 12 residues processed: 152 average time/residue: 0.2449 time to fit residues: 51.7261 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 : 1.125 ------------------------------------------------------------------------------- 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 92 optimal weight: 6.9990 chunk 89 optimal weight: 8.9990 chunk 72 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 18 optimal weight: 8.9990 chunk 77 optimal weight: 6.9990 chunk 90 optimal weight: 6.9990 chunk 7 optimal weight: 0.8980 chunk 0 optimal weight: 8.9990 chunk 88 optimal weight: 0.8980 chunk 104 optimal weight: 4.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- 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 112 ASN B 318 GLN C 50 ASN C 133 ASN C 262 GLN L 68 ASN L 212 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.168179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.121914 restraints weight = 10848.593| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 1.71 r_work: 0.3057 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 10386 Z= 0.434 Angle : 0.765 7.558 14034 Z= 0.397 Chirality : 0.047 0.176 1573 Planarity : 0.006 0.122 1764 Dihedral : 7.320 65.069 1361 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.90 % Favored : 89.77 % Rotamer: Outliers : 2.91 % Allowed : 16.39 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.57 % Twisted General : 0.33 % 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: -3.39 (0.22), residues: 1242 helix: -1.11 (0.26), residues: 359 sheet: -2.24 (0.25), residues: 399 loop : -2.98 (0.25), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 323 HIS 0.005 0.001 HIS A 422 PHE 0.025 0.002 PHE B 18 TYR 0.023 0.002 TYR A 140 ARG 0.005 0.001 ARG B 120 *********************** 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 157 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 124 time to evaluate : 1.201 Fit side-chains REVERT: A 157 ARG cc_start: 0.8112 (ptt90) cc_final: 0.7764 (ptt-90) REVERT: A 266 MET cc_start: 0.9306 (mmt) cc_final: 0.9083 (mmm) REVERT: A 291 MET cc_start: 0.7779 (mmm) cc_final: 0.7468 (tpp) REVERT: A 300 LYS cc_start: 0.8683 (tttt) cc_final: 0.8448 (tttm) REVERT: A 385 ASP cc_start: 0.8633 (m-30) cc_final: 0.8095 (m-30) REVERT: A 390 TYR cc_start: 0.8956 (p90) cc_final: 0.8619 (p90) REVERT: A 446 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8902 (tt) REVERT: B 135 TYR cc_start: 0.8584 (t80) cc_final: 0.8379 (t80) REVERT: B 136 LYS cc_start: 0.8338 (mttp) cc_final: 0.7913 (mmtt) REVERT: B 168 ASP cc_start: 0.8972 (m-30) cc_final: 0.8743 (m-30) REVERT: B 189 MET cc_start: 0.9243 (mmm) cc_final: 0.8617 (mmt) REVERT: B 190 GLU cc_start: 0.8934 (tt0) cc_final: 0.8732 (tt0) REVERT: B 236 GLU cc_start: 0.8559 (mm-30) cc_final: 0.7789 (pm20) REVERT: C 40 MET cc_start: 0.8964 (ptt) cc_final: 0.8696 (ptm) REVERT: C 102 ILE cc_start: 0.8009 (mm) cc_final: 0.7692 (mm) REVERT: C 119 ASP cc_start: 0.8367 (t0) cc_final: 0.8111 (t0) REVERT: C 317 MET cc_start: 0.8018 (tpp) cc_final: 0.7755 (tpp) REVERT: L 13 TYR cc_start: 0.6658 (m-10) cc_final: 0.6122 (m-80) REVERT: L 146 MET cc_start: 0.8567 (ptp) cc_final: 0.8327 (ptm) REVERT: L 168 MET cc_start: 0.8173 (mtp) cc_final: 0.7814 (mtp) REVERT: L 253 ARG cc_start: 0.7933 (ptt-90) cc_final: 0.7644 (ptt-90) REVERT: L 254 TYR cc_start: 0.7478 (t80) cc_final: 0.7073 (t80) outliers start: 33 outliers final: 24 residues processed: 150 average time/residue: 0.2384 time to fit residues: 49.9664 Evaluate side-chains 142 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 117 time to evaluate : 1.170 ------------------------------------------------------------------------------- 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 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 144 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 252 VAL 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 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 85 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 chunk 46 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 28 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 chunk 117 optimal weight: 8.9990 chunk 99 optimal weight: 6.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.3850 r_free = 0.3850 target = 0.169648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.122677 restraints weight = 10756.057| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 1.90 r_work: 0.3084 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 10386 Z= 0.335 Angle : 0.697 8.320 14034 Z= 0.363 Chirality : 0.045 0.165 1573 Planarity : 0.006 0.106 1764 Dihedral : 7.036 68.803 1361 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.34 % Favored : 90.42 % Rotamer: Outliers : 4.14 % Allowed : 16.21 % Favored : 79.65 % 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: -3.04 (0.23), residues: 1242 helix: -0.67 (0.27), residues: 369 sheet: -2.03 (0.26), residues: 386 loop : -2.97 (0.25), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 197 HIS 0.004 0.001 HIS A 310 PHE 0.022 0.002 PHE B 18 TYR 0.019 0.002 TYR B 164 ARG 0.005 0.000 ARG B 120 *********************** 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 174 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 127 time to evaluate : 1.095 Fit side-chains REVERT: A 157 ARG cc_start: 0.8048 (ptt90) cc_final: 0.7743 (ptt180) REVERT: A 266 MET cc_start: 0.9305 (mmt) cc_final: 0.9076 (mmm) REVERT: A 291 MET cc_start: 0.7726 (mmm) cc_final: 0.7432 (tpp) REVERT: A 300 LYS cc_start: 0.8696 (tttt) cc_final: 0.8482 (tttm) REVERT: A 385 ASP cc_start: 0.8546 (m-30) cc_final: 0.7981 (m-30) REVERT: A 390 TYR cc_start: 0.8896 (p90) cc_final: 0.8592 (p90) REVERT: A 446 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8838 (tt) REVERT: B 135 TYR cc_start: 0.8432 (t80) cc_final: 0.8215 (t80) REVERT: B 136 LYS cc_start: 0.8412 (mttp) cc_final: 0.8052 (mmtt) REVERT: B 189 MET cc_start: 0.9231 (mmm) cc_final: 0.8566 (mmt) REVERT: C 11 LYS cc_start: 0.7431 (ptmt) cc_final: 0.7003 (ptmt) REVERT: C 40 MET cc_start: 0.8959 (ptt) cc_final: 0.8706 (ptm) REVERT: C 102 ILE cc_start: 0.7935 (mm) cc_final: 0.7654 (mm) REVERT: C 111 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.7956 (tm-30) REVERT: C 119 ASP cc_start: 0.8333 (t0) cc_final: 0.8063 (t0) REVERT: C 303 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.7495 (pt0) REVERT: C 317 MET cc_start: 0.8078 (tpp) cc_final: 0.7772 (tpp) REVERT: L 13 TYR cc_start: 0.6543 (m-10) cc_final: 0.6023 (m-80) REVERT: L 38 ARG cc_start: 0.7429 (ttp-170) cc_final: 0.7165 (ttp-170) REVERT: L 85 MET cc_start: 0.2244 (mmp) cc_final: 0.1012 (mtp) REVERT: L 146 MET cc_start: 0.8617 (ptp) cc_final: 0.8391 (ptm) REVERT: L 148 TYR cc_start: 0.8247 (OUTLIER) cc_final: 0.7842 (p90) REVERT: L 254 TYR cc_start: 0.7575 (t80) cc_final: 0.7123 (t80) outliers start: 47 outliers final: 30 residues processed: 161 average time/residue: 0.2459 time to fit residues: 54.6767 Evaluate side-chains 152 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 118 time to evaluate : 1.139 ------------------------------------------------------------------------------- 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 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 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 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 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 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 28 optimal weight: 4.9990 chunk 121 optimal weight: 7.9990 chunk 98 optimal weight: 4.9990 chunk 9 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 123 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 2 optimal weight: 6.9990 chunk 10 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.168696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.119897 restraints weight = 10721.618| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 1.75 r_work: 0.3026 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 10386 Z= 0.417 Angle : 0.744 8.239 14034 Z= 0.385 Chirality : 0.047 0.171 1573 Planarity : 0.006 0.111 1764 Dihedral : 7.160 70.234 1361 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.32 % Allowed : 10.47 % Favored : 89.21 % Rotamer: Outliers : 4.41 % Allowed : 17.27 % Favored : 78.33 % 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: -2.99 (0.23), residues: 1242 helix: -0.51 (0.27), residues: 361 sheet: -2.07 (0.25), residues: 398 loop : -2.93 (0.25), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 236 HIS 0.004 0.001 HIS A 310 PHE 0.024 0.002 PHE B 18 TYR 0.022 0.002 TYR B 164 ARG 0.005 0.000 ARG B 120 *********************** 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 168 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 118 time to evaluate : 1.205 Fit side-chains REVERT: A 157 ARG cc_start: 0.7969 (ptt90) cc_final: 0.7616 (ptt-90) REVERT: A 266 MET cc_start: 0.9176 (mmt) cc_final: 0.8936 (mmm) REVERT: A 300 LYS cc_start: 0.8590 (tttt) cc_final: 0.8377 (tttm) REVERT: A 385 ASP cc_start: 0.8430 (m-30) cc_final: 0.7864 (m-30) REVERT: A 390 TYR cc_start: 0.8899 (p90) cc_final: 0.8506 (p90) REVERT: A 446 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8804 (tt) REVERT: B 135 TYR cc_start: 0.8453 (t80) cc_final: 0.8231 (t80) REVERT: B 136 LYS cc_start: 0.8343 (mttp) cc_final: 0.8004 (mmtt) REVERT: B 189 MET cc_start: 0.9167 (mmm) cc_final: 0.8475 (mmt) REVERT: B 236 GLU cc_start: 0.8433 (mm-30) cc_final: 0.7706 (pm20) REVERT: B 312 GLU cc_start: 0.8191 (mt-10) cc_final: 0.7938 (mt-10) REVERT: C 40 MET cc_start: 0.8961 (ptt) cc_final: 0.8728 (ptm) REVERT: C 57 ASP cc_start: 0.8746 (p0) cc_final: 0.8517 (p0) REVERT: C 102 ILE cc_start: 0.8114 (mm) cc_final: 0.7821 (mm) REVERT: C 111 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.7785 (tm-30) REVERT: C 119 ASP cc_start: 0.8079 (t0) cc_final: 0.7802 (t0) REVERT: C 150 TYR cc_start: 0.7604 (m-80) cc_final: 0.7357 (m-80) REVERT: C 303 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.7330 (pt0) REVERT: C 317 MET cc_start: 0.8069 (tpp) cc_final: 0.7821 (tpp) REVERT: L 38 ARG cc_start: 0.7456 (ttp-170) cc_final: 0.7166 (ttp-170) REVERT: L 49 ASN cc_start: 0.7510 (OUTLIER) cc_final: 0.7058 (m-40) REVERT: L 146 MET cc_start: 0.8298 (ptp) cc_final: 0.8043 (ptm) REVERT: L 148 TYR cc_start: 0.8326 (OUTLIER) cc_final: 0.7912 (p90) REVERT: L 168 MET cc_start: 0.8034 (mtp) cc_final: 0.7806 (mtp) REVERT: L 254 TYR cc_start: 0.7611 (t80) cc_final: 0.6987 (t80) REVERT: L 435 TRP cc_start: 0.7296 (OUTLIER) cc_final: 0.5698 (t60) outliers start: 50 outliers final: 32 residues processed: 153 average time/residue: 0.2415 time to fit residues: 51.7564 Evaluate side-chains 156 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 118 time to evaluate : 1.212 ------------------------------------------------------------------------------- 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 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 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 134 THR Chi-restraints excluded: chain C residue 219 VAL 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 148 TYR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 88 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 35 optimal weight: 0.0770 chunk 9 optimal weight: 4.9990 chunk 6 optimal weight: 0.9980 chunk 68 optimal weight: 3.9990 chunk 80 optimal weight: 20.0000 chunk 101 optimal weight: 10.0000 overall best weight: 1.3542 ------------------------------------------------------------------------------- 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 = 0.3865 r_free = 0.3865 target = 0.171244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.121735 restraints weight = 10699.575| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 1.79 r_work: 0.3091 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10386 Z= 0.236 Angle : 0.642 7.605 14034 Z= 0.334 Chirality : 0.043 0.162 1573 Planarity : 0.005 0.102 1764 Dihedral : 6.743 72.045 1361 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.26 % Favored : 90.50 % Rotamer: Outliers : 4.41 % Allowed : 17.44 % Favored : 78.15 % 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: -2.65 (0.23), residues: 1242 helix: -0.16 (0.28), residues: 369 sheet: -1.82 (0.26), residues: 380 loop : -2.90 (0.25), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 197 HIS 0.004 0.001 HIS A 310 PHE 0.025 0.002 PHE L 485 TYR 0.017 0.002 TYR B 164 ARG 0.003 0.000 ARG B 120 *********************** 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 174 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 124 time to evaluate : 1.200 Fit side-chains REVERT: A 157 ARG cc_start: 0.7855 (ptt90) cc_final: 0.7554 (ptt180) REVERT: A 266 MET cc_start: 0.9163 (mmt) cc_final: 0.8910 (mmm) REVERT: A 300 LYS cc_start: 0.8544 (tttt) cc_final: 0.8329 (tttm) REVERT: A 385 ASP cc_start: 0.8293 (m-30) cc_final: 0.7677 (m-30) REVERT: A 390 TYR cc_start: 0.8761 (p90) cc_final: 0.8443 (p90) REVERT: B 136 LYS cc_start: 0.8300 (mttp) cc_final: 0.7947 (mmtt) REVERT: B 189 MET cc_start: 0.9135 (mmm) cc_final: 0.8337 (mmt) REVERT: B 312 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7793 (mt-10) REVERT: C 40 MET cc_start: 0.8920 (ptt) cc_final: 0.8705 (ptm) REVERT: C 102 ILE cc_start: 0.8084 (mm) cc_final: 0.7817 (mm) REVERT: C 111 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7817 (tm-30) REVERT: C 119 ASP cc_start: 0.7996 (t0) cc_final: 0.7705 (t0) REVERT: C 303 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7486 (pt0) REVERT: C 317 MET cc_start: 0.8096 (tpp) cc_final: 0.7839 (tpp) REVERT: L 49 ASN cc_start: 0.7351 (OUTLIER) cc_final: 0.6973 (m-40) REVERT: L 85 MET cc_start: 0.2110 (mmt) cc_final: 0.0270 (ttm) REVERT: L 146 MET cc_start: 0.8321 (ptp) cc_final: 0.8084 (ptm) REVERT: L 166 GLN cc_start: 0.8698 (OUTLIER) cc_final: 0.8321 (mt0) REVERT: L 168 MET cc_start: 0.7998 (mtp) cc_final: 0.7780 (mtp) REVERT: L 231 LEU cc_start: 0.8177 (tt) cc_final: 0.7674 (pp) REVERT: L 254 TYR cc_start: 0.7495 (t80) cc_final: 0.6948 (t80) REVERT: L 304 GLU cc_start: 0.6474 (OUTLIER) cc_final: 0.6178 (pt0) REVERT: L 435 TRP cc_start: 0.7169 (OUTLIER) cc_final: 0.5631 (t60) outliers start: 50 outliers final: 33 residues processed: 155 average time/residue: 0.2432 time to fit residues: 52.9454 Evaluate side-chains 152 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 112 time to evaluate : 1.117 ------------------------------------------------------------------------------- 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 349 LEU Chi-restraints excluded: chain A residue 359 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 B residue 291 SER Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain C residue 41 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 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 148 TYR Chi-restraints excluded: chain L residue 166 GLN Chi-restraints excluded: chain L residue 204 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 42 optimal weight: 3.9990 chunk 64 optimal weight: 0.8980 chunk 98 optimal weight: 4.9990 chunk 63 optimal weight: 5.9990 chunk 92 optimal weight: 0.0070 chunk 7 optimal weight: 0.9990 chunk 114 optimal weight: 0.0470 chunk 53 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 81 optimal weight: 0.2980 chunk 10 optimal weight: 3.9990 overall best weight: 0.4096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 421 ASN ** A 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 318 GLN L 49 ASN L 195 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.181794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.154489 restraints weight = 10791.587| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 1.10 r_work: 0.3283 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.2822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 10386 Z= 0.142 Angle : 0.596 8.926 14034 Z= 0.305 Chirality : 0.041 0.253 1573 Planarity : 0.005 0.093 1764 Dihedral : 6.285 73.452 1361 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.37 % Favored : 91.38 % Rotamer: Outliers : 2.56 % Allowed : 19.30 % Favored : 78.15 % 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: -2.31 (0.24), residues: 1242 helix: 0.18 (0.28), residues: 384 sheet: -1.63 (0.26), residues: 394 loop : -2.85 (0.26), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 301 HIS 0.004 0.000 HIS A 310 PHE 0.025 0.001 PHE L 485 TYR 0.014 0.001 TYR C 260 ARG 0.002 0.000 ARG L 192 *********************** 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 166 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 137 time to evaluate : 1.278 Fit side-chains REVERT: A 266 MET cc_start: 0.9211 (mmt) cc_final: 0.8952 (mmm) REVERT: A 385 ASP cc_start: 0.8273 (m-30) cc_final: 0.7747 (m-30) REVERT: B 136 LYS cc_start: 0.8130 (mttp) cc_final: 0.7752 (mmtt) REVERT: B 178 GLN cc_start: 0.8834 (mt0) cc_final: 0.8590 (tt0) REVERT: B 189 MET cc_start: 0.9111 (mmm) cc_final: 0.8280 (mmt) REVERT: B 312 GLU cc_start: 0.8067 (mt-10) cc_final: 0.7768 (mt-10) REVERT: C 66 ASP cc_start: 0.4532 (p0) cc_final: 0.4278 (p0) REVERT: C 102 ILE cc_start: 0.8065 (mm) cc_final: 0.7834 (mm) REVERT: C 119 ASP cc_start: 0.8216 (t0) cc_final: 0.7942 (t0) REVERT: C 260 TYR cc_start: 0.7918 (t80) cc_final: 0.7717 (t80) REVERT: C 317 MET cc_start: 0.8225 (tpp) cc_final: 0.8014 (tpp) REVERT: L 13 TYR cc_start: 0.6429 (m-10) cc_final: 0.5837 (m-80) REVERT: L 85 MET cc_start: 0.2637 (mmt) cc_final: 0.0613 (ttm) REVERT: L 166 GLN cc_start: 0.8696 (OUTLIER) cc_final: 0.8324 (tt0) REVERT: L 231 LEU cc_start: 0.8229 (tt) cc_final: 0.7792 (pp) REVERT: L 254 TYR cc_start: 0.7569 (t80) cc_final: 0.7083 (t80) outliers start: 29 outliers final: 20 residues processed: 154 average time/residue: 0.2478 time to fit residues: 52.8646 Evaluate side-chains 147 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 126 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 TRP Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 481 LEU 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 252 VAL Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain L residue 49 ASN Chi-restraints excluded: chain L residue 139 LYS Chi-restraints excluded: chain L residue 166 GLN Chi-restraints excluded: chain L residue 204 LEU Chi-restraints excluded: chain L residue 411 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 23 optimal weight: 2.9990 chunk 111 optimal weight: 6.9990 chunk 29 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 95 optimal weight: 10.0000 chunk 41 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 55 optimal weight: 10.0000 chunk 98 optimal weight: 7.9990 chunk 121 optimal weight: 10.0000 overall best weight: 2.5388 ------------------------------------------------------------------------------- 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 L 49 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.170114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 104)---------------| | r_work = 0.3284 r_free = 0.3284 target = 0.122053 restraints weight = 10782.261| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 1.77 r_work: 0.3058 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 10386 Z= 0.384 Angle : 0.728 10.723 14034 Z= 0.372 Chirality : 0.047 0.228 1573 Planarity : 0.006 0.111 1764 Dihedral : 6.841 71.582 1361 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.90 % Favored : 89.77 % Rotamer: Outliers : 3.35 % Allowed : 19.56 % Favored : 77.09 % 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: -2.42 (0.24), residues: 1242 helix: 0.10 (0.28), residues: 363 sheet: -1.67 (0.26), residues: 392 loop : -2.81 (0.26), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 236 HIS 0.004 0.001 HIS A 422 PHE 0.037 0.002 PHE L 298 TYR 0.022 0.002 TYR B 164 ARG 0.007 0.001 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 153 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 115 time to evaluate : 1.259 Fit side-chains REVERT: A 385 ASP cc_start: 0.8259 (m-30) cc_final: 0.7724 (m-30) REVERT: B 93 LYS cc_start: 0.8425 (tttp) cc_final: 0.8211 (ttpt) REVERT: B 136 LYS cc_start: 0.8355 (mttp) cc_final: 0.7961 (mmtt) REVERT: B 189 MET cc_start: 0.9138 (mmm) cc_final: 0.8411 (mmt) REVERT: B 312 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7832 (mt-10) REVERT: C 102 ILE cc_start: 0.8215 (mm) cc_final: 0.7884 (mm) REVERT: C 111 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7807 (tm-30) REVERT: C 119 ASP cc_start: 0.8083 (t0) cc_final: 0.7789 (t0) REVERT: C 317 MET cc_start: 0.8308 (tpp) cc_final: 0.8105 (tpp) REVERT: L 85 MET cc_start: 0.2323 (mmt) cc_final: 0.0277 (ttm) REVERT: L 166 GLN cc_start: 0.8694 (OUTLIER) cc_final: 0.8341 (mt0) REVERT: L 168 MET cc_start: 0.7807 (mtp) cc_final: 0.7573 (mtp) REVERT: L 254 TYR cc_start: 0.7612 (t80) cc_final: 0.7061 (t80) REVERT: L 435 TRP cc_start: 0.7231 (OUTLIER) cc_final: 0.5624 (t60) outliers start: 38 outliers final: 27 residues processed: 141 average time/residue: 0.2437 time to fit residues: 48.3295 Evaluate side-chains 145 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 114 time to evaluate : 1.192 ------------------------------------------------------------------------------- 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 253 SER Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 396 SER 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 252 VAL Chi-restraints excluded: chain B residue 291 SER Chi-restraints excluded: chain B residue 312 GLU 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 39 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 chunk 115 optimal weight: 20.0000 chunk 15 optimal weight: 0.4980 chunk 52 optimal weight: 1.9990 chunk 116 optimal weight: 10.0000 chunk 76 optimal weight: 4.9990 chunk 61 optimal weight: 0.0770 chunk 89 optimal weight: 8.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- 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 = 0.3961 r_free = 0.3961 target = 0.179242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.150958 restraints weight = 10755.856| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 1.11 r_work: 0.3258 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 10386 Z= 0.159 Angle : 0.630 14.924 14034 Z= 0.317 Chirality : 0.042 0.216 1573 Planarity : 0.005 0.094 1764 Dihedral : 6.387 74.225 1361 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.13 % Favored : 91.63 % Rotamer: Outliers : 1.85 % Allowed : 21.06 % Favored : 77.09 % 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: -2.13 (0.24), residues: 1242 helix: 0.34 (0.28), residues: 384 sheet: -1.45 (0.27), residues: 393 loop : -2.83 (0.26), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 301 HIS 0.004 0.000 HIS A 310 PHE 0.029 0.001 PHE L 292 TYR 0.014 0.001 TYR C 260 ARG 0.003 0.000 ARG A 211 *********************** 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 150 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 129 time to evaluate : 1.123 Fit side-chains REVERT: A 266 MET cc_start: 0.9257 (mmt) cc_final: 0.9015 (mmm) REVERT: A 324 MET cc_start: 0.7781 (tpp) cc_final: 0.7480 (mmm) REVERT: A 385 ASP cc_start: 0.8237 (m-30) cc_final: 0.7750 (m-30) REVERT: B 136 LYS cc_start: 0.8249 (mttp) cc_final: 0.7867 (mmtt) REVERT: B 178 GLN cc_start: 0.8814 (mt0) cc_final: 0.8587 (tt0) REVERT: B 189 MET cc_start: 0.9103 (mmm) cc_final: 0.8337 (mmt) REVERT: B 312 GLU cc_start: 0.8190 (mt-10) cc_final: 0.7987 (mt-10) REVERT: C 66 ASP cc_start: 0.4634 (p0) cc_final: 0.4381 (p0) REVERT: C 97 GLU cc_start: 0.5568 (OUTLIER) cc_final: 0.5368 (tp30) REVERT: C 102 ILE cc_start: 0.8290 (mm) cc_final: 0.8010 (mm) REVERT: C 119 ASP cc_start: 0.8380 (t0) cc_final: 0.8093 (t0) REVERT: C 150 TYR cc_start: 0.7965 (m-80) cc_final: 0.7627 (m-80) REVERT: C 260 TYR cc_start: 0.8075 (t80) cc_final: 0.7861 (t80) REVERT: L 85 MET cc_start: 0.2749 (mmt) cc_final: 0.0615 (ttm) REVERT: L 168 MET cc_start: 0.8097 (mtp) cc_final: 0.7883 (mtp) REVERT: L 231 LEU cc_start: 0.8295 (tt) cc_final: 0.7825 (pp) REVERT: L 254 TYR cc_start: 0.7519 (t80) cc_final: 0.7042 (t80) REVERT: L 435 TRP cc_start: 0.7178 (OUTLIER) cc_final: 0.5744 (t60) outliers start: 21 outliers final: 15 residues processed: 141 average time/residue: 0.2436 time to fit residues: 48.1055 Evaluate side-chains 141 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 124 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 TRP Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 396 SER 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 139 ILE Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 284 LEU 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 13 optimal weight: 3.9990 chunk 62 optimal weight: 7.9990 chunk 42 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 99 optimal weight: 0.0770 chunk 59 optimal weight: 0.0870 chunk 8 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 chunk 53 optimal weight: 0.5980 chunk 6 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 overall best weight: 0.9518 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.178445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.149899 restraints weight = 10749.684| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 1.19 r_work: 0.3235 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.2942 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= 0.192 Angle : 0.642 14.403 14034 Z= 0.323 Chirality : 0.042 0.211 1573 Planarity : 0.005 0.101 1764 Dihedral : 6.355 73.408 1361 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.78 % Favored : 90.98 % Rotamer: Outliers : 2.11 % Allowed : 20.62 % Favored : 77.27 % 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: -2.01 (0.24), residues: 1242 helix: 0.54 (0.28), residues: 381 sheet: -1.43 (0.27), residues: 395 loop : -2.80 (0.26), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 301 HIS 0.002 0.000 HIS A 310 PHE 0.027 0.002 PHE L 292 TYR 0.017 0.001 TYR C 140 ARG 0.004 0.000 ARG A 211 ********************** 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 148 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 124 time to evaluate : 1.101 Fit side-chains REVERT: A 266 MET cc_start: 0.9081 (mmt) cc_final: 0.8832 (mmm) REVERT: A 324 MET cc_start: 0.7707 (tpp) cc_final: 0.7432 (mmm) REVERT: A 385 ASP cc_start: 0.8014 (m-30) cc_final: 0.7533 (m-30) REVERT: B 136 LYS cc_start: 0.8198 (mttp) cc_final: 0.7945 (mmtt) REVERT: B 189 MET cc_start: 0.9045 (mmm) cc_final: 0.8185 (mmt) REVERT: C 66 ASP cc_start: 0.4724 (p0) cc_final: 0.4424 (p0) REVERT: C 102 ILE cc_start: 0.8485 (mm) cc_final: 0.8217 (mm) REVERT: C 111 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7899 (tm-30) REVERT: C 119 ASP cc_start: 0.8108 (t0) cc_final: 0.7821 (t0) REVERT: C 260 TYR cc_start: 0.7965 (t80) cc_final: 0.7764 (t80) REVERT: L 85 MET cc_start: 0.2126 (mmt) cc_final: 0.0430 (ttm) REVERT: L 166 GLN cc_start: 0.8496 (OUTLIER) cc_final: 0.8185 (mt0) REVERT: L 231 LEU cc_start: 0.8166 (tt) cc_final: 0.7846 (pp) REVERT: L 254 TYR cc_start: 0.7380 (t80) cc_final: 0.6997 (t80) REVERT: L 435 TRP cc_start: 0.6958 (OUTLIER) cc_final: 0.5741 (t60) outliers start: 24 outliers final: 18 residues processed: 138 average time/residue: 0.2334 time to fit residues: 45.1761 Evaluate side-chains 142 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 121 time to evaluate : 1.123 ------------------------------------------------------------------------------- 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 248 SER Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 396 SER 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 139 ILE Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 69 THR 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 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 115 optimal weight: 20.0000 chunk 75 optimal weight: 0.2980 chunk 108 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 chunk 110 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 69 optimal weight: 0.7980 chunk 65 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.177211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.148577 restraints weight = 10702.067| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 1.10 r_work: 0.3341 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.2953 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= 0.216 Angle : 0.653 14.126 14034 Z= 0.328 Chirality : 0.043 0.203 1573 Planarity : 0.005 0.100 1764 Dihedral : 5.922 54.446 1358 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.86 % Favored : 90.90 % Rotamer: Outliers : 2.47 % Allowed : 20.53 % Favored : 77.00 % 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: -1.94 (0.24), residues: 1242 helix: 0.64 (0.28), residues: 375 sheet: -1.36 (0.27), residues: 391 loop : -2.77 (0.25), residues: 476 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 0.026 0.002 PHE L 292 TYR 0.017 0.001 TYR C 140 ARG 0.004 0.000 ARG A 211 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4808.08 seconds wall clock time: 86 minutes 19.68 seconds (5179.68 seconds total)