Starting phenix.real_space_refine on Sun Jan 19 17:16:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7cky_30394/01_2025/7cky_30394_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cky_30394/01_2025/7cky_30394.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7cky_30394/01_2025/7cky_30394.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cky_30394/01_2025/7cky_30394.map" model { file = "/net/cci-nas-00/data/ceres_data/7cky_30394/01_2025/7cky_30394_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cky_30394/01_2025/7cky_30394_neut.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 7222 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians S 53 5.16 5 C 5171 2.51 5 N 1408 2.21 5 O 1494 1.98 5 F 2 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 8128 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1906 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 6, 'TRANS': 229} Chain breaks: 2 Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 30 Chain: "B" Number of atoms: 2587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2587 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 334} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "G" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 438 Classifications: {'peptide': 58} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 53} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "N" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 970 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "R" Number of atoms: 2171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2171 Classifications: {'peptide': 276} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 9, 'TRANS': 266} Chain breaks: 3 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 23 Chain: "R" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'CLR': 1, 'G3U': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.97, per 1000 atoms: 0.61 Number of scatterers: 8128 At special positions: 0 Unit cell: (90, 86, 123, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 53 16.00 F 2 9.00 O 1494 8.00 N 1408 7.00 C 5171 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=1.96 Simple disulfide: pdb=" SG CYS R 96 " - pdb=" SG CYS R 186 " distance=1.44 Simple disulfide: pdb=" SG CYS R 298 " - pdb=" SG CYS R 307 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.34 Conformation dependent library (CDL) restraints added in 917.8 milliseconds 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1966 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 10 sheets defined 43.0% alpha, 17.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.90 Creating SS restraints... Processing helix chain 'A' and resid 14 through 40 removed outlier: 3.729A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 59 removed outlier: 3.566A pdb=" N ILE A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 238 Processing helix chain 'A' and resid 264 through 278 Processing helix chain 'A' and resid 281 through 285 removed outlier: 4.155A pdb=" N THR A 284 " --> pdb=" O TRP A 281 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE A 285 " --> pdb=" O LEU A 282 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 281 through 285' Processing helix chain 'A' and resid 293 through 304 removed outlier: 4.667A pdb=" N GLU A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N VAL A 301 " --> pdb=" O LEU A 297 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N LEU A 302 " --> pdb=" O ALA A 298 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLY A 304 " --> pdb=" O LYS A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 316 removed outlier: 3.507A pdb=" N PHE A 315 " --> pdb=" O PHE A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 351 removed outlier: 3.934A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 removed outlier: 4.096A pdb=" N ARG A 374 " --> pdb=" O GLU A 370 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP A 381 " --> pdb=" O ASN A 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 25 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.908A pdb=" N ILE B 33 " --> pdb=" O LEU B 30 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR B 34 " --> pdb=" O SER B 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 24 Processing helix chain 'G' and resid 29 through 45 Processing helix chain 'G' and resid 46 through 48 No H-bonds generated for 'chain 'G' and resid 46 through 48' Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.739A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.640A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 23 through 51 removed outlier: 3.505A pdb=" N PHE R 51 " --> pdb=" O ALA R 47 " (cutoff:3.500A) Processing helix chain 'R' and resid 59 through 77 removed outlier: 4.148A pdb=" N VAL R 63 " --> pdb=" O THR R 59 " (cutoff:3.500A) Processing helix chain 'R' and resid 77 through 88 Processing helix chain 'R' and resid 92 through 94 No H-bonds generated for 'chain 'R' and resid 92 through 94' Processing helix chain 'R' and resid 95 through 127 removed outlier: 3.728A pdb=" N ALA R 109 " --> pdb=" O MET R 105 " (cutoff:3.500A) Processing helix chain 'R' and resid 127 through 135 Processing helix chain 'R' and resid 136 through 161 removed outlier: 4.576A pdb=" N ILE R 157 " --> pdb=" O LEU R 153 " (cutoff:3.500A) Proline residue: R 158 - end of helix Processing helix chain 'R' and resid 191 through 203 removed outlier: 3.835A pdb=" N ILE R 196 " --> pdb=" O ARG R 192 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N SER R 197 " --> pdb=" O THR R 193 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ILE R 201 " --> pdb=" O SER R 197 " (cutoff:3.500A) Processing helix chain 'R' and resid 203 through 237 removed outlier: 3.956A pdb=" N ALA R 234 " --> pdb=" O ALA R 230 " (cutoff:3.500A) Processing helix chain 'R' and resid 264 through 295 removed outlier: 3.798A pdb=" N LYS R 269 " --> pdb=" O LYS R 265 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL R 270 " --> pdb=" O ARG R 266 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LEU R 271 " --> pdb=" O GLU R 267 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N VAL R 280 " --> pdb=" O VAL R 276 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N PHE R 281 " --> pdb=" O ILE R 277 " (cutoff:3.500A) Proline residue: R 287 - end of helix removed outlier: 4.079A pdb=" N LEU R 291 " --> pdb=" O PRO R 287 " (cutoff:3.500A) Processing helix chain 'R' and resid 309 through 332 removed outlier: 4.075A pdb=" N VAL R 315 " --> pdb=" O ASN R 311 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE R 316 " --> pdb=" O THR R 312 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASN R 323 " --> pdb=" O PHE R 319 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N SER R 324 " --> pdb=" O GLY R 320 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER R 325 " --> pdb=" O TRP R 321 " (cutoff:3.500A) Proline residue: R 328 - end of helix Processing helix chain 'R' and resid 334 through 344 removed outlier: 3.822A pdb=" N ALA R 340 " --> pdb=" O ASP R 336 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR R 343 " --> pdb=" O LYS R 339 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 210 through 214 removed outlier: 3.523A pdb=" N PHE A 212 " --> pdb=" O PHE A 219 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.738A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 62 removed outlier: 3.611A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 104 through 105 removed outlier: 3.989A pdb=" N ALA B 104 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.893A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.855A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.142A 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: 3.809A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.350A 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: 6.228A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.004A 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 8 Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12 removed outlier: 5.763A pdb=" N GLY N 10 " --> pdb=" O THR N 125 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) 406 hydrogen bonds defined for protein. 1152 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.03 Time building geometry restraints manager: 2.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1308 1.31 - 1.44: 2328 1.44 - 1.56: 4591 1.56 - 1.69: 0 1.69 - 1.81: 72 Bond restraints: 8299 Sorted by residual: bond pdb=" C15 G3U R 502 " pdb=" C19 G3U R 502 " ideal model delta sigma weight residual 1.484 1.386 0.098 2.00e-02 2.50e+03 2.41e+01 bond pdb=" C24 G3U R 502 " pdb=" C26 G3U R 502 " ideal model delta sigma weight residual 1.449 1.372 0.077 2.00e-02 2.50e+03 1.48e+01 bond pdb=" C24 G3U R 502 " pdb=" N23 G3U R 502 " ideal model delta sigma weight residual 1.379 1.316 0.063 2.00e-02 2.50e+03 9.85e+00 bond pdb=" C10 G3U R 502 " pdb=" O11 G3U R 502 " ideal model delta sigma weight residual 1.347 1.406 -0.059 2.00e-02 2.50e+03 8.56e+00 bond pdb=" C19 G3U R 502 " pdb=" N20 G3U R 502 " ideal model delta sigma weight residual 1.382 1.329 0.053 2.00e-02 2.50e+03 7.01e+00 ... (remaining 8294 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.35: 10992 1.35 - 2.70: 227 2.70 - 4.06: 29 4.06 - 5.41: 12 5.41 - 6.76: 3 Bond angle restraints: 11263 Sorted by residual: angle pdb=" C TYR R 214 " pdb=" CA TYR R 214 " pdb=" CB TYR R 214 " ideal model delta sigma weight residual 110.67 115.79 -5.12 1.92e+00 2.71e-01 7.12e+00 angle pdb=" N SER B 227 " pdb=" CA SER B 227 " pdb=" C SER B 227 " ideal model delta sigma weight residual 108.34 111.69 -3.35 1.31e+00 5.83e-01 6.55e+00 angle pdb=" CA ASP B 186 " pdb=" C ASP B 186 " pdb=" O ASP B 186 " ideal model delta sigma weight residual 120.92 118.22 2.70 1.14e+00 7.69e-01 5.62e+00 angle pdb=" N ASN R 292 " pdb=" CA ASN R 292 " pdb=" C ASN R 292 " ideal model delta sigma weight residual 111.75 108.76 2.99 1.28e+00 6.10e-01 5.47e+00 angle pdb=" C21 G3U R 502 " pdb=" N23 G3U R 502 " pdb=" C24 G3U R 502 " ideal model delta sigma weight residual 127.77 121.01 6.76 3.00e+00 1.11e-01 5.08e+00 ... (remaining 11258 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.06: 4401 17.06 - 34.13: 462 34.13 - 51.19: 77 51.19 - 68.26: 24 68.26 - 85.32: 10 Dihedral angle restraints: 4974 sinusoidal: 1949 harmonic: 3025 Sorted by residual: dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual 93.00 60.49 32.51 1 1.00e+01 1.00e-02 1.50e+01 dihedral pdb=" CA ASP R 70 " pdb=" CB ASP R 70 " pdb=" CG ASP R 70 " pdb=" OD1 ASP R 70 " ideal model delta sinusoidal sigma weight residual -30.00 -86.03 56.03 1 2.00e+01 2.50e-03 1.06e+01 dihedral pdb=" C TYR R 214 " pdb=" N TYR R 214 " pdb=" CA TYR R 214 " pdb=" CB TYR R 214 " ideal model delta harmonic sigma weight residual -122.60 -130.64 8.04 0 2.50e+00 1.60e-01 1.03e+01 ... (remaining 4971 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 976 0.042 - 0.084: 236 0.084 - 0.127: 66 0.127 - 0.169: 2 0.169 - 0.211: 1 Chirality restraints: 1281 Sorted by residual: chirality pdb=" CA TYR R 214 " pdb=" N TYR R 214 " pdb=" C TYR R 214 " pdb=" CB TYR R 214 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CA LEU R 190 " pdb=" N LEU R 190 " pdb=" C LEU R 190 " pdb=" CB LEU R 190 " both_signs ideal model delta sigma weight residual False 2.51 2.65 -0.14 2.00e-01 2.50e+01 4.62e-01 chirality pdb=" CA ILE B 232 " pdb=" N ILE B 232 " pdb=" C ILE B 232 " pdb=" CB ILE B 232 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.34e-01 ... (remaining 1278 not shown) Planarity restraints: 1423 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE R 205 " -0.027 5.00e-02 4.00e+02 4.12e-02 2.71e+00 pdb=" N PRO R 206 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO R 206 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO R 206 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN R 327 " -0.019 5.00e-02 4.00e+02 2.92e-02 1.37e+00 pdb=" N PRO R 328 " 0.051 5.00e-02 4.00e+02 pdb=" CA PRO R 328 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO R 328 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS N 87 " -0.016 5.00e-02 4.00e+02 2.43e-02 9.44e-01 pdb=" N PRO N 88 " 0.042 5.00e-02 4.00e+02 pdb=" CA PRO N 88 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO N 88 " -0.014 5.00e-02 4.00e+02 ... (remaining 1420 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 290 2.70 - 3.25: 8429 3.25 - 3.80: 14553 3.80 - 4.35: 18657 4.35 - 4.90: 30677 Nonbonded interactions: 72606 Sorted by model distance: nonbonded pdb=" O PRO R 137 " pdb=" CD2 PHE R 141 " model vdw 2.154 3.340 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.186 3.040 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.239 3.040 nonbonded pdb=" OG1 THR R 108 " pdb=" OG SER R 202 " model vdw 2.262 3.040 nonbonded pdb=" OG1 THR R 59 " pdb=" OD2 ASP R 120 " model vdw 2.282 3.040 ... (remaining 72601 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 21.720 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4872 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 : 0.003 0.098 8299 Z= 0.198 Angle : 0.478 6.761 11263 Z= 0.285 Chirality : 0.039 0.211 1281 Planarity : 0.003 0.041 1423 Dihedral : 14.493 85.325 2996 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 17.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 1.51 % Allowed : 13.24 % Favored : 85.25 % 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: -2.84 (0.24), residues: 1018 helix: -0.77 (0.23), residues: 395 sheet: -2.80 (0.33), residues: 192 loop : -2.40 (0.28), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 234 HIS 0.002 0.000 HIS B 311 PHE 0.006 0.001 PHE B 235 TYR 0.014 0.001 TYR R 214 ARG 0.003 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 189 time to evaluate : 0.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 PHE cc_start: 0.1995 (t80) cc_final: 0.1396 (t80) REVERT: A 343 ASP cc_start: 0.4753 (m-30) cc_final: 0.4339 (m-30) REVERT: B 153 ASP cc_start: 0.6151 (p0) cc_final: 0.5779 (p0) REVERT: B 196 THR cc_start: 0.8127 (OUTLIER) cc_final: 0.7914 (m) REVERT: R 136 THR cc_start: 0.7920 (p) cc_final: 0.7611 (p) outliers start: 13 outliers final: 5 residues processed: 200 average time/residue: 0.2494 time to fit residues: 64.7201 Evaluate side-chains 153 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 147 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain B residue 151 PHE Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 120 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 0.4980 chunk 76 optimal weight: 0.0870 chunk 42 optimal weight: 1.9990 chunk 26 optimal weight: 10.0000 chunk 51 optimal weight: 0.8980 chunk 40 optimal weight: 6.9990 chunk 79 optimal weight: 0.8980 chunk 30 optimal weight: 0.6980 chunk 48 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 267 GLN ** A 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 GLN A 371 ASN A 377 ASN A 390 GLN B 75 GLN B 110 ASN N 13 GLN N 39 GLN R 60 ASN R 323 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4723 r_free = 0.4723 target = 0.255388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.224819 restraints weight = 9847.263| |-----------------------------------------------------------------------------| r_work (start): 0.4448 rms_B_bonded: 2.19 r_work: 0.4306 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.4306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5868 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8299 Z= 0.211 Angle : 0.584 8.661 11263 Z= 0.308 Chirality : 0.042 0.162 1281 Planarity : 0.004 0.038 1423 Dihedral : 5.204 51.743 1210 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 2.09 % Allowed : 18.47 % Favored : 79.44 % 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: -1.70 (0.26), residues: 1018 helix: 0.45 (0.26), residues: 391 sheet: -2.27 (0.37), residues: 175 loop : -2.05 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 211 HIS 0.012 0.002 HIS A 357 PHE 0.032 0.002 PHE R 141 TYR 0.018 0.002 TYR A 318 ARG 0.006 0.001 ARG A 389 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 162 time to evaluate : 0.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 PHE cc_start: 0.3020 (t80) cc_final: 0.2367 (t80) REVERT: B 105 TYR cc_start: 0.8144 (t80) cc_final: 0.7939 (t80) REVERT: B 134 ARG cc_start: 0.7308 (ttm110) cc_final: 0.7081 (ttt180) REVERT: B 153 ASP cc_start: 0.7080 (p0) cc_final: 0.6702 (p0) REVERT: B 188 MET cc_start: 0.4977 (tpt) cc_final: 0.4666 (tpt) REVERT: R 136 THR cc_start: 0.8281 (p) cc_final: 0.8062 (p) REVERT: R 205 ILE cc_start: 0.7801 (mt) cc_final: 0.7494 (mt) outliers start: 18 outliers final: 8 residues processed: 176 average time/residue: 0.1923 time to fit residues: 46.3649 Evaluate side-chains 154 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 146 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 151 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 60 ASN Chi-restraints excluded: chain R residue 120 ASP Chi-restraints excluded: chain R residue 164 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 84 optimal weight: 0.7980 chunk 74 optimal weight: 4.9990 chunk 46 optimal weight: 0.9990 chunk 100 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 16 optimal weight: 9.9990 chunk 88 optimal weight: 0.8980 chunk 87 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS A 254 ASN ** A 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 371 ASN B 110 ASN B 268 ASN N 123 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4605 r_free = 0.4605 target = 0.239462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.204761 restraints weight = 9651.801| |-----------------------------------------------------------------------------| r_work (start): 0.4293 rms_B_bonded: 2.17 r_work: 0.4138 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.4138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6514 moved from start: 0.4249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 8299 Z= 0.267 Angle : 0.608 7.644 11263 Z= 0.322 Chirality : 0.043 0.163 1281 Planarity : 0.004 0.042 1423 Dihedral : 5.203 59.724 1207 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 16.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 3.60 % Allowed : 18.23 % Favored : 78.16 % 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: -1.46 (0.26), residues: 1018 helix: 0.75 (0.26), residues: 399 sheet: -2.47 (0.35), residues: 187 loop : -1.89 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 211 HIS 0.013 0.002 HIS A 357 PHE 0.025 0.002 PHE R 141 TYR 0.010 0.002 TYR N 94 ARG 0.015 0.001 ARG A 336 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 170 time to evaluate : 0.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 PHE cc_start: 0.3864 (t80) cc_final: 0.3286 (t80) REVERT: B 234 PHE cc_start: 0.7981 (OUTLIER) cc_final: 0.7564 (t80) REVERT: N 109 ASP cc_start: 0.6047 (OUTLIER) cc_final: 0.5686 (p0) REVERT: R 136 THR cc_start: 0.8388 (p) cc_final: 0.8148 (p) outliers start: 31 outliers final: 13 residues processed: 189 average time/residue: 0.2177 time to fit residues: 55.0835 Evaluate side-chains 169 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 154 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain N residue 109 ASP Chi-restraints excluded: chain R residue 120 ASP Chi-restraints excluded: chain R residue 190 LEU Chi-restraints excluded: chain R residue 207 VAL Chi-restraints excluded: chain R residue 298 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 15 optimal weight: 0.7980 chunk 89 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 78 optimal weight: 0.6980 chunk 77 optimal weight: 7.9990 chunk 3 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 10 optimal weight: 0.0970 chunk 74 optimal weight: 8.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 268 ASN ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4565 r_free = 0.4565 target = 0.234790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.198879 restraints weight = 9334.368| |-----------------------------------------------------------------------------| r_work (start): 0.4218 rms_B_bonded: 2.22 r_work: 0.4062 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.4062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6653 moved from start: 0.5064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8299 Z= 0.219 Angle : 0.557 7.637 11263 Z= 0.293 Chirality : 0.042 0.157 1281 Planarity : 0.004 0.048 1423 Dihedral : 5.007 55.367 1205 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 14.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 3.14 % Allowed : 21.72 % Favored : 75.15 % 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: -1.07 (0.27), residues: 1018 helix: 1.12 (0.26), residues: 390 sheet: -2.33 (0.37), residues: 159 loop : -1.70 (0.29), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 99 HIS 0.009 0.001 HIS A 357 PHE 0.020 0.001 PHE R 141 TYR 0.011 0.002 TYR B 289 ARG 0.009 0.001 ARG A 336 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 161 time to evaluate : 0.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 PHE cc_start: 0.3946 (t80) cc_final: 0.3370 (t80) REVERT: A 314 GLU cc_start: 0.6813 (mm-30) cc_final: 0.6562 (mp0) REVERT: A 356 ARG cc_start: 0.7926 (mmt180) cc_final: 0.7701 (mmt180) REVERT: B 234 PHE cc_start: 0.8236 (OUTLIER) cc_final: 0.7641 (t80) REVERT: B 339 TRP cc_start: 0.8041 (m100) cc_final: 0.7601 (m100) REVERT: R 136 THR cc_start: 0.8476 (p) cc_final: 0.8260 (p) outliers start: 27 outliers final: 17 residues processed: 177 average time/residue: 0.2134 time to fit residues: 51.1685 Evaluate side-chains 164 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 146 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 359 CYS Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain R residue 120 ASP Chi-restraints excluded: chain R residue 190 LEU Chi-restraints excluded: chain R residue 207 VAL Chi-restraints excluded: chain R residue 298 CYS Chi-restraints excluded: chain R residue 325 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/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-5571/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-5571/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-5571/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-5571/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-5571/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-5571/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-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/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-5571/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-5571/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-5571/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: 69.9505 > 50: distance: 53 - 57: 10.158 distance: 57 - 58: 6.942 distance: 58 - 59: 19.370 distance: 58 - 61: 7.468 distance: 59 - 60: 16.867 distance: 59 - 64: 10.362 distance: 61 - 62: 30.686 distance: 61 - 63: 25.680 distance: 64 - 65: 10.886 distance: 64 - 273: 11.898 distance: 65 - 66: 15.340 distance: 65 - 68: 20.097 distance: 66 - 67: 5.777 distance: 66 - 72: 9.081 distance: 67 - 270: 17.517 distance: 68 - 69: 34.489 distance: 69 - 70: 15.230 distance: 69 - 71: 21.179 distance: 72 - 73: 7.241 distance: 73 - 74: 14.446 distance: 73 - 76: 13.060 distance: 74 - 75: 26.482 distance: 74 - 83: 11.946 distance: 76 - 77: 9.756 distance: 77 - 78: 11.678 distance: 79 - 80: 23.232 distance: 80 - 81: 5.918 distance: 80 - 82: 25.049 distance: 83 - 84: 8.883 distance: 84 - 85: 4.200 distance: 85 - 86: 14.072 distance: 85 - 87: 5.192 distance: 87 - 88: 3.692 distance: 88 - 89: 4.434 distance: 88 - 91: 16.510 distance: 89 - 90: 3.719 distance: 89 - 97: 7.869 distance: 91 - 92: 21.759 distance: 92 - 93: 6.155 distance: 92 - 94: 9.419 distance: 93 - 95: 4.326 distance: 94 - 96: 9.956 distance: 95 - 96: 9.768 distance: 97 - 98: 3.639 distance: 98 - 99: 14.168 distance: 98 - 101: 18.248 distance: 99 - 100: 20.501 distance: 99 - 105: 18.864 distance: 101 - 102: 5.169 distance: 102 - 103: 6.758 distance: 102 - 104: 19.816 distance: 105 - 106: 18.962 distance: 106 - 107: 26.837 distance: 106 - 109: 24.494 distance: 107 - 108: 19.057 distance: 107 - 110: 24.809 distance: 110 - 111: 4.680 distance: 111 - 112: 11.513 distance: 111 - 114: 11.829 distance: 112 - 119: 40.360 distance: 114 - 115: 23.122 distance: 115 - 116: 39.579 distance: 116 - 117: 23.003 distance: 117 - 118: 26.099 distance: 119 - 120: 21.863 distance: 120 - 121: 24.803 distance: 120 - 123: 47.769 distance: 121 - 122: 18.843 distance: 121 - 127: 15.737 distance: 123 - 124: 27.513 distance: 123 - 125: 42.370 distance: 124 - 126: 18.939 distance: 127 - 128: 24.799 distance: 128 - 129: 15.745 distance: 128 - 131: 21.754 distance: 129 - 130: 46.650 distance: 129 - 139: 14.066 distance: 131 - 132: 7.744 distance: 132 - 133: 18.997 distance: 132 - 134: 17.977 distance: 133 - 135: 5.580 distance: 134 - 136: 11.004 distance: 135 - 137: 11.947 distance: 136 - 137: 10.277 distance: 137 - 138: 25.506