Starting phenix.real_space_refine on Sun Aug 24 05:25:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7voo_32052/08_2025/7voo_32052.cif Found real_map, /net/cci-nas-00/data/ceres_data/7voo_32052/08_2025/7voo_32052.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7voo_32052/08_2025/7voo_32052.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7voo_32052/08_2025/7voo_32052.map" model { file = "/net/cci-nas-00/data/ceres_data/7voo_32052/08_2025/7voo_32052.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7voo_32052/08_2025/7voo_32052.cif" } resolution = 3.9 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= 0.007 sd= 0.088 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 9113 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 43 5.16 5 C 6140 2.51 5 N 1609 2.21 5 O 1894 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9686 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 9521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1245, 9521 Classifications: {'peptide': 1245} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 61, 'TRANS': 1183} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 179 Unresolved non-hydrogen angles: 221 Unresolved non-hydrogen dihedrals: 150 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ASP:plan': 1, 'PHE:plan': 1, 'GLN:plan1': 4, 'GLU:plan': 9, 'TYR:plan': 2, 'HIS:plan': 2, 'ASN:plan1': 2, 'MEQ:plan-2': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 107 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 2.09, per 1000 atoms: 0.22 Number of scatterers: 9686 At special positions: 0 Unit cell: (99.84, 125.84, 124.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 43 16.00 O 1894 8.00 N 1609 7.00 C 6140 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 251 " - pdb=" SG CYS A 299 " distance=2.03 Simple disulfide: pdb=" SG CYS A 269 " - pdb=" SG CYS A 287 " distance=2.03 Simple disulfide: pdb=" SG CYS A 470 " - pdb=" SG CYS A 563 " distance=2.03 Simple disulfide: pdb=" SG CYS A 595 " - pdb=" SG CYS A 771 " distance=2.03 Simple disulfide: pdb=" SG CYS A 821 " - pdb=" SG CYS A 849 " distance=2.03 Simple disulfide: pdb=" SG CYS A 847 " - pdb=" SG CYS A 883 " distance=2.03 Simple disulfide: pdb=" SG CYS A 921 " - pdb=" SG CYS A1321 " distance=2.03 Simple disulfide: pdb=" SG CYS A1079 " - pdb=" SG CYS A1127 " 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 Links applied ALPHA1-4 " NAG E 2 " - " MAN E 3 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " NAG-ASN " NAG A2101 " - " ASN A 70 " " NAG A2102 " - " ASN A 247 " " NAG A2103 " - " ASN A 396 " " NAG B 1 " - " ASN A 55 " " NAG C 1 " - " ASN A 410 " " NAG D 1 " - " ASN A 869 " " NAG E 1 " - " ASN A 991 " Time building additional restraints: 0.73 Conformation dependent library (CDL) restraints added in 417.7 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2332 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 24 sheets defined 18.8% alpha, 23.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 601 through 608 removed outlier: 3.673A pdb=" N LEU A 605 " --> pdb=" O ASP A 601 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LYS A 608 " --> pdb=" O VAL A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 622 removed outlier: 3.869A pdb=" N LEU A 621 " --> pdb=" O SER A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 672 Processing helix chain 'A' and resid 960 through 966 removed outlier: 3.905A pdb=" N LEU A 966 " --> pdb=" O GLN A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 972 through 993 removed outlier: 3.671A pdb=" N MET A 977 " --> pdb=" O GLY A 973 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL A 978 " --> pdb=" O GLU A 974 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA A 981 " --> pdb=" O MET A 977 " (cutoff:3.500A) Proline residue: A 982 - end of helix removed outlier: 3.674A pdb=" N TYR A 985 " --> pdb=" O ALA A 981 " (cutoff:3.500A) Processing helix chain 'A' and resid 997 through 1016 removed outlier: 3.589A pdb=" N GLY A1006 " --> pdb=" O SER A1002 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR A1007 " --> pdb=" O LYS A1003 " (cutoff:3.500A) Processing helix chain 'A' and resid 1030 through 1034 Processing helix chain 'A' and resid 1039 through 1053 Processing helix chain 'A' and resid 1059 through 1071 removed outlier: 3.660A pdb=" N ILE A1063 " --> pdb=" O ASP A1059 " (cutoff:3.500A) Processing helix chain 'A' and resid 1097 through 1112 removed outlier: 3.838A pdb=" N ILE A1112 " --> pdb=" O ALA A1108 " (cutoff:3.500A) Processing helix chain 'A' and resid 1118 through 1138 removed outlier: 3.606A pdb=" N PHE A1126 " --> pdb=" O ARG A1122 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N CYS A1127 " --> pdb=" O ASN A1123 " (cutoff:3.500A) Processing helix chain 'A' and resid 1143 through 1157 Processing helix chain 'A' and resid 1159 through 1173 removed outlier: 4.397A pdb=" N GLU A1165 " --> pdb=" O ASP A1161 " (cutoff:3.500A) Processing helix chain 'A' and resid 1204 through 1218 removed outlier: 4.190A pdb=" N MET A1208 " --> pdb=" O ALA A1204 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N THR A1209 " --> pdb=" O GLU A1205 " (cutoff:3.500A) Processing helix chain 'A' and resid 1224 through 1241 removed outlier: 4.054A pdb=" N ASN A1233 " --> pdb=" O THR A1229 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ILE A1234 " --> pdb=" O SER A1230 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N TRP A1237 " --> pdb=" O ASN A1233 " (cutoff:3.500A) Processing helix chain 'A' and resid 1243 through 1247 Processing helix chain 'A' and resid 1251 through 1269 Processing helix chain 'A' and resid 1293 through 1297 Processing sheet with id=AA1, first strand: chain 'A' and resid 85 through 89 removed outlier: 3.861A pdb=" N HIS A 85 " --> pdb=" O VAL A 49 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL A 49 " --> pdb=" O HIS A 85 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N LYS A 46 " --> pdb=" O PRO A 36 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL A 35 " --> pdb=" O LYS A 676 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 74 through 77 removed outlier: 3.925A pdb=" N VAL A 60 " --> pdb=" O LEU A 77 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 98 through 99 Processing sheet with id=AA4, first strand: chain 'A' and resid 128 through 129 Processing sheet with id=AA5, first strand: chain 'A' and resid 137 through 138 removed outlier: 3.641A pdb=" N TYR A 138 " --> pdb=" O THR A 220 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LEU A 164 " --> pdb=" O GLN A 208 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ALA A 176 " --> pdb=" O ILE A 167 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 161 through 162 Processing sheet with id=AA7, first strand: chain 'A' and resid 231 through 233 removed outlier: 3.504A pdb=" N GLN A 232 " --> pdb=" O CYS A 251 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N CYS A 251 " --> pdb=" O GLN A 232 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 238 through 239 removed outlier: 3.610A pdb=" N ILE A 239 " --> pdb=" O GLU A 342 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 287 through 292 removed outlier: 3.514A pdb=" N VAL A 264 " --> pdb=" O GLY A 292 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N HIS A 321 " --> pdb=" O SER A 267 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 349 through 354 removed outlier: 4.592A pdb=" N LEU A 350 " --> pdb=" O VAL A 372 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N VAL A 372 " --> pdb=" O LEU A 350 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N PHE A 352 " --> pdb=" O ARG A 370 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N ARG A 370 " --> pdb=" O PHE A 352 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N PHE A 365 " --> pdb=" O ILE A 409 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N PHE A 407 " --> pdb=" O GLY A 367 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N VAL A 369 " --> pdb=" O VAL A 405 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 358 through 359 removed outlier: 7.592A pdb=" N PHE A 359 " --> pdb=" O THR A 447 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N TYR A 449 " --> pdb=" O PHE A 359 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 458 through 461 removed outlier: 3.732A pdb=" N PHE A 458 " --> pdb=" O ILE A 481 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 474 through 476 Processing sheet with id=AB5, first strand: chain 'A' and resid 493 through 494 Processing sheet with id=AB6, first strand: chain 'A' and resid 504 through 509 removed outlier: 6.767A pdb=" N ILE A 499 " --> pdb=" O VAL A 506 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N THR A 508 " --> pdb=" O TYR A 497 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N TYR A 497 " --> pdb=" O THR A 508 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU A 541 " --> pdb=" O LEU A 498 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ILE A 552 " --> pdb=" O ALA A 544 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 569 through 571 Processing sheet with id=AB8, first strand: chain 'A' and resid 739 through 745 removed outlier: 4.087A pdb=" N ILE A 740 " --> pdb=" O ALA A 599 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 792 through 797 removed outlier: 3.626A pdb=" N GLY A 852 " --> pdb=" O ASN A 816 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 801 through 803 removed outlier: 6.057A pdb=" N VAL A 802 " --> pdb=" O GLU A 906 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'A' and resid 847 through 848 removed outlier: 3.822A pdb=" N ILE A 848 " --> pdb=" O ILE A 822 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE A 822 " --> pdb=" O ILE A 848 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL A 872 " --> pdb=" O VAL A 899 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 910 through 915 Processing sheet with id=AC4, first strand: chain 'A' and resid 910 through 915 Processing sheet with id=AC5, first strand: chain 'A' and resid 925 through 931 removed outlier: 3.634A pdb=" N GLY A 925 " --> pdb=" O GLY A1318 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N TYR A1312 " --> pdb=" O LEU A 931 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 1175 through 1176 325 hydrogen bonds defined for protein. 879 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: 1.56 Time building geometry restraints manager: 0.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3135 1.34 - 1.46: 2226 1.46 - 1.58: 4463 1.58 - 1.70: 0 1.70 - 1.82: 63 Bond restraints: 9887 Sorted by residual: bond pdb=" C1 NAG A2103 " pdb=" O5 NAG A2103 " ideal model delta sigma weight residual 1.406 1.483 -0.077 2.00e-02 2.50e+03 1.49e+01 bond pdb=" C1 NAG E 1 " pdb=" O5 NAG E 1 " ideal model delta sigma weight residual 1.406 1.461 -0.055 2.00e-02 2.50e+03 7.68e+00 bond pdb=" CA GLN A 232 " pdb=" CB GLN A 232 " ideal model delta sigma weight residual 1.524 1.568 -0.044 1.62e-02 3.81e+03 7.45e+00 bond pdb=" CA VAL A 260 " pdb=" C VAL A 260 " ideal model delta sigma weight residual 1.524 1.503 0.021 1.05e-02 9.07e+03 4.03e+00 bond pdb=" CA THR A 656 " pdb=" CB THR A 656 " ideal model delta sigma weight residual 1.530 1.557 -0.027 1.58e-02 4.01e+03 2.96e+00 ... (remaining 9882 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.04: 13407 5.04 - 10.08: 35 10.08 - 15.13: 3 15.13 - 20.17: 0 20.17 - 25.21: 2 Bond angle restraints: 13447 Sorted by residual: angle pdb=" C THR A 656 " pdb=" N PRO A 657 " pdb=" CA PRO A 657 " ideal model delta sigma weight residual 119.84 141.14 -21.30 1.25e+00 6.40e-01 2.90e+02 angle pdb=" N PHE A 309 " pdb=" CA PHE A 309 " pdb=" C PHE A 309 " ideal model delta sigma weight residual 109.62 94.94 14.68 1.50e+00 4.44e-01 9.58e+01 angle pdb=" C THR A 656 " pdb=" N PRO A 657 " pdb=" CD PRO A 657 " ideal model delta sigma weight residual 125.00 99.79 25.21 4.10e+00 5.95e-02 3.78e+01 angle pdb=" N GLY A 652 " pdb=" CA GLY A 652 " pdb=" C GLY A 652 " ideal model delta sigma weight residual 113.18 98.93 14.25 2.37e+00 1.78e-01 3.61e+01 angle pdb=" CA PRO A 261 " pdb=" C PRO A 261 " pdb=" N GLY A 262 " ideal model delta sigma weight residual 115.78 109.68 6.10 1.24e+00 6.50e-01 2.42e+01 ... (remaining 13442 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.18: 5734 24.18 - 48.37: 261 48.37 - 72.55: 22 72.55 - 96.73: 34 96.73 - 120.92: 54 Dihedral angle restraints: 6105 sinusoidal: 2488 harmonic: 3617 Sorted by residual: dihedral pdb=" CB CYS A 821 " pdb=" SG CYS A 821 " pdb=" SG CYS A 849 " pdb=" CB CYS A 849 " ideal model delta sinusoidal sigma weight residual -86.00 -134.01 48.01 1 1.00e+01 1.00e-02 3.18e+01 dihedral pdb=" CA ARG A 684 " pdb=" C ARG A 684 " pdb=" N LYS A 685 " pdb=" CA LYS A 685 " ideal model delta harmonic sigma weight residual 180.00 154.43 25.57 0 5.00e+00 4.00e-02 2.62e+01 dihedral pdb=" C THR A 656 " pdb=" N THR A 656 " pdb=" CA THR A 656 " pdb=" CB THR A 656 " ideal model delta harmonic sigma weight residual -122.00 -133.87 11.87 0 2.50e+00 1.60e-01 2.25e+01 ... (remaining 6102 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 1509 0.098 - 0.196: 72 0.196 - 0.294: 5 0.294 - 0.392: 2 0.392 - 0.490: 2 Chirality restraints: 1590 Sorted by residual: chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN A 410 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.91 -0.49 2.00e-01 2.50e+01 6.00e+00 chirality pdb=" C1 NAG B 1 " pdb=" ND2 ASN A 55 " pdb=" C2 NAG B 1 " pdb=" O5 NAG B 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.97 -0.43 2.00e-01 2.50e+01 4.71e+00 chirality pdb=" CA THR A 656 " pdb=" N THR A 656 " pdb=" C THR A 656 " pdb=" CB THR A 656 " both_signs ideal model delta sigma weight residual False 2.53 2.16 0.37 2.00e-01 2.50e+01 3.41e+00 ... (remaining 1587 not shown) Planarity restraints: 1724 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 656 " -0.080 5.00e-02 4.00e+02 1.14e-01 2.08e+01 pdb=" N PRO A 657 " 0.196 5.00e-02 4.00e+02 pdb=" CA PRO A 657 " -0.075 5.00e-02 4.00e+02 pdb=" CD PRO A 657 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 308 " 0.013 2.00e-02 2.50e+03 2.72e-02 7.38e+00 pdb=" C VAL A 308 " -0.047 2.00e-02 2.50e+03 pdb=" O VAL A 308 " 0.018 2.00e-02 2.50e+03 pdb=" N PHE A 309 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 578 " 0.033 5.00e-02 4.00e+02 4.95e-02 3.92e+00 pdb=" N PRO A 579 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO A 579 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 579 " 0.027 5.00e-02 4.00e+02 ... (remaining 1721 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 98 2.52 - 3.12: 7668 3.12 - 3.71: 15148 3.71 - 4.31: 20366 4.31 - 4.90: 33052 Nonbonded interactions: 76332 Sorted by model distance: nonbonded pdb=" O ASP A 665 " pdb=" OG SER A 668 " model vdw 1.930 3.040 nonbonded pdb=" O GLN A 132 " pdb=" OG1 THR A 133 " model vdw 2.063 3.040 nonbonded pdb=" NH2 ARG A 823 " pdb=" O GLN A 880 " model vdw 2.099 3.120 nonbonded pdb=" O MET A 318 " pdb=" OG SER A 341 " model vdw 2.161 3.040 nonbonded pdb=" O CYS A1079 " pdb=" OG SER A1102 " model vdw 2.172 3.040 ... (remaining 76327 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 'B' selection = chain 'C' selection = chain 'D' } 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 group one per residue 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: 0.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 8.840 Find NCS groups from input model: 0.060 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:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6907 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 : 0.004 0.077 9907 Z= 0.208 Angle : 0.936 25.209 13499 Z= 0.502 Chirality : 0.052 0.490 1590 Planarity : 0.005 0.114 1717 Dihedral : 19.361 120.917 3749 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 21.43 Ramachandran Plot: Outliers : 0.41 % Allowed : 12.72 % Favored : 86.87 % Rotamer: Outliers : 0.29 % Allowed : 0.67 % Favored : 99.04 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -2.96 (0.23), residues: 1234 helix: 0.10 (0.38), residues: 195 sheet: -1.48 (0.26), residues: 405 loop : -3.06 (0.22), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 823 TYR 0.026 0.002 TYR A 667 PHE 0.030 0.002 PHE A1057 TRP 0.021 0.002 TRP A1069 HIS 0.003 0.001 HIS A1259 Details of bonding type rmsd covalent geometry : bond 0.00404 ( 9887) covalent geometry : angle 0.91201 (13447) SS BOND : bond 0.00330 ( 8) SS BOND : angle 1.22117 ( 16) hydrogen bonds : bond 0.23762 ( 319) hydrogen bonds : angle 9.11990 ( 879) link_ALPHA1-4 : bond 0.00549 ( 1) link_ALPHA1-4 : angle 1.77842 ( 3) link_BETA1-4 : bond 0.00390 ( 4) link_BETA1-4 : angle 1.69328 ( 12) link_NAG-ASN : bond 0.01294 ( 7) link_NAG-ASN : angle 5.24381 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 125 time to evaluate : 0.401 Fit side-chains revert: symmetry clash REVERT: A 500 MET cc_start: 0.8231 (mtp) cc_final: 0.7901 (mtp) REVERT: A 673 MET cc_start: 0.8988 (tpp) cc_final: 0.8661 (tpp) REVERT: A 1323 TYR cc_start: 0.7028 (t80) cc_final: 0.6591 (t80) outliers start: 3 outliers final: 0 residues processed: 128 average time/residue: 0.0839 time to fit residues: 16.3326 Evaluate side-chains 99 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 108 optimal weight: 9.9990 chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 4.9990 chunk 113 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 9.9990 chunk 123 optimal weight: 6.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 0.0010 chunk 51 optimal weight: 0.4980 overall best weight: 3.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN A 368 GLN A 474 GLN ** A 635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 963 GLN A 983 ASN ** A1182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1277 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.115213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.092314 restraints weight = 33968.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.094598 restraints weight = 21347.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.096058 restraints weight = 15679.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.097058 restraints weight = 12799.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.097786 restraints weight = 11177.733| |-----------------------------------------------------------------------------| r_work (final): 0.3778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7152 moved from start: 0.1392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 9907 Z= 0.206 Angle : 0.871 16.869 13499 Z= 0.425 Chirality : 0.053 0.404 1590 Planarity : 0.006 0.135 1717 Dihedral : 19.403 109.722 1572 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 17.83 Ramachandran Plot: Outliers : 0.32 % Allowed : 11.99 % Favored : 87.68 % Rotamer: Outliers : 2.50 % Allowed : 8.56 % Favored : 88.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -2.99 (0.23), residues: 1234 helix: 0.18 (0.38), residues: 205 sheet: -1.62 (0.25), residues: 432 loop : -3.11 (0.23), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 787 TYR 0.026 0.002 TYR A 667 PHE 0.016 0.002 PHE A1248 TRP 0.017 0.002 TRP A 739 HIS 0.020 0.001 HIS A 358 Details of bonding type rmsd covalent geometry : bond 0.00465 ( 9887) covalent geometry : angle 0.84055 (13447) SS BOND : bond 0.00401 ( 8) SS BOND : angle 0.83215 ( 16) hydrogen bonds : bond 0.04517 ( 319) hydrogen bonds : angle 6.83307 ( 879) link_ALPHA1-4 : bond 0.00243 ( 1) link_ALPHA1-4 : angle 3.79744 ( 3) link_BETA1-4 : bond 0.00512 ( 4) link_BETA1-4 : angle 2.96990 ( 12) link_NAG-ASN : bond 0.01202 ( 7) link_NAG-ASN : angle 5.26916 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 101 time to evaluate : 0.374 Fit side-chains revert: symmetry clash REVERT: A 989 TYR cc_start: 0.7995 (t80) cc_final: 0.7755 (t80) REVERT: A 1323 TYR cc_start: 0.6968 (t80) cc_final: 0.6380 (t80) outliers start: 26 outliers final: 16 residues processed: 113 average time/residue: 0.0867 time to fit residues: 14.8490 Evaluate side-chains 108 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 92 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 683 ILE Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 983 ASN Chi-restraints excluded: chain A residue 997 THR Chi-restraints excluded: chain A residue 1097 ASP Chi-restraints excluded: chain A residue 1105 ILE Chi-restraints excluded: chain A residue 1251 THR Chi-restraints excluded: chain A residue 1308 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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: 54.9367 > 50: distance: 28 - 175: 15.877 distance: 31 - 172: 11.715 distance: 40 - 161: 3.692 distance: 43 - 158: 8.725 distance: 113 - 118: 5.622 distance: 118 - 119: 5.242 distance: 119 - 120: 5.840 distance: 119 - 122: 8.756 distance: 120 - 121: 5.066 distance: 120 - 127: 4.403 distance: 122 - 123: 11.992 distance: 123 - 124: 3.544 distance: 124 - 125: 13.764 distance: 125 - 126: 4.339 distance: 127 - 128: 8.570 distance: 128 - 129: 28.135 distance: 129 - 130: 21.049 distance: 129 - 131: 11.555 distance: 131 - 132: 9.688 distance: 132 - 133: 5.654 distance: 132 - 135: 4.284 distance: 133 - 134: 9.636 distance: 133 - 141: 11.987 distance: 135 - 136: 8.484 distance: 136 - 137: 12.256 distance: 136 - 138: 5.423 distance: 137 - 139: 11.060 distance: 138 - 140: 7.389 distance: 141 - 142: 3.381 distance: 142 - 143: 12.353 distance: 142 - 145: 5.594 distance: 143 - 144: 18.321 distance: 143 - 152: 16.149 distance: 145 - 146: 10.724 distance: 146 - 147: 5.484 distance: 146 - 148: 8.357 distance: 148 - 150: 8.276 distance: 149 - 151: 12.100 distance: 150 - 151: 9.037 distance: 152 - 153: 11.442 distance: 153 - 154: 21.534 distance: 153 - 156: 34.657 distance: 154 - 155: 8.298 distance: 154 - 158: 21.018 distance: 156 - 157: 16.094 distance: 158 - 159: 10.355 distance: 159 - 160: 6.779 distance: 159 - 162: 8.056 distance: 160 - 166: 12.425 distance: 162 - 163: 11.873 distance: 162 - 164: 10.170 distance: 163 - 165: 14.154 distance: 166 - 167: 8.369 distance: 167 - 168: 5.221 distance: 167 - 170: 7.355 distance: 168 - 169: 11.049 distance: 168 - 172: 5.690 distance: 170 - 171: 10.796 distance: 172 - 173: 4.339 distance: 173 - 174: 7.799 distance: 173 - 176: 4.702 distance: 174 - 175: 7.549 distance: 174 - 180: 3.819 distance: 176 - 177: 6.440 distance: 176 - 178: 21.493 distance: 177 - 179: 23.360 distance: 180 - 181: 7.664 distance: 180 - 186: 12.488 distance: 181 - 182: 21.087 distance: 181 - 184: 21.592 distance: 182 - 183: 44.552 distance: 182 - 187: 16.980 distance: 184 - 185: 17.545 distance: 185 - 186: 13.830 distance: 187 - 188: 15.970 distance: 188 - 189: 18.827 distance: 188 - 191: 17.237 distance: 189 - 190: 21.749 distance: 189 - 194: 13.229 distance: 191 - 192: 19.902 distance: 191 - 193: 39.931