Starting phenix.real_space_refine on Sat Aug 3 14:01:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h4l_34480/08_2024/8h4l_34480_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h4l_34480/08_2024/8h4l_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h4l_34480/08_2024/8h4l_34480.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h4l_34480/08_2024/8h4l_34480.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h4l_34480/08_2024/8h4l_34480_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h4l_34480/08_2024/8h4l_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 Residue "A GLU 344": "OE1" <-> "OE2" Residue "A TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 389": "NH1" <-> "NH2" Residue "R GLU 135": "OE1" <-> "OE2" Residue "R PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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: 4.77, per 1000 atoms: 0.58 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 - 3.50 Amino acid : False - 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: 2.77 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.01 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: 2.30 Time building geometry restraints manager: 3.07 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: 99.46 - 106.39: 188 106.39 - 113.31: 4552 113.31 - 120.24: 3136 120.24 - 127.17: 3361 127.17 - 134.10: 91 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: 1.000 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: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 24.280 Find NCS groups from input model: 0.080 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:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.360 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 2 poor density : 98 time to evaluate : 0.977 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: 0.2420 time to fit residues: 32.2245 Evaluate side-chains 92 residues out of total 909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 91 time to evaluate : 0.918 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 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 6.767 11328 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 *********************** 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 fitting. rotamer outliers: 5 poor density : 99 time to evaluate : 0.962 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 102 average time/residue: 0.2107 time to fit residues: 29.8345 Evaluate side-chains 93 residues out of total 909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 90 time to evaluate : 0.866 ------------------------------------------------------------------------------- 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 51 optimal weight: 2.9990 chunk 29 optimal weight: 0.4980 chunk 77 optimal weight: 0.9980 chunk 63 optimal weight: 0.4980 chunk 25 optimal weight: 9.9990 chunk 93 optimal weight: 0.9990 chunk 101 optimal weight: 0.4980 chunk 83 optimal weight: 0.6980 chunk 92 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 75 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.1550 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= 0.161 Angle : 0.527 5.955 11328 Z= 0.287 Chirality : 0.043 0.137 1322 Planarity : 0.004 0.041 1442 Dihedral : 5.216 56.544 1157 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.04 % Allowed : 5.77 % Favored : 93.19 % 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: 1.89 (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 0.007 0.001 HIS A 357 PHE 0.015 0.002 PHE A 376 TYR 0.013 0.001 TYR R 247 ARG 0.003 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 102 residues out of total 909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 93 time to evaluate : 0.953 Fit side-chains outliers start: 9 outliers final: 7 residues processed: 98 average time/residue: 0.2149 time to fit residues: 28.7333 Evaluate side-chains 95 residues out of total 909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 88 time to evaluate : 0.911 ------------------------------------------------------------------------------- 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 92 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 48 optimal weight: 0.0970 chunk 10 optimal weight: 0.0980 chunk 44 optimal weight: 2.9990 chunk 62 optimal weight: 7.9990 chunk 94 optimal weight: 2.9990 chunk 99 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 89 optimal weight: 0.0980 chunk 26 optimal weight: 0.0170 overall best weight: 0.2616 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8335 Z= 0.116 Angle : 0.468 5.926 11328 Z= 0.253 Chirality : 0.041 0.133 1322 Planarity : 0.003 0.038 1442 Dihedral : 4.795 54.387 1157 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 2.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 0.69 % Allowed : 7.96 % Favored : 91.35 % 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: 1.04 (0.27), residues: 1047 helix: 2.17 (0.27), residues: 404 sheet: 1.01 (0.34), residues: 246 loop : -1.13 (0.30), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.005 0.001 HIS A 357 PHE 0.025 0.001 PHE R 263 TYR 0.011 0.001 TYR R 247 ARG 0.002 0.000 ARG A 280 *********************** 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 102 residues out of total 909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 96 time to evaluate : 0.902 Fit side-chains REVERT: B 333 ASP cc_start: 0.6802 (p0) cc_final: 0.6507 (p0) REVERT: N 80 TYR cc_start: 0.8462 (m-80) cc_final: 0.8223 (m-80) outliers start: 6 outliers final: 4 residues processed: 98 average time/residue: 0.2165 time to fit residues: 28.6751 Evaluate side-chains 93 residues out of total 909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 89 time to evaluate : 0.916 ------------------------------------------------------------------------------- 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 247 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 82 optimal weight: 0.6980 chunk 56 optimal weight: 7.9990 chunk 1 optimal weight: 1.9990 chunk 74 optimal weight: 20.0000 chunk 41 optimal weight: 0.6980 chunk 84 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 89 optimal weight: 0.0170 chunk 25 optimal weight: 8.9990 overall best weight: 0.8822 ------------------------------------------------------------------------------- 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 268 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8335 Z= 0.196 Angle : 0.546 6.484 11328 Z= 0.292 Chirality : 0.043 0.137 1322 Planarity : 0.004 0.036 1442 Dihedral : 4.969 57.679 1157 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.27 % Allowed : 8.30 % Favored : 90.43 % 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: 1.06 (0.27), residues: 1047 helix: 2.16 (0.27), residues: 403 sheet: 1.21 (0.34), residues: 232 loop : -1.14 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.007 0.002 HIS A 357 PHE 0.028 0.002 PHE R 263 TYR 0.013 0.001 TYR R 247 ARG 0.003 0.000 ARG A 39 *********************** 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 103 residues out of total 909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 92 time to evaluate : 0.963 Fit side-chains REVERT: N 28 THR cc_start: 0.8393 (m) cc_final: 0.8149 (m) REVERT: N 80 TYR cc_start: 0.8519 (m-80) cc_final: 0.8274 (m-80) outliers start: 11 outliers final: 8 residues processed: 98 average time/residue: 0.2088 time to fit residues: 28.0560 Evaluate side-chains 99 residues out of total 909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 91 time to evaluate : 0.942 ------------------------------------------------------------------------------- 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 N residue 50 ASP Chi-restraints excluded: chain R residue 42 VAL 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 33 optimal weight: 0.6980 chunk 89 optimal weight: 4.9990 chunk 19 optimal weight: 0.4980 chunk 58 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.1894 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= 0.188 Angle : 0.535 6.544 11328 Z= 0.287 Chirality : 0.043 0.138 1322 Planarity : 0.004 0.035 1442 Dihedral : 5.000 58.342 1157 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.04 % Allowed : 9.69 % 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: 1.10 (0.26), residues: 1047 helix: 2.18 (0.27), residues: 403 sheet: 1.28 (0.34), residues: 231 loop : -1.14 (0.29), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 82 HIS 0.006 0.001 HIS A 357 PHE 0.026 0.002 PHE R 263 TYR 0.013 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 98 residues out of total 909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 89 time to evaluate : 0.944 Fit side-chains REVERT: N 80 TYR cc_start: 0.8506 (m-80) cc_final: 0.8220 (m-80) outliers start: 9 outliers final: 7 residues processed: 95 average time/residue: 0.2153 time to fit residues: 27.9816 Evaluate side-chains 94 residues out of total 909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 87 time to evaluate : 0.964 ------------------------------------------------------------------------------- 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 59 TYR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain N residue 50 ASP 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 96 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 56 optimal weight: 10.0000 chunk 72 optimal weight: 3.9990 chunk 83 optimal weight: 0.6980 chunk 55 optimal weight: 0.9990 chunk 99 optimal weight: 0.9990 chunk 62 optimal weight: 10.0000 chunk 60 optimal weight: 0.0270 chunk 45 optimal weight: 0.9990 chunk 61 optimal weight: 0.7980 overall best weight: 0.7040 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8335 Z= 0.167 Angle : 0.521 5.965 11328 Z= 0.280 Chirality : 0.042 0.134 1322 Planarity : 0.004 0.033 1442 Dihedral : 4.916 58.356 1157 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.04 % Allowed : 9.80 % Favored : 89.16 % 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: 1.13 (0.27), residues: 1047 helix: 2.26 (0.27), residues: 403 sheet: 1.09 (0.34), residues: 240 loop : -1.09 (0.29), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 82 HIS 0.006 0.001 HIS A 357 PHE 0.024 0.002 PHE R 263 TYR 0.013 0.001 TYR R 247 ARG 0.002 0.000 ARG A 280 *********************** 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 94 residues out of total 909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 85 time to evaluate : 0.887 Fit side-chains REVERT: N 80 TYR cc_start: 0.8469 (m-80) cc_final: 0.8190 (m-80) outliers start: 9 outliers final: 9 residues processed: 90 average time/residue: 0.2186 time to fit residues: 26.7194 Evaluate side-chains 94 residues out of total 909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 85 time to evaluate : 0.934 ------------------------------------------------------------------------------- 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 R residue 42 VAL Chi-restraints excluded: chain R residue 56 LEU 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 39 optimal weight: 6.9990 chunk 59 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 9 optimal weight: 0.0060 chunk 78 optimal weight: 1.9990 chunk 90 optimal weight: 5.9990 chunk 95 optimal weight: 0.9980 overall best weight: 0.9798 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.1940 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= 0.212 Angle : 0.561 7.252 11328 Z= 0.299 Chirality : 0.043 0.144 1322 Planarity : 0.004 0.033 1442 Dihedral : 5.062 59.990 1157 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.61 % Allowed : 10.03 % Favored : 88.35 % 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: 1.18 (0.27), residues: 1047 helix: 2.37 (0.27), residues: 397 sheet: 1.16 (0.34), residues: 233 loop : -1.08 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.007 0.001 HIS A 357 PHE 0.024 0.002 PHE R 263 TYR 0.014 0.001 TYR R 247 ARG 0.002 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 101 residues out of total 909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 87 time to evaluate : 0.974 Fit side-chains REVERT: N 80 TYR cc_start: 0.8499 (m-80) cc_final: 0.8185 (m-80) REVERT: R 161 LEU cc_start: 0.6011 (tt) cc_final: 0.5781 (tp) outliers start: 14 outliers final: 14 residues processed: 96 average time/residue: 0.2100 time to fit residues: 27.5234 Evaluate side-chains 99 residues out of total 909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 85 time to evaluate : 0.897 ------------------------------------------------------------------------------- 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 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 86 optimal weight: 0.6980 chunk 92 optimal weight: 0.9980 chunk 95 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 87 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.2050 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= 0.185 Angle : 0.535 6.343 11328 Z= 0.286 Chirality : 0.043 0.145 1322 Planarity : 0.004 0.033 1442 Dihedral : 4.961 59.512 1157 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.61 % Allowed : 10.50 % 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: 1.19 (0.27), residues: 1047 helix: 2.42 (0.27), residues: 400 sheet: 1.03 (0.34), residues: 240 loop : -1.09 (0.29), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 82 HIS 0.006 0.001 HIS A 357 PHE 0.023 0.002 PHE R 263 TYR 0.013 0.001 TYR R 247 ARG 0.002 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 98 residues out of total 909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 84 time to evaluate : 0.944 Fit side-chains REVERT: B 301 LYS cc_start: 0.8635 (mmmt) cc_final: 0.8431 (mtpp) REVERT: N 80 TYR cc_start: 0.8489 (m-80) cc_final: 0.8178 (m-80) REVERT: R 161 LEU cc_start: 0.5999 (tt) cc_final: 0.5746 (tp) outliers start: 14 outliers final: 13 residues processed: 93 average time/residue: 0.2191 time to fit residues: 27.9773 Evaluate side-chains 97 residues out of total 909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 84 time to evaluate : 0.946 ------------------------------------------------------------------------------- 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 B residue 234 PHE 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 ************** Weight determination summary: number of chunks: 103 random chunks: chunk 59 optimal weight: 0.7980 chunk 46 optimal weight: 0.7980 chunk 68 optimal weight: 0.9980 chunk 102 optimal weight: 0.8980 chunk 94 optimal weight: 0.9990 chunk 81 optimal weight: 9.9990 chunk 8 optimal weight: 0.6980 chunk 63 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.2065 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= 0.185 Angle : 0.538 6.685 11328 Z= 0.288 Chirality : 0.043 0.145 1322 Planarity : 0.004 0.034 1442 Dihedral : 4.938 59.595 1157 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.73 % Allowed : 10.38 % 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: 1.19 (0.27), residues: 1047 helix: 2.35 (0.27), residues: 407 sheet: 1.10 (0.33), residues: 238 loop : -1.12 (0.29), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 82 HIS 0.006 0.001 HIS A 357 PHE 0.023 0.002 PHE R 263 TYR 0.013 0.001 TYR R 247 ARG 0.003 0.000 ARG A 39 ********************** 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 100 residues out of total 909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 85 time to evaluate : 0.905 Fit side-chains REVERT: N 80 TYR cc_start: 0.8492 (m-80) cc_final: 0.8157 (m-80) REVERT: R 161 LEU cc_start: 0.5995 (tt) cc_final: 0.5741 (tp) outliers start: 15 outliers final: 15 residues processed: 96 average time/residue: 0.2153 time to fit residues: 28.1012 Evaluate side-chains 100 residues out of total 909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 85 time to evaluate : 0.965 ------------------------------------------------------------------------------- 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 B residue 234 PHE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/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-5409/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-5409/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-5409/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-5409/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-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/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-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 73.4366 > 50: distance: 17 - 38: 36.875 distance: 24 - 46: 33.583 distance: 31 - 38: 33.919 distance: 38 - 39: 51.586 distance: 39 - 40: 46.470 distance: 39 - 42: 59.379 distance: 40 - 41: 56.069 distance: 40 - 46: 59.285 distance: 42 - 43: 41.059 distance: 43 - 44: 56.786 distance: 43 - 45: 40.163 distance: 46 - 47: 39.856 distance: 47 - 48: 16.072 distance: 47 - 50: 51.931 distance: 48 - 49: 38.247 distance: 48 - 58: 47.130 distance: 50 - 51: 47.693 distance: 51 - 52: 31.727 distance: 51 - 53: 6.983 distance: 52 - 54: 56.076 distance: 53 - 55: 66.829 distance: 54 - 56: 40.652 distance: 55 - 56: 37.694 distance: 56 - 57: 61.500 distance: 58 - 59: 26.305 distance: 59 - 60: 49.561 distance: 59 - 62: 37.432 distance: 60 - 61: 61.720 distance: 60 - 69: 42.770 distance: 61 - 85: 39.823 distance: 62 - 63: 14.067 distance: 63 - 64: 34.077 distance: 63 - 65: 27.342 distance: 64 - 66: 42.061 distance: 65 - 67: 22.296 distance: 66 - 68: 38.916 distance: 67 - 68: 60.183 distance: 69 - 70: 48.083 distance: 69 - 75: 49.372 distance: 70 - 71: 31.487 distance: 70 - 73: 62.262 distance: 71 - 72: 36.644 distance: 71 - 76: 41.262 distance: 72 - 96: 46.522 distance: 73 - 74: 57.220 distance: 74 - 75: 40.261 distance: 76 - 77: 18.031 distance: 77 - 78: 39.698 distance: 77 - 80: 58.995 distance: 78 - 79: 28.845 distance: 78 - 85: 58.068 distance: 79 - 101: 40.741 distance: 80 - 81: 70.578 distance: 81 - 82: 41.527 distance: 82 - 83: 21.286 distance: 82 - 84: 55.437 distance: 85 - 86: 48.846 distance: 86 - 87: 38.889 distance: 86 - 89: 41.080 distance: 87 - 88: 47.801 distance: 87 - 96: 64.410 distance: 89 - 90: 13.708 distance: 90 - 91: 59.881 distance: 90 - 92: 53.367 distance: 91 - 93: 51.721 distance: 92 - 94: 43.655 distance: 93 - 95: 56.886 distance: 94 - 95: 37.876 distance: 96 - 97: 40.199 distance: 97 - 98: 57.020 distance: 97 - 100: 53.261 distance: 98 - 99: 63.235 distance: 98 - 101: 58.132 distance: 101 - 102: 39.225 distance: 102 - 103: 56.125 distance: 102 - 105: 52.486 distance: 103 - 104: 56.773 distance: 103 - 112: 44.464 distance: 105 - 106: 56.764 distance: 106 - 107: 55.475 distance: 107 - 108: 56.676 distance: 108 - 109: 53.741 distance: 109 - 110: 41.053 distance: 109 - 111: 31.897 distance: 112 - 113: 43.997 distance: 113 - 114: 38.629 distance: 113 - 116: 66.299 distance: 114 - 124: 57.319 distance: 116 - 117: 39.721 distance: 117 - 118: 27.271 distance: 117 - 119: 31.358 distance: 118 - 120: 58.186 distance: 119 - 121: 42.272 distance: 120 - 122: 32.298 distance: 121 - 122: 32.872 distance: 122 - 123: 48.158 distance: 124 - 125: 57.084 distance: 125 - 126: 57.439 distance: 125 - 128: 48.898 distance: 126 - 127: 69.224 distance: 126 - 131: 33.605 distance: 128 - 129: 59.212 distance: 128 - 130: 42.017