Starting phenix.real_space_refine on Thu Mar 13 16:22:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9iy8_60990/03_2025/9iy8_60990_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9iy8_60990/03_2025/9iy8_60990.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9iy8_60990/03_2025/9iy8_60990.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9iy8_60990/03_2025/9iy8_60990.map" model { file = "/net/cci-nas-00/data/ceres_data/9iy8_60990/03_2025/9iy8_60990_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9iy8_60990/03_2025/9iy8_60990_neut.cif" } resolution = 3.01 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= 0.002 sd= 0.034 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 67 5.16 5 C 5740 2.51 5 N 1540 2.21 5 O 1667 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 9014 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 2594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2594 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 445 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "R" Number of atoms: 2386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2386 Classifications: {'peptide': 294} Link IDs: {'PTRANS': 11, 'TRANS': 282} Chain: "S" Number of atoms: 1802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1802 Classifications: {'peptide': 235} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 224} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 1787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1787 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 3, 'TRANS': 212} Chain breaks: 1 Time building chain proxies: 5.55, per 1000 atoms: 0.62 Number of scatterers: 9014 At special positions: 0 Unit cell: (84.24, 116.48, 141.44, 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 67 16.00 O 1667 8.00 N 1540 7.00 C 5740 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 10 " - pdb=" SG CYS R 260 " distance=2.03 Simple disulfide: pdb=" SG CYS R 94 " - pdb=" SG CYS R 168 " distance=2.04 Simple disulfide: pdb=" SG CYS S 160 " - pdb=" SG CYS S 230 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.42 Conformation dependent library (CDL) restraints added in 1.2 seconds 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2144 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 13 sheets defined 40.6% alpha, 21.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.06 Creating SS restraints... Processing helix chain 'B' and resid 3 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 7 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 Processing helix chain 'R' and resid 12 through 51 removed outlier: 4.272A pdb=" N PHE R 24 " --> pdb=" O LYS R 20 " (cutoff:3.500A) Proline residue: R 29 - end of helix Processing helix chain 'R' and resid 57 through 86 Proline residue: R 78 - end of helix Processing helix chain 'R' and resid 90 through 125 removed outlier: 3.550A pdb=" N CYS R 94 " --> pdb=" O PHE R 90 " (cutoff:3.500A) Processing helix chain 'R' and resid 125 through 132 Processing helix chain 'R' and resid 134 through 164 removed outlier: 3.718A pdb=" N ILE R 154 " --> pdb=" O TRP R 150 " (cutoff:3.500A) Proline residue: R 155 - end of helix removed outlier: 3.948A pdb=" N PHE R 159 " --> pdb=" O PRO R 155 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N HIS R 160 " --> pdb=" O ILE R 156 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL R 163 " --> pdb=" O PHE R 159 " (cutoff:3.500A) Processing helix chain 'R' and resid 178 through 211 Proline residue: R 184 - end of helix removed outlier: 5.298A pdb=" N LEU R 192 " --> pdb=" O PHE R 188 " (cutoff:3.500A) Proline residue: R 193 - end of helix Processing helix chain 'R' and resid 212 through 214 No H-bonds generated for 'chain 'R' and resid 212 through 214' Processing helix chain 'R' and resid 216 through 220 removed outlier: 4.287A pdb=" N VAL R 219 " --> pdb=" O GLN R 216 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLN R 220 " --> pdb=" O ASP R 217 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 216 through 220' Processing helix chain 'R' and resid 221 through 254 Proline residue: R 241 - end of helix Processing helix chain 'R' and resid 259 through 279 Processing helix chain 'R' and resid 279 through 288 Processing helix chain 'R' and resid 292 through 302 removed outlier: 4.247A pdb=" N ARG R 300 " --> pdb=" O ARG R 296 " (cutoff:3.500A) Processing helix chain 'S' and resid 53 through 56 removed outlier: 3.865A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 56' Processing helix chain 'S' and resid 62 through 65 removed outlier: 3.635A pdb=" N LYS S 65 " --> pdb=" O ASP S 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 62 through 65' Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.539A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 48 removed outlier: 3.795A pdb=" N THR A 43 " --> pdb=" O SER A 39 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N TYR A 44 " --> pdb=" O ARG A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 71 removed outlier: 3.527A pdb=" N ILE A 71 " --> pdb=" O GLN A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 236 Processing helix chain 'A' and resid 251 through 263 No H-bonds generated for 'chain 'A' and resid 251 through 263' Processing helix chain 'A' and resid 264 through 277 Processing helix chain 'A' and resid 292 through 301 Processing helix chain 'A' and resid 304 through 309 removed outlier: 4.527A pdb=" N TYR A 308 " --> pdb=" O SER A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 334 removed outlier: 3.547A pdb=" N LYS A 333 " --> pdb=" O CYS A 329 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ARG A 334 " --> pdb=" O PHE A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 374 Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 52 removed outlier: 4.496A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.898A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.581A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.919A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 189 through 192 removed outlier: 3.683A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY B 202 " --> pdb=" O SER B 189 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL B 200 " --> pdb=" O SER B 191 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.571A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.599A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N CYS B 294 " --> pdb=" O LEU B 308 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AA9, first strand: chain 'S' and resid 58 through 60 removed outlier: 5.434A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA S 49 " --> pdb=" O TRP S 36 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL S 97 " --> pdb=" O HIS S 35 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N THR S 115 " --> pdb=" O TYR S 94 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 141 through 142 Processing sheet with id=AB2, first strand: chain 'S' and resid 149 through 150 Processing sheet with id=AB3, first strand: chain 'S' and resid 195 through 196 removed outlier: 6.576A pdb=" N TRP S 177 " --> pdb=" O LEU S 189 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N TYR S 191 " --> pdb=" O LEU S 175 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N LEU S 175 " --> pdb=" O TYR S 191 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 207 through 213 removed outlier: 6.694A pdb=" N VAL A 49 " --> pdb=" O LYS A 219 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N VAL A 221 " --> pdb=" O VAL A 49 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ILE A 51 " --> pdb=" O VAL A 221 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N LYS A 50 " --> pdb=" O SER A 242 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N LEU A 244 " --> pdb=" O LYS A 50 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LEU A 52 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N LEU A 246 " --> pdb=" O LEU A 52 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N LEU A 54 " --> pdb=" O LEU A 246 " (cutoff:3.500A) removed outlier: 8.715A pdb=" N ASP A 248 " --> pdb=" O LEU A 54 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ILE A 243 " --> pdb=" O ILE A 287 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N PHE A 289 " --> pdb=" O ILE A 243 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N PHE A 245 " --> pdb=" O PHE A 289 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ASN A 291 " --> pdb=" O PHE A 245 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N VAL A 247 " --> pdb=" O ASN A 291 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ILE A 286 " --> pdb=" O TYR A 343 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N HIS A 345 " --> pdb=" O ILE A 286 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N LEU A 288 " --> pdb=" O HIS A 345 " (cutoff:3.500A) 448 hydrogen bonds defined for protein. 1290 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: 2.61 Time building geometry restraints manager: 2.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2368 1.33 - 1.45: 1904 1.45 - 1.58: 4842 1.58 - 1.70: 0 1.70 - 1.82: 96 Bond restraints: 9210 Sorted by residual: bond pdb=" N PRO R 29 " pdb=" CD PRO R 29 " ideal model delta sigma weight residual 1.473 1.540 -0.067 1.40e-02 5.10e+03 2.26e+01 bond pdb=" N ASP B 258 " pdb=" CA ASP B 258 " ideal model delta sigma weight residual 1.457 1.473 -0.015 1.29e-02 6.01e+03 1.41e+00 bond pdb=" C LEU R 77 " pdb=" N PRO R 78 " ideal model delta sigma weight residual 1.336 1.350 -0.014 1.23e-02 6.61e+03 1.35e+00 bond pdb=" CG LEU R 36 " pdb=" CD2 LEU R 36 " ideal model delta sigma weight residual 1.521 1.485 0.036 3.30e-02 9.18e+02 1.21e+00 bond pdb=" CD GLN G 11 " pdb=" OE1 GLN G 11 " ideal model delta sigma weight residual 1.231 1.210 0.021 1.90e-02 2.77e+03 1.20e+00 ... (remaining 9205 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.66: 12255 2.66 - 5.32: 169 5.32 - 7.98: 21 7.98 - 10.64: 10 10.64 - 13.30: 4 Bond angle restraints: 12459 Sorted by residual: angle pdb=" CA PRO R 29 " pdb=" N PRO R 29 " pdb=" CD PRO R 29 " ideal model delta sigma weight residual 112.00 98.70 13.30 1.40e+00 5.10e-01 9.02e+01 angle pdb=" CA GLU B 10 " pdb=" CB GLU B 10 " pdb=" CG GLU B 10 " ideal model delta sigma weight residual 114.10 123.49 -9.39 2.00e+00 2.50e-01 2.21e+01 angle pdb=" CA TYR R 62 " pdb=" CB TYR R 62 " pdb=" CG TYR R 62 " ideal model delta sigma weight residual 113.90 120.98 -7.08 1.80e+00 3.09e-01 1.55e+01 angle pdb=" CA LEU R 36 " pdb=" CB LEU R 36 " pdb=" CG LEU R 36 " ideal model delta sigma weight residual 116.30 129.49 -13.19 3.50e+00 8.16e-02 1.42e+01 angle pdb=" CA LEU R 248 " pdb=" CB LEU R 248 " pdb=" CG LEU R 248 " ideal model delta sigma weight residual 116.30 128.68 -12.38 3.50e+00 8.16e-02 1.25e+01 ... (remaining 12454 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.01: 4741 18.01 - 36.03: 545 36.03 - 54.04: 155 54.04 - 72.05: 25 72.05 - 90.06: 7 Dihedral angle restraints: 5473 sinusoidal: 2158 harmonic: 3315 Sorted by residual: dihedral pdb=" CB CYS R 94 " pdb=" SG CYS R 94 " pdb=" SG CYS R 168 " pdb=" CB CYS R 168 " ideal model delta sinusoidal sigma weight residual 93.00 -176.94 -90.06 1 1.00e+01 1.00e-02 9.61e+01 dihedral pdb=" CA TRP R 53 " pdb=" C TRP R 53 " pdb=" N PRO R 54 " pdb=" CA PRO R 54 " ideal model delta harmonic sigma weight residual -180.00 -155.94 -24.06 0 5.00e+00 4.00e-02 2.31e+01 dihedral pdb=" CA ASN A 291 " pdb=" C ASN A 291 " pdb=" N LYS A 292 " pdb=" CA LYS A 292 " ideal model delta harmonic sigma weight residual 180.00 -162.20 -17.80 0 5.00e+00 4.00e-02 1.27e+01 ... (remaining 5470 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1201 0.066 - 0.132: 181 0.132 - 0.198: 12 0.198 - 0.264: 1 0.264 - 0.330: 1 Chirality restraints: 1396 Sorted by residual: chirality pdb=" CG LEU R 248 " pdb=" CB LEU R 248 " pdb=" CD1 LEU R 248 " pdb=" CD2 LEU R 248 " both_signs ideal model delta sigma weight residual False -2.59 -2.26 -0.33 2.00e-01 2.50e+01 2.71e+00 chirality pdb=" CG LEU G 19 " pdb=" CB LEU G 19 " pdb=" CD1 LEU G 19 " pdb=" CD2 LEU G 19 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CG LEU R 22 " pdb=" CB LEU R 22 " pdb=" CD1 LEU R 22 " pdb=" CD2 LEU R 22 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.19 2.00e-01 2.50e+01 9.48e-01 ... (remaining 1393 not shown) Planarity restraints: 1584 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE R 28 " 0.090 5.00e-02 4.00e+02 1.24e-01 2.44e+01 pdb=" N PRO R 29 " -0.213 5.00e-02 4.00e+02 pdb=" CA PRO R 29 " 0.058 5.00e-02 4.00e+02 pdb=" CD PRO R 29 " 0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP R 218 " 0.017 2.00e-02 2.50e+03 1.70e-02 7.26e+00 pdb=" CG TRP R 218 " -0.047 2.00e-02 2.50e+03 pdb=" CD1 TRP R 218 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP R 218 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP R 218 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP R 218 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP R 218 " 0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 218 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 218 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP R 218 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR S 236 " 0.037 5.00e-02 4.00e+02 5.58e-02 4.99e+00 pdb=" N PRO S 237 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO S 237 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO S 237 " 0.031 5.00e-02 4.00e+02 ... (remaining 1581 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 209 2.66 - 3.22: 8819 3.22 - 3.78: 14843 3.78 - 4.34: 19883 4.34 - 4.90: 32465 Nonbonded interactions: 76219 Sorted by model distance: nonbonded pdb=" OH TYR S 176 " pdb=" OE2 GLU A 23 " model vdw 2.102 3.040 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.166 3.040 nonbonded pdb=" N GLU A 229 " pdb=" OE1 GLU A 229 " model vdw 2.176 3.120 nonbonded pdb=" O ILE S 139 " pdb=" OG1 THR S 239 " model vdw 2.199 3.040 nonbonded pdb=" N GLU A 311 " pdb=" OE1 GLU A 311 " model vdw 2.202 3.120 ... (remaining 76214 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: 0.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 24.070 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 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 0.067 9210 Z= 0.226 Angle : 0.793 13.299 12459 Z= 0.395 Chirality : 0.046 0.330 1396 Planarity : 0.006 0.124 1584 Dihedral : 16.608 89.950 3320 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 16.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 0.30 % Allowed : 33.63 % Favored : 66.06 % 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: 0.01 (0.26), residues: 1127 helix: 0.96 (0.25), residues: 419 sheet: 0.01 (0.32), residues: 281 loop : -0.86 (0.32), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP R 218 HIS 0.004 0.001 HIS B 183 PHE 0.029 0.002 PHE R 247 TYR 0.021 0.001 TYR R 62 ARG 0.012 0.001 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 289 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 217 MET cc_start: 0.7958 (ptm) cc_final: 0.7659 (mtp) REVERT: B 264 TYR cc_start: 0.8704 (m-80) cc_final: 0.8175 (m-80) REVERT: B 268 ASN cc_start: 0.8452 (t0) cc_final: 0.8218 (t0) REVERT: G 13 ARG cc_start: 0.8457 (tmm160) cc_final: 0.7843 (tmm160) REVERT: G 17 GLU cc_start: 0.8793 (mm-30) cc_final: 0.8026 (mm-30) REVERT: R 105 MET cc_start: 0.7826 (ttp) cc_final: 0.7538 (ttp) REVERT: R 112 ARG cc_start: 0.8140 (mtm-85) cc_final: 0.7653 (mtm-85) REVERT: R 113 CYS cc_start: 0.8823 (m) cc_final: 0.8502 (m) REVERT: R 280 ASN cc_start: 0.7486 (t0) cc_final: 0.7012 (t0) REVERT: S 46 GLU cc_start: 0.8166 (tt0) cc_final: 0.7873 (pt0) REVERT: S 88 SER cc_start: 0.9155 (m) cc_final: 0.8756 (p) REVERT: S 228 TYR cc_start: 0.8809 (m-80) cc_final: 0.8255 (m-80) REVERT: A 220 MET cc_start: 0.8752 (mtp) cc_final: 0.8523 (ttm) REVERT: A 264 ARG cc_start: 0.8391 (mtp-110) cc_final: 0.7402 (mtp-110) REVERT: A 320 ARG cc_start: 0.8032 (tpp80) cc_final: 0.7534 (tpp80) REVERT: A 343 TYR cc_start: 0.8423 (m-80) cc_final: 0.7819 (m-80) outliers start: 3 outliers final: 3 residues processed: 289 average time/residue: 0.3265 time to fit residues: 119.8058 Evaluate side-chains 271 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 268 time to evaluate : 2.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain R residue 150 TRP Chi-restraints excluded: chain R residue 183 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.7980 chunk 84 optimal weight: 0.9990 chunk 46 optimal weight: 5.9990 chunk 28 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 87 optimal weight: 6.9990 chunk 33 optimal weight: 4.9990 chunk 52 optimal weight: 0.0050 chunk 64 optimal weight: 0.9980 chunk 100 optimal weight: 0.6980 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 220 GLN ** R 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 180 GLN ** A 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 HIS A 377 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.109765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.088461 restraints weight = 16789.260| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 2.54 r_work: 0.3114 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.1135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 9210 Z= 0.238 Angle : 0.669 9.514 12459 Z= 0.344 Chirality : 0.045 0.276 1396 Planarity : 0.005 0.057 1584 Dihedral : 4.850 46.527 1241 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 4.92 % Allowed : 27.01 % Favored : 68.07 % 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: -0.01 (0.26), residues: 1127 helix: 1.00 (0.25), residues: 418 sheet: -0.20 (0.32), residues: 289 loop : -0.77 (0.32), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP R 218 HIS 0.005 0.001 HIS B 183 PHE 0.017 0.002 PHE S 213 TYR 0.020 0.001 TYR R 62 ARG 0.007 0.001 ARG A 279 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 276 time to evaluate : 1.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 96 ARG cc_start: 0.8419 (ttm110) cc_final: 0.8063 (ttm-80) REVERT: B 217 MET cc_start: 0.8247 (ptm) cc_final: 0.7826 (mtp) REVERT: B 268 ASN cc_start: 0.8447 (t0) cc_final: 0.8225 (t0) REVERT: B 298 ASP cc_start: 0.8560 (t70) cc_final: 0.8288 (t70) REVERT: G 13 ARG cc_start: 0.8584 (OUTLIER) cc_final: 0.8013 (tmm160) REVERT: G 17 GLU cc_start: 0.8950 (mm-30) cc_final: 0.8171 (mm-30) REVERT: G 27 ARG cc_start: 0.8658 (tpp-160) cc_final: 0.8389 (tpp-160) REVERT: G 62 ARG cc_start: 0.7660 (ptp90) cc_final: 0.7369 (ptp90) REVERT: R 30 THR cc_start: 0.8884 (t) cc_final: 0.8678 (t) REVERT: R 63 MET cc_start: 0.8916 (OUTLIER) cc_final: 0.7356 (mpp) REVERT: S 46 GLU cc_start: 0.8341 (tt0) cc_final: 0.8136 (pt0) REVERT: S 179 LEU cc_start: 0.8588 (tp) cc_final: 0.8371 (tp) REVERT: S 203 ARG cc_start: 0.8520 (mtm110) cc_final: 0.7619 (mtm110) REVERT: S 221 GLU cc_start: 0.7466 (mp0) cc_final: 0.6492 (mp0) REVERT: A 220 MET cc_start: 0.8661 (mtp) cc_final: 0.8445 (mtm) REVERT: A 252 PHE cc_start: 0.9069 (m-10) cc_final: 0.8816 (m-80) REVERT: A 320 ARG cc_start: 0.8119 (tpp80) cc_final: 0.7726 (tpp80) REVERT: A 337 GLN cc_start: 0.9073 (OUTLIER) cc_final: 0.8498 (mt0) REVERT: A 343 TYR cc_start: 0.8629 (m-80) cc_final: 0.8071 (m-80) REVERT: A 375 MET cc_start: 0.8760 (mmm) cc_final: 0.8418 (mtt) outliers start: 49 outliers final: 22 residues processed: 295 average time/residue: 0.2824 time to fit residues: 106.6745 Evaluate side-chains 299 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 274 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 13 ARG Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain R residue 63 MET Chi-restraints excluded: chain R residue 76 SER Chi-restraints excluded: chain R residue 99 CYS Chi-restraints excluded: chain R residue 150 TRP Chi-restraints excluded: chain R residue 183 PHE Chi-restraints excluded: chain R residue 256 PHE Chi-restraints excluded: chain R residue 268 PHE Chi-restraints excluded: chain R residue 279 VAL Chi-restraints excluded: chain R residue 289 TYR Chi-restraints excluded: chain S residue 139 ILE Chi-restraints excluded: chain S residue 142 THR Chi-restraints excluded: chain S residue 214 THR Chi-restraints excluded: chain S residue 216 THR Chi-restraints excluded: chain S residue 225 VAL Chi-restraints excluded: chain S residue 239 THR Chi-restraints excluded: chain S residue 248 LEU Chi-restraints excluded: chain A residue 24 ASP Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 263 ASN Chi-restraints excluded: chain A residue 337 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 19 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 85 optimal weight: 0.0970 chunk 17 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.109898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.088521 restraints weight = 17053.239| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 2.58 r_work: 0.3101 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9210 Z= 0.251 Angle : 0.638 9.188 12459 Z= 0.327 Chirality : 0.045 0.280 1396 Planarity : 0.004 0.057 1584 Dihedral : 4.777 47.849 1239 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 6.12 % Allowed : 25.60 % Favored : 68.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.26), residues: 1127 helix: 1.11 (0.25), residues: 418 sheet: -0.25 (0.32), residues: 278 loop : -0.74 (0.32), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 150 HIS 0.004 0.001 HIS B 183 PHE 0.019 0.002 PHE A 211 TYR 0.020 0.001 TYR R 62 ARG 0.006 0.001 ARG A 264 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 282 time to evaluate : 0.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 57 LYS cc_start: 0.9048 (OUTLIER) cc_final: 0.8842 (ptpt) REVERT: B 96 ARG cc_start: 0.8421 (ttm110) cc_final: 0.8068 (ttm-80) REVERT: B 188 MET cc_start: 0.8626 (mmm) cc_final: 0.8366 (mmm) REVERT: B 217 MET cc_start: 0.8319 (ptm) cc_final: 0.7852 (mtp) REVERT: B 268 ASN cc_start: 0.8466 (t0) cc_final: 0.8266 (t0) REVERT: B 298 ASP cc_start: 0.8556 (t70) cc_final: 0.8189 (t70) REVERT: G 13 ARG cc_start: 0.8571 (tmm160) cc_final: 0.8026 (tmm160) REVERT: G 17 GLU cc_start: 0.8996 (mm-30) cc_final: 0.8248 (mm-30) REVERT: G 27 ARG cc_start: 0.8630 (tpp-160) cc_final: 0.8313 (tpp-160) REVERT: G 62 ARG cc_start: 0.7795 (ptp90) cc_final: 0.7469 (ptp90) REVERT: R 30 THR cc_start: 0.8881 (t) cc_final: 0.8679 (t) REVERT: R 63 MET cc_start: 0.8913 (OUTLIER) cc_final: 0.7417 (mpp) REVERT: R 79 PHE cc_start: 0.8252 (m-10) cc_final: 0.7977 (m-10) REVERT: R 80 LYS cc_start: 0.8036 (tppt) cc_final: 0.7658 (tppt) REVERT: R 112 ARG cc_start: 0.8101 (mtm-85) cc_final: 0.7737 (mtm-85) REVERT: R 183 PHE cc_start: 0.8167 (OUTLIER) cc_final: 0.7957 (t80) REVERT: S 46 GLU cc_start: 0.8322 (tt0) cc_final: 0.8032 (pt0) REVERT: S 87 ARG cc_start: 0.8804 (mpp80) cc_final: 0.8575 (mpp80) REVERT: S 179 LEU cc_start: 0.8709 (tp) cc_final: 0.8389 (tp) REVERT: S 203 ARG cc_start: 0.8497 (mtm110) cc_final: 0.7255 (mtm110) REVERT: S 221 GLU cc_start: 0.7561 (mp0) cc_final: 0.6332 (mp0) REVERT: A 220 MET cc_start: 0.8664 (mtp) cc_final: 0.8442 (mtm) REVERT: A 252 PHE cc_start: 0.9076 (m-10) cc_final: 0.8640 (m-80) REVERT: A 278 ASN cc_start: 0.8492 (t0) cc_final: 0.8277 (t0) REVERT: A 292 LYS cc_start: 0.8844 (mmtm) cc_final: 0.8531 (mmtm) REVERT: A 320 ARG cc_start: 0.8177 (tpp80) cc_final: 0.7797 (tpp80) REVERT: A 337 GLN cc_start: 0.9145 (OUTLIER) cc_final: 0.8617 (mt0) outliers start: 61 outliers final: 34 residues processed: 314 average time/residue: 0.2718 time to fit residues: 109.3741 Evaluate side-chains 307 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 269 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain R residue 26 VAL Chi-restraints excluded: chain R residue 63 MET Chi-restraints excluded: chain R residue 76 SER Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 96 LEU Chi-restraints excluded: chain R residue 99 CYS Chi-restraints excluded: chain R residue 136 ARG Chi-restraints excluded: chain R residue 150 TRP Chi-restraints excluded: chain R residue 183 PHE Chi-restraints excluded: chain R residue 237 VAL Chi-restraints excluded: chain R residue 256 PHE Chi-restraints excluded: chain R residue 268 PHE Chi-restraints excluded: chain R residue 276 PHE Chi-restraints excluded: chain R residue 279 VAL Chi-restraints excluded: chain R residue 289 TYR Chi-restraints excluded: chain R residue 293 LYS Chi-restraints excluded: chain S residue 139 ILE Chi-restraints excluded: chain S residue 142 THR Chi-restraints excluded: chain S residue 214 THR Chi-restraints excluded: chain S residue 216 THR Chi-restraints excluded: chain S residue 225 VAL Chi-restraints excluded: chain S residue 239 THR Chi-restraints excluded: chain S residue 248 LEU Chi-restraints excluded: chain A residue 24 ASP Chi-restraints excluded: chain A residue 37 CYS Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 214 LYS Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 337 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 35 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 55 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 68 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 104 optimal weight: 0.0980 chunk 0 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.106654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.085498 restraints weight = 16938.500| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 2.52 r_work: 0.3062 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 9210 Z= 0.378 Angle : 0.688 12.194 12459 Z= 0.354 Chirality : 0.047 0.319 1396 Planarity : 0.005 0.053 1584 Dihedral : 4.903 48.536 1239 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 7.03 % Allowed : 25.40 % Favored : 67.57 % 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: -0.06 (0.26), residues: 1127 helix: 1.00 (0.25), residues: 419 sheet: -0.42 (0.31), residues: 291 loop : -0.70 (0.32), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 82 HIS 0.006 0.001 HIS B 62 PHE 0.022 0.002 PHE R 247 TYR 0.018 0.002 TYR R 62 ARG 0.007 0.001 ARG A 331 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 271 time to evaluate : 1.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 96 ARG cc_start: 0.8653 (ttm110) cc_final: 0.8450 (ttm-80) REVERT: B 217 MET cc_start: 0.8588 (ptm) cc_final: 0.8014 (mtp) REVERT: B 298 ASP cc_start: 0.8808 (t70) cc_final: 0.8449 (t70) REVERT: G 11 GLN cc_start: 0.8658 (pm20) cc_final: 0.8395 (pm20) REVERT: G 21 MET cc_start: 0.8542 (mmm) cc_final: 0.8341 (mmm) REVERT: G 30 VAL cc_start: 0.8943 (t) cc_final: 0.8690 (p) REVERT: G 62 ARG cc_start: 0.7976 (ptp90) cc_final: 0.7722 (ptp90) REVERT: R 63 MET cc_start: 0.9054 (OUTLIER) cc_final: 0.7544 (mpp) REVERT: R 75 LEU cc_start: 0.8374 (mp) cc_final: 0.8014 (tt) REVERT: R 79 PHE cc_start: 0.8376 (m-10) cc_final: 0.8166 (m-10) REVERT: R 183 PHE cc_start: 0.8317 (OUTLIER) cc_final: 0.8071 (t80) REVERT: R 255 SER cc_start: 0.8646 (t) cc_final: 0.8330 (m) REVERT: S 46 GLU cc_start: 0.8594 (tt0) cc_final: 0.8319 (pt0) REVERT: S 87 ARG cc_start: 0.8859 (mpp80) cc_final: 0.8531 (mpp80) REVERT: S 141 MET cc_start: 0.8847 (OUTLIER) cc_final: 0.8324 (mmm) REVERT: S 179 LEU cc_start: 0.8879 (tp) cc_final: 0.8522 (tp) REVERT: S 203 ARG cc_start: 0.8563 (mtm110) cc_final: 0.7388 (mtm110) REVERT: S 221 GLU cc_start: 0.7767 (mp0) cc_final: 0.6625 (mp0) REVERT: S 231 MET cc_start: 0.8825 (ttp) cc_final: 0.8449 (ttp) REVERT: A 40 ARG cc_start: 0.8467 (tpp80) cc_final: 0.8100 (mpp80) REVERT: A 61 LYS cc_start: 0.8983 (OUTLIER) cc_final: 0.8582 (ttmm) REVERT: A 220 MET cc_start: 0.8887 (mtp) cc_final: 0.8684 (mtm) REVERT: A 230 ARG cc_start: 0.8405 (mpt90) cc_final: 0.8200 (mmt180) REVERT: A 278 ASN cc_start: 0.8811 (t0) cc_final: 0.8517 (t0) REVERT: A 320 ARG cc_start: 0.8388 (tpp80) cc_final: 0.7972 (tpp80) REVERT: A 328 GLU cc_start: 0.8286 (tp30) cc_final: 0.7604 (tp30) REVERT: A 337 GLN cc_start: 0.9215 (OUTLIER) cc_final: 0.8684 (mt0) outliers start: 70 outliers final: 46 residues processed: 302 average time/residue: 0.2780 time to fit residues: 107.1516 Evaluate side-chains 321 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 270 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 13 ARG Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain R residue 26 VAL Chi-restraints excluded: chain R residue 63 MET Chi-restraints excluded: chain R residue 76 SER Chi-restraints excluded: chain R residue 82 VAL Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 96 LEU Chi-restraints excluded: chain R residue 99 CYS Chi-restraints excluded: chain R residue 150 TRP Chi-restraints excluded: chain R residue 183 PHE Chi-restraints excluded: chain R residue 187 VAL Chi-restraints excluded: chain R residue 196 ILE Chi-restraints excluded: chain R residue 237 VAL Chi-restraints excluded: chain R residue 256 PHE Chi-restraints excluded: chain R residue 268 PHE Chi-restraints excluded: chain R residue 270 LEU Chi-restraints excluded: chain R residue 276 PHE Chi-restraints excluded: chain R residue 279 VAL Chi-restraints excluded: chain R residue 289 TYR Chi-restraints excluded: chain S residue 113 GLN Chi-restraints excluded: chain S residue 139 ILE Chi-restraints excluded: chain S residue 141 MET Chi-restraints excluded: chain S residue 142 THR Chi-restraints excluded: chain S residue 214 THR Chi-restraints excluded: chain S residue 216 THR Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain S residue 225 VAL Chi-restraints excluded: chain S residue 239 THR Chi-restraints excluded: chain S residue 248 LEU Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 24 ASP Chi-restraints excluded: chain A residue 37 CYS Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 61 LYS Chi-restraints excluded: chain A residue 214 LYS Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 337 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 68 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 78 optimal weight: 0.7980 chunk 21 optimal weight: 0.0770 chunk 44 optimal weight: 0.7980 chunk 101 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 chunk 53 optimal weight: 10.0000 chunk 64 optimal weight: 5.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 143 GLN ** S 168 HIS ** 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 = 0.3610 r_free = 0.3610 target = 0.109033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.087535 restraints weight = 16763.513| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 2.55 r_work: 0.3094 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9210 Z= 0.227 Angle : 0.647 10.610 12459 Z= 0.328 Chirality : 0.045 0.263 1396 Planarity : 0.004 0.052 1584 Dihedral : 4.817 50.151 1239 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 5.62 % Allowed : 27.21 % Favored : 67.17 % 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: 0.06 (0.26), residues: 1127 helix: 1.15 (0.26), residues: 419 sheet: -0.43 (0.31), residues: 291 loop : -0.61 (0.33), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 339 HIS 0.004 0.001 HIS B 183 PHE 0.024 0.002 PHE R 247 TYR 0.016 0.001 TYR R 62 ARG 0.006 0.001 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 278 time to evaluate : 1.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 188 MET cc_start: 0.8863 (mmm) cc_final: 0.8605 (mmm) REVERT: B 217 MET cc_start: 0.8606 (ptm) cc_final: 0.8009 (mtp) REVERT: B 237 ASN cc_start: 0.9252 (OUTLIER) cc_final: 0.8998 (p0) REVERT: B 298 ASP cc_start: 0.8817 (t70) cc_final: 0.8430 (t70) REVERT: G 11 GLN cc_start: 0.8621 (pm20) cc_final: 0.8202 (pm20) REVERT: G 21 MET cc_start: 0.8472 (mmm) cc_final: 0.8254 (mmm) REVERT: G 27 ARG cc_start: 0.8656 (tpp-160) cc_final: 0.8408 (tpp-160) REVERT: G 30 VAL cc_start: 0.8910 (t) cc_final: 0.8654 (p) REVERT: G 62 ARG cc_start: 0.7940 (ptp90) cc_final: 0.7636 (ptp90) REVERT: R 63 MET cc_start: 0.9032 (OUTLIER) cc_final: 0.7569 (mpp) REVERT: R 75 LEU cc_start: 0.8355 (mp) cc_final: 0.7984 (tt) REVERT: R 80 LYS cc_start: 0.8081 (tppt) cc_final: 0.7723 (tppt) REVERT: R 112 ARG cc_start: 0.8281 (mtm-85) cc_final: 0.8042 (mtm-85) REVERT: S 46 GLU cc_start: 0.8616 (tt0) cc_final: 0.8238 (pt0) REVERT: S 87 ARG cc_start: 0.8829 (mpp80) cc_final: 0.8497 (mpp80) REVERT: S 141 MET cc_start: 0.8819 (OUTLIER) cc_final: 0.8292 (mmm) REVERT: S 179 LEU cc_start: 0.8783 (tp) cc_final: 0.8459 (tp) REVERT: S 203 ARG cc_start: 0.8570 (mtm110) cc_final: 0.7494 (mtm110) REVERT: S 221 GLU cc_start: 0.7792 (mp0) cc_final: 0.6783 (mp0) REVERT: S 231 MET cc_start: 0.8809 (ttp) cc_final: 0.8439 (ttm) REVERT: A 40 ARG cc_start: 0.8463 (tpp80) cc_final: 0.8106 (mpp80) REVERT: A 68 MET cc_start: 0.8266 (mmm) cc_final: 0.7593 (tmm) REVERT: A 230 ARG cc_start: 0.8429 (mpt90) cc_final: 0.8049 (mmt180) REVERT: A 267 GLU cc_start: 0.8875 (tt0) cc_final: 0.8586 (pt0) REVERT: A 278 ASN cc_start: 0.8682 (t0) cc_final: 0.8387 (t0) REVERT: A 320 ARG cc_start: 0.8384 (tpp80) cc_final: 0.7957 (tpp80) REVERT: A 328 GLU cc_start: 0.8329 (tp30) cc_final: 0.7502 (tp30) REVERT: A 337 GLN cc_start: 0.9215 (OUTLIER) cc_final: 0.8646 (mt0) REVERT: A 375 MET cc_start: 0.8845 (mtt) cc_final: 0.8533 (mtt) outliers start: 56 outliers final: 37 residues processed: 302 average time/residue: 0.2936 time to fit residues: 113.1100 Evaluate side-chains 312 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 271 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain G residue 13 ARG Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain R residue 63 MET Chi-restraints excluded: chain R residue 76 SER Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 96 LEU Chi-restraints excluded: chain R residue 99 CYS Chi-restraints excluded: chain R residue 136 ARG Chi-restraints excluded: chain R residue 150 TRP Chi-restraints excluded: chain R residue 256 PHE Chi-restraints excluded: chain R residue 268 PHE Chi-restraints excluded: chain R residue 270 LEU Chi-restraints excluded: chain R residue 276 PHE Chi-restraints excluded: chain R residue 279 VAL Chi-restraints excluded: chain R residue 289 TYR Chi-restraints excluded: chain S residue 139 ILE Chi-restraints excluded: chain S residue 141 MET Chi-restraints excluded: chain S residue 142 THR Chi-restraints excluded: chain S residue 143 GLN Chi-restraints excluded: chain S residue 216 THR Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain S residue 225 VAL Chi-restraints excluded: chain S residue 239 THR Chi-restraints excluded: chain S residue 248 LEU Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 24 ASP Chi-restraints excluded: chain A residue 214 LYS Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 263 ASN Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 337 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/iotbx/cli_parser.py", line 980, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 51.2467 > 50: distance: 12 - 16: 3.488 distance: 16 - 17: 3.833 distance: 17 - 18: 3.383 distance: 17 - 20: 9.545 distance: 18 - 25: 5.129 distance: 20 - 21: 4.755 distance: 21 - 22: 7.822 distance: 23 - 24: 6.143 distance: 25 - 26: 5.774 distance: 26 - 27: 4.065 distance: 26 - 29: 3.532 distance: 27 - 28: 3.253 distance: 27 - 31: 4.288 distance: 29 - 30: 8.128 distance: 31 - 32: 3.361 distance: 32 - 33: 6.238 distance: 32 - 35: 4.464 distance: 33 - 34: 3.950 distance: 33 - 39: 4.658 distance: 36 - 37: 9.755 distance: 36 - 38: 9.160 distance: 39 - 40: 4.546 distance: 40 - 41: 5.570 distance: 40 - 43: 3.343 distance: 41 - 42: 15.269 distance: 41 - 47: 10.830 distance: 43 - 44: 4.383 distance: 44 - 45: 8.320 distance: 44 - 46: 10.469 distance: 47 - 48: 7.908 distance: 48 - 51: 4.630 distance: 49 - 50: 5.734 distance: 49 - 57: 4.041 distance: 51 - 52: 7.372 distance: 52 - 53: 5.862 distance: 52 - 54: 7.179 distance: 54 - 56: 3.795 distance: 55 - 56: 7.639 distance: 57 - 58: 4.419 distance: 58 - 59: 7.806 distance: 58 - 61: 6.202 distance: 59 - 60: 9.948 distance: 59 - 63: 11.638 distance: 61 - 62: 14.337 distance: 63 - 64: 4.685 distance: 64 - 65: 10.677 distance: 64 - 67: 5.832 distance: 65 - 66: 17.787 distance: 65 - 71: 16.550 distance: 67 - 68: 8.326 distance: 68 - 69: 8.501 distance: 68 - 70: 17.904 distance: 71 - 72: 7.409 distance: 72 - 73: 23.311 distance: 73 - 74: 28.040 distance: 73 - 75: 7.600 distance: 75 - 76: 4.044 distance: 76 - 79: 4.465 distance: 77 - 78: 3.711 distance: 79 - 80: 4.064 distance: 80 - 81: 5.807 distance: 80 - 82: 5.429 distance: 83 - 84: 4.375 distance: 87 - 88: 4.070