Starting phenix.real_space_refine on Fri Aug 22 22:35:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xq8_38569/08_2025/8xq8_38569.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xq8_38569/08_2025/8xq8_38569.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xq8_38569/08_2025/8xq8_38569.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xq8_38569/08_2025/8xq8_38569.map" model { file = "/net/cci-nas-00/data/ceres_data/8xq8_38569/08_2025/8xq8_38569.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xq8_38569/08_2025/8xq8_38569.cif" } resolution = 3.35 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= 0.001 sd= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 46 5.16 5 C 5423 2.51 5 N 1380 2.21 5 O 1469 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8319 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 8297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1051, 8297 Classifications: {'peptide': 1051} Link IDs: {'PTRANS': 32, 'TRANS': 1018} Chain breaks: 5 Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'RNA': 1} Modifications used: {'rna3p': 1} Time building chain proxies: 1.89, per 1000 atoms: 0.23 Number of scatterers: 8319 At special positions: 0 Unit cell: (78.84, 111.24, 124.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 46 16.00 P 1 15.00 O 1469 8.00 N 1380 7.00 C 5423 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: 0.56 Conformation dependent library (CDL) restraints added in 202.2 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1982 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 4 sheets defined 74.9% alpha, 4.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'A' and resid 76 through 95 Processing helix chain 'A' and resid 101 through 120 removed outlier: 3.991A pdb=" N VAL A 105 " --> pdb=" O PRO A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'A' and resid 134 through 153 Proline residue: A 144 - end of helix Processing helix chain 'A' and resid 155 through 162 Processing helix chain 'A' and resid 162 through 189 Processing helix chain 'A' and resid 194 through 206 Processing helix chain 'A' and resid 211 through 220 Processing helix chain 'A' and resid 223 through 253 removed outlier: 3.824A pdb=" N GLY A 227 " --> pdb=" O SER A 223 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N THR A 228 " --> pdb=" O LYS A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 292 Proline residue: A 276 - end of helix removed outlier: 3.707A pdb=" N HIS A 292 " --> pdb=" O PHE A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 318 removed outlier: 3.932A pdb=" N GLU A 300 " --> pdb=" O ASP A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 337 removed outlier: 3.652A pdb=" N ALA A 326 " --> pdb=" O SER A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 375 Processing helix chain 'A' and resid 381 through 406 Processing helix chain 'A' and resid 406 through 412 Processing helix chain 'A' and resid 418 through 428 Processing helix chain 'A' and resid 432 through 447 removed outlier: 3.686A pdb=" N LEU A 436 " --> pdb=" O GLY A 432 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY A 447 " --> pdb=" O GLU A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 481 removed outlier: 4.415A pdb=" N SER A 453 " --> pdb=" O ASP A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 513 Processing helix chain 'A' and resid 522 through 530 removed outlier: 3.738A pdb=" N ALA A 526 " --> pdb=" O ASP A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 558 Processing helix chain 'A' and resid 571 through 600 Processing helix chain 'A' and resid 604 through 621 removed outlier: 3.627A pdb=" N GLU A 621 " --> pdb=" O VAL A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 652 removed outlier: 3.940A pdb=" N TRP A 643 " --> pdb=" O GLY A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 677 removed outlier: 4.148A pdb=" N CYS A 675 " --> pdb=" O MET A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 705 removed outlier: 4.028A pdb=" N VAL A 682 " --> pdb=" O MET A 678 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N THR A 683 " --> pdb=" O ALA A 679 " (cutoff:3.500A) Proline residue: A 694 - end of helix Processing helix chain 'A' and resid 727 through 754 removed outlier: 3.847A pdb=" N LEU A 754 " --> pdb=" O LYS A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 754 through 760 Processing helix chain 'A' and resid 761 through 784 Processing helix chain 'A' and resid 795 through 858 removed outlier: 4.347A pdb=" N LYS A 815 " --> pdb=" O LEU A 811 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ALA A 816 " --> pdb=" O ARG A 812 " (cutoff:3.500A) Proline residue: A 819 - end of helix removed outlier: 5.524A pdb=" N ASP A 855 " --> pdb=" O GLY A 851 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ARG A 856 " --> pdb=" O LYS A 852 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N MET A 857 " --> pdb=" O ILE A 853 " (cutoff:3.500A) Processing helix chain 'A' and resid 860 through 889 removed outlier: 3.701A pdb=" N HIS A 889 " --> pdb=" O LEU A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 889 through 919 Processing helix chain 'A' and resid 923 through 943 Processing helix chain 'A' and resid 952 through 959 Processing helix chain 'A' and resid 960 through 964 removed outlier: 4.145A pdb=" N ALA A 964 " --> pdb=" O SER A 961 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 976 Processing helix chain 'A' and resid 1043 through 1050 removed outlier: 3.559A pdb=" N LYS A1050 " --> pdb=" O GLY A1046 " (cutoff:3.500A) Processing helix chain 'A' and resid 1070 through 1079 Processing helix chain 'A' and resid 1085 through 1108 Proline residue: A1101 - end of helix removed outlier: 3.785A pdb=" N GLN A1106 " --> pdb=" O LEU A1102 " (cutoff:3.500A) Processing helix chain 'A' and resid 1113 through 1123 removed outlier: 3.587A pdb=" N ARG A1123 " --> pdb=" O LEU A1119 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 979 through 982 removed outlier: 6.867A pdb=" N GLN A1064 " --> pdb=" O VAL A1002 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 987 through 989 removed outlier: 6.500A pdb=" N VAL A1057 " --> pdb=" O ILE A 988 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASP A1034 " --> pdb=" O LEU A1008 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY A1010 " --> pdb=" O PHE A1032 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1125 through 1126 removed outlier: 3.531A pdb=" N TYR A1125 " --> pdb=" O VAL A1188 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N VAL A1188 " --> pdb=" O TYR A1125 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ARG A1185 " --> pdb=" O ILE A1148 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL A1189 " --> pdb=" O ASP A1144 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ASP A1144 " --> pdb=" O VAL A1189 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1135 through 1137 removed outlier: 3.590A pdb=" N ASN A1154 " --> pdb=" O GLU A1159 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU A1159 " --> pdb=" O ASN A1154 " (cutoff:3.500A) 616 hydrogen bonds defined for protein. 1833 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.12 Time building geometry restraints manager: 0.73 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: 2003 1.33 - 1.46: 1873 1.46 - 1.58: 4518 1.58 - 1.70: 5 1.70 - 1.83: 83 Bond restraints: 8482 Sorted by residual: bond pdb=" O2P CMP A2001 " pdb=" P CMP A2001 " ideal model delta sigma weight residual 1.510 1.643 -0.133 2.00e-02 2.50e+03 4.41e+01 bond pdb=" C4 CMP A2001 " pdb=" C5 CMP A2001 " ideal model delta sigma weight residual 1.490 1.370 0.120 2.00e-02 2.50e+03 3.62e+01 bond pdb=" C6 CMP A2001 " pdb=" N6 CMP A2001 " ideal model delta sigma weight residual 1.355 1.452 -0.097 2.00e-02 2.50e+03 2.35e+01 bond pdb=" C5 CMP A2001 " pdb=" C6 CMP A2001 " ideal model delta sigma weight residual 1.490 1.421 0.069 2.00e-02 2.50e+03 1.19e+01 bond pdb=" O1P CMP A2001 " pdb=" P CMP A2001 " ideal model delta sigma weight residual 1.510 1.452 0.058 2.00e-02 2.50e+03 8.27e+00 ... (remaining 8477 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.81: 11293 3.81 - 7.63: 172 7.63 - 11.44: 33 11.44 - 15.25: 7 15.25 - 19.07: 1 Bond angle restraints: 11506 Sorted by residual: angle pdb=" CG1 ILE A 652 " pdb=" CB ILE A 652 " pdb=" CG2 ILE A 652 " ideal model delta sigma weight residual 110.70 91.63 19.07 3.00e+00 1.11e-01 4.04e+01 angle pdb=" CA MET A 565 " pdb=" CB MET A 565 " pdb=" CG MET A 565 " ideal model delta sigma weight residual 114.10 125.72 -11.62 2.00e+00 2.50e-01 3.37e+01 angle pdb=" C SER A 487 " pdb=" N ILE A 488 " pdb=" CA ILE A 488 " ideal model delta sigma weight residual 120.24 123.56 -3.32 6.30e-01 2.52e+00 2.77e+01 angle pdb=" CA GLN A1106 " pdb=" CB GLN A1106 " pdb=" CG GLN A1106 " ideal model delta sigma weight residual 114.10 124.22 -10.12 2.00e+00 2.50e-01 2.56e+01 angle pdb=" CB GLN A1106 " pdb=" CG GLN A1106 " pdb=" CD GLN A1106 " ideal model delta sigma weight residual 112.60 121.09 -8.49 1.70e+00 3.46e-01 2.49e+01 ... (remaining 11501 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.26: 4686 26.26 - 52.53: 347 52.53 - 78.79: 32 78.79 - 105.06: 7 105.06 - 131.32: 1 Dihedral angle restraints: 5073 sinusoidal: 2016 harmonic: 3057 Sorted by residual: dihedral pdb=" CA TYR A1083 " pdb=" C TYR A1083 " pdb=" N PRO A1084 " pdb=" CA PRO A1084 " ideal model delta harmonic sigma weight residual 180.00 156.01 23.99 0 5.00e+00 4.00e-02 2.30e+01 dihedral pdb=" CA THR A1049 " pdb=" C THR A1049 " pdb=" N LYS A1050 " pdb=" CA LYS A1050 " ideal model delta harmonic sigma weight residual 180.00 159.76 20.24 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" CA LEU A 754 " pdb=" C LEU A 754 " pdb=" N GLY A 755 " pdb=" CA GLY A 755 " ideal model delta harmonic sigma weight residual 180.00 162.15 17.85 0 5.00e+00 4.00e-02 1.27e+01 ... (remaining 5070 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 1148 0.073 - 0.145: 186 0.145 - 0.218: 38 0.218 - 0.290: 4 0.290 - 0.363: 4 Chirality restraints: 1380 Sorted by residual: chirality pdb=" CB ILE A 652 " pdb=" CA ILE A 652 " pdb=" CG1 ILE A 652 " pdb=" CG2 ILE A 652 " both_signs ideal model delta sigma weight residual False 2.64 3.01 -0.36 2.00e-01 2.50e+01 3.29e+00 chirality pdb=" CB VAL A 116 " pdb=" CA VAL A 116 " pdb=" CG1 VAL A 116 " pdb=" CG2 VAL A 116 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.71e+00 chirality pdb=" CB ILE A 742 " pdb=" CA ILE A 742 " pdb=" CG1 ILE A 742 " pdb=" CG2 ILE A 742 " both_signs ideal model delta sigma weight residual False 2.64 2.97 -0.32 2.00e-01 2.50e+01 2.63e+00 ... (remaining 1377 not shown) Planarity restraints: 1415 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 766 " 0.044 2.00e-02 2.50e+03 4.05e-02 2.87e+01 pdb=" CG PHE A 766 " -0.092 2.00e-02 2.50e+03 pdb=" CD1 PHE A 766 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 PHE A 766 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A 766 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A 766 " 0.018 2.00e-02 2.50e+03 pdb=" CZ PHE A 766 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A1123 " -0.352 9.50e-02 1.11e+02 1.58e-01 1.64e+01 pdb=" NE ARG A1123 " 0.027 2.00e-02 2.50e+03 pdb=" CZ ARG A1123 " -0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG A1123 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG A1123 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 275 " 0.050 5.00e-02 4.00e+02 7.61e-02 9.27e+00 pdb=" N PRO A 276 " -0.132 5.00e-02 4.00e+02 pdb=" CA PRO A 276 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 276 " 0.042 5.00e-02 4.00e+02 ... (remaining 1412 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.78: 1782 2.78 - 3.31: 8007 3.31 - 3.84: 14026 3.84 - 4.37: 15109 4.37 - 4.90: 26778 Nonbonded interactions: 65702 Sorted by model distance: nonbonded pdb=" O ALA A 307 " pdb=" OG1 THR A 311 " model vdw 2.255 3.040 nonbonded pdb=" O SER A 735 " pdb=" OG SER A 735 " model vdw 2.269 3.040 nonbonded pdb=" OE1 GLU A 954 " pdb=" OH TYR A1066 " model vdw 2.280 3.040 nonbonded pdb=" O PHE A 680 " pdb=" OG1 THR A 683 " model vdw 2.302 3.040 nonbonded pdb=" O ILE A 469 " pdb=" OG1 THR A 473 " model vdw 2.306 3.040 ... (remaining 65697 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.150 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 7.810 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:0.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 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 : 0.007 0.133 8482 Z= 0.311 Angle : 1.245 19.067 11506 Z= 0.646 Chirality : 0.061 0.363 1380 Planarity : 0.010 0.158 1415 Dihedral : 17.539 131.319 3091 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.77 % Allowed : 29.61 % Favored : 69.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.52 (0.22), residues: 1039 helix: -0.78 (0.16), residues: 755 sheet: -0.54 (0.69), residues: 50 loop : -1.26 (0.35), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.002 ARG A1123 TYR 0.045 0.002 TYR A 267 PHE 0.092 0.003 PHE A 766 TRP 0.016 0.002 TRP A 427 HIS 0.024 0.002 HIS A1156 Details of bonding type rmsd covalent geometry : bond 0.00666 ( 8482) covalent geometry : angle 1.24462 (11506) hydrogen bonds : bond 0.11763 ( 616) hydrogen bonds : angle 6.25932 ( 1833) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 256 time to evaluate : 0.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 VAL cc_start: 0.8231 (p) cc_final: 0.8025 (m) REVERT: A 174 LEU cc_start: 0.8155 (tp) cc_final: 0.7821 (tp) REVERT: A 263 GLN cc_start: 0.7713 (mt0) cc_final: 0.7115 (mp10) REVERT: A 295 ASN cc_start: 0.8131 (t0) cc_final: 0.7609 (t0) REVERT: A 354 GLU cc_start: 0.7987 (tt0) cc_final: 0.7632 (tm-30) REVERT: A 621 GLU cc_start: 0.7384 (tp30) cc_final: 0.7176 (tp30) REVERT: A 671 MET cc_start: 0.7143 (mtt) cc_final: 0.6775 (mtt) REVERT: A 940 ARG cc_start: 0.8146 (tpp80) cc_final: 0.7810 (ttm-80) REVERT: A 1008 LEU cc_start: 0.7198 (tt) cc_final: 0.6981 (tp) REVERT: A 1161 ILE cc_start: 0.7298 (OUTLIER) cc_final: 0.7020 (pt) outliers start: 7 outliers final: 3 residues processed: 260 average time/residue: 0.0813 time to fit residues: 28.2736 Evaluate side-chains 248 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 244 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1161 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 57.9007 > 50: distance: 13 - 18: 15.277 distance: 18 - 19: 16.640 distance: 19 - 20: 12.044 distance: 19 - 22: 54.140 distance: 20 - 21: 57.901 distance: 20 - 24: 42.592 distance: 21 - 51: 22.864 distance: 22 - 23: 41.186 distance: 24 - 25: 20.240 distance: 24 - 30: 18.456 distance: 25 - 26: 23.065 distance: 25 - 28: 23.194 distance: 26 - 27: 17.110 distance: 26 - 31: 18.125 distance: 27 - 62: 20.322 distance: 28 - 29: 5.029 distance: 29 - 30: 6.411 distance: 31 - 32: 7.924 distance: 32 - 33: 14.173 distance: 32 - 35: 15.862 distance: 33 - 34: 8.779 distance: 33 - 42: 6.521 distance: 34 - 67: 9.146 distance: 35 - 36: 6.867 distance: 42 - 43: 4.745 distance: 43 - 44: 7.281 distance: 43 - 46: 5.684 distance: 44 - 45: 10.502 distance: 44 - 51: 9.485 distance: 45 - 75: 15.564 distance: 46 - 47: 9.078 distance: 48 - 49: 3.979 distance: 51 - 52: 14.123 distance: 52 - 53: 11.328 distance: 52 - 55: 10.908 distance: 53 - 54: 10.455 distance: 53 - 62: 15.188 distance: 54 - 83: 12.418 distance: 55 - 56: 6.635 distance: 56 - 57: 7.830 distance: 56 - 58: 3.986 distance: 57 - 59: 3.968 distance: 58 - 60: 5.509 distance: 60 - 61: 5.957 distance: 62 - 63: 11.428 distance: 63 - 64: 9.235 distance: 63 - 66: 11.721 distance: 64 - 65: 9.388 distance: 64 - 67: 5.672 distance: 65 - 91: 18.661 distance: 67 - 68: 12.445 distance: 68 - 69: 13.244 distance: 68 - 71: 12.534 distance: 69 - 70: 11.273 distance: 70 - 100: 9.607 distance: 71 - 72: 8.273 distance: 72 - 73: 9.433 distance: 72 - 74: 10.499 distance: 75 - 76: 18.092 distance: 76 - 77: 23.028 distance: 76 - 79: 34.289 distance: 77 - 78: 20.212 distance: 77 - 83: 18.708 distance: 78 - 106: 8.357 distance: 79 - 80: 13.573 distance: 80 - 81: 5.914 distance: 81 - 82: 10.168 distance: 83 - 84: 13.947 distance: 84 - 85: 24.949 distance: 84 - 87: 20.944 distance: 85 - 86: 14.432 distance: 85 - 91: 27.914 distance: 86 - 111: 11.096 distance: 87 - 88: 14.650 distance: 88 - 89: 7.036 distance: 91 - 92: 28.940 distance: 92 - 93: 14.768 distance: 92 - 95: 17.025 distance: 93 - 94: 17.796 distance: 93 - 100: 9.037 distance: 94 - 117: 22.129 distance: 95 - 96: 16.317 distance: 97 - 98: 3.228