Starting phenix.real_space_refine on Fri Feb 6 09:41:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kqg_62504/02_2026/9kqg_62504_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kqg_62504/02_2026/9kqg_62504.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9kqg_62504/02_2026/9kqg_62504_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kqg_62504/02_2026/9kqg_62504_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9kqg_62504/02_2026/9kqg_62504.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kqg_62504/02_2026/9kqg_62504.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.090 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: 5 Type Number sf(0) Gaussians S 84 5.16 5 C 7549 2.51 5 N 2035 2.21 5 O 2189 1.98 5 H 11823 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23680 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 6391 Classifications: {'peptide': 403} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 19, 'TRANS': 379} Chain breaks: 1 Chain: "B" Number of atoms: 6285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 6285 Classifications: {'peptide': 396} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 19, 'TRANS': 373} Chain breaks: 1 Chain: "C" Number of atoms: 5386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 5386 Classifications: {'peptide': 347} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 333} Chain breaks: 5 Chain: "D" Number of atoms: 5594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 5594 Classifications: {'peptide': 360} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 344} Chain breaks: 7 Chain: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'D12': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'D12': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.42, per 1000 atoms: 0.19 Number of scatterers: 23680 At special positions: 0 Unit cell: (120.91, 114.49, 131.61, 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 84 16.00 O 2189 8.00 N 2035 7.00 C 7549 6.00 H 11823 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 102 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS B 102 " - pdb=" SG CYS B 141 " 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: 2.48 Conformation dependent library (CDL) restraints added in 971.6 milliseconds 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2818 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 14 sheets defined 38.8% alpha, 17.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'A' and resid 74 through 84 Processing helix chain 'A' and resid 105 through 117 Processing helix chain 'A' and resid 120 through 133 removed outlier: 3.637A pdb=" N VAL A 124 " --> pdb=" O ASN A 120 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ARG A 133 " --> pdb=" O ARG A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 178 removed outlier: 3.518A pdb=" N SER A 168 " --> pdb=" O LEU A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 182 No H-bonds generated for 'chain 'A' and resid 180 through 182' Processing helix chain 'A' and resid 199 through 209 Processing helix chain 'A' and resid 225 through 239 removed outlier: 3.624A pdb=" N ILE A 231 " --> pdb=" O GLY A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 258 removed outlier: 3.797A pdb=" N TYR A 258 " --> pdb=" O THR A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 273 Processing helix chain 'A' and resid 286 through 290 removed outlier: 4.331A pdb=" N SER A 290 " --> pdb=" O ARG A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 313 Processing helix chain 'A' and resid 331 through 352 removed outlier: 3.870A pdb=" N ILE A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) Proline residue: A 349 - end of helix Processing helix chain 'A' and resid 380 through 384 removed outlier: 3.514A pdb=" N GLN A 383 " --> pdb=" O ASP A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 405 removed outlier: 3.550A pdb=" N ILE A 398 " --> pdb=" O GLY A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 423 Processing helix chain 'A' and resid 425 through 427 No H-bonds generated for 'chain 'A' and resid 425 through 427' Processing helix chain 'A' and resid 428 through 440 removed outlier: 3.596A pdb=" N SER A 435 " --> pdb=" O TRP A 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 81 Processing helix chain 'B' and resid 105 through 117 Processing helix chain 'B' and resid 120 through 133 removed outlier: 3.741A pdb=" N ARG B 133 " --> pdb=" O ARG B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 148 removed outlier: 3.889A pdb=" N TYR B 148 " --> pdb=" O ALA B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 178 Processing helix chain 'B' and resid 180 through 184 Processing helix chain 'B' and resid 199 through 209 Processing helix chain 'B' and resid 225 through 241 Processing helix chain 'B' and resid 263 through 266 Processing helix chain 'B' and resid 267 through 273 Processing helix chain 'B' and resid 285 through 289 Processing helix chain 'B' and resid 307 through 312 Processing helix chain 'B' and resid 331 through 347 Processing helix chain 'B' and resid 347 through 352 Processing helix chain 'B' and resid 394 through 406 Processing helix chain 'B' and resid 413 through 423 Processing helix chain 'B' and resid 425 through 427 No H-bonds generated for 'chain 'B' and resid 425 through 427' Processing helix chain 'B' and resid 428 through 440 removed outlier: 3.549A pdb=" N TYR B 432 " --> pdb=" O SER B 428 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 38 Processing helix chain 'C' and resid 58 through 73 Proline residue: C 65 - end of helix removed outlier: 4.100A pdb=" N GLN C 68 " --> pdb=" O ARG C 64 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ASP C 71 " --> pdb=" O PHE C 67 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ILE C 72 " --> pdb=" O GLN C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 78 Processing helix chain 'C' and resid 111 through 118 Processing helix chain 'C' and resid 136 through 140 Processing helix chain 'C' and resid 167 through 184 Processing helix chain 'C' and resid 244 through 255 Processing helix chain 'C' and resid 268 through 282 Processing helix chain 'C' and resid 421 through 434 Processing helix chain 'D' and resid 5 through 9 Processing helix chain 'D' and resid 32 through 38 Processing helix chain 'D' and resid 51 through 55 Processing helix chain 'D' and resid 58 through 73 Proline residue: D 65 - end of helix removed outlier: 4.462A pdb=" N GLN D 68 " --> pdb=" O ARG D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 118 Processing helix chain 'D' and resid 123 through 127 removed outlier: 4.075A pdb=" N CYS D 126 " --> pdb=" O ARG D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 140 Processing helix chain 'D' and resid 167 through 184 Processing helix chain 'D' and resid 244 through 252 Processing helix chain 'D' and resid 268 through 281 Processing helix chain 'D' and resid 330 through 335 Processing helix chain 'D' and resid 367 through 371 removed outlier: 3.720A pdb=" N LEU D 371 " --> pdb=" O VAL D 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 419 through 435 Processing sheet with id=AA1, first strand: chain 'A' and resid 215 through 219 removed outlier: 7.006A pdb=" N ASP A 185 " --> pdb=" O LYS A 215 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N PHE A 217 " --> pdb=" O ASP A 185 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N LEU A 187 " --> pdb=" O PHE A 217 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N LEU A 219 " --> pdb=" O LEU A 187 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N VAL A 189 " --> pdb=" O LEU A 219 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N ILE A 184 " --> pdb=" O ASN A 245 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N VAL A 247 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ILE A 186 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N VAL A 249 " --> pdb=" O ILE A 186 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ILE A 188 " --> pdb=" O VAL A 249 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N THR A 251 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N ASN A 190 " --> pdb=" O THR A 251 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASP A 92 " --> pdb=" O LEU A 281 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N SER A 283 " --> pdb=" O LEU A 90 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N LEU A 90 " --> pdb=" O SER A 283 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N LEU A 296 " --> pdb=" O LYS A 466 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N LYS A 466 " --> pdb=" O LEU A 296 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 148 through 149 removed outlier: 4.304A pdb=" N LEU C 15 " --> pdb=" O ILE A 149 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ARG C 101 " --> pdb=" O VAL C 145 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N PHE C 147 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N VAL C 103 " --> pdb=" O PHE C 147 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N SER C 149 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ALA C 105 " --> pdb=" O SER C 149 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 314 through 318 Processing sheet with id=AA4, first strand: chain 'B' and resid 215 through 219 removed outlier: 6.478A pdb=" N ILE B 186 " --> pdb=" O VAL B 247 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N VAL B 249 " --> pdb=" O ILE B 186 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ILE B 188 " --> pdb=" O VAL B 249 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N THR B 251 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N ASN B 190 " --> pdb=" O THR B 251 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASP B 92 " --> pdb=" O LEU B 281 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N SER B 283 " --> pdb=" O LEU B 90 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N LEU B 90 " --> pdb=" O SER B 283 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N VAL B 88 " --> pdb=" O LEU B 296 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N LEU B 296 " --> pdb=" O LYS B 466 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N LYS B 466 " --> pdb=" O LEU B 296 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 314 through 318 Processing sheet with id=AA6, first strand: chain 'C' and resid 27 through 30 removed outlier: 3.977A pdb=" N GLN C 27 " --> pdb=" O CYS C 95 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 219 through 221 removed outlier: 3.972A pdb=" N ASP C 350 " --> pdb=" O VAL C 221 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 237 through 243 Processing sheet with id=AA9, first strand: chain 'C' and resid 294 through 296 Processing sheet with id=AB1, first strand: chain 'D' and resid 13 through 18 removed outlier: 3.973A pdb=" N ASP D 380 " --> pdb=" O PHE D 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 79 through 81 Processing sheet with id=AB3, first strand: chain 'D' and resid 219 through 221 removed outlier: 4.743A pdb=" N ASP D 350 " --> pdb=" O VAL D 221 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 237 through 243 Processing sheet with id=AB5, first strand: chain 'D' and resid 292 through 295 530 hydrogen bonds defined for protein. 1446 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: 4.71 Time building geometry restraints manager: 3.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 11793 1.03 - 1.23: 61 1.23 - 1.42: 4967 1.42 - 1.62: 6964 1.62 - 1.81: 134 Bond restraints: 23919 Sorted by residual: bond pdb=" C PRO A 144 " pdb=" N ALA A 145 " ideal model delta sigma weight residual 1.332 1.314 0.019 1.40e-02 5.10e+03 1.76e+00 bond pdb=" CB GLU A 410 " pdb=" CG GLU A 410 " ideal model delta sigma weight residual 1.520 1.554 -0.034 3.00e-02 1.11e+03 1.31e+00 bond pdb=" C VAL B 412 " pdb=" N GLU B 413 " ideal model delta sigma weight residual 1.332 1.319 0.013 1.40e-02 5.10e+03 9.23e-01 bond pdb=" CA ASN B 477 " pdb=" CB ASN B 477 " ideal model delta sigma weight residual 1.538 1.526 0.012 1.40e-02 5.10e+03 7.27e-01 bond pdb=" CB GLU B 492 " pdb=" CG GLU B 492 " ideal model delta sigma weight residual 1.520 1.545 -0.025 3.00e-02 1.11e+03 6.93e-01 ... (remaining 23914 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.40: 42193 1.40 - 2.80: 916 2.80 - 4.20: 103 4.20 - 5.60: 20 5.60 - 7.00: 5 Bond angle restraints: 43237 Sorted by residual: angle pdb=" N VAL A 412 " pdb=" CA VAL A 412 " pdb=" C VAL A 412 " ideal model delta sigma weight residual 112.29 108.71 3.58 9.40e-01 1.13e+00 1.45e+01 angle pdb=" N GLY C 387 " pdb=" CA GLY C 387 " pdb=" C GLY C 387 " ideal model delta sigma weight residual 115.08 110.63 4.45 1.64e+00 3.72e-01 7.35e+00 angle pdb=" CB GLU A 410 " pdb=" CG GLU A 410 " pdb=" CD GLU A 410 " ideal model delta sigma weight residual 112.60 116.97 -4.37 1.70e+00 3.46e-01 6.60e+00 angle pdb=" C GLY A 457 " pdb=" N PHE A 458 " pdb=" CA PHE A 458 " ideal model delta sigma weight residual 121.70 126.22 -4.52 1.80e+00 3.09e-01 6.32e+00 angle pdb=" N ASN B 477 " pdb=" CA ASN B 477 " pdb=" C ASN B 477 " ideal model delta sigma weight residual 108.13 110.35 -2.22 9.00e-01 1.23e+00 6.08e+00 ... (remaining 43232 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.27: 10147 17.27 - 34.53: 716 34.53 - 51.80: 309 51.80 - 69.06: 79 69.06 - 86.33: 12 Dihedral angle restraints: 11263 sinusoidal: 6161 harmonic: 5102 Sorted by residual: dihedral pdb=" CA ILE B 149 " pdb=" C ILE B 149 " pdb=" N PRO B 150 " pdb=" CA PRO B 150 " ideal model delta harmonic sigma weight residual 180.00 150.88 29.12 0 5.00e+00 4.00e-02 3.39e+01 dihedral pdb=" CA PRO C 419 " pdb=" C PRO C 419 " pdb=" N GLU C 420 " pdb=" CA GLU C 420 " ideal model delta harmonic sigma weight residual -180.00 -159.65 -20.35 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" CB CYS A 102 " pdb=" SG CYS A 102 " pdb=" SG CYS A 141 " pdb=" CB CYS A 141 " ideal model delta sinusoidal sigma weight residual -86.00 -118.26 32.26 1 1.00e+01 1.00e-02 1.48e+01 ... (remaining 11260 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1115 0.029 - 0.059: 489 0.059 - 0.088: 87 0.088 - 0.118: 101 0.118 - 0.147: 27 Chirality restraints: 1819 Sorted by residual: chirality pdb=" CA ILE B 280 " pdb=" N ILE B 280 " pdb=" C ILE B 280 " pdb=" CB ILE B 280 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.43e-01 chirality pdb=" CA ILE B 186 " pdb=" N ILE B 186 " pdb=" C ILE B 186 " pdb=" CB ILE B 186 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.19e-01 chirality pdb=" CA ILE A 280 " pdb=" N ILE A 280 " pdb=" C ILE A 280 " pdb=" CB ILE A 280 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.15e-01 ... (remaining 1816 not shown) Planarity restraints: 3513 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 129 " -0.142 9.50e-02 1.11e+02 4.76e-02 2.64e+00 pdb=" NE ARG B 129 " 0.011 2.00e-02 2.50e+03 pdb=" CZ ARG B 129 " -0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG B 129 " -0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG B 129 " -0.001 2.00e-02 2.50e+03 pdb="HH11 ARG B 129 " 0.003 2.00e-02 2.50e+03 pdb="HH12 ARG B 129 " 0.000 2.00e-02 2.50e+03 pdb="HH21 ARG B 129 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG B 129 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS B 180 " 0.022 5.00e-02 4.00e+02 3.33e-02 1.78e+00 pdb=" N PRO B 181 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO B 181 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 181 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN D 5 " -0.022 5.00e-02 4.00e+02 3.31e-02 1.75e+00 pdb=" N PRO D 6 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO D 6 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO D 6 " -0.019 5.00e-02 4.00e+02 ... (remaining 3510 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.38: 9905 2.38 - 2.94: 54860 2.94 - 3.49: 62013 3.49 - 4.05: 86844 4.05 - 4.60: 127154 Nonbonded interactions: 340776 Sorted by model distance: nonbonded pdb=" H LYS C 32 " pdb=" HG2 LYS C 32 " model vdw 1.831 2.270 nonbonded pdb=" HE2 PHE C 169 " pdb=" HE ARG C 301 " model vdw 1.844 2.100 nonbonded pdb=" HG3 ARG B 129 " pdb="HH11 ARG B 129 " model vdw 1.865 2.270 nonbonded pdb=" HD2 PHE A 388 " pdb=" HE3 TRP A 450 " model vdw 1.886 2.100 nonbonded pdb=" H THR A 101 " pdb=" H CYS A 102 " model vdw 1.890 2.100 ... (remaining 340771 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 74 through 353 or (resid 380 and (name N or name CA or nam \ e C or name O or name CB or name CG or name OD1 or name OD2 or name HA or name H \ B2 or name HB3)) or resid 381 through 495 or resid 501)) selection = chain 'B' } ncs_group { reference = (chain 'C' and (resid 12 through 83 or resid 88 through 187 or (resid 215 and (n \ ame N or name CA or name C or name O or name CB or name CG or name CD1 or name C \ D2 or name HA or name HB2 or name HB3 or name HG or name HD11 or name HD12 or na \ me HD13 or name HD21 or name HD22 or name HD23)) or resid 216 through 313 or res \ id 341 through 437)) selection = (chain 'D' and ((resid 12 and (name N or name CA or name C or name O or name HA2 \ or name HA3)) or resid 13 through 282 or resid 291 through 313 or resid 335 thr \ ough 399 or (resid 411 and (name N or name CA or name C or name O or name HA2 or \ name HA3)) or resid 412 through 437)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.810 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: 0.090 Extract box with map and model: 0.340 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 22.860 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 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 0.034 12098 Z= 0.132 Angle : 0.539 6.996 16340 Z= 0.277 Chirality : 0.041 0.147 1819 Planarity : 0.004 0.063 2096 Dihedral : 15.527 86.326 4501 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 2.38 % Allowed : 17.22 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.86 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.22), residues: 1470 helix: 0.32 (0.25), residues: 495 sheet: -0.25 (0.30), residues: 302 loop : -0.73 (0.24), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 129 TYR 0.007 0.001 TYR A 208 PHE 0.013 0.001 PHE D 351 TRP 0.013 0.001 TRP B 431 HIS 0.003 0.001 HIS C 41 Details of bonding type rmsd covalent geometry : bond 0.00295 (12096) covalent geometry : angle 0.53861 (16336) SS BOND : bond 0.00378 ( 2) SS BOND : angle 1.16630 ( 4) hydrogen bonds : bond 0.13171 ( 530) hydrogen bonds : angle 7.19985 ( 1446) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 185 time to evaluate : 0.493 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: 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: symmetry clash revert: symmetry clash REVERT: A 93 TYR cc_start: 0.8937 (p90) cc_final: 0.8645 (p90) REVERT: A 113 SER cc_start: 0.7911 (m) cc_final: 0.7410 (p) REVERT: A 243 ASN cc_start: 0.8574 (OUTLIER) cc_final: 0.8303 (t0) REVERT: A 289 ARG cc_start: 0.7935 (tmm-80) cc_final: 0.7702 (tmm-80) REVERT: A 400 GLU cc_start: 0.7036 (tt0) cc_final: 0.6758 (tt0) REVERT: A 485 ARG cc_start: 0.6998 (mtm180) cc_final: 0.6475 (ptm160) REVERT: B 81 PHE cc_start: 0.6979 (m-80) cc_final: 0.6452 (t80) REVERT: B 118 LYS cc_start: 0.7735 (OUTLIER) cc_final: 0.7389 (mttt) REVERT: B 215 LYS cc_start: 0.8411 (mmtt) cc_final: 0.8140 (mtmm) REVERT: B 285 ARG cc_start: 0.8306 (mtt180) cc_final: 0.8043 (mtt90) REVERT: B 312 ARG cc_start: 0.8132 (mmm-85) cc_final: 0.7602 (mmt180) REVERT: B 320 LYS cc_start: 0.8636 (mptp) cc_final: 0.7914 (mtmm) REVERT: B 473 THR cc_start: 0.8271 (m) cc_final: 0.7949 (p) REVERT: C 14 LYS cc_start: 0.6999 (mttt) cc_final: 0.6599 (mmtt) REVERT: C 64 ARG cc_start: 0.8038 (OUTLIER) cc_final: 0.7082 (mmp80) REVERT: C 68 GLN cc_start: 0.8550 (mt0) cc_final: 0.8137 (mp10) REVERT: C 237 LYS cc_start: 0.7270 (OUTLIER) cc_final: 0.6678 (mmpt) REVERT: C 353 MET cc_start: 0.7432 (tmm) cc_final: 0.7069 (tmm) REVERT: D 71 ASP cc_start: 0.8357 (t0) cc_final: 0.8094 (t70) REVERT: D 216 TYR cc_start: 0.6370 (m-80) cc_final: 0.5358 (m-80) REVERT: D 238 THR cc_start: 0.7556 (OUTLIER) cc_final: 0.7277 (p) REVERT: D 239 HIS cc_start: 0.6130 (t-90) cc_final: 0.5733 (t-90) REVERT: D 309 ASP cc_start: 0.6909 (p0) cc_final: 0.6447 (p0) outliers start: 31 outliers final: 20 residues processed: 203 average time/residue: 1.3813 time to fit residues: 299.6743 Evaluate side-chains 205 residues out of total 1301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 180 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 243 ASN Chi-restraints excluded: chain A residue 309 LYS Chi-restraints excluded: chain A residue 381 PHE Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 84 LYS Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain B residue 128 MET Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 64 ARG Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 237 LYS Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 269 PHE Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 384 SER Chi-restraints excluded: chain C residue 417 VAL Chi-restraints excluded: chain D residue 238 THR Chi-restraints excluded: chain D residue 293 THR Chi-restraints excluded: chain D residue 352 ILE Chi-restraints excluded: chain D residue 379 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 461 ASN ** 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 = 0.4197 r_free = 0.4197 target = 0.195294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.127529 restraints weight = 37871.061| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 2.45 r_work: 0.3243 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.0533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 12098 Z= 0.207 Angle : 0.537 5.887 16340 Z= 0.278 Chirality : 0.042 0.152 1819 Planarity : 0.004 0.047 2096 Dihedral : 7.030 56.757 1684 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.05 % Favored : 93.88 % Rotamer: Outliers : 3.23 % Allowed : 16.14 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.86 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.22), residues: 1470 helix: 0.69 (0.24), residues: 510 sheet: -0.28 (0.30), residues: 301 loop : -0.90 (0.24), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 129 TYR 0.010 0.001 TYR A 208 PHE 0.010 0.001 PHE A 454 TRP 0.016 0.001 TRP B 431 HIS 0.004 0.001 HIS A 298 Details of bonding type rmsd covalent geometry : bond 0.00492 (12096) covalent geometry : angle 0.53645 (16336) SS BOND : bond 0.00442 ( 2) SS BOND : angle 1.45095 ( 4) hydrogen bonds : bond 0.04206 ( 530) hydrogen bonds : angle 5.63817 ( 1446) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 188 time to evaluate : 0.667 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 TYR cc_start: 0.8983 (p90) cc_final: 0.8778 (p90) REVERT: A 113 SER cc_start: 0.7947 (m) cc_final: 0.7440 (p) REVERT: A 128 MET cc_start: 0.8258 (OUTLIER) cc_final: 0.8057 (ttm) REVERT: A 185 ASP cc_start: 0.8658 (m-30) cc_final: 0.8388 (m-30) REVERT: A 243 ASN cc_start: 0.8597 (OUTLIER) cc_final: 0.8298 (t0) REVERT: A 289 ARG cc_start: 0.8073 (tmm-80) cc_final: 0.7607 (tmm-80) REVERT: A 295 ARG cc_start: 0.8860 (OUTLIER) cc_final: 0.8305 (ttm170) REVERT: A 400 GLU cc_start: 0.7056 (tt0) cc_final: 0.6769 (tt0) REVERT: A 485 ARG cc_start: 0.7012 (mtm180) cc_final: 0.6339 (ptm160) REVERT: B 81 PHE cc_start: 0.6947 (m-80) cc_final: 0.6554 (t80) REVERT: B 215 LYS cc_start: 0.8468 (mmtt) cc_final: 0.8172 (mtmm) REVERT: B 285 ARG cc_start: 0.8234 (mtt180) cc_final: 0.8002 (mtt90) REVERT: B 312 ARG cc_start: 0.8134 (mmm-85) cc_final: 0.7485 (mmt180) REVERT: B 320 LYS cc_start: 0.8704 (mptp) cc_final: 0.7960 (mtmm) REVERT: B 473 THR cc_start: 0.8288 (m) cc_final: 0.7954 (p) REVERT: C 14 LYS cc_start: 0.7041 (mttt) cc_final: 0.6609 (mmtt) REVERT: C 353 MET cc_start: 0.7415 (tmm) cc_final: 0.7078 (tmm) REVERT: D 71 ASP cc_start: 0.8461 (t0) cc_final: 0.8134 (t0) REVERT: D 118 MET cc_start: 0.2886 (OUTLIER) cc_final: 0.2636 (ttm) REVERT: D 239 HIS cc_start: 0.6118 (t-90) cc_final: 0.5718 (t-90) REVERT: D 309 ASP cc_start: 0.7010 (p0) cc_final: 0.6556 (p0) outliers start: 42 outliers final: 23 residues processed: 216 average time/residue: 1.5408 time to fit residues: 356.4550 Evaluate side-chains 208 residues out of total 1301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 181 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 128 MET Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 243 ASN Chi-restraints excluded: chain A residue 266 MET Chi-restraints excluded: chain A residue 295 ARG Chi-restraints excluded: chain A residue 309 LYS Chi-restraints excluded: chain A residue 381 PHE Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain B residue 128 MET Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 403 LYS Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 269 PHE Chi-restraints excluded: chain C residue 302 GLU Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 417 VAL Chi-restraints excluded: chain D residue 118 MET Chi-restraints excluded: chain D residue 293 THR Chi-restraints excluded: chain D residue 352 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 98 optimal weight: 0.9990 chunk 82 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 106 optimal weight: 20.0000 chunk 64 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 75 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 124 optimal weight: 5.9990 chunk 41 optimal weight: 0.5980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 260 GLN B 461 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.197036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.122964 restraints weight = 37741.231| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 2.10 r_work: 0.3267 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.0639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12098 Z= 0.126 Angle : 0.496 5.862 16340 Z= 0.255 Chirality : 0.041 0.145 1819 Planarity : 0.004 0.045 2096 Dihedral : 6.221 55.923 1665 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 2.31 % Allowed : 17.68 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.86 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.22), residues: 1470 helix: 1.07 (0.24), residues: 506 sheet: -0.32 (0.30), residues: 301 loop : -0.81 (0.24), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 129 TYR 0.007 0.001 TYR A 208 PHE 0.009 0.001 PHE D 174 TRP 0.014 0.001 TRP B 431 HIS 0.002 0.001 HIS C 41 Details of bonding type rmsd covalent geometry : bond 0.00291 (12096) covalent geometry : angle 0.49536 (16336) SS BOND : bond 0.00289 ( 2) SS BOND : angle 1.16797 ( 4) hydrogen bonds : bond 0.03560 ( 530) hydrogen bonds : angle 5.34739 ( 1446) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 183 time to evaluate : 0.698 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 TYR cc_start: 0.8960 (p90) cc_final: 0.8750 (p90) REVERT: A 113 SER cc_start: 0.7969 (m) cc_final: 0.7505 (p) REVERT: A 185 ASP cc_start: 0.8599 (m-30) cc_final: 0.8259 (m-30) REVERT: A 289 ARG cc_start: 0.7988 (tmm-80) cc_final: 0.7680 (tmm-80) REVERT: A 400 GLU cc_start: 0.7058 (tt0) cc_final: 0.6786 (tt0) REVERT: A 485 ARG cc_start: 0.7061 (mtm180) cc_final: 0.6511 (ptm160) REVERT: B 81 PHE cc_start: 0.6888 (m-80) cc_final: 0.6519 (t80) REVERT: B 125 GLU cc_start: 0.7322 (tm-30) cc_final: 0.7046 (tm-30) REVERT: B 215 LYS cc_start: 0.8465 (mmtt) cc_final: 0.8128 (mtmm) REVERT: B 285 ARG cc_start: 0.8243 (mtt180) cc_final: 0.8008 (mtt90) REVERT: B 312 ARG cc_start: 0.8102 (mmm-85) cc_final: 0.7405 (mmt180) REVERT: B 320 LYS cc_start: 0.8630 (mptp) cc_final: 0.7897 (mtmm) REVERT: B 473 THR cc_start: 0.8283 (m) cc_final: 0.7948 (p) REVERT: C 14 LYS cc_start: 0.7093 (mttt) cc_final: 0.6618 (mmtt) REVERT: C 353 MET cc_start: 0.7453 (tmm) cc_final: 0.7119 (tmm) REVERT: D 118 MET cc_start: 0.2795 (OUTLIER) cc_final: 0.2574 (ttm) REVERT: D 239 HIS cc_start: 0.6054 (t-90) cc_final: 0.5700 (t-90) REVERT: D 309 ASP cc_start: 0.6948 (p0) cc_final: 0.6483 (p0) REVERT: D 310 MET cc_start: 0.7931 (OUTLIER) cc_final: 0.7591 (ptp) outliers start: 30 outliers final: 17 residues processed: 204 average time/residue: 1.5614 time to fit residues: 341.0701 Evaluate side-chains 197 residues out of total 1301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 178 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 381 PHE Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain B residue 84 LYS Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain B residue 128 MET Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 254 ASN Chi-restraints excluded: chain C residue 302 GLU Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 417 VAL Chi-restraints excluded: chain D residue 118 MET Chi-restraints excluded: chain D residue 310 MET Chi-restraints excluded: chain D residue 352 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 14 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 129 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 82 optimal weight: 5.9990 chunk 67 optimal weight: 0.0370 chunk 131 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 139 optimal weight: 20.0000 chunk 143 optimal weight: 4.9990 chunk 84 optimal weight: 4.9990 overall best weight: 1.1062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN B 260 GLN B 420 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.196607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.122577 restraints weight = 37911.541| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 2.10 r_work: 0.3267 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.0825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12098 Z= 0.147 Angle : 0.497 5.789 16340 Z= 0.256 Chirality : 0.041 0.146 1819 Planarity : 0.004 0.064 2096 Dihedral : 5.693 58.532 1653 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 3.07 % Allowed : 17.14 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.86 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.22), residues: 1470 helix: 1.17 (0.24), residues: 506 sheet: -0.37 (0.30), residues: 293 loop : -0.79 (0.24), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 416 TYR 0.009 0.001 TYR A 208 PHE 0.012 0.001 PHE D 174 TRP 0.014 0.001 TRP B 431 HIS 0.003 0.001 HIS A 298 Details of bonding type rmsd covalent geometry : bond 0.00349 (12096) covalent geometry : angle 0.49707 (16336) SS BOND : bond 0.00323 ( 2) SS BOND : angle 1.23515 ( 4) hydrogen bonds : bond 0.03391 ( 530) hydrogen bonds : angle 5.18952 ( 1446) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 186 time to evaluate : 0.665 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 SER cc_start: 0.7958 (m) cc_final: 0.7481 (p) REVERT: A 125 GLU cc_start: 0.7528 (OUTLIER) cc_final: 0.7309 (tt0) REVERT: A 185 ASP cc_start: 0.8643 (m-30) cc_final: 0.8386 (m-30) REVERT: A 243 ASN cc_start: 0.8570 (OUTLIER) cc_final: 0.8305 (t0) REVERT: A 289 ARG cc_start: 0.7969 (tmm-80) cc_final: 0.7682 (tmm-80) REVERT: A 400 GLU cc_start: 0.7076 (tt0) cc_final: 0.6792 (tt0) REVERT: A 485 ARG cc_start: 0.7077 (mtm180) cc_final: 0.6519 (ptm160) REVERT: B 81 PHE cc_start: 0.6900 (m-80) cc_final: 0.6550 (t80) REVERT: B 215 LYS cc_start: 0.8482 (mmtt) cc_final: 0.8148 (mtmm) REVERT: B 285 ARG cc_start: 0.8261 (mtt180) cc_final: 0.8022 (mtt90) REVERT: B 312 ARG cc_start: 0.8012 (mmm-85) cc_final: 0.7419 (mmt180) REVERT: B 320 LYS cc_start: 0.8656 (mptp) cc_final: 0.7897 (mtmm) REVERT: B 473 THR cc_start: 0.8285 (m) cc_final: 0.7954 (p) REVERT: C 14 LYS cc_start: 0.7107 (mttt) cc_final: 0.6610 (mmtt) REVERT: C 237 LYS cc_start: 0.7370 (OUTLIER) cc_final: 0.6829 (mmtt) REVERT: D 118 MET cc_start: 0.2801 (OUTLIER) cc_final: 0.2595 (ttm) REVERT: D 182 MET cc_start: 0.7441 (ttt) cc_final: 0.6975 (ttt) REVERT: D 238 THR cc_start: 0.7505 (OUTLIER) cc_final: 0.7228 (p) REVERT: D 239 HIS cc_start: 0.6030 (t-90) cc_final: 0.5519 (t-90) REVERT: D 309 ASP cc_start: 0.6915 (p0) cc_final: 0.6434 (p0) outliers start: 40 outliers final: 23 residues processed: 213 average time/residue: 1.5927 time to fit residues: 362.6267 Evaluate side-chains 204 residues out of total 1301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 176 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 243 ASN Chi-restraints excluded: chain A residue 266 MET Chi-restraints excluded: chain A residue 309 LYS Chi-restraints excluded: chain A residue 381 PHE Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain B residue 128 MET Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 403 LYS Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 237 LYS Chi-restraints excluded: chain C residue 254 ASN Chi-restraints excluded: chain C residue 269 PHE Chi-restraints excluded: chain C residue 302 GLU Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 417 VAL Chi-restraints excluded: chain D residue 118 MET Chi-restraints excluded: chain D residue 238 THR Chi-restraints excluded: chain D residue 352 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 39 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 102 optimal weight: 9.9990 chunk 1 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 136 optimal weight: 10.0000 chunk 64 optimal weight: 2.9990 chunk 131 optimal weight: 9.9990 chunk 16 optimal weight: 0.5980 chunk 139 optimal weight: 20.0000 chunk 14 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 260 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.196600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.130662 restraints weight = 37853.811| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 2.19 r_work: 0.3288 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.0908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12098 Z= 0.141 Angle : 0.497 6.559 16340 Z= 0.255 Chirality : 0.041 0.146 1819 Planarity : 0.004 0.051 2096 Dihedral : 5.680 58.815 1653 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 2.92 % Allowed : 17.14 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.86 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.22), residues: 1470 helix: 1.21 (0.24), residues: 508 sheet: -0.33 (0.29), residues: 301 loop : -0.81 (0.24), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 416 TYR 0.008 0.001 TYR A 208 PHE 0.010 0.001 PHE D 174 TRP 0.014 0.001 TRP B 431 HIS 0.003 0.001 HIS A 298 Details of bonding type rmsd covalent geometry : bond 0.00335 (12096) covalent geometry : angle 0.49675 (16336) SS BOND : bond 0.00303 ( 2) SS BOND : angle 1.24141 ( 4) hydrogen bonds : bond 0.03259 ( 530) hydrogen bonds : angle 5.10507 ( 1446) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 180 time to evaluate : 0.662 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: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.8347 (mmp) cc_final: 0.7973 (mmm) REVERT: A 113 SER cc_start: 0.7947 (m) cc_final: 0.7453 (p) REVERT: A 125 GLU cc_start: 0.7505 (OUTLIER) cc_final: 0.7282 (tt0) REVERT: A 185 ASP cc_start: 0.8632 (m-30) cc_final: 0.8379 (m-30) REVERT: A 243 ASN cc_start: 0.8550 (OUTLIER) cc_final: 0.8279 (t0) REVERT: A 289 ARG cc_start: 0.7928 (tmm-80) cc_final: 0.7629 (tmm-80) REVERT: A 400 GLU cc_start: 0.7100 (OUTLIER) cc_final: 0.6822 (tt0) REVERT: A 485 ARG cc_start: 0.6951 (mtm180) cc_final: 0.6495 (ptm160) REVERT: B 81 PHE cc_start: 0.6838 (m-80) cc_final: 0.6496 (t80) REVERT: B 215 LYS cc_start: 0.8490 (mmtt) cc_final: 0.8153 (mtmm) REVERT: B 285 ARG cc_start: 0.8225 (mtt180) cc_final: 0.7976 (mtt90) REVERT: B 312 ARG cc_start: 0.8169 (mmm-85) cc_final: 0.7495 (mmt180) REVERT: B 473 THR cc_start: 0.8210 (m) cc_final: 0.7897 (p) REVERT: C 14 LYS cc_start: 0.7021 (mttt) cc_final: 0.6557 (mmtt) REVERT: D 182 MET cc_start: 0.7453 (ttt) cc_final: 0.6999 (ttt) REVERT: D 216 TYR cc_start: 0.6357 (m-80) cc_final: 0.5295 (m-80) REVERT: D 238 THR cc_start: 0.7387 (OUTLIER) cc_final: 0.7091 (p) REVERT: D 239 HIS cc_start: 0.6001 (t-90) cc_final: 0.5523 (t-90) REVERT: D 309 ASP cc_start: 0.6812 (p0) cc_final: 0.6322 (p0) outliers start: 38 outliers final: 21 residues processed: 204 average time/residue: 1.6641 time to fit residues: 362.6156 Evaluate side-chains 199 residues out of total 1301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 174 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 211 ARG Chi-restraints excluded: chain A residue 243 ASN Chi-restraints excluded: chain A residue 309 LYS Chi-restraints excluded: chain A residue 381 PHE Chi-restraints excluded: chain A residue 400 GLU Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain B residue 128 MET Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 403 LYS Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 254 ASN Chi-restraints excluded: chain C residue 269 PHE Chi-restraints excluded: chain C residue 302 GLU Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 417 VAL Chi-restraints excluded: chain D residue 238 THR Chi-restraints excluded: chain D residue 293 THR Chi-restraints excluded: chain D residue 352 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 20 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 136 optimal weight: 9.9990 chunk 99 optimal weight: 9.9990 chunk 115 optimal weight: 6.9990 chunk 117 optimal weight: 4.9990 chunk 95 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 chunk 109 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 98 optimal weight: 10.0000 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 GLN ** A 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 260 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.193582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.119170 restraints weight = 38073.253| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 2.09 r_work: 0.3211 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.1211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 12098 Z= 0.267 Angle : 0.568 6.034 16340 Z= 0.296 Chirality : 0.044 0.163 1819 Planarity : 0.005 0.087 2096 Dihedral : 5.790 58.423 1650 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.12 % Favored : 93.81 % Rotamer: Outliers : 3.15 % Allowed : 18.06 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.86 % Cis-general : 0.14 % Twisted Proline : 1.41 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.22), residues: 1470 helix: 0.81 (0.24), residues: 512 sheet: -0.40 (0.31), residues: 282 loop : -0.91 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 416 TYR 0.012 0.002 TYR A 208 PHE 0.015 0.002 PHE C 174 TRP 0.018 0.001 TRP B 431 HIS 0.005 0.001 HIS A 420 Details of bonding type rmsd covalent geometry : bond 0.00644 (12096) covalent geometry : angle 0.56727 (16336) SS BOND : bond 0.00533 ( 2) SS BOND : angle 1.66933 ( 4) hydrogen bonds : bond 0.03979 ( 530) hydrogen bonds : angle 5.29198 ( 1446) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 178 time to evaluate : 0.687 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: symmetry clash REVERT: A 110 MET cc_start: 0.8471 (mmp) cc_final: 0.8080 (mmm) REVERT: A 113 SER cc_start: 0.8061 (m) cc_final: 0.7554 (p) REVERT: A 185 ASP cc_start: 0.8698 (m-30) cc_final: 0.8451 (m-30) REVERT: A 289 ARG cc_start: 0.8119 (tmm-80) cc_final: 0.7845 (tmm-80) REVERT: A 295 ARG cc_start: 0.8831 (OUTLIER) cc_final: 0.8253 (ttm170) REVERT: A 400 GLU cc_start: 0.7154 (OUTLIER) cc_final: 0.6877 (tt0) REVERT: A 485 ARG cc_start: 0.7029 (mtm180) cc_final: 0.6434 (ptm160) REVERT: B 81 PHE cc_start: 0.6907 (m-80) cc_final: 0.6542 (t80) REVERT: B 215 LYS cc_start: 0.8557 (mmtt) cc_final: 0.8251 (mtmm) REVERT: B 285 ARG cc_start: 0.8245 (mtt180) cc_final: 0.8013 (mtt90) REVERT: B 312 ARG cc_start: 0.8127 (mmm-85) cc_final: 0.7566 (mmt180) REVERT: B 473 THR cc_start: 0.8214 (m) cc_final: 0.7923 (p) REVERT: C 14 LYS cc_start: 0.7100 (mttt) cc_final: 0.6641 (mmtt) REVERT: C 66 MET cc_start: 0.8522 (mtp) cc_final: 0.8284 (tpp) REVERT: C 353 MET cc_start: 0.7577 (tmm) cc_final: 0.7166 (tmm) REVERT: D 216 TYR cc_start: 0.6533 (m-80) cc_final: 0.5336 (m-80) REVERT: D 238 THR cc_start: 0.7568 (OUTLIER) cc_final: 0.7281 (p) REVERT: D 239 HIS cc_start: 0.6155 (t-90) cc_final: 0.5722 (t-90) REVERT: D 309 ASP cc_start: 0.6987 (p0) cc_final: 0.6510 (p0) outliers start: 41 outliers final: 27 residues processed: 205 average time/residue: 1.5881 time to fit residues: 348.7936 Evaluate side-chains 204 residues out of total 1301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 174 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 211 ARG Chi-restraints excluded: chain A residue 243 ASN Chi-restraints excluded: chain A residue 295 ARG Chi-restraints excluded: chain A residue 309 LYS Chi-restraints excluded: chain A residue 381 PHE Chi-restraints excluded: chain A residue 400 GLU Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain B residue 128 MET Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 257 ASN Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 254 ASN Chi-restraints excluded: chain C residue 269 PHE Chi-restraints excluded: chain C residue 302 GLU Chi-restraints excluded: chain C residue 417 VAL Chi-restraints excluded: chain D residue 238 THR Chi-restraints excluded: chain D residue 293 THR Chi-restraints excluded: chain D residue 345 LEU Chi-restraints excluded: chain D residue 352 ILE Chi-restraints excluded: chain D residue 359 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 85 optimal weight: 0.7980 chunk 50 optimal weight: 0.9980 chunk 135 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 40 optimal weight: 7.9990 chunk 21 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 42 optimal weight: 0.3980 chunk 0 optimal weight: 4.9990 chunk 58 optimal weight: 0.1980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 260 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.196027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.129401 restraints weight = 37771.932| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 2.41 r_work: 0.3268 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.1230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12098 Z= 0.119 Angle : 0.505 6.157 16340 Z= 0.259 Chirality : 0.041 0.146 1819 Planarity : 0.004 0.067 2096 Dihedral : 5.516 57.677 1650 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.17 % Favored : 94.76 % Rotamer: Outliers : 2.54 % Allowed : 18.75 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.86 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.22), residues: 1470 helix: 1.20 (0.24), residues: 508 sheet: -0.36 (0.30), residues: 291 loop : -0.81 (0.24), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 416 TYR 0.007 0.001 TYR B 96 PHE 0.009 0.001 PHE A 454 TRP 0.015 0.001 TRP B 431 HIS 0.002 0.001 HIS A 298 Details of bonding type rmsd covalent geometry : bond 0.00277 (12096) covalent geometry : angle 0.50493 (16336) SS BOND : bond 0.00286 ( 2) SS BOND : angle 1.22268 ( 4) hydrogen bonds : bond 0.03159 ( 530) hydrogen bonds : angle 5.05759 ( 1446) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 184 time to evaluate : 0.682 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.8285 (mmp) cc_final: 0.7866 (mmm) REVERT: A 113 SER cc_start: 0.7954 (m) cc_final: 0.7449 (p) REVERT: A 185 ASP cc_start: 0.8644 (m-30) cc_final: 0.8414 (m-30) REVERT: A 289 ARG cc_start: 0.7992 (tmm-80) cc_final: 0.7684 (tmm-80) REVERT: A 295 ARG cc_start: 0.8832 (OUTLIER) cc_final: 0.8275 (ttm170) REVERT: A 400 GLU cc_start: 0.7109 (OUTLIER) cc_final: 0.6835 (tt0) REVERT: A 485 ARG cc_start: 0.7065 (mtm180) cc_final: 0.6576 (ptm160) REVERT: B 81 PHE cc_start: 0.6810 (m-80) cc_final: 0.6445 (t80) REVERT: B 215 LYS cc_start: 0.8513 (mmtt) cc_final: 0.8176 (mtmm) REVERT: B 285 ARG cc_start: 0.8201 (mtt180) cc_final: 0.7953 (mtt90) REVERT: B 312 ARG cc_start: 0.8091 (mmm-85) cc_final: 0.7501 (mmt180) REVERT: B 397 VAL cc_start: 0.7896 (m) cc_final: 0.7679 (p) REVERT: B 473 THR cc_start: 0.8206 (m) cc_final: 0.7906 (p) REVERT: C 14 LYS cc_start: 0.7170 (mttt) cc_final: 0.6745 (mmtt) REVERT: C 296 ARG cc_start: 0.7547 (pmm-80) cc_final: 0.7065 (pmm-80) REVERT: C 353 MET cc_start: 0.7595 (tmm) cc_final: 0.7226 (tmm) REVERT: D 182 MET cc_start: 0.7472 (ttt) cc_final: 0.7048 (ttt) REVERT: D 216 TYR cc_start: 0.6518 (m-80) cc_final: 0.5355 (m-80) REVERT: D 238 THR cc_start: 0.7447 (OUTLIER) cc_final: 0.7158 (p) REVERT: D 239 HIS cc_start: 0.6116 (t-90) cc_final: 0.5767 (t-90) REVERT: D 309 ASP cc_start: 0.6912 (p0) cc_final: 0.6407 (p0) outliers start: 33 outliers final: 23 residues processed: 208 average time/residue: 1.5820 time to fit residues: 352.5988 Evaluate side-chains 204 residues out of total 1301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 178 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 211 ARG Chi-restraints excluded: chain A residue 243 ASN Chi-restraints excluded: chain A residue 295 ARG Chi-restraints excluded: chain A residue 309 LYS Chi-restraints excluded: chain A residue 381 PHE Chi-restraints excluded: chain A residue 400 GLU Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain B residue 128 MET Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 254 ASN Chi-restraints excluded: chain C residue 269 PHE Chi-restraints excluded: chain C residue 302 GLU Chi-restraints excluded: chain C residue 352 ILE Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 417 VAL Chi-restraints excluded: chain D residue 238 THR Chi-restraints excluded: chain D residue 352 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 83 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 102 optimal weight: 20.0000 chunk 137 optimal weight: 9.9990 chunk 11 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 131 optimal weight: 6.9990 chunk 50 optimal weight: 0.7980 chunk 3 optimal weight: 0.5980 chunk 129 optimal weight: 0.9980 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 461 ASN ** 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 = 0.4277 r_free = 0.4277 target = 0.199915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.133527 restraints weight = 37336.590| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 2.25 r_work: 0.3307 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.1270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12098 Z= 0.130 Angle : 0.509 6.234 16340 Z= 0.260 Chirality : 0.041 0.144 1819 Planarity : 0.004 0.096 2096 Dihedral : 5.415 56.619 1650 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 2.46 % Allowed : 18.91 % Favored : 78.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.86 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.22), residues: 1470 helix: 1.32 (0.24), residues: 508 sheet: -0.32 (0.30), residues: 291 loop : -0.78 (0.24), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 416 TYR 0.010 0.001 TYR A 259 PHE 0.009 0.001 PHE A 454 TRP 0.014 0.001 TRP B 431 HIS 0.003 0.001 HIS A 298 Details of bonding type rmsd covalent geometry : bond 0.00308 (12096) covalent geometry : angle 0.50852 (16336) SS BOND : bond 0.00293 ( 2) SS BOND : angle 1.18912 ( 4) hydrogen bonds : bond 0.03107 ( 530) hydrogen bonds : angle 4.98149 ( 1446) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 182 time to evaluate : 0.723 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: symmetry clash REVERT: A 110 MET cc_start: 0.8387 (mmp) cc_final: 0.8007 (mmm) REVERT: A 113 SER cc_start: 0.8089 (m) cc_final: 0.7615 (p) REVERT: A 114 ARG cc_start: 0.7886 (mtp85) cc_final: 0.7684 (mtp85) REVERT: A 185 ASP cc_start: 0.8616 (m-30) cc_final: 0.8371 (m-30) REVERT: A 243 ASN cc_start: 0.8637 (OUTLIER) cc_final: 0.8365 (t0) REVERT: A 289 ARG cc_start: 0.8080 (tmm-80) cc_final: 0.7820 (tmm-80) REVERT: A 295 ARG cc_start: 0.8814 (OUTLIER) cc_final: 0.8240 (ttm170) REVERT: A 400 GLU cc_start: 0.7168 (OUTLIER) cc_final: 0.6892 (tt0) REVERT: A 485 ARG cc_start: 0.7144 (mtm180) cc_final: 0.6726 (ptm160) REVERT: B 81 PHE cc_start: 0.6838 (m-80) cc_final: 0.6509 (t80) REVERT: B 215 LYS cc_start: 0.8617 (mmtt) cc_final: 0.8353 (mtmm) REVERT: B 285 ARG cc_start: 0.8389 (mtt180) cc_final: 0.8152 (mtt90) REVERT: B 312 ARG cc_start: 0.8174 (mmm-85) cc_final: 0.7653 (mmt180) REVERT: B 397 VAL cc_start: 0.8011 (m) cc_final: 0.7811 (p) REVERT: B 473 THR cc_start: 0.8263 (m) cc_final: 0.8045 (p) REVERT: C 14 LYS cc_start: 0.7384 (mttt) cc_final: 0.6975 (mmtt) REVERT: C 296 ARG cc_start: 0.7487 (pmm-80) cc_final: 0.7030 (pmm-80) REVERT: C 353 MET cc_start: 0.7627 (tmm) cc_final: 0.7241 (tmm) REVERT: D 182 MET cc_start: 0.7548 (ttt) cc_final: 0.7144 (ttt) REVERT: D 216 TYR cc_start: 0.6543 (m-80) cc_final: 0.5340 (m-80) REVERT: D 238 THR cc_start: 0.7478 (OUTLIER) cc_final: 0.7180 (p) REVERT: D 239 HIS cc_start: 0.6244 (t-90) cc_final: 0.5900 (t-90) REVERT: D 309 ASP cc_start: 0.6528 (p0) cc_final: 0.5691 (p0) REVERT: D 395 LEU cc_start: 0.6995 (OUTLIER) cc_final: 0.6711 (tm) outliers start: 32 outliers final: 22 residues processed: 207 average time/residue: 1.6178 time to fit residues: 358.2882 Evaluate side-chains 205 residues out of total 1301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 178 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 211 ARG Chi-restraints excluded: chain A residue 243 ASN Chi-restraints excluded: chain A residue 295 ARG Chi-restraints excluded: chain A residue 309 LYS Chi-restraints excluded: chain A residue 381 PHE Chi-restraints excluded: chain A residue 400 GLU Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 128 MET Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 262 ASN Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 254 ASN Chi-restraints excluded: chain C residue 269 PHE Chi-restraints excluded: chain C residue 352 ILE Chi-restraints excluded: chain C residue 380 ASP Chi-restraints excluded: chain C residue 417 VAL Chi-restraints excluded: chain D residue 238 THR Chi-restraints excluded: chain D residue 293 THR Chi-restraints excluded: chain D residue 352 ILE Chi-restraints excluded: chain D residue 395 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.1421 > 50: distance: 59 - 73: 33.617 distance: 73 - 74: 8.955 distance: 73 - 79: 51.898 distance: 74 - 75: 10.963 distance: 74 - 77: 30.405 distance: 74 - 80: 41.868 distance: 75 - 76: 17.757 distance: 75 - 84: 31.556 distance: 77 - 81: 17.169 distance: 77 - 82: 34.269 distance: 78 - 83: 50.412 distance: 84 - 85: 41.968 distance: 84 - 95: 61.610 distance: 84 - 283: 29.834 distance: 85 - 86: 40.704 distance: 85 - 88: 4.941 distance: 85 - 96: 35.015 distance: 87 - 280: 32.416 distance: 88 - 97: 39.173 distance: 88 - 98: 15.022 distance: 89 - 90: 5.662 distance: 89 - 99: 28.440 distance: 90 - 91: 4.726 distance: 90 - 101: 6.370 distance: 90 - 102: 5.201 distance: 91 - 103: 40.704 distance: 93 - 104: 39.601 distance: 93 - 105: 11.228 distance: 94 - 106: 4.123 distance: 108 - 109: 55.382 distance: 109 - 110: 36.500 distance: 109 - 112: 38.736 distance: 110 - 111: 12.165 distance: 110 - 129: 32.016 distance: 112 - 113: 12.517 distance: 112 - 122: 52.930 distance: 112 - 123: 35.179 distance: 113 - 114: 29.986 distance: 113 - 115: 22.820 distance: 114 - 116: 18.010 distance: 115 - 117: 25.695 distance: 116 - 126: 40.344 distance: 117 - 118: 14.822 distance: 117 - 127: 14.810 distance: 129 - 130: 39.054 distance: 130 - 133: 56.353 distance: 130 - 138: 40.637 distance: 131 - 132: 38.758 distance: 131 - 143: 39.648 distance: 133 - 134: 40.778 distance: 133 - 139: 39.209 distance: 134 - 135: 38.998 distance: 134 - 136: 57.031 distance: 136 - 141: 39.663 distance: 143 - 144: 6.099 distance: 143 - 147: 39.909 distance: 144 - 145: 41.094 distance: 144 - 148: 35.565 distance: 144 - 149: 35.944 distance: 145 - 146: 44.989 distance: 145 - 150: 33.187 distance: 150 - 151: 41.941 distance: 150 - 159: 66.725 distance: 151 - 152: 50.511 distance: 151 - 154: 41.215 distance: 151 - 160: 61.716 distance: 152 - 167: 56.739 distance: 154 - 155: 13.863 distance: 154 - 161: 13.611 distance: 154 - 162: 12.309 distance: 155 - 156: 32.279 distance: 156 - 157: 7.835 distance: 156 - 158: 11.297 distance: 158 - 165: 39.410 distance: 158 - 166: 10.472 distance: 167 - 178: 40.090 distance: 168 - 169: 56.281 distance: 168 - 171: 7.119 distance: 169 - 170: 41.220 distance: 169 - 191: 36.683 distance: 171 - 172: 41.146 distance: 171 - 180: 39.997 distance: 171 - 181: 34.549 distance: 172 - 173: 45.021 distance: 172 - 182: 56.569 distance: 172 - 183: 49.365 distance: 173 - 174: 19.191 distance: 173 - 184: 17.532 distance: 173 - 185: 22.423 distance: 174 - 175: 52.406 distance: 175 - 177: 16.586 distance: 177 - 189: 23.613 distance: 177 - 190: 20.866 distance: 191 - 192: 39.165 distance: 191 - 200: 40.385 distance: 193 - 194: 56.876 distance: 193 - 206: 27.163 distance: 195 - 202: 3.527 distance: 196 - 205: 56.729 distance: 197 - 199: 39.083 distance: 206 - 207: 26.688 distance: 206 - 214: 13.309 distance: 208 - 209: 41.048 distance: 208 - 220: 38.828 distance: 210 - 211: 15.899 distance: 210 - 216: 69.295 distance: 211 - 212: 40.613 distance: 211 - 213: 46.870 distance: 213 - 218: 40.624 distance: 213 - 219: 39.221 distance: 220 - 221: 20.789 distance: 221 - 222: 36.827 distance: 221 - 224: 45.729 distance: 221 - 230: 18.966 distance: 222 - 223: 22.925 distance: 222 - 235: 30.228 distance: 224 - 225: 5.553 distance: 224 - 231: 9.100 distance: 224 - 232: 3.104 distance: 225 - 226: 22.778 distance: 225 - 233: 15.945 distance: 225 - 234: 17.243 distance: 226 - 227: 13.429