Starting phenix.real_space_refine on Thu Jan 18 05:43:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ies_35392/01_2024/8ies_35392_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ies_35392/01_2024/8ies_35392.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ies_35392/01_2024/8ies_35392.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ies_35392/01_2024/8ies_35392.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ies_35392/01_2024/8ies_35392_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ies_35392/01_2024/8ies_35392_updated.pdb" } resolution = 3.73 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= 0.002 sd= 0.056 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: 8 Type Number sf(0) Gaussians Al 1 5.89 5 P 2 5.49 5 Mg 1 5.21 5 S 53 5.16 5 C 5129 2.51 5 N 1367 2.21 5 O 1408 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "P TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 192": "NH1" <-> "NH2" Residue "P ASP 196": "OD1" <-> "OD2" Residue "P TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 286": "NH1" <-> "NH2" Residue "P ASP 287": "OD1" <-> "OD2" Residue "P GLU 305": "OE1" <-> "OE2" Residue "P ASP 308": "OD1" <-> "OD2" Residue "P ARG 415": "NH1" <-> "NH2" Residue "P PHE 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 487": "NH1" <-> "NH2" Residue "P GLU 542": "OE1" <-> "OE2" Residue "P ARG 627": "NH1" <-> "NH2" Residue "P ARG 709": "NH1" <-> "NH2" Residue "P ASP 710": "OD1" <-> "OD2" Residue "P ARG 745": "NH1" <-> "NH2" Residue "P GLU 771": "OE1" <-> "OE2" Residue "P ARG 853": "NH1" <-> "NH2" Residue "P GLU 861": "OE1" <-> "OE2" Residue "P TYR 871": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 906": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 1029": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 1034": "NH1" <-> "NH2" Residue "P GLU 1046": "OE1" <-> "OE2" Residue "P ARG 1072": "NH1" <-> "NH2" Residue "P PHE 1116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 1135": "OE1" <-> "OE2" Residue "P ARG 1150": "NH1" <-> "NH2" Residue "P GLU 1163": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 7965 Number of models: 1 Model: "" Number of chains: 2 Chain: "P" Number of atoms: 7932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1026, 7932 Classifications: {'peptide': 1026} Link IDs: {'PTRANS': 69, 'TRANS': 956} Chain breaks: 4 Chain: "P" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'ALF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 4.46, per 1000 atoms: 0.56 Number of scatterers: 7965 At special positions: 0 Unit cell: (96.36, 91.98, 131.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 53 16.00 P 2 15.00 Al 1 13.00 Mg 1 11.99 F 4 9.00 O 1408 8.00 N 1367 7.00 C 5129 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.17 Conformation dependent library (CDL) restraints added in 1.5 seconds 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1916 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 34 helices and 8 sheets defined 36.1% alpha, 7.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.01 Creating SS restraints... Processing helix chain 'P' and resid 50 through 57 removed outlier: 4.292A pdb=" N TRP P 55 " --> pdb=" O HIS P 51 " (cutoff:3.500A) Processing helix chain 'P' and resid 60 through 62 No H-bonds generated for 'chain 'P' and resid 60 through 62' Processing helix chain 'P' and resid 69 through 75 removed outlier: 3.592A pdb=" N VAL P 73 " --> pdb=" O PRO P 69 " (cutoff:3.500A) Processing helix chain 'P' and resid 195 through 198 No H-bonds generated for 'chain 'P' and resid 195 through 198' Processing helix chain 'P' and resid 228 through 233 Processing helix chain 'P' and resid 239 through 254 removed outlier: 3.599A pdb=" N ASP P 254 " --> pdb=" O LEU P 250 " (cutoff:3.500A) Processing helix chain 'P' and resid 259 through 286 removed outlier: 3.934A pdb=" N LEU P 285 " --> pdb=" O GLN P 281 " (cutoff:3.500A) Processing helix chain 'P' and resid 403 through 411 Processing helix chain 'P' and resid 424 through 449 Processing helix chain 'P' and resid 457 through 466 Processing helix chain 'P' and resid 473 through 477 removed outlier: 3.507A pdb=" N MET P 477 " --> pdb=" O LEU P 473 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 473 through 477' Processing helix chain 'P' and resid 479 through 488 Processing helix chain 'P' and resid 504 through 506 No H-bonds generated for 'chain 'P' and resid 504 through 506' Processing helix chain 'P' and resid 549 through 556 removed outlier: 4.025A pdb=" N LEU P 552 " --> pdb=" O GLY P 549 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ARG P 553 " --> pdb=" O PRO P 550 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ALA P 554 " --> pdb=" O LEU P 551 " (cutoff:3.500A) Processing helix chain 'P' and resid 572 through 579 Processing helix chain 'P' and resid 610 through 612 No H-bonds generated for 'chain 'P' and resid 610 through 612' Processing helix chain 'P' and resid 657 through 662 removed outlier: 4.256A pdb=" N GLY P 662 " --> pdb=" O GLU P 658 " (cutoff:3.500A) Processing helix chain 'P' and resid 673 through 681 removed outlier: 3.737A pdb=" N GLN P 678 " --> pdb=" O ALA P 674 " (cutoff:3.500A) Processing helix chain 'P' and resid 697 through 703 Processing helix chain 'P' and resid 733 through 740 Processing helix chain 'P' and resid 754 through 764 removed outlier: 3.874A pdb=" N CYS P 764 " --> pdb=" O VAL P 760 " (cutoff:3.500A) Processing helix chain 'P' and resid 827 through 831 Processing helix chain 'P' and resid 841 through 847 removed outlier: 4.045A pdb=" N VAL P 846 " --> pdb=" O PRO P 842 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N GLN P 847 " --> pdb=" O LYS P 843 " (cutoff:3.500A) Processing helix chain 'P' and resid 859 through 869 removed outlier: 3.901A pdb=" N LEU P 869 " --> pdb=" O GLU P 865 " (cutoff:3.500A) Processing helix chain 'P' and resid 883 through 888 removed outlier: 3.826A pdb=" N LYS P 887 " --> pdb=" O CYS P 883 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA P 888 " --> pdb=" O GLY P 884 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 883 through 888' Processing helix chain 'P' and resid 916 through 951 Processing helix chain 'P' and resid 960 through 968 removed outlier: 4.015A pdb=" N LEU P 964 " --> pdb=" O ASP P 960 " (cutoff:3.500A) Processing helix chain 'P' and resid 972 through 978 Processing helix chain 'P' and resid 999 through 1024 Processing helix chain 'P' and resid 1047 through 1065 removed outlier: 4.280A pdb=" N PHE P1056 " --> pdb=" O SER P1052 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLN P1057 " --> pdb=" O LEU P1053 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N TYR P1058 " --> pdb=" O SER P1054 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LEU P1059 " --> pdb=" O SER P1055 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA P1063 " --> pdb=" O LEU P1059 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL P1065 " --> pdb=" O LEU P1061 " (cutoff:3.500A) Processing helix chain 'P' and resid 1079 through 1093 Processing helix chain 'P' and resid 1118 through 1135 removed outlier: 4.148A pdb=" N LEU P1123 " --> pdb=" O LEU P1119 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE P1132 " --> pdb=" O PHE P1128 " (cutoff:3.500A) Processing helix chain 'P' and resid 1142 through 1146 Processing helix chain 'P' and resid 1158 through 1168 removed outlier: 4.088A pdb=" N GLU P1168 " --> pdb=" O ARG P1164 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'P' and resid 39 through 43 removed outlier: 4.355A pdb=" N GLY P 39 " --> pdb=" O ILE P 92 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE P 92 " --> pdb=" O GLY P 39 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU P 88 " --> pdb=" O SER P 43 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'P' and resid 166 through 168 removed outlier: 3.769A pdb=" N TYR P 166 " --> pdb=" O TYR P 173 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N TYR P 173 " --> pdb=" O TYR P 166 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'P' and resid 338 through 340 Processing sheet with id= D, first strand: chain 'P' and resid 745 through 748 Processing sheet with id= E, first strand: chain 'P' and resid 528 through 530 removed outlier: 7.311A pdb=" N LEU P 690 " --> pdb=" O LEU P 719 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N LEU P 721 " --> pdb=" O VAL P 688 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N VAL P 688 " --> pdb=" O LEU P 721 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N VAL P 723 " --> pdb=" O ARG P 686 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N ARG P 686 " --> pdb=" O VAL P 723 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA P 651 " --> pdb=" O LYS P 693 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'P' and resid 584 through 586 removed outlier: 4.073A pdb=" N VAL P 584 " --> pdb=" O MET P 615 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLN P 613 " --> pdb=" O GLU P 586 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'P' and resid 331 through 335 removed outlier: 3.831A pdb=" N VAL P 334 " --> pdb=" O LEU P 392 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N LEU P 392 " --> pdb=" O VAL P 334 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'P' and resid 823 through 825 removed outlier: 7.404A pdb=" N LEU P 825 " --> pdb=" O THR P 849 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N PHE P 851 " --> pdb=" O LEU P 825 " (cutoff:3.500A) 250 hydrogen bonds defined for protein. 729 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: 2.35 Time building geometry restraints manager: 3.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2557 1.34 - 1.46: 1664 1.46 - 1.58: 3832 1.58 - 1.69: 3 1.69 - 1.81: 83 Bond restraints: 8139 Sorted by residual: bond pdb=" F1 ALF P1201 " pdb="AL ALF P1201 " ideal model delta sigma weight residual 1.684 1.785 -0.101 2.00e-02 2.50e+03 2.57e+01 bond pdb=" F2 ALF P1201 " pdb="AL ALF P1201 " ideal model delta sigma weight residual 1.685 1.785 -0.100 2.00e-02 2.50e+03 2.50e+01 bond pdb=" F3 ALF P1201 " pdb="AL ALF P1201 " ideal model delta sigma weight residual 1.685 1.784 -0.099 2.00e-02 2.50e+03 2.47e+01 bond pdb=" F4 ALF P1201 " pdb="AL ALF P1201 " ideal model delta sigma weight residual 1.686 1.785 -0.099 2.00e-02 2.50e+03 2.46e+01 bond pdb=" C LEU P1142 " pdb=" N PRO P1143 " ideal model delta sigma weight residual 1.335 1.355 -0.020 1.28e-02 6.10e+03 2.52e+00 ... (remaining 8134 not shown) Histogram of bond angle deviations from ideal: 89.98 - 107.97: 410 107.97 - 125.97: 10542 125.97 - 143.97: 140 143.97 - 161.96: 0 161.96 - 179.96: 2 Bond angle restraints: 11094 Sorted by residual: angle pdb=" F1 ALF P1201 " pdb="AL ALF P1201 " pdb=" F2 ALF P1201 " ideal model delta sigma weight residual 108.68 179.92 -71.24 3.00e+00 1.11e-01 5.64e+02 angle pdb=" F3 ALF P1201 " pdb="AL ALF P1201 " pdb=" F4 ALF P1201 " ideal model delta sigma weight residual 109.63 179.96 -70.33 3.00e+00 1.11e-01 5.50e+02 angle pdb=" F2 ALF P1201 " pdb="AL ALF P1201 " pdb=" F4 ALF P1201 " ideal model delta sigma weight residual 110.21 89.99 20.22 3.00e+00 1.11e-01 4.54e+01 angle pdb=" F1 ALF P1201 " pdb="AL ALF P1201 " pdb=" F3 ALF P1201 " ideal model delta sigma weight residual 109.69 89.98 19.71 3.00e+00 1.11e-01 4.32e+01 angle pdb=" F2 ALF P1201 " pdb="AL ALF P1201 " pdb=" F3 ALF P1201 " ideal model delta sigma weight residual 109.59 90.02 19.57 3.00e+00 1.11e-01 4.25e+01 ... (remaining 11089 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.02: 4699 27.02 - 54.05: 204 54.05 - 81.07: 10 81.07 - 108.10: 0 108.10 - 135.12: 3 Dihedral angle restraints: 4916 sinusoidal: 1948 harmonic: 2968 Sorted by residual: dihedral pdb=" O2A ADP P1203 " pdb=" O3A ADP P1203 " pdb=" PA ADP P1203 " pdb=" PB ADP P1203 " ideal model delta sinusoidal sigma weight residual -60.00 75.12 -135.12 1 2.00e+01 2.50e-03 4.10e+01 dihedral pdb=" C5' ADP P1203 " pdb=" O5' ADP P1203 " pdb=" PA ADP P1203 " pdb=" O2A ADP P1203 " ideal model delta sinusoidal sigma weight residual -60.00 67.58 -127.57 1 2.00e+01 2.50e-03 3.86e+01 dihedral pdb=" O1B ADP P1203 " pdb=" O3A ADP P1203 " pdb=" PB ADP P1203 " pdb=" PA ADP P1203 " ideal model delta sinusoidal sigma weight residual -60.00 66.52 -126.52 1 2.00e+01 2.50e-03 3.83e+01 ... (remaining 4913 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 754 0.026 - 0.053: 351 0.053 - 0.079: 116 0.079 - 0.105: 78 0.105 - 0.132: 19 Chirality restraints: 1318 Sorted by residual: chirality pdb=" CA ILE P 350 " pdb=" N ILE P 350 " pdb=" C ILE P 350 " pdb=" CB ILE P 350 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.33e-01 chirality pdb=" CA VAL P 469 " pdb=" N VAL P 469 " pdb=" C VAL P 469 " pdb=" CB VAL P 469 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.00e-01 chirality pdb=" CA VAL P 313 " pdb=" N VAL P 313 " pdb=" C VAL P 313 " pdb=" CB VAL P 313 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.69e-01 ... (remaining 1315 not shown) Planarity restraints: 1395 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU P 617 " -0.025 5.00e-02 4.00e+02 3.79e-02 2.30e+00 pdb=" N PRO P 618 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO P 618 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO P 618 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL P 999 " 0.019 5.00e-02 4.00e+02 2.82e-02 1.27e+00 pdb=" N PRO P1000 " -0.049 5.00e-02 4.00e+02 pdb=" CA PRO P1000 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO P1000 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR P 567 " 0.018 5.00e-02 4.00e+02 2.65e-02 1.13e+00 pdb=" N PRO P 568 " -0.046 5.00e-02 4.00e+02 pdb=" CA PRO P 568 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO P 568 " 0.015 5.00e-02 4.00e+02 ... (remaining 1392 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 1962 2.79 - 3.32: 7024 3.32 - 3.85: 12363 3.85 - 4.37: 13043 4.37 - 4.90: 23219 Nonbonded interactions: 57611 Sorted by model distance: nonbonded pdb=" O THR P 515 " pdb=" F2 ALF P1201 " model vdw 2.268 2.390 nonbonded pdb=" N GLY P 879 " pdb="MG MG P1202 " model vdw 2.270 2.250 nonbonded pdb=" O ARG P 553 " pdb=" OG1 THR P 557 " model vdw 2.290 2.440 nonbonded pdb=" OG1 THR P 647 " pdb=" OE1 GLN P 648 " model vdw 2.307 2.440 nonbonded pdb=" O ASP P 967 " pdb=" OG1 THR P 972 " model vdw 2.309 2.440 ... (remaining 57606 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: 1.640 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: 6.060 Check model and map are aligned: 0.130 Set scattering table: 0.060 Process input model: 24.600 Find NCS groups from input model: 0.200 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6520 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 0.101 8139 Z= 0.204 Angle : 1.160 71.242 11094 Z= 0.454 Chirality : 0.039 0.132 1318 Planarity : 0.003 0.038 1395 Dihedral : 13.702 135.121 3000 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % 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: -3.84 (0.22), residues: 1016 helix: -0.87 (0.24), residues: 396 sheet: -2.51 (0.53), residues: 79 loop : -4.08 (0.19), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.000 TRP P 55 HIS 0.001 0.000 HIS P 51 PHE 0.003 0.000 PHE P1128 TYR 0.003 0.000 TYR P 241 ARG 0.001 0.000 ARG P 201 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 205 time to evaluate : 1.021 Fit side-chains revert: symmetry clash REVERT: P 40 TYR cc_start: 0.4402 (m-80) cc_final: 0.3237 (m-80) REVERT: P 437 LEU cc_start: 0.8732 (pp) cc_final: 0.8469 (mp) REVERT: P 641 VAL cc_start: 0.8123 (t) cc_final: 0.7740 (p) REVERT: P 942 LEU cc_start: 0.9024 (tp) cc_final: 0.8574 (tp) REVERT: P 1012 VAL cc_start: 0.7641 (t) cc_final: 0.7411 (t) REVERT: P 1046 GLU cc_start: 0.7213 (mp0) cc_final: 0.6795 (mp0) REVERT: P 1164 ARG cc_start: 0.8838 (tmm160) cc_final: 0.8636 (ptm-80) outliers start: 0 outliers final: 0 residues processed: 205 average time/residue: 0.2361 time to fit residues: 61.8342 Evaluate side-chains 118 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 3.9990 chunk 77 optimal weight: 0.4980 chunk 42 optimal weight: 0.6980 chunk 26 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 59 optimal weight: 6.9990 chunk 92 optimal weight: 4.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 106 GLN P 413 HIS P 534 GLN P 755 GLN P 822 HIS ** P 847 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 858 GLN P 867 GLN P1026 GLN ** P1033 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1057 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P1169 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.3753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 8139 Z= 0.330 Angle : 0.992 33.833 11094 Z= 0.417 Chirality : 0.046 0.254 1318 Planarity : 0.005 0.044 1395 Dihedral : 6.823 128.630 1125 Min Nonbonded Distance : 1.624 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.56 % Favored : 91.44 % Rotamer: Outliers : 2.28 % Allowed : 15.72 % Favored : 82.00 % 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: -2.78 (0.25), residues: 1016 helix: 0.46 (0.28), residues: 380 sheet: -2.97 (0.47), residues: 81 loop : -3.56 (0.21), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP P 55 HIS 0.010 0.002 HIS P 84 PHE 0.015 0.002 PHE P 512 TYR 0.025 0.002 TYR P 241 ARG 0.011 0.001 ARG P 627 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 141 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 267 SER cc_start: 0.7787 (m) cc_final: 0.7519 (p) REVERT: P 437 LEU cc_start: 0.8712 (pp) cc_final: 0.8419 (mp) REVERT: P 893 ILE cc_start: 0.8846 (mm) cc_final: 0.8581 (mm) REVERT: P 1046 GLU cc_start: 0.7395 (mp0) cc_final: 0.7038 (mp0) outliers start: 20 outliers final: 13 residues processed: 154 average time/residue: 0.1878 time to fit residues: 39.7016 Evaluate side-chains 123 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 110 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 278 THR Chi-restraints excluded: chain P residue 373 THR Chi-restraints excluded: chain P residue 424 HIS Chi-restraints excluded: chain P residue 434 VAL Chi-restraints excluded: chain P residue 464 LEU Chi-restraints excluded: chain P residue 634 LEU Chi-restraints excluded: chain P residue 735 VAL Chi-restraints excluded: chain P residue 750 THR Chi-restraints excluded: chain P residue 873 VAL Chi-restraints excluded: chain P residue 946 ILE Chi-restraints excluded: chain P residue 986 VAL Chi-restraints excluded: chain P residue 1049 VAL Chi-restraints excluded: chain P residue 1138 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 51 optimal weight: 0.0980 chunk 28 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 92 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 82 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 91 optimal weight: 0.6980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 847 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P1057 GLN P1127 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.4506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 8139 Z= 0.198 Angle : 0.903 29.656 11094 Z= 0.363 Chirality : 0.042 0.158 1318 Planarity : 0.004 0.063 1395 Dihedral : 6.405 126.786 1125 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 2.39 % Allowed : 19.59 % Favored : 78.02 % 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: -2.38 (0.26), residues: 1016 helix: 0.83 (0.29), residues: 391 sheet: -2.67 (0.50), residues: 81 loop : -3.46 (0.22), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP P1028 HIS 0.002 0.001 HIS P 836 PHE 0.015 0.001 PHE P 246 TYR 0.013 0.001 TYR P 241 ARG 0.004 0.000 ARG P 199 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 131 time to evaluate : 0.785 Fit side-chains REVERT: P 267 SER cc_start: 0.7838 (m) cc_final: 0.7621 (p) REVERT: P 437 LEU cc_start: 0.8659 (pp) cc_final: 0.8391 (mp) REVERT: P 485 GLN cc_start: 0.8056 (tt0) cc_final: 0.7749 (tt0) REVERT: P 573 MET cc_start: 0.7105 (ttm) cc_final: 0.6887 (ttt) REVERT: P 861 GLU cc_start: 0.7703 (tm-30) cc_final: 0.7320 (tp30) REVERT: P 893 ILE cc_start: 0.8811 (mm) cc_final: 0.8168 (mm) REVERT: P 894 SER cc_start: 0.8929 (m) cc_final: 0.8528 (t) REVERT: P 960 ASP cc_start: 0.7690 (t0) cc_final: 0.7390 (t0) REVERT: P 1046 GLU cc_start: 0.7340 (mp0) cc_final: 0.7073 (mp0) outliers start: 21 outliers final: 15 residues processed: 144 average time/residue: 0.1964 time to fit residues: 38.7433 Evaluate side-chains 130 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 115 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 40 TYR Chi-restraints excluded: chain P residue 262 CYS Chi-restraints excluded: chain P residue 318 LEU Chi-restraints excluded: chain P residue 338 CYS Chi-restraints excluded: chain P residue 424 HIS Chi-restraints excluded: chain P residue 464 LEU Chi-restraints excluded: chain P residue 551 LEU Chi-restraints excluded: chain P residue 634 LEU Chi-restraints excluded: chain P residue 735 VAL Chi-restraints excluded: chain P residue 750 THR Chi-restraints excluded: chain P residue 759 THR Chi-restraints excluded: chain P residue 871 TYR Chi-restraints excluded: chain P residue 873 VAL Chi-restraints excluded: chain P residue 1096 VAL Chi-restraints excluded: chain P residue 1138 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 69 optimal weight: 0.0270 chunk 48 optimal weight: 1.9990 chunk 10 optimal weight: 7.9990 chunk 44 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 93 optimal weight: 0.6980 chunk 98 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 overall best weight: 1.1242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 847 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.5666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8139 Z= 0.261 Angle : 0.938 30.681 11094 Z= 0.384 Chirality : 0.043 0.156 1318 Planarity : 0.005 0.062 1395 Dihedral : 6.135 115.699 1125 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.46 % Favored : 91.54 % Rotamer: Outliers : 3.53 % Allowed : 21.87 % Favored : 74.60 % 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: -2.12 (0.26), residues: 1016 helix: 0.93 (0.29), residues: 390 sheet: -2.46 (0.54), residues: 77 loop : -3.21 (0.23), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP P 55 HIS 0.003 0.001 HIS P 369 PHE 0.009 0.001 PHE P 851 TYR 0.021 0.002 TYR P 183 ARG 0.008 0.001 ARG P 76 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 118 time to evaluate : 1.374 Fit side-chains revert: symmetry clash REVERT: P 243 PHE cc_start: 0.8483 (t80) cc_final: 0.8231 (t80) REVERT: P 246 PHE cc_start: 0.8908 (t80) cc_final: 0.8612 (t80) REVERT: P 267 SER cc_start: 0.7960 (m) cc_final: 0.7753 (p) REVERT: P 333 LEU cc_start: 0.9105 (OUTLIER) cc_final: 0.8889 (tt) REVERT: P 437 LEU cc_start: 0.8668 (pp) cc_final: 0.8346 (mp) REVERT: P 861 GLU cc_start: 0.7780 (tm-30) cc_final: 0.7452 (tp30) REVERT: P 894 SER cc_start: 0.9034 (m) cc_final: 0.8536 (t) REVERT: P 1046 GLU cc_start: 0.7431 (mp0) cc_final: 0.7180 (mp0) outliers start: 31 outliers final: 22 residues processed: 143 average time/residue: 0.2516 time to fit residues: 52.9260 Evaluate side-chains 128 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 105 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 40 TYR Chi-restraints excluded: chain P residue 262 CYS Chi-restraints excluded: chain P residue 318 LEU Chi-restraints excluded: chain P residue 333 LEU Chi-restraints excluded: chain P residue 338 CYS Chi-restraints excluded: chain P residue 424 HIS Chi-restraints excluded: chain P residue 434 VAL Chi-restraints excluded: chain P residue 464 LEU Chi-restraints excluded: chain P residue 551 LEU Chi-restraints excluded: chain P residue 634 LEU Chi-restraints excluded: chain P residue 653 VAL Chi-restraints excluded: chain P residue 669 VAL Chi-restraints excluded: chain P residue 681 THR Chi-restraints excluded: chain P residue 735 VAL Chi-restraints excluded: chain P residue 750 THR Chi-restraints excluded: chain P residue 759 THR Chi-restraints excluded: chain P residue 871 TYR Chi-restraints excluded: chain P residue 873 VAL Chi-restraints excluded: chain P residue 903 VAL Chi-restraints excluded: chain P residue 933 VAL Chi-restraints excluded: chain P residue 986 VAL Chi-restraints excluded: chain P residue 1029 PHE Chi-restraints excluded: chain P residue 1138 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/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-1.21-5211/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-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/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-1.21-5211/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/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-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 61.8707 > 50: distance: 63 - 65: 14.031 distance: 65 - 66: 8.651 distance: 65 - 71: 6.026 distance: 66 - 67: 5.617 distance: 66 - 69: 13.383 distance: 67 - 68: 13.914 distance: 67 - 72: 30.573 distance: 69 - 70: 19.139 distance: 70 - 71: 15.463 distance: 72 - 73: 49.158 distance: 73 - 74: 32.235 distance: 73 - 76: 43.404 distance: 74 - 75: 31.382 distance: 74 - 77: 24.411 distance: 77 - 78: 44.970 distance: 78 - 79: 29.369 distance: 78 - 81: 49.600 distance: 79 - 80: 19.030 distance: 79 - 85: 36.204 distance: 81 - 82: 32.062 distance: 82 - 83: 14.427 distance: 82 - 84: 12.333 distance: 85 - 86: 23.431 distance: 86 - 87: 45.666 distance: 86 - 89: 43.109 distance: 87 - 88: 47.506 distance: 87 - 92: 23.727 distance: 89 - 90: 27.541 distance: 89 - 91: 22.340 distance: 92 - 93: 31.230 distance: 93 - 94: 10.940 distance: 93 - 96: 24.321 distance: 94 - 95: 21.212 distance: 94 - 100: 5.075 distance: 96 - 97: 21.282 distance: 97 - 98: 3.741 distance: 97 - 99: 3.698 distance: 100 - 101: 12.643 distance: 101 - 102: 5.878 distance: 102 - 103: 21.934 distance: 102 - 104: 8.558 distance: 104 - 105: 31.573 distance: 105 - 106: 23.913 distance: 105 - 108: 38.936 distance: 106 - 107: 34.018 distance: 106 - 115: 27.887 distance: 108 - 109: 26.651 distance: 109 - 110: 5.888 distance: 110 - 111: 4.767 distance: 115 - 116: 34.513 distance: 116 - 117: 40.580 distance: 116 - 119: 20.996 distance: 117 - 118: 20.991 distance: 117 - 122: 23.059 distance: 119 - 120: 20.117 distance: 119 - 121: 11.051 distance: 122 - 123: 26.928 distance: 123 - 124: 34.469 distance: 123 - 126: 38.921 distance: 124 - 125: 33.699 distance: 124 - 133: 38.268 distance: 126 - 127: 19.483 distance: 127 - 128: 7.416 distance: 128 - 129: 7.542 distance: 130 - 131: 3.878 distance: 130 - 132: 3.258 distance: 133 - 134: 46.181 distance: 133 - 139: 25.145 distance: 134 - 135: 42.005 distance: 134 - 137: 20.789 distance: 135 - 136: 19.384 distance: 135 - 140: 22.732 distance: 137 - 138: 6.144 distance: 138 - 139: 22.995