Starting phenix.real_space_refine on Thu Jul 2 21:39:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8ibz_35350/07_2026/8ibz_35350.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ibz_35350/07_2026/8ibz_35350.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8ibz_35350/07_2026/8ibz_35350.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8ibz_35350/07_2026/8ibz_35350.cif" model { file = "/net/cci-nas-00/data/ceres_data/8ibz_35350/07_2026/8ibz_35350.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ibz_35350/07_2026/8ibz_35350.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ibz_35350/07_2026/8ibz_35350.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ibz_35350/07_2026/8ibz_35350.map" } resolution = 3.04 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= 0.069 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 180 5.49 5 S 33 5.16 5 C 5747 2.51 5 N 1936 2.21 5 O 2376 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10273 Number of models: 1 Model: "" Number of chains: 3 Chain: "C" Number of atoms: 6419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 817, 6419 Classifications: {'peptide': 817} Link IDs: {'PTRANS': 40, 'TRANS': 776} Chain breaks: 2 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 5, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "E" Number of atoms: 3853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 3853 Classifications: {'RNA': 180} Modifications used: {'rna2p_pur': 15, 'rna2p_pyr': 13, 'rna3p_pur': 84, 'rna3p_pyr': 68} Link IDs: {'rna2p': 27, 'rna3p': 152} Chain breaks: 3 Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5049 SG CYS C 934 23.361 91.141 71.596 1.00 19.77 S ATOM 5075 SG CYS C 938 21.307 94.372 71.712 1.00 27.76 S ATOM 5180 SG CYS C 951 24.106 93.871 74.236 1.00 14.04 S Time building chain proxies: 2.02, per 1000 atoms: 0.20 Number of scatterers: 10273 At special positions: 0 Unit cell: (114.745, 142.89, 123.405, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 33 16.00 P 180 15.00 O 2376 8.00 N 1936 7.00 C 5747 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: 0.75 Conformation dependent library (CDL) restraints added in 167.0 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C1201 " pdb="ZN ZN C1201 " - pdb=" NE2 HIS C 946 " pdb="ZN ZN C1201 " - pdb=" SG CYS C 938 " pdb="ZN ZN C1201 " - pdb=" SG CYS C 951 " pdb="ZN ZN C1201 " - pdb=" SG CYS C 934 " Number of angles added : 3 1622 Ramachandran restraints generated. 811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1512 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 7 sheets defined 55.8% alpha, 9.7% beta 46 base pairs and 94 stacking pairs defined. Time for finding SS restraints: 1.14 Creating SS restraints... Processing helix chain 'C' and resid 260 through 283 Processing helix chain 'C' and resid 306 through 324 Processing helix chain 'C' and resid 324 through 335 Processing helix chain 'C' and resid 347 through 356 Proline residue: C 353 - end of helix Processing helix chain 'C' and resid 365 through 374 Processing helix chain 'C' and resid 393 through 399 removed outlier: 3.675A pdb=" N LYS C 397 " --> pdb=" O VAL C 393 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 436 Processing helix chain 'C' and resid 439 through 444 removed outlier: 3.649A pdb=" N GLN C 444 " --> pdb=" O GLU C 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 460 No H-bonds generated for 'chain 'C' and resid 458 through 460' Processing helix chain 'C' and resid 469 through 487 removed outlier: 3.662A pdb=" N ILE C 478 " --> pdb=" O HIS C 474 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU C 479 " --> pdb=" O PHE C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 503 through 519 removed outlier: 4.322A pdb=" N ALA C 507 " --> pdb=" O LEU C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 538 through 549 Processing helix chain 'C' and resid 552 through 565 Processing helix chain 'C' and resid 592 through 607 removed outlier: 3.850A pdb=" N ASN C 598 " --> pdb=" O PRO C 594 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL C 599 " --> pdb=" O ILE C 595 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL C 600 " --> pdb=" O LEU C 596 " (cutoff:3.500A) Processing helix chain 'C' and resid 636 through 654 Processing helix chain 'C' and resid 719 through 730 Processing helix chain 'C' and resid 733 through 744 Processing helix chain 'C' and resid 745 through 750 Processing helix chain 'C' and resid 751 through 755 Processing helix chain 'C' and resid 759 through 779 removed outlier: 3.806A pdb=" N LEU C 763 " --> pdb=" O SER C 759 " (cutoff:3.500A) Processing helix chain 'C' and resid 785 through 791 removed outlier: 4.047A pdb=" N TYR C 789 " --> pdb=" O PRO C 785 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N HIS C 790 " --> pdb=" O LYS C 786 " (cutoff:3.500A) Processing helix chain 'C' and resid 802 through 817 Proline residue: C 808 - end of helix removed outlier: 4.394A pdb=" N GLY C 817 " --> pdb=" O ARG C 813 " (cutoff:3.500A) Processing helix chain 'C' and resid 818 through 821 Processing helix chain 'C' and resid 823 through 831 removed outlier: 3.839A pdb=" N ARG C 827 " --> pdb=" O TRP C 823 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS C 831 " --> pdb=" O ARG C 827 " (cutoff:3.500A) Processing helix chain 'C' and resid 833 through 849 Processing helix chain 'C' and resid 861 through 871 Processing helix chain 'C' and resid 878 through 883 removed outlier: 4.096A pdb=" N THR C 882 " --> pdb=" O ARG C 879 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG C 883 " --> pdb=" O GLU C 880 " (cutoff:3.500A) Processing helix chain 'C' and resid 884 through 889 removed outlier: 3.615A pdb=" N THR C 888 " --> pdb=" O PRO C 885 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LYS C 889 " --> pdb=" O THR C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 899 through 911 Processing helix chain 'C' and resid 918 through 922 removed outlier: 3.513A pdb=" N SER C 921 " --> pdb=" O ILE C 918 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ARG C 922 " --> pdb=" O ARG C 919 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 918 through 922' Processing helix chain 'C' and resid 928 through 932 Processing helix chain 'C' and resid 943 through 950 Processing helix chain 'C' and resid 951 through 953 No H-bonds generated for 'chain 'C' and resid 951 through 953' Processing helix chain 'C' and resid 954 through 976 Processing helix chain 'C' and resid 1018 through 1032 removed outlier: 3.507A pdb=" N LEU C1022 " --> pdb=" O SER C1018 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LYS C1029 " --> pdb=" O GLU C1025 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N TYR C1030 " --> pdb=" O LYS C1026 " (cutoff:3.500A) Processing helix chain 'C' and resid 1035 through 1045 Processing helix chain 'C' and resid 1066 through 1076 Processing helix chain 'C' and resid 1080 through 1085 Processing helix chain 'C' and resid 1086 through 1105 removed outlier: 3.711A pdb=" N MET C1105 " --> pdb=" O ARG C1101 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 462 through 467 Processing sheet with id=AA2, first strand: chain 'C' and resid 623 through 625 Processing sheet with id=AA3, first strand: chain 'C' and resid 623 through 625 Processing sheet with id=AA4, first strand: chain 'C' and resid 614 through 615 Processing sheet with id=AA5, first strand: chain 'C' and resid 686 through 687 removed outlier: 3.644A pdb=" N LYS C 690 " --> pdb=" O ILE C 687 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 851 through 852 Processing sheet with id=AA7, first strand: chain 'C' and resid 981 through 982 removed outlier: 6.894A pdb=" N GLY C1005 " --> pdb=" O ARG C1053 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N THR C1055 " --> pdb=" O GLY C1005 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ILE C1007 " --> pdb=" O THR C1055 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N CYS C1057 " --> pdb=" O ILE C1007 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ASP C1009 " --> pdb=" O CYS C1057 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N ILE C1059 " --> pdb=" O ASP C1009 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N GLN C1011 " --> pdb=" O ILE C1059 " (cutoff:3.500A) 329 hydrogen bonds defined for protein. 936 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 116 hydrogen bonds 208 hydrogen bond angles 0 basepair planarities 46 basepair parallelities 94 stacking parallelities Total time for adding SS restraints: 1.63 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: 1.21 - 1.33: 2312 1.33 - 1.45: 3196 1.45 - 1.57: 4946 1.57 - 1.69: 356 1.69 - 1.81: 47 Bond restraints: 10857 Sorted by residual: bond pdb=" CG PRO C 822 " pdb=" CD PRO C 822 " ideal model delta sigma weight residual 1.503 1.571 -0.068 3.40e-02 8.65e+02 4.02e+00 bond pdb=" C SER C 821 " pdb=" N PRO C 822 " ideal model delta sigma weight residual 1.331 1.343 -0.011 7.90e-03 1.60e+04 2.03e+00 bond pdb=" C3' A E 179 " pdb=" O3' A E 179 " ideal model delta sigma weight residual 1.427 1.446 -0.019 1.50e-02 4.44e+03 1.58e+00 bond pdb=" CB GLU C 975 " pdb=" CG GLU C 975 " ideal model delta sigma weight residual 1.520 1.555 -0.035 3.00e-02 1.11e+03 1.40e+00 bond pdb=" C3' A E 181 " pdb=" O3' A E 181 " ideal model delta sigma weight residual 1.427 1.444 -0.017 1.50e-02 4.44e+03 1.23e+00 ... (remaining 10852 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.26: 15354 2.26 - 4.52: 171 4.52 - 6.78: 26 6.78 - 9.04: 3 9.04 - 11.30: 1 Bond angle restraints: 15555 Sorted by residual: angle pdb=" C3' U E 114 " pdb=" O3' U E 114 " pdb=" P A E 115 " ideal model delta sigma weight residual 120.20 125.61 -5.41 1.50e+00 4.44e-01 1.30e+01 angle pdb=" C3' A E 179 " pdb=" O3' A E 179 " pdb=" P A E 180 " ideal model delta sigma weight residual 120.20 125.38 -5.18 1.50e+00 4.44e-01 1.19e+01 angle pdb=" CA PRO C 822 " pdb=" N PRO C 822 " pdb=" CD PRO C 822 " ideal model delta sigma weight residual 112.00 107.33 4.67 1.40e+00 5.10e-01 1.11e+01 angle pdb=" CA LEU C 755 " pdb=" CB LEU C 755 " pdb=" CG LEU C 755 " ideal model delta sigma weight residual 116.30 127.60 -11.30 3.50e+00 8.16e-02 1.04e+01 angle pdb=" O3' C E 186 " pdb=" C3' C E 186 " pdb=" C2' C E 186 " ideal model delta sigma weight residual 109.50 114.08 -4.58 1.50e+00 4.44e-01 9.33e+00 ... (remaining 15550 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.58: 5793 35.58 - 71.17: 320 71.17 - 106.75: 24 106.75 - 142.33: 4 142.33 - 177.91: 5 Dihedral angle restraints: 6146 sinusoidal: 3805 harmonic: 2341 Sorted by residual: dihedral pdb=" C4' C E 186 " pdb=" C3' C E 186 " pdb=" C2' C E 186 " pdb=" C1' C E 186 " ideal model delta sinusoidal sigma weight residual -35.00 35.06 -70.06 1 8.00e+00 1.56e-02 9.88e+01 dihedral pdb=" C5' C E 186 " pdb=" C4' C E 186 " pdb=" C3' C E 186 " pdb=" O3' C E 186 " ideal model delta sinusoidal sigma weight residual 147.00 80.84 66.16 1 8.00e+00 1.56e-02 8.94e+01 dihedral pdb=" O4' C E 186 " pdb=" C4' C E 186 " pdb=" C3' C E 186 " pdb=" C2' C E 186 " ideal model delta sinusoidal sigma weight residual 24.00 -34.97 58.97 1 8.00e+00 1.56e-02 7.27e+01 ... (remaining 6143 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1676 0.060 - 0.121: 183 0.121 - 0.181: 15 0.181 - 0.241: 3 0.241 - 0.302: 1 Chirality restraints: 1878 Sorted by residual: chirality pdb=" C3' C E 186 " pdb=" C4' C E 186 " pdb=" O3' C E 186 " pdb=" C2' C E 186 " both_signs ideal model delta sigma weight residual False -2.74 -2.44 -0.30 2.00e-01 2.50e+01 2.28e+00 chirality pdb=" C2' C E 186 " pdb=" C3' C E 186 " pdb=" O2' C E 186 " pdb=" C1' C E 186 " both_signs ideal model delta sigma weight residual False -2.52 -2.74 0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" C1' C E 78 " pdb=" O4' C E 78 " pdb=" C2' C E 78 " pdb=" N1 C E 78 " both_signs ideal model delta sigma weight residual False 2.47 2.26 0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 1875 not shown) Planarity restraints: 1322 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 701 " 0.021 2.00e-02 2.50e+03 1.84e-02 8.46e+00 pdb=" CG TRP C 701 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 TRP C 701 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP C 701 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP C 701 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP C 701 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C 701 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 701 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 701 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP C 701 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C E 78 " -0.032 2.00e-02 2.50e+03 1.67e-02 6.30e+00 pdb=" N1 C E 78 " 0.035 2.00e-02 2.50e+03 pdb=" C2 C E 78 " -0.004 2.00e-02 2.50e+03 pdb=" O2 C E 78 " 0.006 2.00e-02 2.50e+03 pdb=" N3 C E 78 " 0.004 2.00e-02 2.50e+03 pdb=" C4 C E 78 " -0.011 2.00e-02 2.50e+03 pdb=" N4 C E 78 " -0.008 2.00e-02 2.50e+03 pdb=" C5 C E 78 " 0.001 2.00e-02 2.50e+03 pdb=" C6 C E 78 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C E 117 " -0.006 2.00e-02 2.50e+03 1.58e-02 5.62e+00 pdb=" N1 C E 117 " 0.003 2.00e-02 2.50e+03 pdb=" C2 C E 117 " 0.039 2.00e-02 2.50e+03 pdb=" O2 C E 117 " -0.021 2.00e-02 2.50e+03 pdb=" N3 C E 117 " -0.006 2.00e-02 2.50e+03 pdb=" C4 C E 117 " 0.008 2.00e-02 2.50e+03 pdb=" N4 C E 117 " -0.008 2.00e-02 2.50e+03 pdb=" C5 C E 117 " -0.003 2.00e-02 2.50e+03 pdb=" C6 C E 117 " -0.006 2.00e-02 2.50e+03 ... (remaining 1319 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 932 2.73 - 3.27: 9727 3.27 - 3.82: 18691 3.82 - 4.36: 21932 4.36 - 4.90: 33764 Nonbonded interactions: 85046 Sorted by model distance: nonbonded pdb=" O ALA C1091 " pdb=" OG SER C1095 " model vdw 2.190 3.040 nonbonded pdb=" O2 U E 109 " pdb=" O2' G E 110 " model vdw 2.193 3.040 nonbonded pdb=" O2' U E 131 " pdb=" OP1 G E 132 " model vdw 2.214 3.040 nonbonded pdb=" O2' A E 79 " pdb=" O4' A E 80 " model vdw 2.248 3.040 nonbonded pdb=" O LEU C 878 " pdb=" OG SER C 881 " model vdw 2.254 3.040 ... (remaining 85041 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.340 Find NCS groups from input model: 0.090 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:0.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 10861 Z= 0.152 Angle : 0.603 11.303 15558 Z= 0.308 Chirality : 0.038 0.302 1878 Planarity : 0.005 0.055 1322 Dihedral : 19.078 177.913 4634 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.32 % Favored : 95.56 % Rotamer: Outliers : 0.29 % Allowed : 23.75 % Favored : 75.96 % 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 are not related in a simple way. whole: 0.68 (0.31), residues: 811 helix: 1.83 (0.27), residues: 390 sheet: -0.13 (0.66), residues: 62 loop : -1.02 (0.34), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 748 TYR 0.012 0.002 TYR C 703 PHE 0.015 0.002 PHE C 753 TRP 0.050 0.002 TRP C 701 HIS 0.005 0.001 HIS C 868 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 (10857) covalent geometry : angle 0.60257 / 0.31 (15555) hydrogen bonds : bond 0.14567 / 9.69 ( 431) hydrogen bonds : angle 5.30120 / 3.82 ( 1144) metal coordination : bond 0.00247 / 0.12 ( 4) metal coordination : angle 1.24801 / 0.66 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1622 Ramachandran restraints generated. 811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1622 Ramachandran restraints generated. 811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 57 time to evaluate : 0.250 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 59 average time/residue: 0.1019 time to fit residues: 8.1883 Evaluate side-chains 54 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 53 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 1021 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 7.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.0030 chunk 65 optimal weight: 0.0040 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 10.0000 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 0.9990 overall best weight: 0.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 653 GLN C 769 GLN ** C 946 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.185864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.141112 restraints weight = 15617.438| |-----------------------------------------------------------------------------| r_work (start): 0.3926 rms_B_bonded: 2.42 r_work: 0.3499 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.0876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10861 Z= 0.115 Angle : 0.596 8.908 15558 Z= 0.296 Chirality : 0.037 0.218 1878 Planarity : 0.005 0.064 1322 Dihedral : 17.930 171.240 3069 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.82 % Favored : 96.05 % Rotamer: Outliers : 2.51 % Allowed : 23.45 % Favored : 74.04 % 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 are not related in a simple way. whole: 0.83 (0.31), residues: 811 helix: 2.04 (0.27), residues: 396 sheet: 0.54 (0.71), residues: 56 loop : -1.21 (0.34), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 814 TYR 0.011 0.001 TYR C 703 PHE 0.013 0.001 PHE C 749 TRP 0.021 0.001 TRP C 701 HIS 0.004 0.001 HIS C1096 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.12 (10857) covalent geometry : angle 0.59606 / 0.30 (15555) hydrogen bonds : bond 0.06238 / 3.47 ( 431) hydrogen bonds : angle 3.62411 / 2.63 ( 1144) metal coordination : bond 0.01335 / 0.67 ( 4) metal coordination : angle 1.59215 / 0.82 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1622 Ramachandran restraints generated. 811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1622 Ramachandran restraints generated. 811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 59 time to evaluate : 0.294 Fit side-chains REVERT: C 401 PHE cc_start: 0.7333 (t80) cc_final: 0.7096 (t80) REVERT: C 704 LEU cc_start: 0.6910 (OUTLIER) cc_final: 0.6514 (pp) REVERT: C 1072 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7545 (mt-10) REVERT: C 1105 MET cc_start: 0.7484 (ppp) cc_final: 0.6760 (ppp) outliers start: 17 outliers final: 8 residues processed: 75 average time/residue: 0.1125 time to fit residues: 11.5924 Evaluate side-chains 63 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 53 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 410 ASP Chi-restraints excluded: chain C residue 677 HIS Chi-restraints excluded: chain C residue 701 TRP Chi-restraints excluded: chain C residue 704 LEU Chi-restraints excluded: chain C residue 706 VAL Chi-restraints excluded: chain C residue 861 VAL Chi-restraints excluded: chain C residue 1004 VAL Chi-restraints excluded: chain C residue 1013 VAL Chi-restraints excluded: chain C residue 1046 LEU Chi-restraints excluded: chain C residue 1072 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 58.1443 > 50: distance: 49 - 65: 25.210 distance: 61 - 65: 23.545 distance: 65 - 66: 15.252 distance: 66 - 67: 30.371 distance: 66 - 69: 25.039 distance: 67 - 68: 4.943 distance: 67 - 70: 19.055 distance: 70 - 71: 10.838 distance: 70 - 76: 37.216 distance: 71 - 72: 17.805 distance: 71 - 74: 22.381 distance: 72 - 73: 19.157 distance: 72 - 77: 10.660 distance: 74 - 75: 26.532 distance: 75 - 76: 42.051 distance: 77 - 78: 26.398 distance: 78 - 79: 30.293 distance: 78 - 81: 19.205 distance: 79 - 80: 11.111 distance: 79 - 85: 14.909 distance: 82 - 83: 4.901 distance: 82 - 84: 39.788 distance: 85 - 86: 11.065 distance: 86 - 87: 26.432 distance: 86 - 89: 21.231 distance: 87 - 88: 14.820 distance: 87 - 94: 16.057 distance: 88 - 119: 21.946 distance: 89 - 90: 37.353 distance: 90 - 91: 38.878 distance: 91 - 92: 21.375 distance: 92 - 93: 14.011 distance: 94 - 95: 18.908 distance: 94 - 100: 16.936 distance: 95 - 96: 19.062 distance: 95 - 98: 24.577 distance: 96 - 97: 16.663 distance: 96 - 101: 29.458 distance: 97 - 130: 21.457 distance: 98 - 99: 19.055 distance: 99 - 100: 41.400 distance: 101 - 102: 12.266 distance: 102 - 103: 11.572 distance: 102 - 105: 17.640 distance: 103 - 104: 22.873 distance: 103 - 110: 23.121 distance: 104 - 138: 27.946 distance: 105 - 106: 12.384 distance: 106 - 107: 13.242 distance: 107 - 108: 5.939 distance: 107 - 109: 12.095 distance: 110 - 111: 17.610 distance: 111 - 112: 21.464 distance: 111 - 114: 29.683 distance: 112 - 113: 22.832 distance: 112 - 119: 26.006 distance: 113 - 147: 35.549 distance: 114 - 115: 36.656 distance: 115 - 116: 6.625 distance: 116 - 117: 11.780 distance: 116 - 118: 17.932 distance: 119 - 120: 16.488 distance: 120 - 121: 25.079 distance: 120 - 123: 19.806 distance: 121 - 122: 18.735 distance: 121 - 130: 10.708 distance: 122 - 155: 14.063 distance: 123 - 124: 14.547 distance: 124 - 125: 21.311 distance: 125 - 126: 16.241 distance: 126 - 127: 9.145 distance: 127 - 128: 8.024 distance: 127 - 129: 8.269 distance: 130 - 131: 14.826 distance: 131 - 132: 5.759 distance: 131 - 134: 16.993 distance: 132 - 133: 10.763 distance: 132 - 138: 15.959 distance: 133 - 162: 32.227 distance: 134 - 135: 15.818 distance: 135 - 136: 12.594 distance: 135 - 137: 4.887 distance: 138 - 139: 12.109 distance: 139 - 140: 5.309 distance: 139 - 142: 7.907 distance: 140 - 141: 11.727 distance: 140 - 147: 9.131 distance: 141 - 173: 12.618 distance: 142 - 143: 18.117 distance: 143 - 144: 3.659 distance: 144 - 145: 13.016 distance: 144 - 146: 8.986