Starting phenix.real_space_refine on Sun May 11 17:54:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h4l_34480/05_2025/8h4l_34480_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h4l_34480/05_2025/8h4l_34480.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8h4l_34480/05_2025/8h4l_34480.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h4l_34480/05_2025/8h4l_34480.map" model { file = "/net/cci-nas-00/data/ceres_data/8h4l_34480/05_2025/8h4l_34480_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h4l_34480/05_2025/8h4l_34480_neut.cif" } resolution = 3.07 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= 0.034 sd= 0.130 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 48 5.16 5 C 5212 2.51 5 N 1409 2.21 5 O 1502 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 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: 8171 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1904 Classifications: {'peptide': 234} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 6, 'TRANS': 227} Chain breaks: 1 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "B" Number of atoms: 2547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2547 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 41 Chain: "G" Number of atoms: 408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 408 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "N" Number of atoms: 963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 963 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "R" Number of atoms: 2325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2325 Classifications: {'peptide': 302} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 13, 'TRANS': 288} Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 55 Chain: "R" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'HXA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.25, per 1000 atoms: 0.64 Number of scatterers: 8171 At special positions: 0 Unit cell: (78.1, 103.4, 139.7, 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 48 16.00 O 1502 8.00 N 1409 7.00 C 5212 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 111 " - pdb=" SG CYS R 194 " distance=2.04 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: 2.27 Conformation dependent library (CDL) restraints added in 912.2 milliseconds 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1998 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 11 sheets defined 41.8% alpha, 21.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.06 Creating SS restraints... Processing helix chain 'A' and resid 15 through 38 removed outlier: 4.174A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 61 Processing helix chain 'A' and resid 235 through 239 removed outlier: 3.760A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 removed outlier: 3.561A pdb=" N ALA A 269 " --> pdb=" O ARG A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 283 removed outlier: 4.080A pdb=" N ARG A 283 " --> pdb=" O ARG A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 304 removed outlier: 3.568A pdb=" N LEU A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLY A 304 " --> pdb=" O LYS A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 311 Processing helix chain 'A' and resid 312 through 317 Processing helix chain 'A' and resid 331 through 351 removed outlier: 3.813A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 4 through 25 removed outlier: 3.849A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.748A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 23 Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.728A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N HIS G 44 " --> pdb=" O TYR G 40 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 48 removed outlier: 3.751A pdb=" N ASP G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 48' Processing helix chain 'G' and resid 55 through 59 Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.562A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.641A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 35 through 68 removed outlier: 3.957A pdb=" N ARG R 68 " --> pdb=" O LEU R 64 " (cutoff:3.500A) Processing helix chain 'R' and resid 72 through 89 removed outlier: 3.985A pdb=" N CYS R 76 " --> pdb=" O GLY R 72 " (cutoff:3.500A) Processing helix chain 'R' and resid 91 through 102 removed outlier: 3.765A pdb=" N VAL R 95 " --> pdb=" O ALA R 91 " (cutoff:3.500A) Processing helix chain 'R' and resid 107 through 145 removed outlier: 5.661A pdb=" N PHE R 115 " --> pdb=" O CYS R 111 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N TYR R 116 " --> pdb=" O HIS R 112 " (cutoff:3.500A) Processing helix chain 'R' and resid 151 through 170 Processing helix chain 'R' and resid 171 through 176 removed outlier: 4.029A pdb=" N VAL R 175 " --> pdb=" O LEU R 171 " (cutoff:3.500A) Processing helix chain 'R' and resid 200 through 214 removed outlier: 3.602A pdb=" N GLU R 204 " --> pdb=" O THR R 200 " (cutoff:3.500A) Processing helix chain 'R' and resid 216 through 244 removed outlier: 4.212A pdb=" N LEU R 241 " --> pdb=" O SER R 237 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N THR R 242 " --> pdb=" O ARG R 238 " (cutoff:3.500A) Processing helix chain 'R' and resid 251 through 256 Processing helix chain 'R' and resid 258 through 270 removed outlier: 3.966A pdb=" N LEU R 262 " --> pdb=" O GLN R 258 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N PHE R 267 " --> pdb=" O PHE R 263 " (cutoff:3.500A) Processing helix chain 'R' and resid 271 through 277 Processing helix chain 'R' and resid 277 through 293 removed outlier: 3.988A pdb=" N ILE R 281 " --> pdb=" O TRP R 277 " (cutoff:3.500A) Processing helix chain 'R' and resid 299 through 311 Processing helix chain 'R' and resid 312 through 321 Proline residue: R 318 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 4.911A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.965A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.831A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.757A 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: 6.784A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASN B 125 " --> pdb=" O ARG B 134 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.947A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 189 through 192 removed outlier: 3.903A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.833A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.719A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.207A pdb=" N GLY N 10 " --> pdb=" O THR N 125 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 177 through 183 409 hydrogen bonds defined for protein. 1167 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: 2.24 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: 1.22 - 1.34: 2673 1.34 - 1.47: 2024 1.47 - 1.59: 3572 1.59 - 1.72: 0 1.72 - 1.84: 66 Bond restraints: 8335 Sorted by residual: bond pdb=" N HIS A 357 " pdb=" CA HIS A 357 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.21e-02 6.83e+03 8.07e+00 bond pdb=" N ILE A 348 " pdb=" CA ILE A 348 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.98e+00 bond pdb=" N ARG A 389 " pdb=" CA ARG A 389 " ideal model delta sigma weight residual 1.456 1.488 -0.033 1.32e-02 5.74e+03 6.15e+00 bond pdb=" N GLY A 353 " pdb=" CA GLY A 353 " ideal model delta sigma weight residual 1.448 1.475 -0.028 1.13e-02 7.83e+03 6.01e+00 bond pdb=" N GLU A 390 " pdb=" CA GLU A 390 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.27e-02 6.20e+03 5.94e+00 ... (remaining 8330 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.24: 10980 2.24 - 4.49: 300 4.49 - 6.73: 36 6.73 - 8.98: 9 8.98 - 11.22: 3 Bond angle restraints: 11328 Sorted by residual: angle pdb=" CA TRP B 82 " pdb=" CB TRP B 82 " pdb=" CG TRP B 82 " ideal model delta sigma weight residual 113.60 121.12 -7.52 1.90e+00 2.77e-01 1.57e+01 angle pdb=" N ASP N 109 " pdb=" CA ASP N 109 " pdb=" C ASP N 109 " ideal model delta sigma weight residual 110.06 115.63 -5.57 1.43e+00 4.89e-01 1.51e+01 angle pdb=" N ALA B 309 " pdb=" CA ALA B 309 " pdb=" C ALA B 309 " ideal model delta sigma weight residual 107.48 116.05 -8.57 2.29e+00 1.91e-01 1.40e+01 angle pdb=" N ALA B 203 " pdb=" CA ALA B 203 " pdb=" C ALA B 203 " ideal model delta sigma weight residual 110.06 115.39 -5.33 1.43e+00 4.89e-01 1.39e+01 angle pdb=" N THR A 350 " pdb=" CA THR A 350 " pdb=" C THR A 350 " ideal model delta sigma weight residual 114.04 109.46 4.58 1.24e+00 6.50e-01 1.36e+01 ... (remaining 11323 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 4584 17.71 - 35.41: 292 35.41 - 53.12: 47 53.12 - 70.83: 10 70.83 - 88.54: 10 Dihedral angle restraints: 4943 sinusoidal: 1863 harmonic: 3080 Sorted by residual: dihedral pdb=" CA ASP N 109 " pdb=" C ASP N 109 " pdb=" N VAL N 110 " pdb=" CA VAL N 110 " ideal model delta harmonic sigma weight residual 180.00 160.13 19.87 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA ALA B 203 " pdb=" C ALA B 203 " pdb=" N CYS B 204 " pdb=" CA CYS B 204 " ideal model delta harmonic sigma weight residual 180.00 160.36 19.64 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA GLY B 202 " pdb=" C GLY B 202 " pdb=" N ALA B 203 " pdb=" CA ALA B 203 " ideal model delta harmonic sigma weight residual -180.00 -160.52 -19.48 0 5.00e+00 4.00e-02 1.52e+01 ... (remaining 4940 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1017 0.059 - 0.118: 264 0.118 - 0.177: 36 0.177 - 0.236: 4 0.236 - 0.295: 1 Chirality restraints: 1322 Sorted by residual: chirality pdb=" CA THR R 101 " pdb=" N THR R 101 " pdb=" C THR R 101 " pdb=" CB THR R 101 " both_signs ideal model delta sigma weight residual False 2.53 2.23 0.30 2.00e-01 2.50e+01 2.18e+00 chirality pdb=" CA SER A 251 " pdb=" N SER A 251 " pdb=" C SER A 251 " pdb=" CB SER A 251 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CA PRO R 93 " pdb=" N PRO R 93 " pdb=" C PRO R 93 " pdb=" CB PRO R 93 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.19 2.00e-01 2.50e+01 9.29e-01 ... (remaining 1319 not shown) Planarity restraints: 1442 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE R 92 " -0.073 5.00e-02 4.00e+02 1.08e-01 1.86e+01 pdb=" N PRO R 93 " 0.187 5.00e-02 4.00e+02 pdb=" CA PRO R 93 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO R 93 " -0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP G 48 " -0.045 5.00e-02 4.00e+02 6.78e-02 7.36e+00 pdb=" N PRO G 49 " 0.117 5.00e-02 4.00e+02 pdb=" CA PRO G 49 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO G 49 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 82 " 0.025 2.00e-02 2.50e+03 1.47e-02 5.37e+00 pdb=" CG TRP B 82 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TRP B 82 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 TRP B 82 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP B 82 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP B 82 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 82 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 82 " 0.007 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 82 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP B 82 " 0.002 2.00e-02 2.50e+03 ... (remaining 1439 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 72 2.64 - 3.20: 7036 3.20 - 3.77: 11220 3.77 - 4.33: 15666 4.33 - 4.90: 27374 Nonbonded interactions: 61368 Sorted by model distance: nonbonded pdb=" O PRO R 108 " pdb=" ND1 HIS R 112 " model vdw 2.069 3.120 nonbonded pdb=" OG1 THR R 74 " pdb=" OE1 GLU R 135 " model vdw 2.194 3.040 nonbonded pdb=" OE2 GLU A 27 " pdb=" NZ LYS B 89 " model vdw 2.230 3.120 nonbonded pdb=" O CYS A 359 " pdb=" OH TYR R 247 " model vdw 2.230 3.040 nonbonded pdb=" O ALA R 66 " pdb=" NH2 ARG R 71 " model vdw 2.236 3.120 ... (remaining 61363 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: 1.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 21.980 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 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 : 0.007 0.059 8336 Z= 0.327 Angle : 0.900 11.221 11330 Z= 0.522 Chirality : 0.052 0.295 1322 Planarity : 0.006 0.108 1442 Dihedral : 12.790 88.536 2942 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 0.23 % Allowed : 0.92 % Favored : 98.85 % 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: 1047 helix: 0.74 (0.27), residues: 393 sheet: 0.50 (0.33), residues: 237 loop : -1.61 (0.28), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP B 82 HIS 0.008 0.002 HIS B 91 PHE 0.023 0.003 PHE B 199 TYR 0.021 0.003 TYR B 59 ARG 0.006 0.001 ARG N 72 Details of bonding type rmsd hydrogen bonds : bond 0.15188 ( 409) hydrogen bonds : angle 5.73862 ( 1167) SS BOND : bond 0.00646 ( 1) SS BOND : angle 2.78139 ( 2) covalent geometry : bond 0.00727 ( 8335) covalent geometry : angle 0.89972 (11328) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 98 time to evaluate : 0.864 Fit side-chains REVERT: N 46 GLU cc_start: 0.7509 (tt0) cc_final: 0.7182 (tt0) outliers start: 2 outliers final: 1 residues processed: 100 average time/residue: 0.2247 time to fit residues: 29.9926 Evaluate side-chains 92 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 91 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 388 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 86 optimal weight: 0.9990 chunk 78 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 26 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 49 optimal weight: 0.6980 chunk 60 optimal weight: 0.0170 chunk 93 optimal weight: 0.7980 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.124568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.095186 restraints weight = 12547.964| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 2.18 r_work: 0.3124 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.1156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8336 Z= 0.131 Angle : 0.561 6.767 11330 Z= 0.307 Chirality : 0.044 0.146 1322 Planarity : 0.005 0.054 1442 Dihedral : 5.595 52.687 1159 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 0.58 % Allowed : 3.92 % Favored : 95.50 % 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: 1047 helix: 1.60 (0.27), residues: 397 sheet: 1.01 (0.34), residues: 231 loop : -1.57 (0.28), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 82 HIS 0.006 0.001 HIS A 357 PHE 0.022 0.002 PHE R 263 TYR 0.014 0.001 TYR R 247 ARG 0.002 0.000 ARG A 280 Details of bonding type rmsd hydrogen bonds : bond 0.05957 ( 409) hydrogen bonds : angle 4.21449 ( 1167) SS BOND : bond 0.00325 ( 1) SS BOND : angle 1.89151 ( 2) covalent geometry : bond 0.00270 ( 8335) covalent geometry : angle 0.56048 (11328) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 99 time to evaluate : 0.885 Fit side-chains REVERT: N 106 ASP cc_start: 0.7994 (p0) cc_final: 0.7781 (p0) REVERT: R 239 LYS cc_start: 0.7942 (tttt) cc_final: 0.7733 (tptt) outliers start: 5 outliers final: 3 residues processed: 102 average time/residue: 0.2176 time to fit residues: 30.4233 Evaluate side-chains 93 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 90 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain R residue 247 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 2 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 79 optimal weight: 0.5980 chunk 93 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 chunk 97 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 60 optimal weight: 0.0060 chunk 5 optimal weight: 0.8980 chunk 54 optimal weight: 0.3980 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.125324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.095457 restraints weight = 12861.842| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 2.23 r_work: 0.3134 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8336 Z= 0.118 Angle : 0.524 5.841 11330 Z= 0.285 Chirality : 0.042 0.137 1322 Planarity : 0.004 0.042 1442 Dihedral : 5.222 55.984 1157 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 2.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 0.92 % Allowed : 6.00 % Favored : 93.08 % 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: 0.71 (0.27), residues: 1047 helix: 1.88 (0.27), residues: 401 sheet: 1.03 (0.35), residues: 231 loop : -1.33 (0.28), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.006 0.001 HIS A 357 PHE 0.015 0.002 PHE A 376 TYR 0.012 0.001 TYR R 247 ARG 0.002 0.000 ARG A 280 Details of bonding type rmsd hydrogen bonds : bond 0.05309 ( 409) hydrogen bonds : angle 3.95617 ( 1167) SS BOND : bond 0.00485 ( 1) SS BOND : angle 2.16890 ( 2) covalent geometry : bond 0.00241 ( 8335) covalent geometry : angle 0.52357 (11328) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 93 time to evaluate : 0.852 Fit side-chains REVERT: N 106 ASP cc_start: 0.7924 (p0) cc_final: 0.7695 (p0) outliers start: 8 outliers final: 6 residues processed: 97 average time/residue: 0.2123 time to fit residues: 28.2244 Evaluate side-chains 94 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 88 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain R residue 42 VAL Chi-restraints excluded: chain R residue 247 TYR Chi-restraints excluded: chain R residue 275 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 10 optimal weight: 0.0670 chunk 93 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 overall best weight: 1.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.123142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.093523 restraints weight = 12704.640| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 2.18 r_work: 0.3098 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.1470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8336 Z= 0.164 Angle : 0.586 7.896 11330 Z= 0.315 Chirality : 0.044 0.142 1322 Planarity : 0.004 0.040 1442 Dihedral : 5.434 59.963 1157 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.15 % Allowed : 7.84 % Favored : 91.00 % 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: 0.78 (0.26), residues: 1047 helix: 1.92 (0.27), residues: 401 sheet: 1.16 (0.34), residues: 228 loop : -1.32 (0.28), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 82 HIS 0.008 0.002 HIS A 357 PHE 0.030 0.002 PHE R 263 TYR 0.015 0.002 TYR R 247 ARG 0.003 0.000 ARG N 72 Details of bonding type rmsd hydrogen bonds : bond 0.06090 ( 409) hydrogen bonds : angle 4.02701 ( 1167) SS BOND : bond 0.00667 ( 1) SS BOND : angle 2.31934 ( 2) covalent geometry : bond 0.00383 ( 8335) covalent geometry : angle 0.58508 (11328) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 97 time to evaluate : 0.952 Fit side-chains REVERT: B 333 ASP cc_start: 0.7525 (p0) cc_final: 0.7194 (p0) REVERT: N 106 ASP cc_start: 0.8013 (p0) cc_final: 0.7760 (p0) outliers start: 10 outliers final: 9 residues processed: 102 average time/residue: 0.2156 time to fit residues: 30.2498 Evaluate side-chains 101 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 92 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain N residue 13 GLN Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain R residue 138 VAL Chi-restraints excluded: chain R residue 247 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 59 optimal weight: 0.9980 chunk 81 optimal weight: 9.9990 chunk 93 optimal weight: 0.9980 chunk 57 optimal weight: 6.9990 chunk 49 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 77 optimal weight: 4.9990 chunk 47 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.123839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.094193 restraints weight = 12678.939| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 2.19 r_work: 0.3115 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8336 Z= 0.135 Angle : 0.550 6.809 11330 Z= 0.296 Chirality : 0.043 0.139 1322 Planarity : 0.004 0.039 1442 Dihedral : 5.247 59.606 1157 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.61 % Allowed : 8.88 % Favored : 89.50 % 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: 0.91 (0.26), residues: 1047 helix: 2.07 (0.27), residues: 401 sheet: 1.24 (0.34), residues: 228 loop : -1.30 (0.28), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 82 HIS 0.006 0.001 HIS A 357 PHE 0.028 0.002 PHE R 263 TYR 0.014 0.001 TYR R 247 ARG 0.002 0.000 ARG N 72 Details of bonding type rmsd hydrogen bonds : bond 0.05514 ( 409) hydrogen bonds : angle 3.93207 ( 1167) SS BOND : bond 0.00438 ( 1) SS BOND : angle 2.05407 ( 2) covalent geometry : bond 0.00302 ( 8335) covalent geometry : angle 0.54957 (11328) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 91 time to evaluate : 0.876 Fit side-chains REVERT: N 106 ASP cc_start: 0.7974 (p0) cc_final: 0.7707 (p0) outliers start: 14 outliers final: 11 residues processed: 99 average time/residue: 0.2213 time to fit residues: 29.6913 Evaluate side-chains 99 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain R residue 42 VAL Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 233 ILE Chi-restraints excluded: chain R residue 247 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 74 optimal weight: 20.0000 chunk 57 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 90 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 84 optimal weight: 0.8980 chunk 100 optimal weight: 7.9990 chunk 51 optimal weight: 1.9990 chunk 89 optimal weight: 6.9990 chunk 3 optimal weight: 3.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS B 88 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.118270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.088819 restraints weight = 12742.410| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 2.17 r_work: 0.3022 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.066 8336 Z= 0.340 Angle : 0.802 11.624 11330 Z= 0.424 Chirality : 0.051 0.161 1322 Planarity : 0.006 0.051 1442 Dihedral : 5.938 51.618 1157 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 2.19 % Allowed : 9.92 % Favored : 87.89 % 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: 0.47 (0.26), residues: 1047 helix: 1.68 (0.27), residues: 394 sheet: 0.99 (0.35), residues: 216 loop : -1.39 (0.28), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP B 82 HIS 0.008 0.002 HIS A 362 PHE 0.032 0.004 PHE R 263 TYR 0.018 0.003 TYR N 95 ARG 0.007 0.001 ARG N 72 Details of bonding type rmsd hydrogen bonds : bond 0.08552 ( 409) hydrogen bonds : angle 4.41945 ( 1167) SS BOND : bond 0.00970 ( 1) SS BOND : angle 3.07844 ( 2) covalent geometry : bond 0.00855 ( 8335) covalent geometry : angle 0.80065 (11328) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 97 time to evaluate : 0.959 Fit side-chains outliers start: 19 outliers final: 17 residues processed: 107 average time/residue: 0.2150 time to fit residues: 31.4461 Evaluate side-chains 104 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 87 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain R residue 42 VAL Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 233 ILE Chi-restraints excluded: chain R residue 247 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 87 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 chunk 82 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 90 optimal weight: 5.9990 chunk 12 optimal weight: 0.9980 chunk 77 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 237 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.123568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.093816 restraints weight = 12770.039| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 2.23 r_work: 0.3080 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8336 Z= 0.157 Angle : 0.592 7.590 11330 Z= 0.319 Chirality : 0.044 0.144 1322 Planarity : 0.004 0.038 1442 Dihedral : 5.429 56.056 1157 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.50 % Allowed : 11.19 % Favored : 87.31 % 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: 0.67 (0.26), residues: 1047 helix: 1.93 (0.27), residues: 395 sheet: 1.06 (0.34), residues: 230 loop : -1.43 (0.28), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 82 HIS 0.007 0.001 HIS A 357 PHE 0.025 0.002 PHE R 263 TYR 0.015 0.001 TYR R 247 ARG 0.002 0.000 ARG N 72 Details of bonding type rmsd hydrogen bonds : bond 0.06236 ( 409) hydrogen bonds : angle 4.07684 ( 1167) SS BOND : bond 0.00617 ( 1) SS BOND : angle 2.41013 ( 2) covalent geometry : bond 0.00359 ( 8335) covalent geometry : angle 0.59096 (11328) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 0.962 Fit side-chains REVERT: R 161 LEU cc_start: 0.6152 (tt) cc_final: 0.5945 (tp) outliers start: 13 outliers final: 10 residues processed: 93 average time/residue: 0.2180 time to fit residues: 27.7140 Evaluate side-chains 94 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 84 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain R residue 42 VAL Chi-restraints excluded: chain R residue 233 ILE Chi-restraints excluded: chain R residue 247 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 82 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 16 optimal weight: 6.9990 chunk 94 optimal weight: 0.1980 chunk 87 optimal weight: 0.8980 chunk 90 optimal weight: 5.9990 chunk 54 optimal weight: 0.6980 chunk 18 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 237 ASN B 239 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.122902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.093404 restraints weight = 12741.470| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 2.18 r_work: 0.3100 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8336 Z= 0.141 Angle : 0.566 6.887 11330 Z= 0.304 Chirality : 0.043 0.141 1322 Planarity : 0.004 0.038 1442 Dihedral : 5.255 58.356 1157 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 1.61 % Allowed : 11.30 % Favored : 87.08 % 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: 0.84 (0.27), residues: 1047 helix: 2.11 (0.27), residues: 395 sheet: 1.11 (0.35), residues: 230 loop : -1.35 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 82 HIS 0.006 0.001 HIS A 357 PHE 0.024 0.002 PHE R 263 TYR 0.015 0.001 TYR R 247 ARG 0.002 0.000 ARG N 72 Details of bonding type rmsd hydrogen bonds : bond 0.05667 ( 409) hydrogen bonds : angle 3.94473 ( 1167) SS BOND : bond 0.00526 ( 1) SS BOND : angle 2.28546 ( 2) covalent geometry : bond 0.00319 ( 8335) covalent geometry : angle 0.56491 (11328) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 87 time to evaluate : 0.996 Fit side-chains REVERT: A 229 ASP cc_start: 0.7907 (OUTLIER) cc_final: 0.7670 (t0) outliers start: 14 outliers final: 12 residues processed: 95 average time/residue: 0.2220 time to fit residues: 29.0119 Evaluate side-chains 99 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 86 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain R residue 42 VAL Chi-restraints excluded: chain R residue 233 ILE Chi-restraints excluded: chain R residue 247 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 75 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 46 optimal weight: 0.0980 chunk 86 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 90 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.122062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.092433 restraints weight = 12862.018| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 2.19 r_work: 0.3086 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8336 Z= 0.165 Angle : 0.597 7.786 11330 Z= 0.320 Chirality : 0.044 0.146 1322 Planarity : 0.004 0.037 1442 Dihedral : 5.329 57.409 1157 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.61 % Allowed : 11.53 % Favored : 86.85 % 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: 0.83 (0.26), residues: 1047 helix: 2.13 (0.27), residues: 395 sheet: 1.09 (0.34), residues: 230 loop : -1.38 (0.28), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 82 HIS 0.006 0.002 HIS A 220 PHE 0.024 0.002 PHE R 263 TYR 0.016 0.001 TYR R 247 ARG 0.003 0.000 ARG A 39 Details of bonding type rmsd hydrogen bonds : bond 0.06068 ( 409) hydrogen bonds : angle 3.98715 ( 1167) SS BOND : bond 0.00628 ( 1) SS BOND : angle 2.40345 ( 2) covalent geometry : bond 0.00387 ( 8335) covalent geometry : angle 0.59641 (11328) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 86 time to evaluate : 0.944 Fit side-chains REVERT: R 161 LEU cc_start: 0.6209 (tt) cc_final: 0.5959 (tp) outliers start: 14 outliers final: 13 residues processed: 94 average time/residue: 0.2205 time to fit residues: 28.7031 Evaluate side-chains 98 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain R residue 42 VAL Chi-restraints excluded: chain R residue 138 VAL Chi-restraints excluded: chain R residue 233 ILE Chi-restraints excluded: chain R residue 247 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 46 optimal weight: 0.5980 chunk 98 optimal weight: 0.6980 chunk 50 optimal weight: 0.3980 chunk 54 optimal weight: 0.9980 chunk 68 optimal weight: 0.0970 chunk 90 optimal weight: 3.9990 chunk 56 optimal weight: 7.9990 chunk 67 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 19 optimal weight: 0.0270 chunk 74 optimal weight: 9.9990 overall best weight: 0.3636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN A 220 HIS B 237 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.126459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.097024 restraints weight = 12732.904| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 2.19 r_work: 0.3161 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8336 Z= 0.103 Angle : 0.504 6.067 11330 Z= 0.271 Chirality : 0.042 0.141 1322 Planarity : 0.004 0.038 1442 Dihedral : 4.825 57.119 1157 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.27 % Allowed : 12.00 % Favored : 86.74 % 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: 1.11 (0.27), residues: 1047 helix: 2.43 (0.27), residues: 397 sheet: 0.97 (0.34), residues: 241 loop : -1.19 (0.29), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 82 HIS 0.005 0.001 HIS A 220 PHE 0.021 0.001 PHE R 263 TYR 0.011 0.001 TYR R 247 ARG 0.002 0.000 ARG A 39 Details of bonding type rmsd hydrogen bonds : bond 0.04404 ( 409) hydrogen bonds : angle 3.70442 ( 1167) SS BOND : bond 0.00426 ( 1) SS BOND : angle 2.05992 ( 2) covalent geometry : bond 0.00206 ( 8335) covalent geometry : angle 0.50284 (11328) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 95 time to evaluate : 1.042 Fit side-chains REVERT: B 333 ASP cc_start: 0.7255 (p0) cc_final: 0.6971 (p0) REVERT: N 50 ASP cc_start: 0.8165 (OUTLIER) cc_final: 0.7870 (p0) REVERT: R 138 VAL cc_start: 0.7220 (OUTLIER) cc_final: 0.7014 (t) REVERT: R 161 LEU cc_start: 0.6199 (tt) cc_final: 0.5920 (tp) outliers start: 11 outliers final: 8 residues processed: 102 average time/residue: 0.2174 time to fit residues: 30.6254 Evaluate side-chains 101 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 91 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain R residue 42 VAL Chi-restraints excluded: chain R residue 138 VAL Chi-restraints excluded: chain R residue 247 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 67 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 64 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 71 optimal weight: 0.2980 chunk 42 optimal weight: 0.6980 chunk 52 optimal weight: 0.9980 chunk 35 optimal weight: 0.1980 chunk 5 optimal weight: 0.2980 chunk 85 optimal weight: 3.9990 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS B 237 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.126756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.097221 restraints weight = 12818.814| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 2.20 r_work: 0.3163 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8336 Z= 0.104 Angle : 0.507 6.296 11330 Z= 0.272 Chirality : 0.042 0.137 1322 Planarity : 0.004 0.037 1442 Dihedral : 4.643 55.954 1157 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.38 % Allowed : 12.46 % Favored : 86.16 % 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: 1.27 (0.27), residues: 1047 helix: 2.52 (0.26), residues: 406 sheet: 1.01 (0.34), residues: 241 loop : -1.12 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 82 HIS 0.004 0.001 HIS A 357 PHE 0.021 0.001 PHE R 263 TYR 0.011 0.001 TYR R 247 ARG 0.005 0.000 ARG A 39 Details of bonding type rmsd hydrogen bonds : bond 0.04306 ( 409) hydrogen bonds : angle 3.65530 ( 1167) SS BOND : bond 0.00348 ( 1) SS BOND : angle 2.01063 ( 2) covalent geometry : bond 0.00215 ( 8335) covalent geometry : angle 0.50635 (11328) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4860.83 seconds wall clock time: 84 minutes 58.00 seconds (5098.00 seconds total)