Starting phenix.real_space_refine on Fri Jul 19 09:10:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8huj_35041/07_2024/8huj_35041_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8huj_35041/07_2024/8huj_35041.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8huj_35041/07_2024/8huj_35041.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8huj_35041/07_2024/8huj_35041.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8huj_35041/07_2024/8huj_35041_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8huj_35041/07_2024/8huj_35041_neut.cif" } resolution = 3.76 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 99 5.49 5 Mg 3 5.21 5 S 35 5.16 5 C 4108 2.51 5 N 1261 2.21 5 O 1637 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 95": "OE1" <-> "OE2" Residue "A ASP 125": "OD1" <-> "OD2" Residue "A ASP 164": "OD1" <-> "OD2" Residue "A TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 244": "OE1" <-> "OE2" Residue "A TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 254": "OE1" <-> "OE2" Residue "A ASP 265": "OD1" <-> "OD2" Residue "A TYR 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 268": "OE1" <-> "OE2" Residue "A GLU 310": "OE1" <-> "OE2" Residue "A ASP 337": "OD1" <-> "OD2" Residue "A ARG 362": "NH1" <-> "NH2" Residue "A PHE 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 380": "OD1" <-> "OD2" Residue "A ARG 382": "NH1" <-> "NH2" Residue "A GLU 388": "OE1" <-> "OE2" Residue "A TYR 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 396": "OE1" <-> "OE2" Residue "A ASP 404": "OD1" <-> "OD2" Residue "B GLU 791": "OE1" <-> "OE2" Residue "B ASP 799": "OD1" <-> "OD2" Residue "B GLU 808": "OE1" <-> "OE2" Residue "B ASP 856": "OD1" <-> "OD2" Residue "B GLU 859": "OE1" <-> "OE2" Residue "B GLU 870": "OE1" <-> "OE2" Residue "B GLU 875": "OE1" <-> "OE2" Residue "B GLU 882": "OE1" <-> "OE2" Residue "B GLU 883": "OE1" <-> "OE2" Residue "B GLU 904": "OE1" <-> "OE2" Residue "B GLU 930": "OE1" <-> "OE2" Residue "B ARG 937": "NH1" <-> "NH2" Residue "B TYR 958": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 968": "OE1" <-> "OE2" Residue "B PHE 977": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 7143 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3067 Classifications: {'peptide': 383} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 372} Chain: "B" Number of atoms: 1951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1951 Classifications: {'peptide': 238} Link IDs: {'PTRANS': 5, 'TRANS': 232} Chain: "C" Number of atoms: 2121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 2121 Classifications: {'RNA': 99} Modifications used: {'rna2p_pur': 11, 'rna2p_pyr': 3, 'rna3p_pur': 44, 'rna3p_pyr': 41} Link IDs: {'rna2p': 14, 'rna3p': 84} Chain breaks: 2 Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3, 'water': 1} Link IDs: {None: 3} Time building chain proxies: 4.41, per 1000 atoms: 0.62 Number of scatterers: 7143 At special positions: 0 Unit cell: (100.98, 94.095, 119.34, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 35 16.00 P 99 15.00 Mg 3 11.99 O 1637 8.00 N 1261 7.00 C 4108 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 - 3.50 Amino acid : False - 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: 3.39 Conformation dependent library (CDL) restraints added in 975.4 milliseconds 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1186 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 3 sheets defined 65.1% alpha, 6.9% beta 37 base pairs and 55 stacking pairs defined. Time for finding SS restraints: 2.82 Creating SS restraints... Processing helix chain 'A' and resid 34 through 38 removed outlier: 4.101A pdb=" N ASN A 38 " --> pdb=" O ASP A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 51 Processing helix chain 'A' and resid 56 through 62 Processing helix chain 'A' and resid 63 through 69 removed outlier: 3.564A pdb=" N GLY A 69 " --> pdb=" O PRO A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 94 removed outlier: 4.207A pdb=" N PHE A 86 " --> pdb=" O LYS A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 123 Processing helix chain 'A' and resid 139 through 150 Processing helix chain 'A' and resid 158 through 167 Processing helix chain 'A' and resid 183 through 191 Processing helix chain 'A' and resid 192 through 203 Processing helix chain 'A' and resid 217 through 228 removed outlier: 3.585A pdb=" N LYS A 225 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 246 Processing helix chain 'A' and resid 257 through 269 removed outlier: 4.416A pdb=" N ASP A 261 " --> pdb=" O GLU A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 295 removed outlier: 3.570A pdb=" N ASP A 286 " --> pdb=" O ARG A 282 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG A 295 " --> pdb=" O LYS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 321 Processing helix chain 'A' and resid 329 through 336 Processing helix chain 'A' and resid 354 through 361 removed outlier: 3.926A pdb=" N HIS A 358 " --> pdb=" O GLU A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 365 removed outlier: 3.555A pdb=" N ARG A 365 " --> pdb=" O ARG A 362 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 362 through 365' Processing helix chain 'A' and resid 377 through 379 No H-bonds generated for 'chain 'A' and resid 377 through 379' Processing helix chain 'A' and resid 380 through 391 Processing helix chain 'A' and resid 401 through 406 removed outlier: 4.310A pdb=" N LEU A 405 " --> pdb=" O ASN A 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 771 Processing helix chain 'B' and resid 775 through 785 removed outlier: 3.714A pdb=" N LEU B 779 " --> pdb=" O MET B 775 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LYS B 781 " --> pdb=" O GLN B 777 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N GLN B 782 " --> pdb=" O GLN B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 790 through 808 Processing helix chain 'B' and resid 811 through 822 removed outlier: 3.574A pdb=" N LEU B 822 " --> pdb=" O MET B 818 " (cutoff:3.500A) Processing helix chain 'B' and resid 838 through 852 Processing helix chain 'B' and resid 853 through 871 removed outlier: 3.807A pdb=" N ASP B 858 " --> pdb=" O ASP B 854 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N GLU B 859 " --> pdb=" O LYS B 855 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS B 866 " --> pdb=" O GLU B 862 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N GLU B 867 " --> pdb=" O LYS B 863 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N MET B 868 " --> pdb=" O LYS B 864 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASP B 869 " --> pdb=" O GLN B 865 " (cutoff:3.500A) Processing helix chain 'B' and resid 873 through 908 removed outlier: 3.609A pdb=" N LEU B 908 " --> pdb=" O GLU B 904 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 926 removed outlier: 3.591A pdb=" N MET B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL B 921 " --> pdb=" O HIS B 917 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS B 922 " --> pdb=" O ASP B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 928 through 947 removed outlier: 5.967A pdb=" N LYS B 944 " --> pdb=" O THR B 940 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N ASP B 945 " --> pdb=" O THR B 941 " (cutoff:3.500A) Processing helix chain 'B' and resid 948 through 950 No H-bonds generated for 'chain 'B' and resid 948 through 950' Processing helix chain 'B' and resid 951 through 969 removed outlier: 3.570A pdb=" N PHE B 959 " --> pdb=" O MET B 955 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ASN B 960 " --> pdb=" O ASP B 956 " (cutoff:3.500A) Processing helix chain 'B' and resid 972 through 988 Processing sheet with id=AA1, first strand: chain 'A' and resid 131 through 133 removed outlier: 6.462A pdb=" N HIS A 132 " --> pdb=" O VAL A 156 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N LEU A 104 " --> pdb=" O VAL A 180 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N ASP A 182 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N LEU A 106 " --> pdb=" O ASP A 182 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N PHE A 179 " --> pdb=" O VAL A 210 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N LEU A 212 " --> pdb=" O PHE A 179 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N LEU A 181 " --> pdb=" O LEU A 212 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N VAL A 72 " --> pdb=" O LEU A 211 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N SER A 213 " --> pdb=" O VAL A 72 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ALA A 74 " --> pdb=" O SER A 213 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 300 through 301 removed outlier: 6.490A pdb=" N SER A 300 " --> pdb=" O ILE A 327 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ALA A 275 " --> pdb=" O LEU A 326 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N THR A 328 " --> pdb=" O ALA A 275 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ILE A 277 " --> pdb=" O THR A 328 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 827 through 828 269 hydrogen bonds defined for protein. 792 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 93 hydrogen bonds 146 hydrogen bond angles 0 basepair planarities 37 basepair parallelities 55 stacking parallelities Total time for adding SS restraints: 2.66 Time building geometry restraints manager: 3.65 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: 1756 1.33 - 1.46: 1895 1.46 - 1.58: 3551 1.58 - 1.70: 195 1.70 - 1.82: 60 Bond restraints: 7457 Sorted by residual: bond pdb=" N VAL B 835 " pdb=" CA VAL B 835 " ideal model delta sigma weight residual 1.455 1.493 -0.038 1.32e-02 5.74e+03 8.07e+00 bond pdb=" N THR B 829 " pdb=" CA THR B 829 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.23e-02 6.61e+03 6.87e+00 bond pdb=" N MET A 187 " pdb=" CA MET A 187 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.21e-02 6.83e+03 6.79e+00 bond pdb=" N LYS A 369 " pdb=" CA LYS A 369 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.19e-02 7.06e+03 6.73e+00 bond pdb=" N VAL A 180 " pdb=" CA VAL A 180 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.19e-02 7.06e+03 6.41e+00 ... (remaining 7452 not shown) Histogram of bond angle deviations from ideal: 96.27 - 103.80: 334 103.80 - 111.34: 3470 111.34 - 118.87: 2956 118.87 - 126.40: 3437 126.40 - 133.94: 330 Bond angle restraints: 10527 Sorted by residual: angle pdb=" CA PHE B 839 " pdb=" CB PHE B 839 " pdb=" CG PHE B 839 " ideal model delta sigma weight residual 113.80 119.00 -5.20 1.00e+00 1.00e+00 2.70e+01 angle pdb=" O3' U C 778 " pdb=" C3' U C 778 " pdb=" C2' U C 778 " ideal model delta sigma weight residual 113.70 121.48 -7.78 1.50e+00 4.44e-01 2.69e+01 angle pdb=" N ARG A 368 " pdb=" CA ARG A 368 " pdb=" C ARG A 368 " ideal model delta sigma weight residual 111.28 106.15 5.13 1.09e+00 8.42e-01 2.22e+01 angle pdb=" C4' U C 778 " pdb=" C3' U C 778 " pdb=" O3' U C 778 " ideal model delta sigma weight residual 113.00 119.98 -6.98 1.50e+00 4.44e-01 2.17e+01 angle pdb=" CA VAL B 835 " pdb=" C VAL B 835 " pdb=" O VAL B 835 " ideal model delta sigma weight residual 121.92 117.02 4.90 1.17e+00 7.31e-01 1.75e+01 ... (remaining 10522 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.18: 4196 31.18 - 62.37: 405 62.37 - 93.55: 108 93.55 - 124.74: 2 124.74 - 155.92: 1 Dihedral angle restraints: 4712 sinusoidal: 2893 harmonic: 1819 Sorted by residual: dihedral pdb=" C5' A C 687 " pdb=" C4' A C 687 " pdb=" C3' A C 687 " pdb=" O3' A C 687 " ideal model delta sinusoidal sigma weight residual 147.00 108.10 38.90 1 8.00e+00 1.56e-02 3.33e+01 dihedral pdb=" O4' A C 687 " pdb=" C4' A C 687 " pdb=" C3' A C 687 " pdb=" C2' A C 687 " ideal model delta sinusoidal sigma weight residual 24.00 -8.41 32.41 1 8.00e+00 1.56e-02 2.34e+01 dihedral pdb=" O4' A C 687 " pdb=" C1' A C 687 " pdb=" N9 A C 687 " pdb=" C4 A C 687 " ideal model delta sinusoidal sigma weight residual -106.00 -172.85 66.85 1 1.70e+01 3.46e-03 2.02e+01 ... (remaining 4709 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 1157 0.101 - 0.202: 94 0.202 - 0.302: 22 0.302 - 0.403: 1 0.403 - 0.504: 1 Chirality restraints: 1275 Sorted by residual: chirality pdb=" C3' U C 778 " pdb=" C4' U C 778 " pdb=" O3' U C 778 " pdb=" C2' U C 778 " both_signs ideal model delta sigma weight residual False -2.48 -1.97 -0.50 2.00e-01 2.50e+01 6.35e+00 chirality pdb=" C3' A C 771 " pdb=" C4' A C 771 " pdb=" O3' A C 771 " pdb=" C2' A C 771 " both_signs ideal model delta sigma weight residual False -2.48 -2.78 0.31 2.00e-01 2.50e+01 2.33e+00 chirality pdb=" P G C 766 " pdb=" OP1 G C 766 " pdb=" OP2 G C 766 " pdb=" O5' G C 766 " both_signs ideal model delta sigma weight residual True 2.41 -2.69 -0.28 2.00e-01 2.50e+01 2.01e+00 ... (remaining 1272 not shown) Planarity restraints: 979 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 158 " -0.014 2.00e-02 2.50e+03 2.74e-02 7.48e+00 pdb=" C THR A 158 " 0.047 2.00e-02 2.50e+03 pdb=" O THR A 158 " -0.017 2.00e-02 2.50e+03 pdb=" N PRO A 159 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 64 " 0.032 5.00e-02 4.00e+02 4.84e-02 3.74e+00 pdb=" N PRO A 65 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 65 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 65 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 86 " 0.013 2.00e-02 2.50e+03 1.39e-02 3.37e+00 pdb=" CG PHE A 86 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 PHE A 86 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE A 86 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE A 86 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 86 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 86 " 0.002 2.00e-02 2.50e+03 ... (remaining 976 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 829 2.74 - 3.28: 7178 3.28 - 3.82: 13651 3.82 - 4.36: 15716 4.36 - 4.90: 22689 Nonbonded interactions: 60063 Sorted by model distance: nonbonded pdb=" O ASP A 348 " pdb=" NH1 ARG A 359 " model vdw 2.203 2.520 nonbonded pdb=" O CYS B 936 " pdb=" OG1 THR B 940 " model vdw 2.209 2.440 nonbonded pdb=" O ILE A 246 " pdb=" NE2 GLN A 248 " model vdw 2.244 2.520 nonbonded pdb=" O2 C C 746 " pdb=" N6 A C 750 " model vdw 2.249 2.520 nonbonded pdb=" N GLU A 379 " pdb=" OE1 GLU A 379 " model vdw 2.278 2.520 ... (remaining 60058 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.100 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: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 25.100 Find NCS groups from input model: 0.070 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:2.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 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 : 0.005 0.038 7457 Z= 0.314 Angle : 0.828 9.832 10527 Z= 0.518 Chirality : 0.062 0.504 1275 Planarity : 0.004 0.048 979 Dihedral : 22.476 155.919 3526 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.51 % Allowed : 26.21 % Favored : 71.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.34), residues: 617 helix: 0.44 (0.28), residues: 340 sheet: -0.76 (0.64), residues: 61 loop : -1.08 (0.43), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 287 HIS 0.003 0.001 HIS A 303 PHE 0.032 0.003 PHE A 86 TYR 0.009 0.002 TYR A 170 ARG 0.007 0.001 ARG A 190 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 62 time to evaluate : 0.673 Fit side-chains revert: symmetry clash REVERT: A 178 MET cc_start: 0.5083 (mtm) cc_final: 0.4264 (mtm) REVERT: A 228 MET cc_start: 0.4751 (tmm) cc_final: 0.4451 (tmm) REVERT: B 845 ASN cc_start: 0.8227 (OUTLIER) cc_final: 0.7996 (t0) REVERT: B 890 ILE cc_start: 0.8839 (mm) cc_final: 0.8495 (mm) outliers start: 14 outliers final: 5 residues processed: 75 average time/residue: 0.2211 time to fit residues: 21.7285 Evaluate side-chains 66 residues out of total 557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 60 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 HIS Chi-restraints excluded: chain A residue 368 ARG Chi-restraints excluded: chain B residue 827 VAL Chi-restraints excluded: chain B residue 829 THR Chi-restraints excluded: chain B residue 845 ASN Chi-restraints excluded: chain B residue 893 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 59 optimal weight: 10.0000 chunk 53 optimal weight: 7.9990 chunk 29 optimal weight: 10.0000 chunk 18 optimal weight: 1.9990 chunk 35 optimal weight: 9.9990 chunk 28 optimal weight: 9.9990 chunk 54 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 40 optimal weight: 6.9990 chunk 63 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 GLN ** A 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 777 GLN B 960 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.1206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7457 Z= 0.252 Angle : 0.635 8.116 10527 Z= 0.322 Chirality : 0.038 0.181 1275 Planarity : 0.004 0.043 979 Dihedral : 21.829 159.970 2234 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 15.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 4.13 % Allowed : 25.85 % Favored : 70.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.35), residues: 617 helix: 0.77 (0.27), residues: 356 sheet: -0.78 (0.60), residues: 68 loop : -0.66 (0.50), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 287 HIS 0.003 0.001 HIS A 303 PHE 0.032 0.003 PHE B 977 TYR 0.014 0.002 TYR A 48 ARG 0.005 0.000 ARG A 362 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 67 time to evaluate : 0.637 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 187 MET cc_start: 0.6381 (tmm) cc_final: 0.5940 (ppp) REVERT: A 228 MET cc_start: 0.4643 (tmm) cc_final: 0.4262 (tmm) REVERT: A 293 HIS cc_start: 0.7760 (t-90) cc_final: 0.7533 (t-90) REVERT: B 853 LYS cc_start: 0.7208 (OUTLIER) cc_final: 0.6789 (ptpt) REVERT: B 890 ILE cc_start: 0.8772 (mm) cc_final: 0.8468 (mm) outliers start: 23 outliers final: 15 residues processed: 87 average time/residue: 0.2017 time to fit residues: 23.2941 Evaluate side-chains 80 residues out of total 557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 64 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 798 ILE Chi-restraints excluded: chain B residue 827 VAL Chi-restraints excluded: chain B residue 829 THR Chi-restraints excluded: chain B residue 834 THR Chi-restraints excluded: chain B residue 853 LYS Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 893 ARG Chi-restraints excluded: chain B residue 899 ILE Chi-restraints excluded: chain B residue 940 THR Chi-restraints excluded: chain B residue 975 ILE Chi-restraints excluded: chain B residue 981 ASP Chi-restraints excluded: chain B residue 982 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 35 optimal weight: 9.9990 chunk 19 optimal weight: 6.9990 chunk 52 optimal weight: 6.9990 chunk 43 optimal weight: 7.9990 chunk 17 optimal weight: 10.0000 chunk 63 optimal weight: 10.0000 chunk 68 optimal weight: 20.0000 chunk 56 optimal weight: 0.9990 chunk 21 optimal weight: 8.9990 chunk 51 optimal weight: 20.0000 chunk 62 optimal weight: 10.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 7457 Z= 0.326 Angle : 0.672 8.900 10527 Z= 0.340 Chirality : 0.039 0.210 1275 Planarity : 0.004 0.041 979 Dihedral : 21.863 158.602 2226 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 16.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 6.46 % Allowed : 26.21 % Favored : 67.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.35), residues: 617 helix: 0.74 (0.27), residues: 357 sheet: -0.76 (0.61), residues: 68 loop : -0.64 (0.50), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 287 HIS 0.004 0.001 HIS A 303 PHE 0.048 0.003 PHE B 977 TYR 0.019 0.002 TYR A 48 ARG 0.008 0.001 ARG A 362 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 64 time to evaluate : 0.747 Fit side-chains REVERT: A 181 LEU cc_start: 0.7867 (OUTLIER) cc_final: 0.7318 (tp) REVERT: A 187 MET cc_start: 0.6598 (tmm) cc_final: 0.6039 (ppp) REVERT: A 193 LYS cc_start: 0.4902 (OUTLIER) cc_final: 0.4663 (tptt) REVERT: B 791 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7981 (tt0) REVERT: B 855 LYS cc_start: 0.7203 (mmtm) cc_final: 0.6813 (mttm) REVERT: B 890 ILE cc_start: 0.8839 (mm) cc_final: 0.8544 (mm) REVERT: B 986 ARG cc_start: 0.7475 (OUTLIER) cc_final: 0.6941 (ttt-90) outliers start: 36 outliers final: 22 residues processed: 96 average time/residue: 0.2152 time to fit residues: 27.8308 Evaluate side-chains 88 residues out of total 557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 62 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 193 LYS Chi-restraints excluded: chain A residue 230 ASP Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 791 GLU Chi-restraints excluded: chain B residue 798 ILE Chi-restraints excluded: chain B residue 827 VAL Chi-restraints excluded: chain B residue 834 THR Chi-restraints excluded: chain B residue 869 ASP Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 889 ASP Chi-restraints excluded: chain B residue 893 ARG Chi-restraints excluded: chain B residue 899 ILE Chi-restraints excluded: chain B residue 918 ASP Chi-restraints excluded: chain B residue 927 HIS Chi-restraints excluded: chain B residue 936 CYS Chi-restraints excluded: chain B residue 940 THR Chi-restraints excluded: chain B residue 975 ILE Chi-restraints excluded: chain B residue 982 VAL Chi-restraints excluded: chain B residue 986 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 47 optimal weight: 7.9990 chunk 33 optimal weight: 5.9990 chunk 7 optimal weight: 40.0000 chunk 30 optimal weight: 7.9990 chunk 42 optimal weight: 2.9990 chunk 63 optimal weight: 10.0000 chunk 67 optimal weight: 30.0000 chunk 60 optimal weight: 6.9990 chunk 18 optimal weight: 10.0000 chunk 56 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7457 Z= 0.231 Angle : 0.593 8.910 10527 Z= 0.300 Chirality : 0.037 0.189 1275 Planarity : 0.004 0.042 979 Dihedral : 21.604 159.076 2225 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 15.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 7.90 % Allowed : 25.31 % Favored : 66.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.35), residues: 617 helix: 1.01 (0.27), residues: 356 sheet: -0.82 (0.61), residues: 68 loop : -0.64 (0.51), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 27 HIS 0.003 0.001 HIS A 303 PHE 0.033 0.002 PHE B 977 TYR 0.012 0.002 TYR A 48 ARG 0.006 0.000 ARG A 362 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 69 time to evaluate : 0.709 Fit side-chains revert: symmetry clash REVERT: A 143 GLU cc_start: 0.2355 (OUTLIER) cc_final: 0.2082 (mt-10) REVERT: A 181 LEU cc_start: 0.7834 (OUTLIER) cc_final: 0.7415 (tp) REVERT: A 187 MET cc_start: 0.6648 (tmm) cc_final: 0.6153 (ppp) REVERT: A 293 HIS cc_start: 0.7732 (t-90) cc_final: 0.7517 (t-90) REVERT: B 855 LYS cc_start: 0.7142 (mmtm) cc_final: 0.6744 (mttm) REVERT: B 890 ILE cc_start: 0.8817 (mm) cc_final: 0.8610 (mm) REVERT: B 986 ARG cc_start: 0.7447 (OUTLIER) cc_final: 0.7016 (ttt-90) outliers start: 44 outliers final: 29 residues processed: 105 average time/residue: 0.1884 time to fit residues: 26.5478 Evaluate side-chains 96 residues out of total 557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 64 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 143 GLU Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 230 ASP Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 353 ARG Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain B residue 772 THR Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 798 ILE Chi-restraints excluded: chain B residue 827 VAL Chi-restraints excluded: chain B residue 829 THR Chi-restraints excluded: chain B residue 834 THR Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 899 ILE Chi-restraints excluded: chain B residue 918 ASP Chi-restraints excluded: chain B residue 927 HIS Chi-restraints excluded: chain B residue 936 CYS Chi-restraints excluded: chain B residue 940 THR Chi-restraints excluded: chain B residue 981 ASP Chi-restraints excluded: chain B residue 982 VAL Chi-restraints excluded: chain B residue 986 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1477, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1379, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1260, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 58.7637 > 50: distance: 25 - 153: 21.104 distance: 36 - 156: 20.626 distance: 64 - 149: 9.354 distance: 84 - 88: 31.823 distance: 88 - 89: 25.838 distance: 89 - 90: 29.153 distance: 90 - 91: 39.558 distance: 90 - 92: 36.047 distance: 92 - 93: 9.206 distance: 93 - 94: 31.557 distance: 94 - 95: 12.150 distance: 94 - 96: 8.423 distance: 96 - 97: 4.281 distance: 97 - 98: 21.468 distance: 97 - 100: 27.854 distance: 98 - 99: 23.558 distance: 98 - 107: 11.987 distance: 100 - 101: 30.905 distance: 101 - 102: 12.621 distance: 102 - 103: 21.700 distance: 103 - 104: 3.085 distance: 104 - 105: 3.698 distance: 107 - 108: 15.107 distance: 108 - 109: 23.738 distance: 108 - 111: 16.131 distance: 109 - 110: 25.333 distance: 109 - 118: 15.226 distance: 111 - 112: 13.105 distance: 112 - 113: 12.519 distance: 112 - 114: 10.072 distance: 113 - 115: 10.969 distance: 114 - 116: 4.969 distance: 115 - 117: 12.191 distance: 116 - 117: 16.149 distance: 118 - 119: 15.336 distance: 119 - 120: 29.536 distance: 120 - 121: 20.664 distance: 120 - 122: 15.841 distance: 122 - 123: 19.232 distance: 123 - 124: 19.452 distance: 123 - 126: 7.136 distance: 124 - 125: 26.409 distance: 124 - 133: 35.163 distance: 126 - 127: 8.214 distance: 127 - 128: 17.851 distance: 129 - 130: 11.209 distance: 130 - 131: 6.911 distance: 130 - 132: 9.381 distance: 133 - 134: 13.750 distance: 134 - 135: 32.258 distance: 134 - 137: 5.386 distance: 135 - 136: 32.248 distance: 135 - 142: 16.276 distance: 137 - 138: 28.106 distance: 138 - 139: 24.334 distance: 139 - 140: 29.456 distance: 140 - 141: 22.326 distance: 142 - 143: 17.220 distance: 143 - 144: 16.934 distance: 144 - 145: 14.801 distance: 144 - 146: 25.788 distance: 146 - 147: 23.303 distance: 147 - 148: 32.759 distance: 147 - 150: 29.305 distance: 148 - 149: 33.553 distance: 148 - 153: 12.216 distance: 150 - 151: 40.717 distance: 150 - 152: 34.242 distance: 153 - 154: 11.383 distance: 154 - 155: 20.649 distance: 154 - 157: 21.891 distance: 155 - 156: 8.339 distance: 155 - 158: 20.183