Starting phenix.real_space_refine on Sun Aug 24 13:18:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yz4_14387/08_2025/7yz4_14387.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yz4_14387/08_2025/7yz4_14387.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7yz4_14387/08_2025/7yz4_14387.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yz4_14387/08_2025/7yz4_14387.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7yz4_14387/08_2025/7yz4_14387.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yz4_14387/08_2025/7yz4_14387.map" } resolution = 3.84 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.048 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 55 5.16 5 C 6325 2.51 5 N 1675 2.21 5 O 1797 1.98 5 H 9953 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 19805 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 19805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1234, 19805 Classifications: {'peptide': 1234} Link IDs: {'PTRANS': 75, 'TRANS': 1158} Chain breaks: 12 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 21 Time building chain proxies: 3.74, per 1000 atoms: 0.19 Number of scatterers: 19805 At special positions: 0 Unit cell: (97.704, 104.328, 163.944, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 55 16.00 O 1797 8.00 N 1675 7.00 C 6325 6.00 H 9953 1.00 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: 2.13 Conformation dependent library (CDL) restraints added in 681.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2370 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 12 sheets defined 54.1% alpha, 11.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'A' and resid 46 through 58 Processing helix chain 'A' and resid 66 through 81 removed outlier: 3.563A pdb=" N LYS A 70 " --> pdb=" O THR A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 86 Processing helix chain 'A' and resid 89 through 93 removed outlier: 3.534A pdb=" N ALA A 93 " --> pdb=" O ASN A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 117 Processing helix chain 'A' and resid 126 through 132 Processing helix chain 'A' and resid 134 through 144 removed outlier: 3.877A pdb=" N SER A 139 " --> pdb=" O LYS A 135 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN A 140 " --> pdb=" O GLU A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 162 Processing helix chain 'A' and resid 176 through 182 Processing helix chain 'A' and resid 184 through 195 removed outlier: 4.285A pdb=" N GLU A 188 " --> pdb=" O HIS A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 231 removed outlier: 4.936A pdb=" N GLU A 220 " --> pdb=" O PRO A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 280 removed outlier: 3.552A pdb=" N PHE A 280 " --> pdb=" O ALA A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 313 removed outlier: 4.057A pdb=" N LEU A 313 " --> pdb=" O VAL A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 336 removed outlier: 3.652A pdb=" N ALA A 318 " --> pdb=" O GLY A 314 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS A 331 " --> pdb=" O ARG A 327 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LYS A 334 " --> pdb=" O GLN A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 358 removed outlier: 4.323A pdb=" N LYS A 354 " --> pdb=" O THR A 350 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N ILE A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N HIS A 356 " --> pdb=" O LEU A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 362 Processing helix chain 'A' and resid 374 through 387 Processing helix chain 'A' and resid 450 through 468 Processing helix chain 'A' and resid 498 through 510 removed outlier: 3.564A pdb=" N GLU A 503 " --> pdb=" O ARG A 499 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL A 504 " --> pdb=" O LYS A 500 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU A 505 " --> pdb=" O GLN A 501 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG A 506 " --> pdb=" O GLU A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 524 removed outlier: 3.889A pdb=" N GLU A 524 " --> pdb=" O VAL A 521 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 521 through 524' Processing helix chain 'A' and resid 542 through 552 removed outlier: 3.827A pdb=" N ARG A 552 " --> pdb=" O GLN A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 591 Processing helix chain 'A' and resid 626 through 628 No H-bonds generated for 'chain 'A' and resid 626 through 628' Processing helix chain 'A' and resid 629 through 641 Processing helix chain 'A' and resid 686 through 705 Processing helix chain 'A' and resid 782 through 786 Processing helix chain 'A' and resid 839 through 854 removed outlier: 3.712A pdb=" N PHE A 854 " --> pdb=" O HIS A 850 " (cutoff:3.500A) Processing helix chain 'A' and resid 893 through 903 removed outlier: 3.592A pdb=" N SER A 903 " --> pdb=" O ASP A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 928 Processing helix chain 'A' and resid 967 through 976 Processing helix chain 'A' and resid 1034 through 1036 No H-bonds generated for 'chain 'A' and resid 1034 through 1036' Processing helix chain 'A' and resid 1044 through 1053 Processing helix chain 'A' and resid 1053 through 1076 removed outlier: 3.634A pdb=" N ILE A1057 " --> pdb=" O CYS A1053 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N THR A1074 " --> pdb=" O LEU A1070 " (cutoff:3.500A) Processing helix chain 'A' and resid 1293 through 1302 Processing helix chain 'A' and resid 1303 through 1307 Processing helix chain 'A' and resid 1312 through 1335 Processing helix chain 'A' and resid 1339 through 1351 Processing helix chain 'A' and resid 1352 through 1363 Processing helix chain 'A' and resid 1364 through 1369 removed outlier: 4.084A pdb=" N MET A1369 " --> pdb=" O PRO A1366 " (cutoff:3.500A) Processing helix chain 'A' and resid 1552 through 1570 Processing helix chain 'A' and resid 1571 through 1583 removed outlier: 3.504A pdb=" N GLY A1583 " --> pdb=" O LEU A1579 " (cutoff:3.500A) Processing helix chain 'A' and resid 1650 through 1658 Processing helix chain 'A' and resid 1662 through 1667 Processing helix chain 'A' and resid 1674 through 1681 removed outlier: 3.673A pdb=" N LEU A1678 " --> pdb=" O LYS A1674 " (cutoff:3.500A) Processing helix chain 'A' and resid 1695 through 1716 removed outlier: 3.644A pdb=" N LEU A1701 " --> pdb=" O ARG A1697 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ALA A1704 " --> pdb=" O PHE A1700 " (cutoff:3.500A) Processing helix chain 'A' and resid 1722 through 1734 Processing helix chain 'A' and resid 1735 through 1746 Processing helix chain 'A' and resid 1747 through 1752 Processing helix chain 'A' and resid 1756 through 1773 Processing helix chain 'A' and resid 1799 through 1816 removed outlier: 4.106A pdb=" N GLY A1803 " --> pdb=" O PRO A1799 " (cutoff:3.500A) Processing helix chain 'A' and resid 1821 through 1842 Proline residue: A1830 - end of helix Proline residue: A1834 - end of helix Processing helix chain 'A' and resid 1846 through 1855 Processing helix chain 'A' and resid 1890 through 1910 Processing sheet with id=AA1, first strand: chain 'A' and resid 205 through 206 removed outlier: 7.712A pdb=" N THR A 206 " --> pdb=" O THR A 60 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N VAL A 62 " --> pdb=" O THR A 206 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 121 through 124 removed outlier: 3.804A pdb=" N THR A 151 " --> pdb=" O TYR A 124 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N ARG A 95 " --> pdb=" O ILE A 169 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N LEU A 171 " --> pdb=" O ARG A 95 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 252 through 257 removed outlier: 6.152A pdb=" N VAL A 534 " --> pdb=" O VAL A 561 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N LEU A 563 " --> pdb=" O VAL A 534 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 446 through 448 removed outlier: 5.716A pdb=" N ILE A 446 " --> pdb=" O ALA A 518 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ASN A 477 " --> pdb=" O ILE A 517 " (cutoff:3.500A) removed outlier: 9.003A pdb=" N THR A 519 " --> pdb=" O ASN A 477 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 666 through 667 Processing sheet with id=AA6, first strand: chain 'A' and resid 746 through 750 removed outlier: 3.587A pdb=" N GLN A 747 " --> pdb=" O ILE A1550 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 777 through 780 removed outlier: 6.469A pdb=" N GLU A 824 " --> pdb=" O THR A 778 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 777 through 780 removed outlier: 6.469A pdb=" N GLU A 824 " --> pdb=" O THR A 778 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N ILE A 829 " --> pdb=" O GLY A 774 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N GLY A 774 " --> pdb=" O ILE A 829 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N LEU A 831 " --> pdb=" O VAL A 772 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N VAL A 772 " --> pdb=" O LEU A 831 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LYS A 833 " --> pdb=" O LEU A 770 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N PHE A 802 " --> pdb=" O ILE A 773 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N CYS A 877 " --> pdb=" O LEU A 805 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 865 through 867 removed outlier: 3.503A pdb=" N VAL A1386 " --> pdb=" O GLU A 866 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 987 through 992 removed outlier: 3.574A pdb=" N LEU A 987 " --> pdb=" O TYR A 951 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ASP A 949 " --> pdb=" O ASP A 989 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ASP A 991 " --> pdb=" O VAL A 947 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N VAL A 947 " --> pdb=" O ASP A 991 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1859 through 1861 Processing sheet with id=AB3, first strand: chain 'A' and resid 1859 through 1861 492 hydrogen bonds defined for protein. 1398 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.50 Time building geometry restraints manager: 2.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 9919 1.03 - 1.23: 38 1.23 - 1.43: 4101 1.43 - 1.62: 5885 1.62 - 1.82: 76 Bond restraints: 20019 Sorted by residual: bond pdb=" CG LEU A1312 " pdb=" CD1 LEU A1312 " ideal model delta sigma weight residual 1.521 1.475 0.046 3.30e-02 9.18e+02 1.94e+00 bond pdb=" ND2 ASN A1311 " pdb="HD22 ASN A1311 " ideal model delta sigma weight residual 0.860 0.832 0.028 2.00e-02 2.50e+03 1.93e+00 bond pdb=" CB LEU A1312 " pdb=" CG LEU A1312 " ideal model delta sigma weight residual 1.530 1.502 0.028 2.00e-02 2.50e+03 1.91e+00 bond pdb=" C ALA A 555 " pdb=" N PRO A 556 " ideal model delta sigma weight residual 1.334 1.354 -0.020 1.51e-02 4.39e+03 1.70e+00 bond pdb=" ND2 ASN A 161 " pdb="HD22 ASN A 161 " ideal model delta sigma weight residual 0.860 0.835 0.025 2.00e-02 2.50e+03 1.54e+00 ... (remaining 20014 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.54: 36293 7.54 - 15.07: 2 15.07 - 22.61: 0 22.61 - 30.15: 1 30.15 - 37.69: 2 Bond angle restraints: 36298 Sorted by residual: angle pdb=" N ASP A1764 " pdb=" CA ASP A1764 " pdb=" HA ASP A1764 " ideal model delta sigma weight residual 110.00 72.31 37.69 3.00e+00 1.11e-01 1.58e+02 angle pdb=" CB ASP A1764 " pdb=" CA ASP A1764 " pdb=" HA ASP A1764 " ideal model delta sigma weight residual 109.00 73.25 35.75 3.00e+00 1.11e-01 1.42e+02 angle pdb=" C ASP A1764 " pdb=" CA ASP A1764 " pdb=" HA ASP A1764 " ideal model delta sigma weight residual 109.00 78.99 30.01 3.00e+00 1.11e-01 1.00e+02 angle pdb=" N LEU A 313 " pdb=" CA LEU A 313 " pdb=" C LEU A 313 " ideal model delta sigma weight residual 107.73 115.46 -7.73 1.34e+00 5.57e-01 3.32e+01 angle pdb=" N GLU A1313 " pdb=" CA GLU A1313 " pdb=" C GLU A1313 " ideal model delta sigma weight residual 111.37 117.30 -5.93 1.65e+00 3.67e-01 1.29e+01 ... (remaining 36293 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.19: 8728 17.19 - 34.37: 519 34.37 - 51.56: 152 51.56 - 68.74: 35 68.74 - 85.93: 9 Dihedral angle restraints: 9443 sinusoidal: 5179 harmonic: 4264 Sorted by residual: dihedral pdb=" N ASP A1764 " pdb=" C ASP A1764 " pdb=" CA ASP A1764 " pdb=" CB ASP A1764 " ideal model delta harmonic sigma weight residual 122.80 131.36 -8.56 0 2.50e+00 1.60e-01 1.17e+01 dihedral pdb=" C ASP A1764 " pdb=" N ASP A1764 " pdb=" CA ASP A1764 " pdb=" CB ASP A1764 " ideal model delta harmonic sigma weight residual -122.60 -130.83 8.23 0 2.50e+00 1.60e-01 1.08e+01 dihedral pdb=" CG ARG A 269 " pdb=" CD ARG A 269 " pdb=" NE ARG A 269 " pdb=" CZ ARG A 269 " ideal model delta sinusoidal sigma weight residual -90.00 -133.47 43.47 2 1.50e+01 4.44e-03 1.01e+01 ... (remaining 9440 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1340 0.065 - 0.130: 193 0.130 - 0.195: 17 0.195 - 0.261: 1 0.261 - 0.326: 1 Chirality restraints: 1552 Sorted by residual: chirality pdb=" CA ASP A1764 " pdb=" N ASP A1764 " pdb=" C ASP A1764 " pdb=" CB ASP A1764 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.65e+00 chirality pdb=" CA HIS A1655 " pdb=" N HIS A1655 " pdb=" C HIS A1655 " pdb=" CB HIS A1655 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA ILE A 479 " pdb=" N ILE A 479 " pdb=" C ILE A 479 " pdb=" CB ILE A 479 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 8.13e-01 ... (remaining 1549 not shown) Planarity restraints: 2880 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A1311 " -0.052 2.00e-02 2.50e+03 6.82e-02 6.97e+01 pdb=" CG ASN A1311 " 0.037 2.00e-02 2.50e+03 pdb=" OD1 ASN A1311 " 0.003 2.00e-02 2.50e+03 pdb=" ND2 ASN A1311 " 0.111 2.00e-02 2.50e+03 pdb="HD21 ASN A1311 " 0.007 2.00e-02 2.50e+03 pdb="HD22 ASN A1311 " -0.106 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 161 " 0.047 2.00e-02 2.50e+03 6.37e-02 6.08e+01 pdb=" CG ASN A 161 " -0.023 2.00e-02 2.50e+03 pdb=" OD1 ASN A 161 " -0.012 2.00e-02 2.50e+03 pdb=" ND2 ASN A 161 " -0.104 2.00e-02 2.50e+03 pdb="HD21 ASN A 161 " -0.011 2.00e-02 2.50e+03 pdb="HD22 ASN A 161 " 0.102 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 985 " -0.040 2.00e-02 2.50e+03 5.12e-02 3.93e+01 pdb=" CD GLN A 985 " 0.030 2.00e-02 2.50e+03 pdb=" OE1 GLN A 985 " 0.003 2.00e-02 2.50e+03 pdb=" NE2 GLN A 985 " 0.083 2.00e-02 2.50e+03 pdb="HE21 GLN A 985 " 0.003 2.00e-02 2.50e+03 pdb="HE22 GLN A 985 " -0.079 2.00e-02 2.50e+03 ... (remaining 2877 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.23: 1475 2.23 - 2.82: 44609 2.82 - 3.42: 50832 3.42 - 4.01: 66736 4.01 - 4.60: 104009 Nonbonded interactions: 267661 Sorted by model distance: nonbonded pdb="HE22 GLN A1679 " pdb=" OD1 ASP A1693 " model vdw 1.641 2.450 nonbonded pdb=" HG1 THR A1867 " pdb=" OD1 ASP A1869 " model vdw 1.669 2.450 nonbonded pdb=" O GLU A 542 " pdb=" HG SER A 545 " model vdw 1.683 2.450 nonbonded pdb=" HA ASP A1764 " pdb=" HB3 ASP A1764 " model vdw 1.683 1.952 nonbonded pdb=" OD2 ASP A 319 " pdb=" HH TYR A 362 " model vdw 1.686 2.450 ... (remaining 267656 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 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: 3.970 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: 0.120 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 20.380 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6269 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 0.046 10066 Z= 0.188 Angle : 0.780 9.299 13634 Z= 0.425 Chirality : 0.046 0.326 1552 Planarity : 0.009 0.123 1732 Dihedral : 11.946 85.927 3798 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 1.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.92 % Allowed : 6.98 % Favored : 92.10 % 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: -2.13 (0.22), residues: 1208 helix: -0.99 (0.19), residues: 598 sheet: -1.46 (0.47), residues: 135 loop : -1.78 (0.26), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.032 0.003 ARG A 790 TYR 0.032 0.003 TYR A1695 PHE 0.030 0.003 PHE A1700 TRP 0.027 0.005 TRP A 133 HIS 0.013 0.002 HIS A 58 Details of bonding type rmsd covalent geometry : bond 0.00432 (10066) covalent geometry : angle 0.78015 (13634) hydrogen bonds : bond 0.15257 ( 489) hydrogen bonds : angle 6.07495 ( 1398) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 160 is missing expected H atoms. Skipping. Residue THR 655 is missing expected H atoms. Skipping. Residue LEU 658 is missing expected H atoms. Skipping. Residue ILE 907 is missing expected H atoms. Skipping. Residue ILE 909 is missing expected H atoms. Skipping. Residue SER 911 is missing expected H atoms. Skipping. Residue THR 912 is missing expected H atoms. Skipping. Residue LYS 913 is missing expected H atoms. Skipping. Residue TYR 914 is missing expected H atoms. Skipping. Residue SER 915 is missing expected H atoms. Skipping. Residue LYS 916 is missing expected H atoms. Skipping. Evaluate side-chains 220 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 210 time to evaluate : 0.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 GLU cc_start: 0.6978 (tp30) cc_final: 0.6621 (tt0) REVERT: A 144 LYS cc_start: 0.8235 (mttt) cc_final: 0.7962 (mttp) REVERT: A 193 CYS cc_start: 0.7425 (t) cc_final: 0.7103 (t) REVERT: A 219 LEU cc_start: 0.8013 (tp) cc_final: 0.7777 (tp) REVERT: A 222 LYS cc_start: 0.7640 (mmtt) cc_final: 0.7427 (ttpt) REVERT: A 225 LYS cc_start: 0.8156 (tttp) cc_final: 0.7955 (tttt) REVERT: A 307 ARG cc_start: 0.7995 (ptp-110) cc_final: 0.7678 (ptp-110) REVERT: A 324 MET cc_start: 0.6766 (mpp) cc_final: 0.6319 (tpp) REVERT: A 325 MET cc_start: 0.7579 (mtt) cc_final: 0.7274 (mtt) REVERT: A 477 ASN cc_start: 0.7991 (t0) cc_final: 0.7292 (m-40) REVERT: A 546 TYR cc_start: 0.8037 (t80) cc_final: 0.7763 (t80) REVERT: A 578 THR cc_start: 0.8371 (m) cc_final: 0.8133 (p) REVERT: A 771 TYR cc_start: 0.6920 (m-80) cc_final: 0.6390 (m-80) REVERT: A 791 LYS cc_start: 0.8418 (pttt) cc_final: 0.7967 (ptmm) REVERT: A 851 GLN cc_start: 0.7235 (pt0) cc_final: 0.6847 (pt0) REVERT: A 1066 THR cc_start: 0.7757 (m) cc_final: 0.7475 (p) REVERT: A 1345 TYR cc_start: 0.6926 (t80) cc_final: 0.6710 (t80) REVERT: A 1768 LYS cc_start: 0.7039 (mttt) cc_final: 0.6706 (mmmt) outliers start: 10 outliers final: 3 residues processed: 217 average time/residue: 0.3270 time to fit residues: 91.2161 Evaluate side-chains 169 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 166 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 1372 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 108 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 0.2980 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 6.9990 chunk 117 optimal weight: 6.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 HIS A 184 HIS A 356 HIS A 985 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.197290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.166490 restraints weight = 52418.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.172370 restraints weight = 23085.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.175980 restraints weight = 13062.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.178209 restraints weight = 8869.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.179068 restraints weight = 6899.241| |-----------------------------------------------------------------------------| r_work (final): 0.4235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6230 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10066 Z= 0.176 Angle : 0.585 5.329 13634 Z= 0.312 Chirality : 0.041 0.325 1552 Planarity : 0.005 0.050 1732 Dihedral : 4.022 34.575 1355 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 0.83 % Allowed : 10.19 % Favored : 88.98 % 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: -0.72 (0.23), residues: 1208 helix: 0.33 (0.20), residues: 603 sheet: -1.14 (0.49), residues: 131 loop : -1.25 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 137 TYR 0.020 0.001 TYR A1335 PHE 0.023 0.001 PHE A1700 TRP 0.014 0.002 TRP A 316 HIS 0.007 0.001 HIS A 356 Details of bonding type rmsd covalent geometry : bond 0.00379 (10066) covalent geometry : angle 0.58485 (13634) hydrogen bonds : bond 0.04950 ( 489) hydrogen bonds : angle 4.84009 ( 1398) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 160 is missing expected H atoms. Skipping. Residue THR 655 is missing expected H atoms. Skipping. Residue LEU 658 is missing expected H atoms. Skipping. Residue ILE 907 is missing expected H atoms. Skipping. Residue ILE 909 is missing expected H atoms. Skipping. Residue SER 911 is missing expected H atoms. Skipping. Residue THR 912 is missing expected H atoms. Skipping. Residue LYS 913 is missing expected H atoms. Skipping. Residue TYR 914 is missing expected H atoms. Skipping. Residue SER 915 is missing expected H atoms. Skipping. Residue LYS 916 is missing expected H atoms. Skipping. Evaluate side-chains 176 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 167 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 ARG cc_start: 0.6530 (ptm160) cc_final: 0.6261 (ptm160) REVERT: A 307 ARG cc_start: 0.8056 (ptp-110) cc_final: 0.7787 (ptp-110) REVERT: A 325 MET cc_start: 0.7225 (mtt) cc_final: 0.7019 (mtt) REVERT: A 477 ASN cc_start: 0.8003 (t0) cc_final: 0.7439 (m-40) REVERT: A 771 TYR cc_start: 0.7248 (m-80) cc_final: 0.6600 (m-80) REVERT: A 791 LYS cc_start: 0.8408 (pttt) cc_final: 0.8099 (ptmm) REVERT: A 851 GLN cc_start: 0.7332 (pt0) cc_final: 0.7051 (pt0) REVERT: A 1066 THR cc_start: 0.7772 (m) cc_final: 0.7516 (p) REVERT: A 1345 TYR cc_start: 0.7061 (t80) cc_final: 0.6739 (t80) REVERT: A 1547 GLU cc_start: 0.7151 (mt-10) cc_final: 0.6702 (mt-10) REVERT: A 1746 TYR cc_start: 0.7616 (m-80) cc_final: 0.7394 (m-80) REVERT: A 1768 LYS cc_start: 0.6977 (mttt) cc_final: 0.6678 (mmmt) outliers start: 9 outliers final: 6 residues processed: 172 average time/residue: 0.3310 time to fit residues: 73.3443 Evaluate side-chains 167 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 161 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 703 HIS Chi-restraints excluded: chain A residue 1657 ILE 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: 72.0878 > 50: distance: 32 - 410: 36.307 distance: 204 - 254: 36.179 distance: 210 - 276: 33.138 distance: 224 - 295: 37.738 distance: 239 - 254: 34.583 distance: 240 - 310: 35.776 distance: 254 - 255: 56.312 distance: 255 - 256: 57.432 distance: 255 - 258: 56.093 distance: 255 - 264: 57.047 distance: 256 - 257: 56.647 distance: 256 - 276: 40.027 distance: 257 - 334: 39.645 distance: 258 - 259: 39.818 distance: 259 - 260: 39.149 distance: 259 - 267: 40.914 distance: 260 - 270: 40.943 distance: 261 - 272: 40.078 distance: 262 - 275: 40.649 distance: 276 - 284: 39.260 distance: 277 - 278: 56.395 distance: 277 - 280: 39.557 distance: 277 - 285: 40.347 distance: 278 - 279: 40.585 distance: 278 - 295: 40.764 distance: 279 - 353: 71.235 distance: 280 - 281: 57.899 distance: 280 - 286: 55.888 distance: 281 - 283: 39.439 distance: 281 - 288: 39.834 distance: 282 - 289: 39.609 distance: 282 - 290: 56.807 distance: 282 - 291: 56.655 distance: 283 - 294: 39.684 distance: 295 - 296: 40.156 distance: 296 - 297: 39.198 distance: 296 - 299: 68.926 distance: 296 - 305: 40.327 distance: 298 - 372: 39.158 distance: 299 - 306: 39.776 distance: 299 - 307: 40.315 distance: 301 - 302: 56.412 distance: 310 - 311: 41.162 distance: 310 - 321: 40.105 distance: 311 - 314: 39.324 distance: 312 - 313: 40.112 distance: 314 - 315: 56.201 distance: 314 - 323: 56.313 distance: 314 - 324: 40.306 distance: 315 - 316: 39.585 distance: 315 - 325: 40.668 distance: 316 - 327: 57.229 distance: 316 - 328: 39.937 distance: 317 - 318: 56.795 distance: 317 - 329: 40.631 distance: 318 - 319: 56.717 distance: 319 - 330: 57.325 distance: 319 - 331: 39.438 distance: 335 - 343: 40.355 distance: 338 - 339: 40.454 distance: 338 - 344: 69.518 distance: 340 - 347: 57.092 distance: 340 - 348: 40.123 distance: 340 - 349: 40.690 distance: 353 - 361: 39.979 distance: 354 - 355: 57.029 distance: 357 - 358: 57.655 distance: 357 - 364: 39.369 distance: 358 - 359: 56.842 distance: 358 - 360: 55.717 distance: 360 - 369: 39.939 distance: 360 - 370: 39.885 distance: 360 - 371: 40.416 distance: 374 - 375: 39.659 distance: 374 - 396: 7.920 distance: 377 - 378: 40.195 distance: 377 - 388: 39.832 distance: 378 - 390: 40.448 distance: 396 - 397: 30.704 distance: 396 - 402: 9.675 distance: 397 - 398: 39.203 distance: 397 - 403: 39.609 distance: 398 - 407: 69.905 distance: 400 - 404: 45.534 distance: 407 - 408: 56.217 distance: 407 - 415: 40.518 distance: 408 - 411: 56.476 distance: 408 - 416: 40.547 distance: 409 - 410: 56.511 distance: 412 - 414: 56.726 distance: 419 - 420: 40.186 distance: 419 - 424: 39.979 distance: 420 - 421: 56.536 distance: 420 - 423: 40.463 distance: 421 - 422: 40.685 distance: 421 - 429: 33.966 distance: 423 - 426: 69.470 distance: 423 - 427: 40.731 distance: 423 - 428: 40.493