Starting phenix.real_space_refine on Sat Aug 23 05:05:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iz9_35836/08_2025/8iz9_35836_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iz9_35836/08_2025/8iz9_35836.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8iz9_35836/08_2025/8iz9_35836_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iz9_35836/08_2025/8iz9_35836_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8iz9_35836/08_2025/8iz9_35836.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iz9_35836/08_2025/8iz9_35836.map" } resolution = 2.95 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= 0.004 sd= 0.075 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 43 5.16 5 C 6351 2.51 5 N 1638 2.21 5 O 1747 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 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: 9779 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 9754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1224, 9754 Classifications: {'peptide': 1224} Link IDs: {'PCIS': 1, 'PTRANS': 37, 'TRANS': 1185} Chain breaks: 2 Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'XPG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.11, per 1000 atoms: 0.22 Number of scatterers: 9779 At special positions: 0 Unit cell: (74.385, 103.455, 153.9, 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 1747 8.00 N 1638 7.00 C 6351 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: 0.65 Conformation dependent library (CDL) restraints added in 225.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2312 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 3 sheets defined 70.0% alpha, 2.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 17 through 24 Processing helix chain 'A' and resid 27 through 37 removed outlier: 3.575A pdb=" N LYS A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 44 removed outlier: 3.516A pdb=" N ASP A 43 " --> pdb=" O GLU A 40 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N MET A 44 " --> pdb=" O GLU A 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 40 through 44' Processing helix chain 'A' and resid 48 through 51 Processing helix chain 'A' and resid 52 through 74 removed outlier: 3.622A pdb=" N LEU A 56 " --> pdb=" O ARG A 52 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASP A 74 " --> pdb=" O ARG A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 122 removed outlier: 5.801A pdb=" N LYS A 90 " --> pdb=" O LYS A 86 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N SER A 91 " --> pdb=" O CYS A 87 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N VAL A 94 " --> pdb=" O LYS A 90 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU A 95 " --> pdb=" O SER A 91 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE A 98 " --> pdb=" O VAL A 94 " (cutoff:3.500A) Proline residue: A 110 - end of helix removed outlier: 3.602A pdb=" N TYR A 119 " --> pdb=" O LYS A 115 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N PHE A 120 " --> pdb=" O ILE A 116 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLU A 121 " --> pdb=" O ILE A 117 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ASN A 122 " --> pdb=" O ASN A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 179 removed outlier: 3.817A pdb=" N LEU A 131 " --> pdb=" O ASP A 127 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N HIS A 153 " --> pdb=" O ALA A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 189 Processing helix chain 'A' and resid 190 through 213 removed outlier: 3.501A pdb=" N ILE A 194 " --> pdb=" O THR A 190 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N VAL A 202 " --> pdb=" O LEU A 198 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N ASN A 203 " --> pdb=" O SER A 199 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N PHE A 205 " --> pdb=" O ASP A 201 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ASP A 206 " --> pdb=" O VAL A 202 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLN A 207 " --> pdb=" O ASN A 203 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N THR A 209 " --> pdb=" O PHE A 205 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N VAL A 210 " --> pdb=" O ASP A 206 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N PHE A 211 " --> pdb=" O GLN A 207 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N HIS A 213 " --> pdb=" O THR A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 234 Proline residue: A 219 - end of helix Processing helix chain 'A' and resid 236 through 282 removed outlier: 4.420A pdb=" N GLY A 240 " --> pdb=" O SER A 236 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LEU A 248 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Proline residue: A 249 - end of helix removed outlier: 3.769A pdb=" N PHE A 268 " --> pdb=" O LYS A 264 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLY A 282 " --> pdb=" O GLU A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 290 removed outlier: 3.546A pdb=" N ILE A 286 " --> pdb=" O GLY A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 343 removed outlier: 4.067A pdb=" N LYS A 309 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N SER A 328 " --> pdb=" O PHE A 324 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N LYS A 329 " --> pdb=" O PHE A 325 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLY A 343 " --> pdb=" O TYR A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 391 removed outlier: 4.092A pdb=" N PHE A 369 " --> pdb=" O VAL A 365 " (cutoff:3.500A) Proline residue: A 370 - end of helix Processing helix chain 'A' and resid 450 through 459 removed outlier: 3.683A pdb=" N LEU A 459 " --> pdb=" O LEU A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 495 Processing helix chain 'A' and resid 500 through 510 Processing helix chain 'A' and resid 513 through 520 Processing helix chain 'A' and resid 522 through 526 removed outlier: 3.983A pdb=" N THR A 526 " --> pdb=" O GLY A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 550 Processing helix chain 'A' and resid 566 through 578 Processing helix chain 'A' and resid 581 through 585 removed outlier: 4.316A pdb=" N GLU A 584 " --> pdb=" O ILE A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 597 removed outlier: 3.524A pdb=" N LEU A 597 " --> pdb=" O LEU A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 617 through 622 Processing helix chain 'A' and resid 697 through 709 removed outlier: 4.018A pdb=" N TYR A 701 " --> pdb=" O GLY A 697 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N GLY A 708 " --> pdb=" O TYR A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 751 removed outlier: 3.922A pdb=" N ASP A 732 " --> pdb=" O TYR A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 807 removed outlier: 3.602A pdb=" N TYR A 764 " --> pdb=" O ASP A 760 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS A 807 " --> pdb=" O GLU A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 809 through 816 removed outlier: 4.092A pdb=" N PHE A 813 " --> pdb=" O PRO A 809 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 861 removed outlier: 3.914A pdb=" N ASP A 828 " --> pdb=" O ARG A 824 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ILE A 829 " --> pdb=" O PHE A 825 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N LEU A 836 " --> pdb=" O LEU A 832 " (cutoff:3.500A) Proline residue: A 837 - end of helix Processing helix chain 'A' and resid 862 through 866 removed outlier: 3.894A pdb=" N ALA A 865 " --> pdb=" O PRO A 862 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE A 866 " --> pdb=" O TRP A 863 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 862 through 866' Processing helix chain 'A' and resid 867 through 910 removed outlier: 3.940A pdb=" N THR A 885 " --> pdb=" O TYR A 881 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ASP A 888 " --> pdb=" O GLU A 884 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N SER A 898 " --> pdb=" O SER A 894 " (cutoff:3.500A) Proline residue: A 899 - end of helix removed outlier: 3.547A pdb=" N GLY A 910 " --> pdb=" O SER A 906 " (cutoff:3.500A) Processing helix chain 'A' and resid 910 through 918 Processing helix chain 'A' and resid 919 through 970 removed outlier: 4.057A pdb=" N CYS A 923 " --> pdb=" O ALA A 919 " (cutoff:3.500A) Processing helix chain 'A' and resid 971 through 974 removed outlier: 3.797A pdb=" N LEU A 974 " --> pdb=" O ALA A 971 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 971 through 974' Processing helix chain 'A' and resid 975 through 987 Processing helix chain 'A' and resid 991 through 1018 removed outlier: 4.436A pdb=" N ILE A1008 " --> pdb=" O GLU A1004 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N SER A1009 " --> pdb=" O ASN A1005 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N VAL A1010 " --> pdb=" O MET A1006 " (cutoff:3.500A) Processing helix chain 'A' and resid 1080 through 1090 Processing helix chain 'A' and resid 1130 through 1136 Processing helix chain 'A' and resid 1142 through 1153 removed outlier: 4.294A pdb=" N LEU A1146 " --> pdb=" O THR A1142 " (cutoff:3.500A) Processing helix chain 'A' and resid 1155 through 1160 removed outlier: 3.718A pdb=" N ILE A1159 " --> pdb=" O LEU A1155 " (cutoff:3.500A) Processing helix chain 'A' and resid 1178 through 1193 Processing helix chain 'A' and resid 1208 through 1223 Processing helix chain 'A' and resid 1258 through 1264 removed outlier: 3.597A pdb=" N ASN A1264 " --> pdb=" O VAL A1260 " (cutoff:3.500A) Processing helix chain 'A' and resid 1267 through 1276 removed outlier: 3.893A pdb=" N LYS A1271 " --> pdb=" O SER A1267 " (cutoff:3.500A) Processing helix chain 'A' and resid 1277 through 1297 removed outlier: 3.513A pdb=" N TYR A1297 " --> pdb=" O PHE A1293 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 475 through 477 removed outlier: 4.383A pdb=" N ALA A 476 " --> pdb=" O ILE A 555 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N LEU A 557 " --> pdb=" O ALA A 476 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LEU A 558 " --> pdb=" O ILE A 588 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL A 590 " --> pdb=" O LEU A 558 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N LEU A 441 " --> pdb=" O LEU A 589 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL A 444 " --> pdb=" O LEU A 604 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE A 603 " --> pdb=" O GLY A 615 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N GLY A 615 " --> pdb=" O ILE A 603 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1041 through 1042 removed outlier: 4.175A pdb=" N TRP A1099 " --> pdb=" O ILE A1042 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1228 through 1232 removed outlier: 6.486A pdb=" N VAL A1071 " --> pdb=" O THR A1230 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N ALA A1232 " --> pdb=" O VAL A1071 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ILE A1073 " --> pdb=" O ALA A1232 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N MET A1245 " --> pdb=" O GLY A1072 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N VAL A1074 " --> pdb=" O MET A1245 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N LEU A1247 " --> pdb=" O VAL A1074 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ASP A1256 " --> pdb=" O ILE A1244 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N VAL A1246 " --> pdb=" O GLU A1254 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N GLU A1254 " --> pdb=" O VAL A1246 " (cutoff:3.500A) 608 hydrogen bonds defined for protein. 1806 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: 1.15 Time building geometry restraints manager: 0.82 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: 1616 1.32 - 1.45: 2596 1.45 - 1.57: 5705 1.57 - 1.69: 0 1.69 - 1.81: 70 Bond restraints: 9987 Sorted by residual: bond pdb=" C13 XPG A1401 " pdb=" C14 XPG A1401 " ideal model delta sigma weight residual 1.328 1.292 0.036 2.00e-02 2.50e+03 3.30e+00 bond pdb=" C18 XPG A1401 " pdb=" C19 XPG A1401 " ideal model delta sigma weight residual 1.524 1.497 0.027 2.00e-02 2.50e+03 1.86e+00 bond pdb=" C2 XPG A1401 " pdb=" C3 XPG A1401 " ideal model delta sigma weight residual 1.520 1.495 0.025 2.00e-02 2.50e+03 1.61e+00 bond pdb=" N ASN A1139 " pdb=" CA ASN A1139 " ideal model delta sigma weight residual 1.457 1.472 -0.015 1.29e-02 6.01e+03 1.32e+00 bond pdb=" C17 XPG A1401 " pdb=" C18 XPG A1401 " ideal model delta sigma weight residual 1.524 1.501 0.023 2.00e-02 2.50e+03 1.28e+00 ... (remaining 9982 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 13363 2.03 - 4.07: 137 4.07 - 6.10: 29 6.10 - 8.13: 1 8.13 - 10.17: 3 Bond angle restraints: 13533 Sorted by residual: angle pdb=" CA LEU A 13 " pdb=" CB LEU A 13 " pdb=" CG LEU A 13 " ideal model delta sigma weight residual 116.30 126.47 -10.17 3.50e+00 8.16e-02 8.44e+00 angle pdb=" C12 XPG A1401 " pdb=" C8 XPG A1401 " pdb=" C7 XPG A1401 " ideal model delta sigma weight residual 114.63 123.33 -8.70 3.00e+00 1.11e-01 8.42e+00 angle pdb=" C7 XPG A1401 " pdb=" C8 XPG A1401 " pdb=" C9 XPG A1401 " ideal model delta sigma weight residual 115.09 106.64 8.45 3.00e+00 1.11e-01 7.92e+00 angle pdb=" N LYS A1156 " pdb=" CA LYS A1156 " pdb=" C LYS A1156 " ideal model delta sigma weight residual 111.36 113.96 -2.60 1.09e+00 8.42e-01 5.68e+00 angle pdb=" N GLY A1072 " pdb=" CA GLY A1072 " pdb=" C GLY A1072 " ideal model delta sigma weight residual 111.46 115.55 -4.09 1.75e+00 3.27e-01 5.46e+00 ... (remaining 13528 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.80: 5420 18.80 - 37.61: 458 37.61 - 56.41: 70 56.41 - 75.21: 19 75.21 - 94.02: 11 Dihedral angle restraints: 5978 sinusoidal: 2407 harmonic: 3571 Sorted by residual: dihedral pdb=" CA ASP A1212 " pdb=" CB ASP A1212 " pdb=" CG ASP A1212 " pdb=" OD1 ASP A1212 " ideal model delta sinusoidal sigma weight residual -30.00 -89.05 59.05 1 2.00e+01 2.50e-03 1.17e+01 dihedral pdb=" C15 XPG A1401 " pdb=" C16 XPG A1401 " pdb=" C17 XPG A1401 " pdb=" C18 XPG A1401 " ideal model delta sinusoidal sigma weight residual -176.15 -82.13 -94.02 1 3.00e+01 1.11e-03 1.14e+01 dihedral pdb=" CB LYS A1194 " pdb=" CG LYS A1194 " pdb=" CD LYS A1194 " pdb=" CE LYS A1194 " ideal model delta sinusoidal sigma weight residual 60.00 117.92 -57.92 3 1.50e+01 4.44e-03 9.45e+00 ... (remaining 5975 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1124 0.036 - 0.072: 352 0.072 - 0.108: 79 0.108 - 0.144: 17 0.144 - 0.180: 1 Chirality restraints: 1573 Sorted by residual: chirality pdb=" CB VAL A1153 " pdb=" CA VAL A1153 " pdb=" CG1 VAL A1153 " pdb=" CG2 VAL A1153 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 8.06e-01 chirality pdb=" C15 XPG A1401 " pdb=" C14 XPG A1401 " pdb=" C16 XPG A1401 " pdb=" O15 XPG A1401 " both_signs ideal model delta sigma weight residual False 2.25 2.39 -0.14 2.00e-01 2.50e+01 5.13e-01 chirality pdb=" CA ILE A1073 " pdb=" N ILE A1073 " pdb=" C ILE A1073 " pdb=" CB ILE A1073 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.51e-01 ... (remaining 1570 not shown) Planarity restraints: 1682 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C12 XPG A1401 " 0.101 2.00e-02 2.50e+03 2.09e-01 4.36e+02 pdb=" C13 XPG A1401 " -0.285 2.00e-02 2.50e+03 pdb=" C14 XPG A1401 " 0.274 2.00e-02 2.50e+03 pdb=" C15 XPG A1401 " -0.090 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A 11 " -0.020 5.00e-02 4.00e+02 3.08e-02 1.51e+00 pdb=" N PRO A 12 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 12 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 12 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 898 " 0.017 5.00e-02 4.00e+02 2.62e-02 1.10e+00 pdb=" N PRO A 899 " -0.045 5.00e-02 4.00e+02 pdb=" CA PRO A 899 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 899 " 0.015 5.00e-02 4.00e+02 ... (remaining 1679 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 2439 2.80 - 3.32: 9552 3.32 - 3.85: 16149 3.85 - 4.37: 17170 4.37 - 4.90: 30635 Nonbonded interactions: 75945 Sorted by model distance: nonbonded pdb=" OG1 THR A 269 " pdb=" OE2 GLU A 306 " model vdw 2.273 3.040 nonbonded pdb=" NE2 HIS A 153 " pdb=" OD2 ASP A 953 " model vdw 2.285 3.120 nonbonded pdb=" O GLY A 450 " pdb=" OG SER A 453 " model vdw 2.286 3.040 nonbonded pdb=" O VAL A 484 " pdb=" OG SER A 906 " model vdw 2.287 3.040 nonbonded pdb=" OH TYR A 504 " pdb=" OD2 ASP A 524 " model vdw 2.308 3.040 ... (remaining 75940 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 1.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 8.300 Find NCS groups from input model: 0.030 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:6.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5823 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 0.036 9987 Z= 0.126 Angle : 0.562 10.169 13533 Z= 0.310 Chirality : 0.037 0.180 1573 Planarity : 0.006 0.209 1682 Dihedral : 14.569 94.017 3666 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: -0.94 (0.23), residues: 1218 helix: 0.38 (0.18), residues: 784 sheet: -1.45 (0.81), residues: 37 loop : -2.59 (0.26), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 317 TYR 0.017 0.001 TYR A1270 PHE 0.006 0.001 PHE A1043 TRP 0.008 0.001 TRP A 763 HIS 0.003 0.000 HIS A 592 Details of bonding type rmsd covalent geometry : bond 0.00220 ( 9987) covalent geometry : angle 0.56150 (13533) hydrogen bonds : bond 0.10781 ( 608) hydrogen bonds : angle 4.24158 ( 1806) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1145 GLU cc_start: 0.6429 (mp0) cc_final: 0.6208 (pm20) outliers start: 0 outliers final: 2 residues processed: 137 average time/residue: 0.5040 time to fit residues: 74.0373 Evaluate side-chains 82 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 80 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 380 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- 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: 54.7229 > 50: distance: 15 - 18: 10.239 distance: 18 - 19: 11.321 distance: 19 - 20: 14.575 distance: 19 - 22: 5.806 distance: 20 - 21: 17.405 distance: 20 - 25: 11.508 distance: 22 - 23: 9.828 distance: 22 - 24: 9.470 distance: 25 - 26: 7.581 distance: 26 - 27: 16.823 distance: 26 - 29: 18.946 distance: 27 - 28: 12.268 distance: 27 - 30: 14.987 distance: 31 - 32: 11.724 distance: 31 - 34: 4.425 distance: 32 - 33: 14.326 distance: 32 - 38: 10.057 distance: 34 - 35: 6.164 distance: 35 - 36: 4.647 distance: 35 - 37: 3.123 distance: 38 - 39: 16.434 distance: 39 - 42: 11.013 distance: 40 - 41: 5.723 distance: 42 - 43: 28.005 distance: 42 - 44: 16.216 distance: 46 - 47: 12.255 distance: 46 - 49: 7.806 distance: 47 - 48: 27.673 distance: 47 - 53: 9.905 distance: 48 - 78: 21.881 distance: 49 - 50: 10.348 distance: 50 - 51: 18.755 distance: 50 - 52: 11.838 distance: 53 - 54: 15.262 distance: 54 - 55: 10.026 distance: 54 - 57: 16.766 distance: 55 - 56: 21.018 distance: 55 - 60: 13.218 distance: 56 - 86: 23.526 distance: 57 - 58: 6.818 distance: 58 - 59: 6.563 distance: 60 - 61: 5.255 distance: 61 - 62: 7.059 distance: 61 - 64: 12.319 distance: 62 - 63: 8.329 distance: 62 - 71: 12.049 distance: 63 - 95: 3.999 distance: 64 - 65: 17.571 distance: 65 - 66: 6.853 distance: 66 - 67: 3.895 distance: 67 - 68: 4.330 distance: 68 - 69: 3.552 distance: 71 - 72: 14.247 distance: 72 - 73: 18.491 distance: 72 - 75: 16.064 distance: 73 - 74: 26.290 distance: 73 - 78: 24.877 distance: 74 - 103: 13.546 distance: 75 - 76: 10.301 distance: 75 - 77: 11.058 distance: 78 - 79: 5.672 distance: 79 - 80: 36.870 distance: 79 - 82: 28.856 distance: 80 - 81: 36.345 distance: 80 - 86: 49.344 distance: 81 - 111: 17.773 distance: 82 - 83: 27.862 distance: 83 - 84: 21.378 distance: 83 - 85: 13.042 distance: 86 - 87: 6.172 distance: 87 - 88: 21.230 distance: 87 - 90: 41.195 distance: 88 - 89: 24.767 distance: 88 - 95: 11.269 distance: 89 - 117: 20.010 distance: 90 - 91: 29.375 distance: 91 - 92: 20.474 distance: 92 - 93: 4.987 distance: 92 - 94: 5.669