Starting phenix.real_space_refine on Sun May 11 20:39:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b5y_44229/05_2025/9b5y_44229.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b5y_44229/05_2025/9b5y_44229.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b5y_44229/05_2025/9b5y_44229.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b5y_44229/05_2025/9b5y_44229.map" model { file = "/net/cci-nas-00/data/ceres_data/9b5y_44229/05_2025/9b5y_44229.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b5y_44229/05_2025/9b5y_44229.cif" } resolution = 3.49 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= 0.001 sd= 0.020 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 49 5.16 5 C 5370 2.51 5 N 1441 2.21 5 O 1569 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 8429 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 1844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1844 Classifications: {'peptide': 249} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 4, 'TRANS': 244} Chain breaks: 3 Unresolved non-hydrogen bonds: 200 Unresolved non-hydrogen angles: 246 Unresolved non-hydrogen dihedrals: 169 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 3, 'GLU:plan': 6, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 120 Chain: "A" Number of atoms: 1607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1607 Classifications: {'peptide': 222} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 5, 'TRANS': 216} Chain breaks: 1 Unresolved non-hydrogen bonds: 230 Unresolved non-hydrogen angles: 289 Unresolved non-hydrogen dihedrals: 198 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 6, 'PHE:plan': 3, 'GLU:plan': 9, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 169 Chain: "L" Number of atoms: 179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 179 Classifications: {'peptide': 26} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'TRANS': 25} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 3, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "B" Number of atoms: 2593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2593 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "N" Number of atoms: 1770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1770 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Time building chain proxies: 5.27, per 1000 atoms: 0.63 Number of scatterers: 8429 At special positions: 0 Unit cell: (89.424, 122.544, 133.308, 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 49 16.00 O 1569 8.00 N 1441 7.00 C 5370 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 281 " - pdb=" SG CYS R 351 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 160 " - pdb=" SG CYS N 230 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.22 Conformation dependent library (CDL) restraints added in 1.1 seconds 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2106 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 14 sheets defined 35.3% alpha, 20.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'R' and resid 179 through 212 removed outlier: 3.828A pdb=" N ALA R 200 " --> pdb=" O SER R 196 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA R 205 " --> pdb=" O SER R 201 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE R 212 " --> pdb=" O ILE R 208 " (cutoff:3.500A) Processing helix chain 'R' and resid 217 through 244 Processing helix chain 'R' and resid 280 through 310 removed outlier: 3.667A pdb=" N ALA R 284 " --> pdb=" O GLY R 280 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU R 300 " --> pdb=" O TYR R 296 " (cutoff:3.500A) Processing helix chain 'R' and resid 317 through 322 removed outlier: 4.000A pdb=" N LEU R 321 " --> pdb=" O GLU R 317 " (cutoff:3.500A) Processing helix chain 'R' and resid 322 through 339 removed outlier: 3.608A pdb=" N VAL R 326 " --> pdb=" O TRP R 322 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE R 327 " --> pdb=" O GLY R 323 " (cutoff:3.500A) Proline residue: R 332 - end of helix removed outlier: 3.602A pdb=" N PHE R 335 " --> pdb=" O LEU R 331 " (cutoff:3.500A) Processing helix chain 'R' and resid 364 through 391 removed outlier: 3.530A pdb=" N THR R 387 " --> pdb=" O ARG R 383 " (cutoff:3.500A) Processing helix chain 'R' and resid 403 through 418 Proline residue: R 415 - end of helix Processing helix chain 'R' and resid 434 through 445 Processing helix chain 'R' and resid 455 through 460 Processing helix chain 'R' and resid 465 through 470 Processing helix chain 'A' and resid 12 through 35 Processing helix chain 'A' and resid 53 through 60 Processing helix chain 'A' and resid 217 through 222 removed outlier: 3.522A pdb=" N GLU A 221 " --> pdb=" O HIS A 218 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ASN A 222 " --> pdb=" O CYS A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 235 No H-bonds generated for 'chain 'A' and resid 233 through 235' Processing helix chain 'A' and resid 247 through 260 Processing helix chain 'A' and resid 275 through 286 removed outlier: 3.520A pdb=" N LEU A 279 " --> pdb=" O LYS A 275 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N MET A 284 " --> pdb=" O GLU A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 302 removed outlier: 3.669A pdb=" N ALA A 302 " --> pdb=" O GLN A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 316 removed outlier: 3.963A pdb=" N LEU A 316 " --> pdb=" O MET A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 356 Processing helix chain 'L' and resid 2 through 21 removed outlier: 3.686A pdb=" N ARG L 19 " --> pdb=" O ILE L 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 25 removed outlier: 3.594A pdb=" N GLN B 9 " --> pdb=" O ASP B 5 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLU B 10 " --> pdb=" O GLN B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.838A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 53 through 56 removed outlier: 3.783A pdb=" N GLY N 56 " --> pdb=" O SER N 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 53 through 56' Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.815A pdb=" N ASP N 90 " --> pdb=" O ARG N 87 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N THR N 91 " --> pdb=" O SER N 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 87 through 91' Processing helix chain 'N' and resid 221 through 225 removed outlier: 3.891A pdb=" N VAL N 225 " --> pdb=" O ALA N 222 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 24 removed outlier: 3.818A pdb=" N GLN G 11 " --> pdb=" O ALA G 7 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA G 12 " --> pdb=" O SER G 8 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 43 Processing helix chain 'G' and resid 44 through 48 Processing sheet with id=AA1, first strand: chain 'A' and resid 203 through 206 removed outlier: 6.258A pdb=" N LEU A 40 " --> pdb=" O VAL A 204 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N VAL A 206 " --> pdb=" O LEU A 40 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N LEU A 42 " --> pdb=" O VAL A 206 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LYS A 41 " --> pdb=" O SER A 225 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N MET A 227 " --> pdb=" O LYS A 41 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N LEU A 43 " --> pdb=" O MET A 227 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N LEU A 229 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N LEU A 45 " --> pdb=" O LEU A 229 " (cutoff:3.500A) removed outlier: 8.908A pdb=" N ALA A 231 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL A 230 " --> pdb=" O PHE A 272 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 49 through 50 removed outlier: 3.725A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL B 327 " --> pdb=" O TRP B 339 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 62 removed outlier: 6.988A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.882A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 4.295A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.576A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 232 removed outlier: 6.594A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.766A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.518A pdb=" N THR N 69 " --> pdb=" O GLN N 82 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 11 through 12 removed outlier: 3.863A pdb=" N VAL N 97 " --> pdb=" O HIS N 35 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N MET N 34 " --> pdb=" O TYR N 50 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N TYR N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 11 through 12 removed outlier: 4.434A pdb=" N PHE N 110 " --> pdb=" O ARG N 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'N' and resid 147 through 149 removed outlier: 6.409A pdb=" N VAL N 148 " --> pdb=" O GLU N 247 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE N 190 " --> pdb=" O TRP N 177 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LEU N 179 " --> pdb=" O LEU N 188 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N LEU N 188 " --> pdb=" O LEU N 179 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'N' and resid 156 through 157 removed outlier: 3.584A pdb=" N CYS N 160 " --> pdb=" O PHE N 213 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'N' and resid 156 through 157 removed outlier: 3.668A pdb=" N SER N 207 " --> pdb=" O THR N 214 " (cutoff:3.500A) 378 hydrogen bonds defined for protein. 1071 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.51 Time building geometry restraints manager: 2.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1977 1.33 - 1.45: 1852 1.45 - 1.57: 4699 1.57 - 1.69: 0 1.69 - 1.81: 72 Bond restraints: 8600 Sorted by residual: bond pdb=" N LEU R 331 " pdb=" CA LEU R 331 " ideal model delta sigma weight residual 1.461 1.494 -0.033 9.20e-03 1.18e+04 1.30e+01 bond pdb=" N GLY N 241 " pdb=" CA GLY N 241 " ideal model delta sigma weight residual 1.445 1.470 -0.026 9.90e-03 1.02e+04 6.73e+00 bond pdb=" CA SER R 308 " pdb=" CB SER R 308 " ideal model delta sigma weight residual 1.536 1.484 0.052 2.01e-02 2.48e+03 6.58e+00 bond pdb=" N PHE R 327 " pdb=" CA PHE R 327 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.20e-02 6.94e+03 6.32e+00 bond pdb=" N LEU R 306 " pdb=" CA LEU R 306 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.21e-02 6.83e+03 6.15e+00 ... (remaining 8595 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.34: 11644 4.34 - 8.67: 43 8.67 - 13.01: 3 13.01 - 17.35: 2 17.35 - 21.68: 2 Bond angle restraints: 11694 Sorted by residual: angle pdb=" C PRO N 14 " pdb=" CA PRO N 14 " pdb=" CB PRO N 14 " ideal model delta sigma weight residual 111.23 129.61 -18.38 1.28e+00 6.10e-01 2.06e+02 angle pdb=" N PRO N 14 " pdb=" CA PRO N 14 " pdb=" C PRO N 14 " ideal model delta sigma weight residual 111.21 89.53 21.68 1.59e+00 3.96e-01 1.86e+02 angle pdb=" N GLY N 15 " pdb=" CA GLY N 15 " pdb=" C GLY N 15 " ideal model delta sigma weight residual 115.59 130.96 -15.37 1.32e+00 5.74e-01 1.36e+02 angle pdb=" N PRO N 237 " pdb=" CA PRO N 237 " pdb=" C PRO N 237 " ideal model delta sigma weight residual 112.47 96.26 16.21 2.06e+00 2.36e-01 6.19e+01 angle pdb=" N LEU N 238 " pdb=" CA LEU N 238 " pdb=" C LEU N 238 " ideal model delta sigma weight residual 109.71 99.47 10.24 1.41e+00 5.03e-01 5.28e+01 ... (remaining 11689 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.62: 4240 14.62 - 29.23: 508 29.23 - 43.85: 216 43.85 - 58.46: 66 58.46 - 73.08: 14 Dihedral angle restraints: 5044 sinusoidal: 1787 harmonic: 3257 Sorted by residual: dihedral pdb=" CB CYS N 22 " pdb=" SG CYS N 22 " pdb=" SG CYS N 96 " pdb=" CB CYS N 96 " ideal model delta sinusoidal sigma weight residual 93.00 162.73 -69.73 1 1.00e+01 1.00e-02 6.27e+01 dihedral pdb=" CB CYS R 281 " pdb=" SG CYS R 281 " pdb=" SG CYS R 351 " pdb=" CB CYS R 351 " ideal model delta sinusoidal sigma weight residual 93.00 29.61 63.39 1 1.00e+01 1.00e-02 5.30e+01 dihedral pdb=" C GLU N 235 " pdb=" N GLU N 235 " pdb=" CA GLU N 235 " pdb=" CB GLU N 235 " ideal model delta harmonic sigma weight residual -122.60 -135.54 12.94 0 2.50e+00 1.60e-01 2.68e+01 ... (remaining 5041 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1166 0.062 - 0.125: 174 0.125 - 0.187: 10 0.187 - 0.249: 4 0.249 - 0.311: 5 Chirality restraints: 1359 Sorted by residual: chirality pdb=" CA LEU N 238 " pdb=" N LEU N 238 " pdb=" C LEU N 238 " pdb=" CB LEU N 238 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.42e+00 chirality pdb=" CA GLU N 235 " pdb=" N GLU N 235 " pdb=" C GLU N 235 " pdb=" CB GLU N 235 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.31 2.00e-01 2.50e+01 2.33e+00 chirality pdb=" CA TYR N 236 " pdb=" N TYR N 236 " pdb=" C TYR N 236 " pdb=" CB TYR N 236 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.27 2.00e-01 2.50e+01 1.89e+00 ... (remaining 1356 not shown) Planarity restraints: 1485 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE R 324 " -0.023 2.00e-02 2.50e+03 2.47e-02 1.07e+01 pdb=" CG PHE R 324 " 0.057 2.00e-02 2.50e+03 pdb=" CD1 PHE R 324 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 PHE R 324 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE R 324 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE R 324 " -0.009 2.00e-02 2.50e+03 pdb=" CZ PHE R 324 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS R 319 " -0.014 2.00e-02 2.50e+03 2.83e-02 8.01e+00 pdb=" C LYS R 319 " 0.049 2.00e-02 2.50e+03 pdb=" O LYS R 319 " -0.018 2.00e-02 2.50e+03 pdb=" N TYR R 320 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU R 306 " -0.014 2.00e-02 2.50e+03 2.83e-02 8.01e+00 pdb=" C LEU R 306 " 0.049 2.00e-02 2.50e+03 pdb=" O LEU R 306 " -0.018 2.00e-02 2.50e+03 pdb=" N HIS R 307 " -0.017 2.00e-02 2.50e+03 ... (remaining 1482 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1484 2.76 - 3.30: 7895 3.30 - 3.83: 14155 3.83 - 4.37: 15963 4.37 - 4.90: 28030 Nonbonded interactions: 67527 Sorted by model distance: nonbonded pdb=" OG SER B 147 " pdb=" O SER B 160 " model vdw 2.230 3.040 nonbonded pdb=" O GLU R 444 " pdb=" ND2 ASN R 448 " model vdw 2.249 3.120 nonbonded pdb=" NE2 GLN N 232 " pdb=" O PRO N 237 " model vdw 2.253 3.120 nonbonded pdb=" N PRO N 14 " pdb=" O PRO N 14 " model vdw 2.261 2.496 nonbonded pdb=" ND2 ASN A 317 " pdb=" OD1 ASP A 319 " model vdw 2.304 3.120 ... (remaining 67522 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: 1.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.390 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 22.350 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6491 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 : 0.004 0.052 8603 Z= 0.234 Angle : 0.777 21.681 11700 Z= 0.484 Chirality : 0.048 0.311 1359 Planarity : 0.004 0.048 1485 Dihedral : 16.505 73.078 2929 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 1.30 % Allowed : 28.57 % Favored : 70.13 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.27), residues: 1103 helix: 1.49 (0.29), residues: 360 sheet: -0.95 (0.32), residues: 289 loop : -1.42 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP B 82 HIS 0.009 0.001 HIS R 307 PHE 0.057 0.002 PHE R 324 TYR 0.031 0.002 TYR R 191 ARG 0.009 0.000 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.17761 ( 371) hydrogen bonds : angle 7.20927 ( 1071) SS BOND : bond 0.00169 ( 3) SS BOND : angle 0.68165 ( 6) covalent geometry : bond 0.00439 ( 8600) covalent geometry : angle 0.77667 (11694) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 140 time to evaluate : 0.901 Fit side-chains REVERT: A 26 ASP cc_start: 0.7329 (t0) cc_final: 0.6970 (m-30) REVERT: B 258 ASP cc_start: 0.6505 (t0) cc_final: 0.5870 (t0) REVERT: N 192 ARG cc_start: 0.7543 (mtt90) cc_final: 0.7291 (mtm180) outliers start: 11 outliers final: 5 residues processed: 147 average time/residue: 0.1892 time to fit residues: 39.1798 Evaluate side-chains 142 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 137 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain A residue 319 ASP Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 234 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 chunk 55 optimal weight: 0.4980 chunk 44 optimal weight: 0.2980 chunk 85 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 63 optimal weight: 1.9990 chunk 98 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 216 HIS R 295 ASN ** R 442 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 317 ASN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 ASN N 39 GLN G 18 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.172925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.149413 restraints weight = 11244.271| |-----------------------------------------------------------------------------| r_work (start): 0.3808 rms_B_bonded: 1.76 r_work: 0.3695 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3533 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7007 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8603 Z= 0.183 Angle : 0.561 7.351 11700 Z= 0.303 Chirality : 0.042 0.155 1359 Planarity : 0.004 0.053 1485 Dihedral : 4.906 43.682 1210 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 4.60 % Allowed : 24.44 % Favored : 70.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.27), residues: 1103 helix: 1.56 (0.29), residues: 368 sheet: -0.87 (0.31), residues: 299 loop : -1.45 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 82 HIS 0.004 0.001 HIS B 142 PHE 0.061 0.002 PHE R 324 TYR 0.020 0.002 TYR R 191 ARG 0.006 0.000 ARG B 314 Details of bonding type rmsd hydrogen bonds : bond 0.04116 ( 371) hydrogen bonds : angle 4.94140 ( 1071) SS BOND : bond 0.00285 ( 3) SS BOND : angle 0.67600 ( 6) covalent geometry : bond 0.00420 ( 8600) covalent geometry : angle 0.56129 (11694) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 148 time to evaluate : 0.808 Fit side-chains REVERT: R 457 ILE cc_start: 0.8349 (OUTLIER) cc_final: 0.8141 (tp) REVERT: B 49 ARG cc_start: 0.7746 (OUTLIER) cc_final: 0.7241 (mtt-85) REVERT: B 83 ASP cc_start: 0.8103 (t0) cc_final: 0.7760 (t70) REVERT: B 129 ARG cc_start: 0.7736 (OUTLIER) cc_final: 0.7349 (mtt90) REVERT: B 159 THR cc_start: 0.7986 (OUTLIER) cc_final: 0.7344 (p) REVERT: N 18 ARG cc_start: 0.6444 (ttt180) cc_final: 0.6195 (ttt180) REVERT: N 89 GLU cc_start: 0.6730 (OUTLIER) cc_final: 0.6190 (pp20) outliers start: 39 outliers final: 19 residues processed: 172 average time/residue: 0.1782 time to fit residues: 43.2118 Evaluate side-chains 171 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 147 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain R residue 384 VAL Chi-restraints excluded: chain R residue 427 THR Chi-restraints excluded: chain R residue 457 ILE Chi-restraints excluded: chain R residue 460 CYS Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain B residue 49 ARG Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 129 ARG Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 89 GLU Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 116 THR Chi-restraints excluded: chain N residue 119 VAL Chi-restraints excluded: chain N residue 160 CYS Chi-restraints excluded: chain N residue 234 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 36 optimal weight: 0.0070 chunk 68 optimal weight: 0.5980 chunk 52 optimal weight: 0.7980 chunk 100 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 48 optimal weight: 7.9990 chunk 24 optimal weight: 0.9980 chunk 92 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 442 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** 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 = 0.4128 r_free = 0.4128 target = 0.172380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.148515 restraints weight = 11470.778| |-----------------------------------------------------------------------------| r_work (start): 0.3828 rms_B_bonded: 1.80 r_work: 0.3715 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3555 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6995 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8603 Z= 0.151 Angle : 0.522 6.569 11700 Z= 0.279 Chirality : 0.040 0.148 1359 Planarity : 0.004 0.051 1485 Dihedral : 4.739 45.434 1207 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 5.55 % Allowed : 24.91 % Favored : 69.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.26), residues: 1103 helix: 1.76 (0.29), residues: 366 sheet: -0.81 (0.31), residues: 291 loop : -1.48 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.003 0.001 HIS R 420 PHE 0.031 0.002 PHE R 324 TYR 0.019 0.001 TYR N 191 ARG 0.004 0.000 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.03722 ( 371) hydrogen bonds : angle 4.63219 ( 1071) SS BOND : bond 0.00304 ( 3) SS BOND : angle 0.57990 ( 6) covalent geometry : bond 0.00345 ( 8600) covalent geometry : angle 0.52157 (11694) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 147 time to evaluate : 0.928 Fit side-chains REVERT: R 457 ILE cc_start: 0.8292 (OUTLIER) cc_final: 0.8074 (tp) REVERT: A 356 TYR cc_start: 0.5380 (OUTLIER) cc_final: 0.5069 (t80) REVERT: B 49 ARG cc_start: 0.7767 (OUTLIER) cc_final: 0.7182 (mtt-85) REVERT: B 83 ASP cc_start: 0.8121 (t0) cc_final: 0.7336 (t0) REVERT: B 105 TYR cc_start: 0.8568 (t80) cc_final: 0.8364 (t80) REVERT: B 159 THR cc_start: 0.7970 (OUTLIER) cc_final: 0.7298 (p) REVERT: B 247 ASP cc_start: 0.7934 (p0) cc_final: 0.7732 (p0) REVERT: N 89 GLU cc_start: 0.6663 (OUTLIER) cc_final: 0.6251 (pp20) outliers start: 47 outliers final: 28 residues processed: 176 average time/residue: 0.1956 time to fit residues: 48.5463 Evaluate side-chains 177 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 144 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain R residue 325 THR Chi-restraints excluded: chain R residue 427 THR Chi-restraints excluded: chain R residue 457 ILE Chi-restraints excluded: chain R residue 460 CYS Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain A residue 356 TYR Chi-restraints excluded: chain B residue 49 ARG Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain N residue 63 THR Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 89 GLU Chi-restraints excluded: chain N residue 116 THR Chi-restraints excluded: chain N residue 119 VAL Chi-restraints excluded: chain N residue 150 VAL Chi-restraints excluded: chain N residue 151 THR Chi-restraints excluded: chain N residue 160 CYS Chi-restraints excluded: chain N residue 173 THR Chi-restraints excluded: chain N residue 234 LEU Chi-restraints excluded: chain N residue 239 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 32 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 88 optimal weight: 0.0870 chunk 89 optimal weight: 0.9990 chunk 87 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 70 optimal weight: 0.5980 chunk 18 optimal weight: 10.0000 chunk 101 optimal weight: 6.9990 chunk 40 optimal weight: 7.9990 chunk 91 optimal weight: 0.5980 overall best weight: 0.6360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 223 HIS ** R 442 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.171604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.147659 restraints weight = 11251.623| |-----------------------------------------------------------------------------| r_work (start): 0.3822 rms_B_bonded: 1.82 r_work: 0.3708 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3546 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7010 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8603 Z= 0.159 Angle : 0.525 6.655 11700 Z= 0.279 Chirality : 0.040 0.149 1359 Planarity : 0.004 0.050 1485 Dihedral : 4.784 47.058 1207 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 5.08 % Allowed : 26.09 % Favored : 68.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.26), residues: 1103 helix: 1.67 (0.29), residues: 371 sheet: -0.83 (0.31), residues: 289 loop : -1.47 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 169 HIS 0.003 0.001 HIS A 218 PHE 0.028 0.002 PHE R 324 TYR 0.021 0.001 TYR R 191 ARG 0.004 0.000 ARG B 314 Details of bonding type rmsd hydrogen bonds : bond 0.03564 ( 371) hydrogen bonds : angle 4.52750 ( 1071) SS BOND : bond 0.00288 ( 3) SS BOND : angle 0.67282 ( 6) covalent geometry : bond 0.00368 ( 8600) covalent geometry : angle 0.52473 (11694) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 154 time to evaluate : 0.916 Fit side-chains REVERT: R 421 TYR cc_start: 0.6298 (OUTLIER) cc_final: 0.5918 (p90) REVERT: R 457 ILE cc_start: 0.8307 (OUTLIER) cc_final: 0.8082 (tp) REVERT: A 271 LEU cc_start: 0.8201 (OUTLIER) cc_final: 0.7800 (tp) REVERT: A 356 TYR cc_start: 0.5331 (OUTLIER) cc_final: 0.4963 (t80) REVERT: B 49 ARG cc_start: 0.7763 (OUTLIER) cc_final: 0.7111 (mtt-85) REVERT: B 83 ASP cc_start: 0.8118 (t0) cc_final: 0.7343 (t0) REVERT: B 105 TYR cc_start: 0.8559 (t80) cc_final: 0.8331 (t80) REVERT: B 247 ASP cc_start: 0.7883 (p0) cc_final: 0.7653 (p0) outliers start: 43 outliers final: 30 residues processed: 180 average time/residue: 0.1793 time to fit residues: 45.8873 Evaluate side-chains 189 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 154 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 294 THR Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain R residue 373 LEU Chi-restraints excluded: chain R residue 421 TYR Chi-restraints excluded: chain R residue 457 ILE Chi-restraints excluded: chain R residue 460 CYS Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 356 TYR Chi-restraints excluded: chain B residue 49 ARG Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 116 THR Chi-restraints excluded: chain N residue 119 VAL Chi-restraints excluded: chain N residue 150 VAL Chi-restraints excluded: chain N residue 151 THR Chi-restraints excluded: chain N residue 160 CYS Chi-restraints excluded: chain N residue 173 THR Chi-restraints excluded: chain N residue 193 MET Chi-restraints excluded: chain N residue 234 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 10 optimal weight: 0.0670 chunk 50 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 17 optimal weight: 0.4980 chunk 87 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 chunk 106 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 108 optimal weight: 2.9990 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 442 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** 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 = 0.4131 r_free = 0.4131 target = 0.172817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.149226 restraints weight = 11307.375| |-----------------------------------------------------------------------------| r_work (start): 0.3823 rms_B_bonded: 1.77 r_work: 0.3711 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3544 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7011 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8603 Z= 0.157 Angle : 0.523 6.618 11700 Z= 0.277 Chirality : 0.040 0.150 1359 Planarity : 0.004 0.050 1485 Dihedral : 4.783 47.388 1207 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 5.67 % Allowed : 26.09 % Favored : 68.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.26), residues: 1103 helix: 1.68 (0.29), residues: 371 sheet: -0.85 (0.31), residues: 289 loop : -1.45 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 169 HIS 0.003 0.001 HIS A 218 PHE 0.024 0.002 PHE R 324 TYR 0.022 0.001 TYR R 191 ARG 0.008 0.000 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.03459 ( 371) hydrogen bonds : angle 4.46100 ( 1071) SS BOND : bond 0.00342 ( 3) SS BOND : angle 0.58545 ( 6) covalent geometry : bond 0.00364 ( 8600) covalent geometry : angle 0.52275 (11694) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 152 time to evaluate : 0.804 Fit side-chains REVERT: R 421 TYR cc_start: 0.6286 (OUTLIER) cc_final: 0.5865 (p90) REVERT: R 457 ILE cc_start: 0.8293 (OUTLIER) cc_final: 0.8068 (tp) REVERT: A 271 LEU cc_start: 0.8195 (OUTLIER) cc_final: 0.7797 (tp) REVERT: A 356 TYR cc_start: 0.5371 (OUTLIER) cc_final: 0.5071 (t80) REVERT: B 49 ARG cc_start: 0.7746 (OUTLIER) cc_final: 0.7068 (mtt-85) REVERT: B 83 ASP cc_start: 0.8101 (t0) cc_final: 0.7382 (t0) REVERT: B 105 TYR cc_start: 0.8529 (t80) cc_final: 0.8305 (t80) REVERT: B 217 MET cc_start: 0.7846 (ptt) cc_final: 0.7623 (ptt) REVERT: B 247 ASP cc_start: 0.7883 (p0) cc_final: 0.7664 (p0) outliers start: 48 outliers final: 33 residues processed: 180 average time/residue: 0.1801 time to fit residues: 45.9363 Evaluate side-chains 190 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 152 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 294 THR Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain R residue 345 THR Chi-restraints excluded: chain R residue 373 LEU Chi-restraints excluded: chain R residue 421 TYR Chi-restraints excluded: chain R residue 457 ILE Chi-restraints excluded: chain R residue 460 CYS Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 356 TYR Chi-restraints excluded: chain B residue 49 ARG Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 116 THR Chi-restraints excluded: chain N residue 119 VAL Chi-restraints excluded: chain N residue 150 VAL Chi-restraints excluded: chain N residue 151 THR Chi-restraints excluded: chain N residue 160 CYS Chi-restraints excluded: chain N residue 173 THR Chi-restraints excluded: chain N residue 193 MET Chi-restraints excluded: chain N residue 234 LEU Chi-restraints excluded: chain N residue 239 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 35 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 8 optimal weight: 0.1980 chunk 22 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 chunk 16 optimal weight: 0.5980 chunk 78 optimal weight: 2.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 442 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** 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 = 0.4115 r_free = 0.4115 target = 0.171332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.147095 restraints weight = 11323.213| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 1.83 r_work: 0.3676 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3514 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7032 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8603 Z= 0.173 Angle : 0.534 7.169 11700 Z= 0.283 Chirality : 0.041 0.158 1359 Planarity : 0.004 0.050 1485 Dihedral : 4.824 46.608 1207 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 5.19 % Allowed : 26.80 % Favored : 68.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.26), residues: 1103 helix: 1.60 (0.29), residues: 373 sheet: -0.81 (0.31), residues: 283 loop : -1.47 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 169 HIS 0.004 0.001 HIS A 218 PHE 0.022 0.002 PHE R 324 TYR 0.023 0.002 TYR R 191 ARG 0.008 0.000 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.03536 ( 371) hydrogen bonds : angle 4.47789 ( 1071) SS BOND : bond 0.00325 ( 3) SS BOND : angle 0.69428 ( 6) covalent geometry : bond 0.00403 ( 8600) covalent geometry : angle 0.53378 (11694) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 148 time to evaluate : 0.865 Fit side-chains REVERT: R 421 TYR cc_start: 0.6403 (OUTLIER) cc_final: 0.5838 (p90) REVERT: A 271 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7807 (tp) REVERT: A 356 TYR cc_start: 0.5306 (OUTLIER) cc_final: 0.5042 (t80) REVERT: B 49 ARG cc_start: 0.7757 (OUTLIER) cc_final: 0.7076 (mtt-85) REVERT: B 83 ASP cc_start: 0.8108 (t0) cc_final: 0.7426 (t0) REVERT: B 105 TYR cc_start: 0.8518 (t80) cc_final: 0.8301 (t80) REVERT: B 217 MET cc_start: 0.7909 (ptt) cc_final: 0.7693 (ptt) REVERT: B 234 PHE cc_start: 0.7895 (OUTLIER) cc_final: 0.7153 (m-80) REVERT: B 247 ASP cc_start: 0.7866 (p0) cc_final: 0.7651 (p0) REVERT: B 280 LYS cc_start: 0.8329 (tttp) cc_final: 0.8125 (tttm) REVERT: N 52 SER cc_start: 0.8033 (m) cc_final: 0.7680 (t) outliers start: 44 outliers final: 32 residues processed: 175 average time/residue: 0.1919 time to fit residues: 47.0190 Evaluate side-chains 184 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 147 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 294 THR Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain R residue 345 THR Chi-restraints excluded: chain R residue 373 LEU Chi-restraints excluded: chain R residue 421 TYR Chi-restraints excluded: chain R residue 460 CYS Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 356 TYR Chi-restraints excluded: chain B residue 49 ARG Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 116 THR Chi-restraints excluded: chain N residue 119 VAL Chi-restraints excluded: chain N residue 150 VAL Chi-restraints excluded: chain N residue 151 THR Chi-restraints excluded: chain N residue 160 CYS Chi-restraints excluded: chain N residue 173 THR Chi-restraints excluded: chain N residue 193 MET Chi-restraints excluded: chain N residue 234 LEU Chi-restraints excluded: chain N residue 239 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 83 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 44 optimal weight: 0.5980 chunk 4 optimal weight: 0.6980 chunk 60 optimal weight: 0.6980 chunk 18 optimal weight: 7.9990 chunk 10 optimal weight: 7.9990 chunk 32 optimal weight: 0.5980 chunk 82 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 40 optimal weight: 8.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 442 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** 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 = 0.4127 r_free = 0.4127 target = 0.172351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.148799 restraints weight = 11317.410| |-----------------------------------------------------------------------------| r_work (start): 0.3812 rms_B_bonded: 1.76 r_work: 0.3697 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3537 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7015 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8603 Z= 0.169 Angle : 0.535 7.058 11700 Z= 0.283 Chirality : 0.041 0.160 1359 Planarity : 0.004 0.051 1485 Dihedral : 4.818 45.429 1207 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 5.08 % Allowed : 27.15 % Favored : 67.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.26), residues: 1103 helix: 1.66 (0.29), residues: 370 sheet: -0.80 (0.31), residues: 287 loop : -1.45 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 169 HIS 0.004 0.001 HIS A 218 PHE 0.020 0.002 PHE R 324 TYR 0.023 0.002 TYR R 191 ARG 0.008 0.000 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.03473 ( 371) hydrogen bonds : angle 4.44125 ( 1071) SS BOND : bond 0.00310 ( 3) SS BOND : angle 0.64408 ( 6) covalent geometry : bond 0.00394 ( 8600) covalent geometry : angle 0.53470 (11694) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 150 time to evaluate : 0.912 Fit side-chains REVERT: R 421 TYR cc_start: 0.6456 (OUTLIER) cc_final: 0.5846 (p90) REVERT: A 271 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.7795 (tp) REVERT: A 356 TYR cc_start: 0.5203 (OUTLIER) cc_final: 0.4940 (t80) REVERT: B 49 ARG cc_start: 0.7748 (OUTLIER) cc_final: 0.7014 (mtt-85) REVERT: B 83 ASP cc_start: 0.8099 (t0) cc_final: 0.7451 (t0) REVERT: B 105 TYR cc_start: 0.8520 (t80) cc_final: 0.8293 (t80) REVERT: B 217 MET cc_start: 0.7885 (ptt) cc_final: 0.7650 (ptt) REVERT: B 234 PHE cc_start: 0.7910 (OUTLIER) cc_final: 0.7145 (m-80) REVERT: B 247 ASP cc_start: 0.7817 (p0) cc_final: 0.7605 (p0) REVERT: N 52 SER cc_start: 0.8051 (m) cc_final: 0.7704 (t) REVERT: N 89 GLU cc_start: 0.6691 (OUTLIER) cc_final: 0.6424 (pp20) outliers start: 43 outliers final: 31 residues processed: 176 average time/residue: 0.2000 time to fit residues: 48.8646 Evaluate side-chains 185 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 148 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 294 THR Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain R residue 345 THR Chi-restraints excluded: chain R residue 373 LEU Chi-restraints excluded: chain R residue 421 TYR Chi-restraints excluded: chain R residue 460 CYS Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 356 TYR Chi-restraints excluded: chain B residue 49 ARG Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 89 GLU Chi-restraints excluded: chain N residue 116 THR Chi-restraints excluded: chain N residue 119 VAL Chi-restraints excluded: chain N residue 150 VAL Chi-restraints excluded: chain N residue 151 THR Chi-restraints excluded: chain N residue 160 CYS Chi-restraints excluded: chain N residue 173 THR Chi-restraints excluded: chain N residue 193 MET Chi-restraints excluded: chain N residue 234 LEU Chi-restraints excluded: chain N residue 239 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 65 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 82 optimal weight: 0.6980 chunk 75 optimal weight: 0.4980 chunk 80 optimal weight: 0.0570 chunk 107 optimal weight: 0.9990 chunk 108 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 79 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 216 HIS ** R 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.172088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.148522 restraints weight = 11373.348| |-----------------------------------------------------------------------------| r_work (start): 0.3822 rms_B_bonded: 1.77 r_work: 0.3702 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3542 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7012 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8603 Z= 0.146 Angle : 0.518 7.376 11700 Z= 0.273 Chirality : 0.040 0.128 1359 Planarity : 0.004 0.050 1485 Dihedral : 4.724 44.800 1207 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 5.55 % Allowed : 26.92 % Favored : 67.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.26), residues: 1103 helix: 1.72 (0.29), residues: 369 sheet: -0.75 (0.31), residues: 287 loop : -1.45 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 169 HIS 0.003 0.001 HIS A 218 PHE 0.019 0.001 PHE R 324 TYR 0.020 0.001 TYR R 191 ARG 0.007 0.000 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.03304 ( 371) hydrogen bonds : angle 4.36902 ( 1071) SS BOND : bond 0.00295 ( 3) SS BOND : angle 0.56350 ( 6) covalent geometry : bond 0.00340 ( 8600) covalent geometry : angle 0.51797 (11694) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 146 time to evaluate : 0.954 Fit side-chains REVERT: R 192 THR cc_start: 0.7955 (m) cc_final: 0.7684 (m) REVERT: R 421 TYR cc_start: 0.6488 (OUTLIER) cc_final: 0.5850 (p90) REVERT: A 271 LEU cc_start: 0.8193 (OUTLIER) cc_final: 0.7816 (tp) REVERT: B 49 ARG cc_start: 0.7739 (OUTLIER) cc_final: 0.6971 (mtt-85) REVERT: B 83 ASP cc_start: 0.8083 (t0) cc_final: 0.7388 (t0) REVERT: B 105 TYR cc_start: 0.8502 (t80) cc_final: 0.8263 (t80) REVERT: B 217 MET cc_start: 0.7894 (ptt) cc_final: 0.7642 (ptt) REVERT: B 234 PHE cc_start: 0.7893 (OUTLIER) cc_final: 0.7155 (m-80) REVERT: N 52 SER cc_start: 0.8058 (m) cc_final: 0.7814 (t) REVERT: N 89 GLU cc_start: 0.6708 (OUTLIER) cc_final: 0.6465 (pp20) outliers start: 47 outliers final: 38 residues processed: 175 average time/residue: 0.1820 time to fit residues: 45.4947 Evaluate side-chains 189 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 146 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 223 HIS Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 294 THR Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain R residue 345 THR Chi-restraints excluded: chain R residue 373 LEU Chi-restraints excluded: chain R residue 421 TYR Chi-restraints excluded: chain R residue 429 TYR Chi-restraints excluded: chain R residue 460 CYS Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain B residue 49 ARG Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 89 GLU Chi-restraints excluded: chain N residue 116 THR Chi-restraints excluded: chain N residue 119 VAL Chi-restraints excluded: chain N residue 150 VAL Chi-restraints excluded: chain N residue 151 THR Chi-restraints excluded: chain N residue 160 CYS Chi-restraints excluded: chain N residue 173 THR Chi-restraints excluded: chain N residue 193 MET Chi-restraints excluded: chain N residue 234 LEU Chi-restraints excluded: chain N residue 239 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 64 optimal weight: 0.6980 chunk 107 optimal weight: 0.7980 chunk 87 optimal weight: 3.9990 chunk 5 optimal weight: 0.5980 chunk 2 optimal weight: 0.7980 chunk 89 optimal weight: 0.8980 chunk 93 optimal weight: 4.9990 chunk 20 optimal weight: 0.0030 chunk 100 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 78 optimal weight: 0.0370 overall best weight: 0.4068 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 442 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** 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 = 0.4142 r_free = 0.4142 target = 0.173878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.151153 restraints weight = 11418.854| |-----------------------------------------------------------------------------| r_work (start): 0.3834 rms_B_bonded: 1.69 r_work: 0.3721 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3568 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6964 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8603 Z= 0.120 Angle : 0.509 7.593 11700 Z= 0.269 Chirality : 0.040 0.126 1359 Planarity : 0.003 0.049 1485 Dihedral : 4.592 44.877 1207 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 5.08 % Allowed : 27.27 % Favored : 67.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.27), residues: 1103 helix: 1.78 (0.29), residues: 369 sheet: -0.66 (0.32), residues: 287 loop : -1.41 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 169 HIS 0.005 0.001 HIS R 442 PHE 0.016 0.001 PHE R 324 TYR 0.020 0.001 TYR R 191 ARG 0.007 0.000 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.03184 ( 371) hydrogen bonds : angle 4.24454 ( 1071) SS BOND : bond 0.00272 ( 3) SS BOND : angle 0.60762 ( 6) covalent geometry : bond 0.00279 ( 8600) covalent geometry : angle 0.50940 (11694) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 146 time to evaluate : 0.815 Fit side-chains REVERT: R 192 THR cc_start: 0.7931 (m) cc_final: 0.7649 (m) REVERT: R 421 TYR cc_start: 0.6429 (OUTLIER) cc_final: 0.5766 (p90) REVERT: B 49 ARG cc_start: 0.7723 (OUTLIER) cc_final: 0.6933 (mtt-85) REVERT: B 83 ASP cc_start: 0.8066 (t0) cc_final: 0.7637 (t0) REVERT: B 105 TYR cc_start: 0.8504 (t80) cc_final: 0.8224 (t80) REVERT: B 234 PHE cc_start: 0.7883 (OUTLIER) cc_final: 0.7156 (m-80) REVERT: B 247 ASP cc_start: 0.7844 (p0) cc_final: 0.7611 (p0) REVERT: N 52 SER cc_start: 0.8060 (m) cc_final: 0.7821 (t) REVERT: N 89 GLU cc_start: 0.6689 (OUTLIER) cc_final: 0.6455 (pp20) outliers start: 43 outliers final: 35 residues processed: 175 average time/residue: 0.1817 time to fit residues: 44.9445 Evaluate side-chains 182 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 143 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 223 HIS Chi-restraints excluded: chain R residue 294 THR Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain R residue 345 THR Chi-restraints excluded: chain R residue 373 LEU Chi-restraints excluded: chain R residue 421 TYR Chi-restraints excluded: chain R residue 429 TYR Chi-restraints excluded: chain R residue 460 CYS Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain B residue 49 ARG Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 89 GLU Chi-restraints excluded: chain N residue 116 THR Chi-restraints excluded: chain N residue 119 VAL Chi-restraints excluded: chain N residue 150 VAL Chi-restraints excluded: chain N residue 151 THR Chi-restraints excluded: chain N residue 160 CYS Chi-restraints excluded: chain N residue 173 THR Chi-restraints excluded: chain N residue 193 MET Chi-restraints excluded: chain N residue 234 LEU Chi-restraints excluded: chain N residue 239 THR Chi-restraints excluded: chain G residue 21 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 55 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 chunk 57 optimal weight: 0.7980 chunk 105 optimal weight: 2.9990 chunk 101 optimal weight: 4.9990 chunk 5 optimal weight: 0.5980 chunk 103 optimal weight: 0.0670 chunk 104 optimal weight: 5.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 442 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.173439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.149448 restraints weight = 11254.942| |-----------------------------------------------------------------------------| r_work (start): 0.3818 rms_B_bonded: 1.84 r_work: 0.3690 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3525 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7035 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8603 Z= 0.155 Angle : 0.555 12.675 11700 Z= 0.285 Chirality : 0.041 0.131 1359 Planarity : 0.004 0.050 1485 Dihedral : 4.709 44.275 1207 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 4.49 % Allowed : 27.98 % Favored : 67.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.26), residues: 1103 helix: 1.75 (0.29), residues: 368 sheet: -0.66 (0.32), residues: 283 loop : -1.47 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 169 HIS 0.005 0.001 HIS R 442 PHE 0.018 0.001 PHE R 324 TYR 0.020 0.002 TYR R 191 ARG 0.009 0.000 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.03313 ( 371) hydrogen bonds : angle 4.31300 ( 1071) SS BOND : bond 0.00287 ( 3) SS BOND : angle 0.57507 ( 6) covalent geometry : bond 0.00363 ( 8600) covalent geometry : angle 0.55450 (11694) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 146 time to evaluate : 0.925 Fit side-chains REVERT: R 192 THR cc_start: 0.7982 (m) cc_final: 0.7709 (m) REVERT: R 421 TYR cc_start: 0.6499 (OUTLIER) cc_final: 0.5885 (p90) REVERT: B 49 ARG cc_start: 0.7765 (OUTLIER) cc_final: 0.6971 (mtt-85) REVERT: B 83 ASP cc_start: 0.8100 (t0) cc_final: 0.7691 (t0) REVERT: B 234 PHE cc_start: 0.7917 (OUTLIER) cc_final: 0.7159 (m-80) REVERT: N 52 SER cc_start: 0.8074 (m) cc_final: 0.7840 (t) outliers start: 38 outliers final: 33 residues processed: 169 average time/residue: 0.1762 time to fit residues: 42.6106 Evaluate side-chains 182 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 146 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 223 HIS Chi-restraints excluded: chain R residue 281 CYS Chi-restraints excluded: chain R residue 294 THR Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain R residue 345 THR Chi-restraints excluded: chain R residue 373 LEU Chi-restraints excluded: chain R residue 421 TYR Chi-restraints excluded: chain R residue 429 TYR Chi-restraints excluded: chain R residue 460 CYS Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain B residue 49 ARG Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 116 THR Chi-restraints excluded: chain N residue 119 VAL Chi-restraints excluded: chain N residue 150 VAL Chi-restraints excluded: chain N residue 151 THR Chi-restraints excluded: chain N residue 160 CYS Chi-restraints excluded: chain N residue 173 THR Chi-restraints excluded: chain N residue 193 MET Chi-restraints excluded: chain N residue 234 LEU Chi-restraints excluded: chain N residue 239 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 74 optimal weight: 0.0030 chunk 68 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 17 optimal weight: 6.9990 chunk 65 optimal weight: 0.0570 chunk 11 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 36 optimal weight: 0.6980 overall best weight: 0.4308 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 442 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** 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 = 0.4143 r_free = 0.4143 target = 0.173999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.151334 restraints weight = 11435.478| |-----------------------------------------------------------------------------| r_work (start): 0.3836 rms_B_bonded: 1.69 r_work: 0.3723 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3568 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6971 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8603 Z= 0.124 Angle : 0.517 7.307 11700 Z= 0.272 Chirality : 0.040 0.130 1359 Planarity : 0.004 0.049 1485 Dihedral : 4.606 43.718 1207 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 4.49 % Allowed : 27.98 % Favored : 67.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.27), residues: 1103 helix: 1.83 (0.29), residues: 366 sheet: -0.61 (0.32), residues: 283 loop : -1.46 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 169 HIS 0.004 0.001 HIS R 442 PHE 0.029 0.001 PHE R 324 TYR 0.020 0.001 TYR R 191 ARG 0.010 0.000 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.03185 ( 371) hydrogen bonds : angle 4.22143 ( 1071) SS BOND : bond 0.00264 ( 3) SS BOND : angle 0.60090 ( 6) covalent geometry : bond 0.00289 ( 8600) covalent geometry : angle 0.51689 (11694) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4703.09 seconds wall clock time: 82 minutes 5.92 seconds (4925.92 seconds total)