Starting phenix.real_space_refine on Sun Apr 5 01:31:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9r4x_53571/04_2026/9r4x_53571.cif Found real_map, /net/cci-nas-00/data/ceres_data/9r4x_53571/04_2026/9r4x_53571.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9r4x_53571/04_2026/9r4x_53571.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9r4x_53571/04_2026/9r4x_53571.map" model { file = "/net/cci-nas-00/data/ceres_data/9r4x_53571/04_2026/9r4x_53571.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9r4x_53571/04_2026/9r4x_53571.cif" } resolution = 3.2 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= 0.001 sd= 0.008 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 P 5 5.49 5 Mg 1 5.21 5 S 55 5.16 5 C 4254 2.51 5 N 1146 2.21 5 O 1301 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6762 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3318 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 18, 'TRANS': 408} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 3321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3321 Classifications: {'peptide': 423} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 403} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 62 Unusual residues: {'TA1': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.76, per 1000 atoms: 0.26 Number of scatterers: 6762 At special positions: 0 Unit cell: (73.623, 73.623, 110.968, 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 55 16.00 P 5 15.00 Mg 1 11.99 O 1301 8.00 N 1146 7.00 C 4254 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.77 Conformation dependent library (CDL) restraints added in 264.8 milliseconds 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1570 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 7 sheets defined 52.2% alpha, 11.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 10 through 28 removed outlier: 3.648A pdb=" N ALA A 19 " --> pdb=" O GLN A 15 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU A 26 " --> pdb=" O GLU A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 51 removed outlier: 3.693A pdb=" N ASN A 50 " --> pdb=" O ASP A 47 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR A 51 " --> pdb=" O ALA A 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 47 through 51' Processing helix chain 'A' and resid 72 through 81 Processing helix chain 'A' and resid 82 through 86 removed outlier: 4.381A pdb=" N GLN A 85 " --> pdb=" O THR A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 108 Processing helix chain 'A' and resid 110 through 113 Processing helix chain 'A' and resid 114 through 129 removed outlier: 3.592A pdb=" N ASN A 128 " --> pdb=" O LYS A 124 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N CYS A 129 " --> pdb=" O LEU A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 161 removed outlier: 3.564A pdb=" N VAL A 159 " --> pdb=" O GLU A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 195 removed outlier: 3.881A pdb=" N SER A 193 " --> pdb=" O LEU A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 216 Processing helix chain 'A' and resid 223 through 244 removed outlier: 4.186A pdb=" N LEU A 227 " --> pdb=" O THR A 223 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N SER A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N LEU A 242 " --> pdb=" O LEU A 238 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG A 243 " --> pdb=" O THR A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 260 removed outlier: 3.731A pdb=" N VAL A 260 " --> pdb=" O GLN A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 296 Processing helix chain 'A' and resid 297 through 301 removed outlier: 3.715A pdb=" N MET A 301 " --> pdb=" O PRO A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 324 through 338 Processing helix chain 'A' and resid 383 through 401 removed outlier: 3.896A pdb=" N VAL A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N MET A 391 " --> pdb=" O VAL A 387 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N LYS A 401 " --> pdb=" O LEU A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.556A pdb=" N GLY A 410 " --> pdb=" O HIS A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 437 removed outlier: 4.300A pdb=" N PHE A 418 " --> pdb=" O GLU A 414 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER A 419 " --> pdb=" O GLU A 415 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ILE A 437 " --> pdb=" O GLU A 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 29 Processing helix chain 'B' and resid 41 through 47 removed outlier: 3.846A pdb=" N ARG B 46 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 79 Processing helix chain 'B' and resid 86 through 88 No H-bonds generated for 'chain 'B' and resid 86 through 88' Processing helix chain 'B' and resid 100 through 106 Processing helix chain 'B' and resid 108 through 126 removed outlier: 4.089A pdb=" N LEU B 112 " --> pdb=" O GLU B 108 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ASP B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N ALA B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL B 119 " --> pdb=" O ALA B 115 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS B 122 " --> pdb=" O ASP B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 159 Processing helix chain 'B' and resid 180 through 193 removed outlier: 3.662A pdb=" N GLN B 191 " --> pdb=" O LEU B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 214 Processing helix chain 'B' and resid 221 through 237 removed outlier: 3.859A pdb=" N LEU B 225 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N HIS B 227 " --> pdb=" O GLY B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 258 Processing helix chain 'B' and resid 277 through 282 removed outlier: 3.721A pdb=" N GLN B 280 " --> pdb=" O GLY B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 294 Processing helix chain 'B' and resid 304 through 308 Processing helix chain 'B' and resid 322 through 337 removed outlier: 3.853A pdb=" N VAL B 326 " --> pdb=" O SER B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 341 Processing helix chain 'B' and resid 373 through 391 removed outlier: 4.158A pdb=" N MET B 377 " --> pdb=" O ALA B 373 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ARG B 391 " --> pdb=" O ALA B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 400 Processing helix chain 'B' and resid 405 through 425 removed outlier: 3.769A pdb=" N THR B 409 " --> pdb=" O GLU B 405 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 92 through 94 removed outlier: 7.945A pdb=" N ILE A 93 " --> pdb=" O CYS A 65 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N PHE A 67 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N VAL A 66 " --> pdb=" O VAL A 4 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ALA A 140 " --> pdb=" O VAL A 9 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N PHE A 135 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N PHE A 169 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N MET A 137 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N CYS A 171 " --> pdb=" O MET A 137 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N SER A 139 " --> pdb=" O CYS A 171 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA3, first strand: chain 'A' and resid 271 through 272 Processing sheet with id=AA4, first strand: chain 'B' and resid 90 through 92 removed outlier: 7.996A pdb=" N VAL B 91 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N LEU B 65 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 8.280A pdb=" N ILE B 64 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N HIS B 6 " --> pdb=" O ILE B 64 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N MET B 66 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N GLN B 8 " --> pdb=" O MET B 66 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N GLU B 3 " --> pdb=" O GLY B 132 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N GLN B 134 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N VAL B 5 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N THR B 136 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ILE B 7 " --> pdb=" O THR B 136 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N GLN B 131 " --> pdb=" O ILE B 163 " (cutoff:3.500A) removed outlier: 8.321A pdb=" N GLU B 165 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N PHE B 133 " --> pdb=" O GLU B 165 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N PHE B 167 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ILE B 135 " --> pdb=" O PHE B 167 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N VAL B 199 " --> pdb=" O PHE B 266 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 51 through 53 Processing sheet with id=AA6, first strand: chain 'B' and resid 169 through 170 Processing sheet with id=AA7, first strand: chain 'B' and resid 349 through 354 removed outlier: 6.138A pdb=" N ALA B 313 " --> pdb=" O LYS B 350 " (cutoff:3.500A) removed outlier: 8.096A pdb=" N SER B 352 " --> pdb=" O ALA B 313 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ALA B 315 " --> pdb=" O SER B 352 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N CYS B 354 " --> pdb=" O ALA B 315 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N PHE B 317 " --> pdb=" O CYS B 354 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA B 364 " --> pdb=" O ARG B 318 " (cutoff:3.500A) 305 hydrogen bonds defined for protein. 873 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: 1.12 Time building geometry restraints manager: 0.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1221 1.32 - 1.44: 1791 1.44 - 1.57: 3804 1.57 - 1.69: 12 1.69 - 1.81: 87 Bond restraints: 6915 Sorted by residual: bond pdb=" CA VAL B 286 " pdb=" CB VAL B 286 " ideal model delta sigma weight residual 1.539 1.531 0.008 5.40e-03 3.43e+04 2.37e+00 bond pdb=" CA PRO A 359 " pdb=" C PRO A 359 " ideal model delta sigma weight residual 1.517 1.525 -0.008 6.70e-03 2.23e+04 1.35e+00 bond pdb=" C5 GDP B 501 " pdb=" C4 GDP B 501 " ideal model delta sigma weight residual 1.490 1.468 0.022 2.00e-02 2.50e+03 1.19e+00 bond pdb=" CB GLN A 256 " pdb=" CG GLN A 256 " ideal model delta sigma weight residual 1.520 1.496 0.024 3.00e-02 1.11e+03 6.52e-01 bond pdb=" CG GLN A 256 " pdb=" CD GLN A 256 " ideal model delta sigma weight residual 1.516 1.499 0.017 2.50e-02 1.60e+03 4.85e-01 ... (remaining 6910 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.20: 9142 1.20 - 2.40: 179 2.40 - 3.60: 49 3.60 - 4.80: 13 4.80 - 6.00: 7 Bond angle restraints: 9390 Sorted by residual: angle pdb=" C2' GTP A 501 " pdb=" C3' GTP A 501 " pdb=" C4' GTP A 501 " ideal model delta sigma weight residual 111.00 105.00 6.00 3.00e+00 1.11e-01 4.00e+00 angle pdb=" C20 TA1 B 502 " pdb=" C21 TA1 B 502 " pdb=" C24 TA1 B 502 " ideal model delta sigma weight residual 107.07 112.59 -5.52 3.00e+00 1.11e-01 3.39e+00 angle pdb=" C1' GTP A 501 " pdb=" C2' GTP A 501 " pdb=" C3' GTP A 501 " ideal model delta sigma weight residual 111.00 105.57 5.43 3.00e+00 1.11e-01 3.28e+00 angle pdb=" C4' GDP B 501 " pdb=" C3' GDP B 501 " pdb=" C2' GDP B 501 " ideal model delta sigma weight residual 111.00 105.64 5.36 3.00e+00 1.11e-01 3.20e+00 angle pdb=" C3' GDP B 501 " pdb=" C2' GDP B 501 " pdb=" C1' GDP B 501 " ideal model delta sigma weight residual 111.00 106.01 4.99 3.00e+00 1.11e-01 2.77e+00 ... (remaining 9385 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.25: 4100 34.25 - 68.49: 51 68.49 - 102.74: 15 102.74 - 136.98: 11 136.98 - 171.23: 6 Dihedral angle restraints: 4183 sinusoidal: 1738 harmonic: 2445 Sorted by residual: dihedral pdb=" C8 GTP A 501 " pdb=" C1' GTP A 501 " pdb=" N9 GTP A 501 " pdb=" O4' GTP A 501 " ideal model delta sinusoidal sigma weight residual 104.59 -66.63 171.23 1 2.00e+01 2.50e-03 4.77e+01 dihedral pdb=" O2G GTP A 501 " pdb=" O3B GTP A 501 " pdb=" PG GTP A 501 " pdb=" PB GTP A 501 " ideal model delta sinusoidal sigma weight residual 177.30 -16.98 -165.72 1 2.00e+01 2.50e-03 4.73e+01 dihedral pdb=" C4' GTP A 501 " pdb=" C5' GTP A 501 " pdb=" O5' GTP A 501 " pdb=" PA GTP A 501 " ideal model delta sinusoidal sigma weight residual 260.87 141.85 119.02 1 2.00e+01 2.50e-03 3.56e+01 ... (remaining 4180 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 688 0.033 - 0.067: 232 0.067 - 0.100: 73 0.100 - 0.133: 31 0.133 - 0.167: 1 Chirality restraints: 1025 Sorted by residual: chirality pdb=" C10 TA1 B 502 " pdb=" C02 TA1 B 502 " pdb=" C11 TA1 B 502 " pdb=" C18 TA1 B 502 " both_signs ideal model delta sigma weight residual False 2.54 2.38 0.17 2.00e-01 2.50e+01 6.95e-01 chirality pdb=" CA VAL A 363 " pdb=" N VAL A 363 " pdb=" C VAL A 363 " pdb=" CB VAL A 363 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.01e-01 chirality pdb=" CA ILE A 378 " pdb=" N ILE A 378 " pdb=" C ILE A 378 " pdb=" CB ILE A 378 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.68e-01 ... (remaining 1022 not shown) Planarity restraints: 1217 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG B 86 " -0.035 5.00e-02 4.00e+02 5.33e-02 4.55e+00 pdb=" N PRO B 87 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO B 87 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 87 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 31 " -0.022 5.00e-02 4.00e+02 3.33e-02 1.78e+00 pdb=" N PRO A 32 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 32 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 32 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 260 " 0.017 5.00e-02 4.00e+02 2.55e-02 1.04e+00 pdb=" N PRO A 261 " -0.044 5.00e-02 4.00e+02 pdb=" CA PRO A 261 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 261 " 0.014 5.00e-02 4.00e+02 ... (remaining 1214 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.58: 53 2.58 - 3.16: 5669 3.16 - 3.74: 10990 3.74 - 4.32: 15220 4.32 - 4.90: 25557 Nonbonded interactions: 57489 Sorted by model distance: nonbonded pdb=" O2G GTP A 501 " pdb="MG MG A 502 " model vdw 2.006 2.170 nonbonded pdb=" O1B GTP A 501 " pdb="MG MG A 502 " model vdw 2.049 2.170 nonbonded pdb=" OE2 GLU A 71 " pdb="MG MG A 502 " model vdw 2.066 2.170 nonbonded pdb=" O ILE B 210 " pdb=" OG1 THR B 214 " model vdw 2.199 3.040 nonbonded pdb=" OE2 GLU A 27 " pdb=" OG SER A 236 " model vdw 2.219 3.040 ... (remaining 57484 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: 11.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.520 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 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 : 0.002 0.031 6915 Z= 0.098 Angle : 0.480 6.001 9390 Z= 0.234 Chirality : 0.040 0.167 1025 Planarity : 0.003 0.053 1217 Dihedral : 16.270 171.225 2613 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.66 % Allowed : 4.16 % Favored : 94.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % 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: 0.52 (0.30), residues: 842 helix: 1.74 (0.28), residues: 365 sheet: -0.55 (0.46), residues: 142 loop : -0.77 (0.35), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 121 TYR 0.008 0.001 TYR B 310 PHE 0.006 0.001 PHE B 394 TRP 0.011 0.002 TRP B 397 HIS 0.005 0.001 HIS A 88 Details of bonding type rmsd covalent geometry : bond 0.00202 ( 6915) covalent geometry : angle 0.48008 ( 9390) hydrogen bonds : bond 0.17074 ( 305) hydrogen bonds : angle 6.32560 ( 873) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 87 time to evaluate : 0.258 Fit side-chains REVERT: A 217 LEU cc_start: 0.8174 (OUTLIER) cc_final: 0.7477 (mp) REVERT: B 137 HIS cc_start: 0.7789 (t-170) cc_final: 0.7497 (t-170) REVERT: B 215 LEU cc_start: 0.8038 (OUTLIER) cc_final: 0.7816 (mm) REVERT: B 267 MET cc_start: 0.8174 (mtp) cc_final: 0.7961 (mtt) REVERT: B 397 TRP cc_start: 0.7035 (m100) cc_final: 0.6753 (m-10) outliers start: 12 outliers final: 5 residues processed: 97 average time/residue: 0.0815 time to fit residues: 10.9286 Evaluate side-chains 64 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 57 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 222 TYR Chi-restraints excluded: chain B residue 323 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 49 optimal weight: 0.0070 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 10.0000 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 0.0670 chunk 45 optimal weight: 0.6980 chunk 74 optimal weight: 5.9990 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 GLN A 300 ASN B 298 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.101901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.087083 restraints weight = 12476.067| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 2.57 r_work: 0.3577 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.1246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6915 Z= 0.101 Angle : 0.545 9.645 9390 Z= 0.257 Chirality : 0.042 0.283 1025 Planarity : 0.004 0.038 1217 Dihedral : 15.786 169.063 1061 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.94 % Allowed : 7.63 % Favored : 90.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % 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: 0.44 (0.30), residues: 842 helix: 1.59 (0.27), residues: 376 sheet: -1.00 (0.44), residues: 133 loop : -0.57 (0.35), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 320 TYR 0.013 0.001 TYR B 51 PHE 0.014 0.001 PHE A 149 TRP 0.010 0.001 TRP A 21 HIS 0.003 0.001 HIS A 8 Details of bonding type rmsd covalent geometry : bond 0.00217 ( 6915) covalent geometry : angle 0.54502 ( 9390) hydrogen bonds : bond 0.03439 ( 305) hydrogen bonds : angle 4.54677 ( 873) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 62 time to evaluate : 0.252 Fit side-chains REVERT: A 217 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.7569 (mp) REVERT: B 211 CYS cc_start: 0.7445 (m) cc_final: 0.7241 (m) REVERT: B 215 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.8101 (mm) REVERT: B 397 TRP cc_start: 0.7555 (m100) cc_final: 0.7122 (m-10) REVERT: B 414 ASN cc_start: 0.7125 (m-40) cc_final: 0.6640 (t0) REVERT: B 415 MET cc_start: 0.7374 (tpp) cc_final: 0.7163 (tpp) outliers start: 14 outliers final: 6 residues processed: 72 average time/residue: 0.0703 time to fit residues: 7.2983 Evaluate side-chains 63 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 55 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 323 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 51 optimal weight: 9.9990 chunk 66 optimal weight: 10.0000 chunk 60 optimal weight: 0.9990 chunk 20 optimal weight: 9.9990 chunk 19 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 67 optimal weight: 9.9990 chunk 58 optimal weight: 3.9990 chunk 9 optimal weight: 10.0000 chunk 52 optimal weight: 9.9990 chunk 80 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 300 ASN B 298 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.095836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.081001 restraints weight = 12876.354| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 2.56 r_work: 0.3467 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 6915 Z= 0.223 Angle : 0.634 8.485 9390 Z= 0.306 Chirality : 0.048 0.468 1025 Planarity : 0.004 0.038 1217 Dihedral : 13.041 168.871 1058 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.64 % Allowed : 8.60 % Favored : 88.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % 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: -0.09 (0.30), residues: 842 helix: 1.03 (0.27), residues: 379 sheet: -1.18 (0.46), residues: 125 loop : -0.77 (0.35), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 243 TYR 0.014 0.002 TYR B 310 PHE 0.018 0.002 PHE B 394 TRP 0.013 0.002 TRP A 21 HIS 0.005 0.002 HIS B 264 Details of bonding type rmsd covalent geometry : bond 0.00518 ( 6915) covalent geometry : angle 0.63430 ( 9390) hydrogen bonds : bond 0.04390 ( 305) hydrogen bonds : angle 4.59134 ( 873) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 53 time to evaluate : 0.275 Fit side-chains REVERT: A 217 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.7871 (mp) REVERT: B 211 CYS cc_start: 0.7702 (m) cc_final: 0.7462 (m) REVERT: B 321 MET cc_start: 0.7949 (OUTLIER) cc_final: 0.6070 (ptm) REVERT: B 414 ASN cc_start: 0.7101 (m-40) cc_final: 0.6615 (t0) outliers start: 19 outliers final: 13 residues processed: 68 average time/residue: 0.0644 time to fit residues: 6.6104 Evaluate side-chains 65 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 50 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 321 MET Chi-restraints excluded: chain B residue 323 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 39 optimal weight: 8.9990 chunk 24 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 82 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 chunk 23 optimal weight: 9.9990 chunk 33 optimal weight: 5.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 300 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.097747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.082754 restraints weight = 12757.190| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 2.60 r_work: 0.3495 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6915 Z= 0.136 Angle : 0.563 8.427 9390 Z= 0.267 Chirality : 0.044 0.371 1025 Planarity : 0.004 0.042 1217 Dihedral : 12.232 168.849 1056 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.94 % Allowed : 9.29 % Favored : 88.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % 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: 0.13 (0.30), residues: 842 helix: 1.28 (0.27), residues: 379 sheet: -1.16 (0.46), residues: 125 loop : -0.70 (0.36), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 62 TYR 0.010 0.001 TYR B 310 PHE 0.012 0.001 PHE A 138 TRP 0.015 0.002 TRP A 21 HIS 0.003 0.001 HIS B 264 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 6915) covalent geometry : angle 0.56284 ( 9390) hydrogen bonds : bond 0.03541 ( 305) hydrogen bonds : angle 4.29366 ( 873) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 54 time to evaluate : 0.279 Fit side-chains REVERT: A 217 LEU cc_start: 0.8335 (OUTLIER) cc_final: 0.7896 (mp) REVERT: A 279 GLU cc_start: 0.7708 (mp0) cc_final: 0.7298 (mp0) REVERT: A 301 MET cc_start: 0.7693 (mmt) cc_final: 0.7180 (mmp) REVERT: B 211 CYS cc_start: 0.7629 (m) cc_final: 0.7393 (m) REVERT: B 414 ASN cc_start: 0.7081 (m-40) cc_final: 0.6622 (t0) outliers start: 14 outliers final: 9 residues processed: 65 average time/residue: 0.0663 time to fit residues: 6.3629 Evaluate side-chains 64 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 323 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/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-2.1rc1-6017/lib/python3.9/site-packages/iotbx/cli_parser.py", line 995, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/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-2.1rc1-6017/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-2.1rc1-6017/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-2.1rc1-6017/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-2.1rc1-6017/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-2.1rc1-6017/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-2.1rc1-6017/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-2.1rc1-6017/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-2.1rc1-6017/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-2.1rc1-6017/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-2.1rc1-6017/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-2.1rc1-6017/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-2.1rc1-6017/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-2.1rc1-6017/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-2.1rc1-6017/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-2.1rc1-6017/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1590, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1493, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1374, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 51.9615 > 50: distance: 80 - 84: 12.928 distance: 84 - 85: 8.094 distance: 85 - 86: 13.833 distance: 85 - 88: 8.434 distance: 86 - 87: 16.904 distance: 86 - 92: 22.442 distance: 88 - 89: 9.697 distance: 88 - 90: 12.784 distance: 89 - 91: 13.158 distance: 92 - 93: 13.471 distance: 93 - 94: 12.341 distance: 93 - 96: 21.702 distance: 94 - 95: 11.628 distance: 94 - 100: 18.087 distance: 95 - 206: 14.072 distance: 96 - 97: 22.373 distance: 97 - 98: 15.351 distance: 98 - 99: 8.059 distance: 100 - 101: 24.445 distance: 101 - 102: 11.202 distance: 101 - 104: 17.374 distance: 102 - 103: 28.114 distance: 102 - 109: 19.541 distance: 104 - 105: 15.291 distance: 105 - 106: 14.967 distance: 106 - 107: 6.509 distance: 106 - 108: 8.308 distance: 109 - 110: 25.767 distance: 109 - 209: 27.301 distance: 110 - 111: 24.248 distance: 110 - 113: 20.621 distance: 111 - 112: 15.460 distance: 111 - 116: 25.046 distance: 112 - 222: 4.650 distance: 113 - 114: 18.872 distance: 113 - 115: 13.104 distance: 116 - 117: 24.015 distance: 117 - 118: 14.835 distance: 117 - 120: 12.549 distance: 118 - 119: 28.131 distance: 118 - 127: 7.065 distance: 120 - 121: 14.130 distance: 121 - 122: 7.592 distance: 122 - 124: 14.750 distance: 123 - 125: 19.403 distance: 124 - 126: 10.458 distance: 125 - 126: 10.086 distance: 127 - 128: 10.802 distance: 128 - 129: 15.614 distance: 128 - 131: 6.632 distance: 129 - 130: 11.620 distance: 129 - 133: 18.756 distance: 131 - 132: 13.653 distance: 133 - 134: 15.775 distance: 134 - 135: 5.241 distance: 134 - 137: 16.136 distance: 135 - 136: 21.979 distance: 135 - 140: 7.799 distance: 137 - 138: 20.044 distance: 137 - 139: 24.883 distance: 140 - 141: 13.130 distance: 140 - 239: 3.983 distance: 141 - 142: 19.415 distance: 141 - 144: 9.534 distance: 142 - 143: 25.824 distance: 142 - 151: 28.541 distance: 144 - 145: 8.051 distance: 145 - 146: 7.989 distance: 145 - 147: 6.947 distance: 146 - 148: 6.993 distance: 147 - 149: 7.828 distance: 148 - 150: 4.455 distance: 149 - 150: 3.460 distance: 151 - 152: 12.777 distance: 151 - 157: 13.877 distance: 152 - 153: 10.908 distance: 152 - 155: 28.088 distance: 153 - 154: 23.742 distance: 153 - 158: 16.614 distance: 155 - 156: 22.282 distance: 156 - 157: 19.998 distance: 158 - 159: 32.365 distance: 159 - 160: 12.466 distance: 159 - 162: 21.620 distance: 160 - 161: 24.199 distance: 160 - 164: 20.626 distance: 162 - 163: 10.908