Starting phenix.real_space_refine on Wed Mar 12 20:35:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h4l_34480/03_2025/8h4l_34480_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h4l_34480/03_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_34480/03_2025/8h4l_34480.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h4l_34480/03_2025/8h4l_34480.map" model { file = "/net/cci-nas-00/data/ceres_data/8h4l_34480/03_2025/8h4l_34480_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h4l_34480/03_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-5624/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: 4.86, per 1000 atoms: 0.59 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: 2.12 Conformation dependent library (CDL) restraints added in 984.0 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: 0.86 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: 2.17 Time building geometry restraints manager: 2.52 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: 0.960 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: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 21.040 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.120 ------------------------------------------------------------------------------- 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 8335 Z= 0.472 Angle : 0.900 11.221 11328 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 *********************** 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 : 0.852 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: 0.2336 time to fit residues: 31.1986 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 : 0.781 ------------------------------------------------------------------------------- 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 = 0.095184 restraints weight = 12547.956| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 2.18 r_work: 0.3123 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 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 8335 Z= 0.175 Angle : 0.560 6.769 11328 Z= 0.307 Chirality : 0.044 0.146 1322 Planarity : 0.005 0.054 1442 Dihedral : 5.596 52.686 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 *********************** 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 : 0.925 Fit side-chains REVERT: N 106 ASP cc_start: 0.7989 (p0) cc_final: 0.7776 (p0) REVERT: R 239 LYS cc_start: 0.7944 (tttt) cc_final: 0.7734 (tptt) outliers start: 5 outliers final: 3 residues processed: 102 average time/residue: 0.2146 time to fit residues: 30.2990 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 : 0.798 ------------------------------------------------------------------------------- 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: 0.0770 chunk 68 optimal weight: 3.9990 chunk 79 optimal weight: 0.7980 chunk 93 optimal weight: 0.9990 chunk 63 optimal weight: 0.8980 chunk 97 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 54 optimal weight: 0.4980 overall best weight: 0.5938 ------------------------------------------------------------------------------- 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 = 0.3721 r_free = 0.3721 target = 0.125397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.096113 restraints weight = 12880.824| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 2.14 r_work: 0.3145 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8335 Z= 0.158 Angle : 0.525 5.916 11328 Z= 0.286 Chirality : 0.043 0.137 1322 Planarity : 0.004 0.042 1442 Dihedral : 5.244 55.931 1157 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.04 % Allowed : 5.88 % 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 (0.26), residues: 1047 helix: 1.86 (0.27), residues: 401 sheet: 1.11 (0.34), residues: 230 loop : -1.35 (0.28), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.007 0.001 HIS A 357 PHE 0.015 0.002 PHE A 376 TYR 0.013 0.001 TYR R 247 ARG 0.002 0.000 ARG A 280 *********************** 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: 9 poor density : 92 time to evaluate : 0.810 Fit side-chains REVERT: N 106 ASP cc_start: 0.7933 (p0) cc_final: 0.7706 (p0) outliers start: 9 outliers final: 7 residues processed: 97 average time/residue: 0.2184 time to fit residues: 28.8855 Evaluate side-chains 95 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 88 time to evaluate : 0.918 ------------------------------------------------------------------------------- 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 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: 0.0770 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: 3.9990 chunk 60 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 overall best weight: 1.3744 ------------------------------------------------------------------------------- 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 = 0.3684 r_free = 0.3684 target = 0.122609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.093068 restraints weight = 12720.363| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 2.18 r_work: 0.3086 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8335 Z= 0.276 Angle : 0.608 8.366 11328 Z= 0.326 Chirality : 0.045 0.147 1322 Planarity : 0.004 0.041 1442 Dihedral : 5.514 59.253 1157 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.27 % Allowed : 7.84 % Favored : 90.89 % 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: 0.72 (0.26), residues: 1047 helix: 1.87 (0.27), residues: 401 sheet: 1.13 (0.34), residues: 228 loop : -1.34 (0.28), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 82 HIS 0.009 0.002 HIS A 357 PHE 0.018 0.002 PHE B 199 TYR 0.015 0.002 TYR R 247 ARG 0.004 0.000 ARG N 72 *********************** 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: 11 poor density : 96 time to evaluate : 0.891 Fit side-chains outliers start: 11 outliers final: 10 residues processed: 101 average time/residue: 0.2165 time to fit residues: 29.9287 Evaluate side-chains 103 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 93 time to evaluate : 0.863 ------------------------------------------------------------------------------- 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 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 50 ASP 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 59 optimal weight: 2.9990 chunk 81 optimal weight: 9.9990 chunk 93 optimal weight: 0.8980 chunk 57 optimal weight: 6.9990 chunk 49 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 = 0.123211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.093548 restraints weight = 12692.547| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 2.19 r_work: 0.3099 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8335 Z= 0.228 Angle : 0.574 7.415 11328 Z= 0.308 Chirality : 0.044 0.145 1322 Planarity : 0.004 0.039 1442 Dihedral : 5.348 59.102 1157 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 1.27 % Allowed : 9.46 % Favored : 89.27 % 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: 0.82 (0.26), residues: 1047 helix: 1.98 (0.27), residues: 401 sheet: 1.19 (0.34), residues: 228 loop : -1.34 (0.28), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 82 HIS 0.007 0.002 HIS A 357 PHE 0.017 0.002 PHE B 199 TYR 0.015 0.001 TYR R 247 ARG 0.003 0.000 ARG N 72 *********************** 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 99 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 0.835 Fit side-chains outliers start: 11 outliers final: 9 residues processed: 96 average time/residue: 0.2178 time to fit residues: 28.3910 Evaluate side-chains 94 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 85 time to evaluate : 0.833 ------------------------------------------------------------------------------- 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 N residue 50 ASP Chi-restraints excluded: chain R residue 56 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 74 optimal weight: 20.0000 chunk 57 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 90 optimal weight: 8.9990 chunk 53 optimal weight: 0.5980 chunk 68 optimal weight: 3.9990 chunk 84 optimal weight: 0.6980 chunk 100 optimal weight: 9.9990 chunk 51 optimal weight: 1.9990 chunk 89 optimal weight: 0.0010 chunk 3 optimal weight: 2.9990 overall best weight: 0.8388 ------------------------------------------------------------------------------- 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 = 0.3704 r_free = 0.3704 target = 0.124122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.094633 restraints weight = 12678.065| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 2.18 r_work: 0.3115 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8335 Z= 0.190 Angle : 0.541 6.447 11328 Z= 0.292 Chirality : 0.043 0.137 1322 Planarity : 0.004 0.037 1442 Dihedral : 5.204 59.924 1157 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 1.15 % Allowed : 9.80 % Favored : 89.04 % 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: 0.88 (0.27), residues: 1047 helix: 2.05 (0.27), residues: 401 sheet: 1.10 (0.35), residues: 231 loop : -1.25 (0.29), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 82 HIS 0.006 0.001 HIS A 357 PHE 0.015 0.002 PHE B 199 TYR 0.014 0.001 TYR R 247 ARG 0.002 0.000 ARG N 72 *********************** 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 101 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 91 time to evaluate : 0.871 Fit side-chains REVERT: B 323 ASP cc_start: 0.7779 (p0) cc_final: 0.7501 (p0) outliers start: 10 outliers final: 8 residues processed: 99 average time/residue: 0.2197 time to fit residues: 29.9608 Evaluate side-chains 97 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 89 time to evaluate : 0.917 ------------------------------------------------------------------------------- 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 N residue 50 ASP 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: 0.7980 chunk 36 optimal weight: 5.9990 chunk 82 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 77 optimal weight: 6.9990 chunk 60 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 31 optimal weight: 0.4980 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 = 0.3688 r_free = 0.3688 target = 0.123036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.093421 restraints weight = 12799.204| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 2.19 r_work: 0.3101 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8335 Z= 0.222 Angle : 0.570 7.245 11328 Z= 0.305 Chirality : 0.043 0.140 1322 Planarity : 0.004 0.036 1442 Dihedral : 5.239 58.957 1157 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.61 % Allowed : 10.38 % Favored : 88.00 % 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: 0.96 (0.27), residues: 1047 helix: 2.17 (0.27), residues: 396 sheet: 1.14 (0.34), residues: 230 loop : -1.23 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 82 HIS 0.006 0.001 HIS A 357 PHE 0.016 0.002 PHE B 199 TYR 0.015 0.001 TYR R 247 ARG 0.002 0.000 ARG N 72 *********************** 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 106 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 92 time to evaluate : 0.857 Fit side-chains REVERT: R 161 LEU cc_start: 0.6214 (tt) cc_final: 0.5961 (tp) outliers start: 14 outliers final: 12 residues processed: 101 average time/residue: 0.2110 time to fit residues: 29.3645 Evaluate side-chains 99 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 87 time to evaluate : 0.830 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- 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: 0.6980 chunk 58 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 16 optimal weight: 10.0000 chunk 94 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 chunk 90 optimal weight: 6.9990 chunk 54 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 = 0.3677 r_free = 0.3677 target = 0.122177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.092642 restraints weight = 12772.696| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 2.18 r_work: 0.3084 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8335 Z= 0.268 Angle : 0.603 8.085 11328 Z= 0.322 Chirality : 0.044 0.145 1322 Planarity : 0.004 0.036 1442 Dihedral : 5.350 57.342 1157 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.73 % Allowed : 10.27 % Favored : 88.00 % 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: 0.95 (0.26), residues: 1047 helix: 2.13 (0.27), residues: 396 sheet: 1.16 (0.34), residues: 228 loop : -1.21 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 82 HIS 0.005 0.002 HIS A 220 PHE 0.018 0.002 PHE R 273 TYR 0.016 0.002 TYR R 247 ARG 0.003 0.000 ARG N 72 *********************** 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 103 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 88 time to evaluate : 0.891 Fit side-chains outliers start: 15 outliers final: 14 residues processed: 97 average time/residue: 0.2205 time to fit residues: 29.1274 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 : 0.875 ------------------------------------------------------------------------------- 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 70 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 322 ASP 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 75 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 46 optimal weight: 0.6980 chunk 86 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 chunk 58 optimal weight: 0.9980 chunk 90 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 = 0.3684 r_free = 0.3684 target = 0.122744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.093470 restraints weight = 12859.343| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 2.12 r_work: 0.3104 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8335 Z= 0.238 Angle : 0.577 7.476 11328 Z= 0.309 Chirality : 0.044 0.143 1322 Planarity : 0.004 0.036 1442 Dihedral : 5.259 57.741 1157 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.50 % Allowed : 10.73 % Favored : 87.77 % 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: 0.99 (0.26), residues: 1047 helix: 2.19 (0.27), residues: 396 sheet: 1.19 (0.34), residues: 228 loop : -1.21 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 82 HIS 0.005 0.001 HIS A 357 PHE 0.016 0.002 PHE B 199 TYR 0.015 0.001 TYR R 247 ARG 0.003 0.000 ARG N 72 *********************** 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 95 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 0.978 Fit side-chains outliers start: 13 outliers final: 13 residues processed: 90 average time/residue: 0.2310 time to fit residues: 28.2472 Evaluate side-chains 94 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 81 time to evaluate : 0.860 ------------------------------------------------------------------------------- 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 70 LEU 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 56 LEU 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 ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/iotbx/cli_parser.py", line 980, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 58.8897 > 50: distance: 48 - 152: 27.103 distance: 75 - 156: 22.713 distance: 78 - 153: 15.449 distance: 88 - 142: 25.153 distance: 91 - 139: 14.426 distance: 101 - 128: 22.619 distance: 104 - 125: 26.728 distance: 113 - 116: 19.983 distance: 116 - 117: 25.921 distance: 117 - 118: 15.602 distance: 117 - 120: 15.993 distance: 118 - 119: 26.114 distance: 118 - 125: 31.647 distance: 120 - 121: 47.834 distance: 121 - 122: 45.048 distance: 122 - 123: 48.237 distance: 122 - 124: 48.224 distance: 125 - 126: 31.557 distance: 126 - 127: 35.621 distance: 126 - 129: 37.983 distance: 127 - 128: 29.098 distance: 127 - 133: 51.064 distance: 129 - 130: 39.868 distance: 129 - 131: 35.153 distance: 130 - 132: 42.626 distance: 133 - 134: 35.247 distance: 134 - 135: 16.710 distance: 134 - 137: 41.742 distance: 135 - 136: 21.161 distance: 135 - 139: 17.658 distance: 137 - 138: 36.695 distance: 139 - 140: 26.247 distance: 140 - 141: 35.335 distance: 140 - 143: 36.312 distance: 141 - 142: 35.648 distance: 141 - 147: 19.684 distance: 143 - 144: 50.251 distance: 143 - 145: 41.110 distance: 144 - 146: 36.008 distance: 147 - 148: 15.290 distance: 148 - 149: 27.108 distance: 148 - 151: 41.206 distance: 149 - 150: 35.749 distance: 149 - 153: 12.211 distance: 151 - 152: 32.024 distance: 153 - 154: 9.735 distance: 154 - 155: 11.167 distance: 154 - 157: 13.075 distance: 155 - 156: 21.299 distance: 155 - 160: 23.737 distance: 157 - 158: 37.326 distance: 157 - 159: 57.184 distance: 160 - 161: 11.267 distance: 161 - 162: 13.790 distance: 161 - 164: 29.322 distance: 162 - 163: 7.763 distance: 162 - 168: 15.059 distance: 164 - 165: 38.060 distance: 165 - 166: 41.065 distance: 165 - 167: 37.372 distance: 168 - 169: 14.271 distance: 169 - 170: 21.864 distance: 169 - 172: 22.418 distance: 170 - 171: 24.981 distance: 170 - 176: 9.337 distance: 172 - 173: 34.185 distance: 172 - 174: 27.441 distance: 173 - 175: 34.382 distance: 176 - 177: 11.014 distance: 177 - 178: 17.411 distance: 177 - 180: 36.342 distance: 178 - 179: 33.382 distance: 178 - 190: 20.103 distance: 180 - 181: 15.216 distance: 181 - 182: 39.312 distance: 181 - 183: 24.200 distance: 182 - 184: 20.552 distance: 183 - 185: 11.054 distance: 183 - 186: 10.329 distance: 185 - 187: 6.438 distance: 186 - 188: 9.091 distance: 187 - 189: 4.570 distance: 188 - 189: 3.643 distance: 190 - 191: 8.777 distance: 190 - 196: 15.698 distance: 191 - 192: 5.217 distance: 191 - 194: 24.895 distance: 192 - 193: 26.701 distance: 192 - 197: 20.847 distance: 194 - 195: 32.375 distance: 195 - 196: 24.974