Starting phenix.real_space_refine on Sat Jun 14 14:41:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xz6_33526/06_2025/7xz6_33526_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xz6_33526/06_2025/7xz6_33526.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xz6_33526/06_2025/7xz6_33526.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xz6_33526/06_2025/7xz6_33526.map" model { file = "/net/cci-nas-00/data/ceres_data/7xz6_33526/06_2025/7xz6_33526_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xz6_33526/06_2025/7xz6_33526_trim.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.007 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: 6 Type Number sf(0) Gaussians S 57 5.16 5 C 5238 2.51 5 N 1437 2.21 5 O 1533 1.98 5 F 1 1.80 5 H 8192 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 66 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 16458 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 3910 Classifications: {'peptide': 237} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 230} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 5109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 5109 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 885 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 1909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1909 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "R" Number of atoms: 4609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 4609 Classifications: {'peptide': 292} Link IDs: {'PTRANS': 9, 'TRANS': 282} Chain breaks: 1 Chain: "R" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 36 Unusual residues: {'I7J': 1} Classifications: {'undetermined': 1, 'water': 1} Link IDs: {None: 1} Time building chain proxies: 7.51, per 1000 atoms: 0.46 Number of scatterers: 16458 At special positions: 0 Unit cell: (100.32, 98.23, 115.995, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 57 16.00 F 1 9.00 O 1533 8.00 N 1437 7.00 C 5238 6.00 H 8192 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 78 " - pdb=" SG CYS R 155 " distance=2.03 Simple disulfide: pdb=" SG CYS R 251 " - pdb=" SG CYS R 254 " distance=2.05 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: 4.06 Conformation dependent library (CDL) restraints added in 1.3 seconds 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1970 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 10 sheets defined 45.2% alpha, 20.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.36 Creating SS restraints... Processing helix chain 'A' and resid 9 through 39 Processing helix chain 'A' and resid 52 through 62 Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.559A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 279 Processing helix chain 'A' and resid 280 through 283 removed outlier: 3.592A pdb=" N ARG A 283 " --> pdb=" O LYS A 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 280 through 283' Processing helix chain 'A' and resid 293 through 303 Processing helix chain 'A' and resid 307 through 312 removed outlier: 4.238A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 316 Processing helix chain 'A' and resid 331 through 353 removed outlier: 4.469A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N SER A 349 " --> pdb=" O PHE A 345 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N GLY A 353 " --> pdb=" O SER A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 391 removed outlier: 4.313A pdb=" N ARG A 373 " --> pdb=" O THR A 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 7 through 24 removed outlier: 4.271A pdb=" N ALA G 12 " --> pdb=" O SER G 8 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'R' and resid 2 through 36 Processing helix chain 'R' and resid 39 through 66 removed outlier: 3.690A pdb=" N PHE R 43 " --> pdb=" O VAL R 39 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU R 62 " --> pdb=" O ILE R 58 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N THR R 63 " --> pdb=" O SER R 59 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N ASP R 64 " --> pdb=" O GLY R 60 " (cutoff:3.500A) Processing helix chain 'R' and resid 71 through 73 No H-bonds generated for 'chain 'R' and resid 71 through 73' Processing helix chain 'R' and resid 74 through 109 Processing helix chain 'R' and resid 109 through 117 removed outlier: 3.623A pdb=" N LEU R 114 " --> pdb=" O PRO R 110 " (cutoff:3.500A) Processing helix chain 'R' and resid 118 through 143 Proline residue: R 140 - end of helix Processing helix chain 'R' and resid 156 through 161 Processing helix chain 'R' and resid 162 through 172 removed outlier: 3.966A pdb=" N VAL R 166 " --> pdb=" O HIS R 162 " (cutoff:3.500A) Processing helix chain 'R' and resid 173 through 210 Processing helix chain 'R' and resid 220 through 251 removed outlier: 4.065A pdb=" N LEU R 224 " --> pdb=" O ASP R 220 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N TRP R 238 " --> pdb=" O PHE R 234 " (cutoff:3.500A) Proline residue: R 240 - end of helix Processing helix chain 'R' and resid 256 through 263 Processing helix chain 'R' and resid 263 through 280 removed outlier: 3.823A pdb=" N LEU R 267 " --> pdb=" O TYR R 263 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLY R 268 " --> pdb=" O LEU R 264 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N SER R 272 " --> pdb=" O GLY R 268 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU R 273 " --> pdb=" O VAL R 269 " (cutoff:3.500A) Proline residue: R 276 - end of helix Processing helix chain 'R' and resid 283 through 299 Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214 removed outlier: 9.239A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 3.736A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASN B 340 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.983A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.443A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.749A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 189 through 192 removed outlier: 3.929A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLY B 202 " --> pdb=" O SER B 189 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.730A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.565A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.172A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) 458 hydrogen bonds defined for protein. 1311 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: 5.95 Time building geometry restraints manager: 4.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 8169 1.04 - 1.25: 1337 1.25 - 1.46: 2546 1.46 - 1.66: 4487 1.66 - 1.87: 83 Bond restraints: 16622 Sorted by residual: bond pdb=" C18 I7J R 401 " pdb=" S1 I7J R 401 " ideal model delta sigma weight residual 1.781 1.867 -0.086 2.00e-02 2.50e+03 1.85e+01 bond pdb=" C12 I7J R 401 " pdb=" N5 I7J R 401 " ideal model delta sigma weight residual 1.353 1.422 -0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" C4 I7J R 401 " pdb=" N1 I7J R 401 " ideal model delta sigma weight residual 1.357 1.425 -0.068 2.00e-02 2.50e+03 1.17e+01 bond pdb=" C10 I7J R 401 " pdb=" O3 I7J R 401 " ideal model delta sigma weight residual 1.313 1.372 -0.059 2.00e-02 2.50e+03 8.65e+00 bond pdb=" C15 I7J R 401 " pdb=" N5 I7J R 401 " ideal model delta sigma weight residual 1.402 1.458 -0.056 2.00e-02 2.50e+03 7.72e+00 ... (remaining 16617 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 29752 1.95 - 3.90: 123 3.90 - 5.85: 27 5.85 - 7.80: 3 7.80 - 9.75: 7 Bond angle restraints: 29912 Sorted by residual: angle pdb=" CA CYS R 254 " pdb=" CB CYS R 254 " pdb=" SG CYS R 254 " ideal model delta sigma weight residual 114.40 124.15 -9.75 2.30e+00 1.89e-01 1.80e+01 angle pdb=" N VAL N 110 " pdb=" CA VAL N 110 " pdb=" C VAL N 110 " ideal model delta sigma weight residual 112.29 108.54 3.75 9.40e-01 1.13e+00 1.59e+01 angle pdb=" CA CYS R 251 " pdb=" CB CYS R 251 " pdb=" SG CYS R 251 " ideal model delta sigma weight residual 114.40 122.30 -7.90 2.30e+00 1.89e-01 1.18e+01 angle pdb=" N ALA B 203 " pdb=" CA ALA B 203 " pdb=" C ALA B 203 " ideal model delta sigma weight residual 110.44 114.13 -3.69 1.20e+00 6.94e-01 9.47e+00 angle pdb=" N VAL R 160 " pdb=" CA VAL R 160 " pdb=" C VAL R 160 " ideal model delta sigma weight residual 112.96 109.90 3.06 1.00e+00 1.00e+00 9.35e+00 ... (remaining 29907 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.51: 7231 17.51 - 35.01: 437 35.01 - 52.52: 121 52.52 - 70.02: 45 70.02 - 87.53: 14 Dihedral angle restraints: 7848 sinusoidal: 4236 harmonic: 3612 Sorted by residual: dihedral pdb=" CB CYS R 251 " pdb=" SG CYS R 251 " pdb=" SG CYS R 254 " pdb=" CB CYS R 254 " ideal model delta sinusoidal sigma weight residual -86.00 0.40 -86.40 1 1.00e+01 1.00e-02 9.00e+01 dihedral pdb=" CA GLU R 253 " pdb=" C GLU R 253 " pdb=" N CYS R 254 " pdb=" CA CYS R 254 " ideal model delta harmonic sigma weight residual -180.00 -150.20 -29.80 0 5.00e+00 4.00e-02 3.55e+01 dihedral pdb=" CA LEU G 19 " pdb=" C LEU G 19 " pdb=" N LYS G 20 " pdb=" CA LYS G 20 " ideal model delta harmonic sigma weight residual 180.00 158.20 21.80 0 5.00e+00 4.00e-02 1.90e+01 ... (remaining 7845 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 880 0.030 - 0.060: 263 0.060 - 0.089: 87 0.089 - 0.119: 50 0.119 - 0.149: 9 Chirality restraints: 1289 Sorted by residual: 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 -2.74 0.15 2.00e-01 2.50e+01 5.56e-01 chirality pdb=" CA ILE R 143 " pdb=" N ILE R 143 " pdb=" C ILE R 143 " pdb=" CB ILE R 143 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.20e-01 chirality pdb=" CA VAL G 54 " pdb=" N VAL G 54 " pdb=" C VAL G 54 " pdb=" CB VAL G 54 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.83e-01 ... (remaining 1286 not shown) Planarity restraints: 2466 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS R 162 " -0.021 5.00e-02 4.00e+02 3.24e-02 1.68e+00 pdb=" N PRO R 163 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO R 163 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO R 163 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN G 59 " -0.021 5.00e-02 4.00e+02 3.13e-02 1.57e+00 pdb=" N PRO G 60 " 0.054 5.00e-02 4.00e+02 pdb=" CA PRO G 60 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO G 60 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE R 175 " 0.018 5.00e-02 4.00e+02 2.68e-02 1.15e+00 pdb=" N PRO R 176 " -0.046 5.00e-02 4.00e+02 pdb=" CA PRO R 176 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO R 176 " 0.015 5.00e-02 4.00e+02 ... (remaining 2463 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.13: 456 2.13 - 2.74: 30563 2.74 - 3.36: 49540 3.36 - 3.98: 63574 3.98 - 4.60: 99183 Nonbonded interactions: 243316 Sorted by model distance: nonbonded pdb="HD21 ASN B 340 " pdb="HD22 ASN G 59 " model vdw 1.507 2.100 nonbonded pdb=" OE1 GLN R 109 " pdb="HH21 ARG R 112 " model vdw 1.534 2.450 nonbonded pdb=" O ALA R 91 " pdb=" HG1 THR R 95 " model vdw 1.538 2.450 nonbonded pdb=" OD1 ASP B 290 " pdb=" HE ARG B 314 " model vdw 1.592 2.450 nonbonded pdb=" H PHE B 235 " pdb=" O ALA B 240 " model vdw 1.592 2.450 ... (remaining 243311 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: 0.550 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: 0.260 Extract box with map and model: 0.660 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 35.810 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 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 0.086 8434 Z= 0.183 Angle : 0.560 9.747 11421 Z= 0.310 Chirality : 0.038 0.149 1289 Planarity : 0.002 0.032 1451 Dihedral : 12.807 87.527 3065 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.27), residues: 1036 helix: 2.81 (0.26), residues: 407 sheet: 0.07 (0.36), residues: 216 loop : 0.47 (0.33), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 281 HIS 0.008 0.001 HIS R 292 PHE 0.013 0.001 PHE B 234 TYR 0.008 0.001 TYR R 185 ARG 0.004 0.001 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.16892 ( 458) hydrogen bonds : angle 6.66026 ( 1311) SS BOND : bond 0.00878 ( 4) SS BOND : angle 1.13889 ( 8) covalent geometry : bond 0.00344 ( 8430) covalent geometry : angle 0.55911 (11413) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 366 is missing expected H atoms. Skipping. Evaluate side-chains 193 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 1.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 186 ASP cc_start: 0.7277 (m-30) cc_final: 0.7049 (m-30) outliers start: 0 outliers final: 1 residues processed: 193 average time/residue: 2.3752 time to fit residues: 489.8641 Evaluate side-chains 149 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 148 time to evaluate : 1.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 10 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 92 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: B 220 GLN B 259 GLN G 18 GLN N 31 ASN N 77 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.148329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.116281 restraints weight = 26192.371| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 1.60 r_work: 0.3171 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8434 Z= 0.186 Angle : 0.558 8.674 11421 Z= 0.300 Chirality : 0.041 0.150 1289 Planarity : 0.004 0.037 1451 Dihedral : 5.059 27.584 1174 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.46 % Allowed : 10.66 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.27), residues: 1036 helix: 2.45 (0.26), residues: 411 sheet: -0.30 (0.35), residues: 221 loop : 0.27 (0.32), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 277 HIS 0.006 0.001 HIS A 357 PHE 0.014 0.002 PHE G 61 TYR 0.016 0.002 TYR B 59 ARG 0.003 0.000 ARG G 13 Details of bonding type rmsd hydrogen bonds : bond 0.04592 ( 458) hydrogen bonds : angle 5.07442 ( 1311) SS BOND : bond 0.00951 ( 4) SS BOND : angle 1.24955 ( 8) covalent geometry : bond 0.00396 ( 8430) covalent geometry : angle 0.55716 (11413) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 366 is missing expected H atoms. Skipping. Evaluate side-chains 167 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 154 time to evaluate : 1.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 265 ARG cc_start: 0.7740 (mmt-90) cc_final: 0.7442 (mtp85) REVERT: B 155 ASN cc_start: 0.8314 (t0) cc_final: 0.7915 (t0) REVERT: B 186 ASP cc_start: 0.8174 (m-30) cc_final: 0.7864 (m-30) REVERT: B 219 ARG cc_start: 0.7923 (ttm-80) cc_final: 0.7543 (mmm160) REVERT: G 16 VAL cc_start: 0.7004 (OUTLIER) cc_final: 0.6760 (t) REVERT: N 5 GLN cc_start: 0.7252 (OUTLIER) cc_final: 0.6646 (tm-30) REVERT: N 33 LYS cc_start: 0.8768 (tttt) cc_final: 0.8510 (tttp) REVERT: N 109 ASP cc_start: 0.7900 (p0) cc_final: 0.7567 (p0) REVERT: N 120 GLN cc_start: 0.7799 (mm-40) cc_final: 0.7561 (mm-40) REVERT: R 175 PHE cc_start: 0.7802 (m-10) cc_final: 0.7533 (m-10) outliers start: 13 outliers final: 8 residues processed: 162 average time/residue: 2.5989 time to fit residues: 448.5528 Evaluate side-chains 144 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 134 time to evaluate : 1.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 311 TYR Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain R residue 254 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/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-5710/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-5710/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-5710/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-5710/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-5710/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-5710/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-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/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-5710/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-5710/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-5710/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: 62.4544 > 50: distance: 295 - 303: 20.161 distance: 298 - 416: 25.884 distance: 303 - 304: 16.632 distance: 303 - 309: 11.799 distance: 304 - 305: 23.342 distance: 304 - 307: 20.899 distance: 304 - 310: 19.887 distance: 305 - 306: 10.992 distance: 305 - 317: 32.178 distance: 307 - 308: 9.044 distance: 307 - 311: 18.202 distance: 307 - 312: 12.712 distance: 308 - 309: 16.116 distance: 308 - 313: 16.517 distance: 308 - 314: 7.510 distance: 309 - 315: 28.599 distance: 309 - 316: 30.638 distance: 317 - 318: 48.439 distance: 317 - 322: 48.559 distance: 318 - 319: 10.552 distance: 318 - 321: 42.823 distance: 319 - 320: 25.291 distance: 319 - 327: 49.565 distance: 321 - 324: 23.053 distance: 321 - 325: 18.630 distance: 321 - 326: 34.786 distance: 327 - 328: 31.578 distance: 327 - 333: 14.189 distance: 328 - 329: 27.039 distance: 328 - 331: 12.852 distance: 328 - 334: 9.572 distance: 329 - 330: 17.383 distance: 329 - 341: 20.779 distance: 331 - 332: 17.956 distance: 331 - 335: 28.042 distance: 331 - 336: 22.235 distance: 332 - 333: 21.013 distance: 332 - 337: 19.287 distance: 332 - 338: 14.698 distance: 333 - 339: 22.453 distance: 333 - 340: 10.743 distance: 341 - 342: 36.713 distance: 341 - 352: 12.458 distance: 342 - 343: 21.028 distance: 342 - 345: 24.026 distance: 342 - 353: 26.499 distance: 343 - 344: 37.462 distance: 343 - 361: 20.212 distance: 345 - 346: 16.097 distance: 345 - 354: 12.084 distance: 345 - 355: 20.712 distance: 346 - 347: 3.598 distance: 346 - 348: 8.672 distance: 347 - 349: 12.005 distance: 347 - 356: 12.953 distance: 348 - 350: 13.107 distance: 348 - 357: 4.239 distance: 349 - 351: 8.846 distance: 349 - 358: 3.787 distance: 350 - 351: 9.776 distance: 350 - 359: 7.076 distance: 351 - 360: 7.597 distance: 361 - 362: 9.814 distance: 361 - 368: 16.291 distance: 362 - 363: 17.422 distance: 362 - 365: 26.474 distance: 362 - 369: 33.349 distance: 363 - 375: 45.701 distance: 365 - 366: 8.662 distance: 365 - 367: 19.071 distance: 365 - 370: 7.691 distance: 366 - 371: 6.145 distance: 367 - 372: 11.751 distance: 367 - 373: 9.522 distance: 367 - 374: 7.666 distance: 375 - 376: 22.746 distance: 375 - 386: 24.179 distance: 376 - 377: 32.956 distance: 376 - 379: 15.946 distance: 376 - 387: 21.603 distance: 377 - 378: 23.745 distance: 377 - 399: 10.283 distance: 379 - 380: 29.819 distance: 379 - 388: 12.923 distance: 379 - 389: 15.725 distance: 380 - 381: 4.825 distance: 380 - 390: 19.143 distance: 380 - 391: 20.321 distance: 381 - 382: 7.743 distance: 381 - 392: 10.622 distance: 381 - 393: 10.280 distance: 382 - 394: 9.343 distance: 383 - 384: 3.727 distance: 383 - 385: 3.867 distance: 384 - 395: 3.728 distance: 384 - 396: 3.772 distance: 385 - 398: 3.621 distance: 399 - 407: 15.023 distance: 400 - 401: 15.100 distance: 400 - 403: 30.990 distance: 400 - 408: 20.092 distance: 401 - 402: 8.161 distance: 401 - 411: 45.524 distance: 403 - 404: 16.604 distance: 403 - 409: 19.933 distance: 403 - 410: 34.559 distance: 404 - 405: 25.676 distance: 404 - 406: 14.331 distance: 411 - 412: 10.255 distance: 411 - 417: 21.941 distance: 412 - 413: 11.267 distance: 412 - 415: 37.714 distance: 412 - 418: 5.707 distance: 413 - 414: 28.099 distance: 413 - 421: 43.224 distance: 415 - 416: 7.757 distance: 415 - 419: 19.783 distance: 415 - 420: 11.820 distance: 421 - 422: 23.949 distance: 421 - 432: 6.650 distance: 422 - 423: 29.034 distance: 422 - 425: 9.744 distance: 422 - 433: 14.078 distance: 423 - 424: 9.125 distance: 423 - 441: 46.600 distance: 425 - 426: 12.777 distance: 425 - 434: 20.458 distance: 425 - 435: 15.979 distance: 426 - 427: 4.419 distance: 427 - 429: 3.367 distance: 441 - 442: 36.163 distance: 441 - 449: 7.413 distance: 442 - 443: 29.519 distance: 442 - 445: 10.892 distance: 442 - 450: 37.551 distance: 443 - 453: 28.838 distance: 445 - 446: 25.981 distance: 445 - 451: 23.588 distance: 445 - 452: 25.739 distance: 446 - 447: 17.482 distance: 446 - 448: 15.744