Starting phenix.real_space_refine on Fri Jul 3 12:26:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7yna_33956/07_2026/7yna_33956.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yna_33956/07_2026/7yna_33956.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7yna_33956/07_2026/7yna_33956.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yna_33956/07_2026/7yna_33956.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7yna_33956/07_2026/7yna_33956.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7yna_33956/07_2026/7yna_33956.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7yna_33956/07_2026/7yna_33956.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yna_33956/07_2026/7yna_33956.map" } resolution = 3.64 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= 0.000 sd= 0.003 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 63 5.49 5 S 57 5.16 5 C 8468 2.51 5 N 2454 2.21 5 O 2742 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 46 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13784 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 12447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1536, 12447 Classifications: {'peptide': 1536} Link IDs: {'PTRANS': 84, 'TRANS': 1451} Chain breaks: 4 Chain: "B" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 810 Classifications: {'RNA': 38} Modifications used: {'rna2p_pur': 14, 'rna2p_pyr': 6, 'rna3p_pur': 7, 'rna3p_pyr': 11} Link IDs: {'rna2p': 20, 'rna3p': 17} Chain: "C" Number of atoms: 527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 527 Classifications: {'RNA': 25} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 2, 'rna3p_pur': 10, 'rna3p_pyr': 12} Link IDs: {'rna2p': 3, 'rna3p': 21} Time building chain proxies: 2.95, per 1000 atoms: 0.21 Number of scatterers: 13784 At special positions: 0 Unit cell: (92.02, 171.2, 132.68, 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 57 16.00 P 63 15.00 O 2742 8.00 N 2454 7.00 C 8468 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: 1.37 Conformation dependent library (CDL) restraints added in 609.1 milliseconds 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2858 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 20 sheets defined 22.2% alpha, 15.3% beta 16 base pairs and 23 stacking pairs defined. Time for finding SS restraints: 1.61 Creating SS restraints... Processing helix chain 'A' and resid 58 through 74 removed outlier: 3.510A pdb=" N THR A 74 " --> pdb=" O GLU A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 77 No H-bonds generated for 'chain 'A' and resid 75 through 77' Processing helix chain 'A' and resid 123 through 130 Processing helix chain 'A' and resid 163 through 167 Processing helix chain 'A' and resid 213 through 225 Processing helix chain 'A' and resid 261 through 276 Processing helix chain 'A' and resid 281 through 290 Processing helix chain 'A' and resid 291 through 295 removed outlier: 4.037A pdb=" N ARG A 294 " --> pdb=" O SER A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 302 removed outlier: 3.945A pdb=" N LEU A 302 " --> pdb=" O VAL A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 336 Processing helix chain 'A' and resid 344 through 365 removed outlier: 4.080A pdb=" N ASP A 365 " --> pdb=" O LEU A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 459 removed outlier: 3.613A pdb=" N VAL A 447 " --> pdb=" O PRO A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 554 Processing helix chain 'A' and resid 562 through 566 Processing helix chain 'A' and resid 587 through 594 removed outlier: 3.562A pdb=" N ASN A 594 " --> pdb=" O ASP A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 607 Processing helix chain 'A' and resid 642 through 649 Processing helix chain 'A' and resid 675 through 688 removed outlier: 3.651A pdb=" N PHE A 679 " --> pdb=" O LYS A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 713 Processing helix chain 'A' and resid 780 through 784 Processing helix chain 'A' and resid 787 through 801 Processing helix chain 'A' and resid 809 through 813 removed outlier: 3.650A pdb=" N GLY A 813 " --> pdb=" O SER A 810 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 962 removed outlier: 3.986A pdb=" N LEU A 950 " --> pdb=" O PRO A 946 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N THR A 962 " --> pdb=" O TYR A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 1101 through 1109 removed outlier: 4.178A pdb=" N GLU A1106 " --> pdb=" O ASN A1102 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N LYS A1107 " --> pdb=" O PHE A1103 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU A1108 " --> pdb=" O ASP A1104 " (cutoff:3.500A) Processing helix chain 'A' and resid 1231 through 1246 removed outlier: 3.980A pdb=" N ARG A1235 " --> pdb=" O PRO A1231 " (cutoff:3.500A) Processing helix chain 'A' and resid 1259 through 1265 Processing helix chain 'A' and resid 1300 through 1305 removed outlier: 4.132A pdb=" N MET A1305 " --> pdb=" O GLY A1302 " (cutoff:3.500A) Processing helix chain 'A' and resid 1420 through 1427 removed outlier: 3.975A pdb=" N ILE A1424 " --> pdb=" O ALA A1420 " (cutoff:3.500A) Processing helix chain 'A' and resid 1466 through 1476 removed outlier: 3.646A pdb=" N GLN A1476 " --> pdb=" O ILE A1472 " (cutoff:3.500A) Processing helix chain 'A' and resid 1515 through 1517 No H-bonds generated for 'chain 'A' and resid 1515 through 1517' Processing helix chain 'A' and resid 1518 through 1534 Processing helix chain 'A' and resid 1538 through 1548 Processing helix chain 'A' and resid 1565 through 1569 removed outlier: 4.032A pdb=" N ASP A1568 " --> pdb=" O ARG A1565 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ASP A1569 " --> pdb=" O LYS A1566 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1565 through 1569' Processing helix chain 'A' and resid 1575 through 1580 Processing helix chain 'A' and resid 1588 through 1595 removed outlier: 3.569A pdb=" N THR A1594 " --> pdb=" O GLN A1590 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 148 through 150 Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 17 removed outlier: 3.709A pdb=" N MET A 17 " --> pdb=" O TYR A 190 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N TYR A 190 " --> pdb=" O MET A 17 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ARG A 171 " --> pdb=" O ALA A 189 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 41 through 44 Processing sheet with id=AA4, first strand: chain 'A' and resid 483 through 484 removed outlier: 3.630A pdb=" N TYR A 577 " --> pdb=" O ASN A 611 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASN A 611 " --> pdb=" O TYR A 577 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 527 through 529 Processing sheet with id=AA6, first strand: chain 'A' and resid 497 through 504 removed outlier: 3.742A pdb=" N GLU A 497 " --> pdb=" O VAL A 521 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ARG A 503 " --> pdb=" O ALA A 515 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ALA A 515 " --> pdb=" O ARG A 503 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 723 through 724 removed outlier: 3.743A pdb=" N VAL A 630 " --> pdb=" O GLY A 774 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ASN A 629 " --> pdb=" O ILE A 822 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ILE A 822 " --> pdb=" O ASN A 629 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N SER A 631 " --> pdb=" O LEU A 820 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N LEU A 820 " --> pdb=" O SER A 631 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N GLU A 633 " --> pdb=" O LYS A 818 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 659 through 660 removed outlier: 3.518A pdb=" N LEU A 728 " --> pdb=" O TYR A 674 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 739 through 744 removed outlier: 3.594A pdb=" N PHE A 757 " --> pdb=" O HIS A 741 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N LYS A 755 " --> pdb=" O ALA A 743 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 861 through 862 Processing sheet with id=AB2, first strand: chain 'A' and resid 944 through 945 removed outlier: 3.603A pdb=" N SER A1363 " --> pdb=" O SER A1455 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 944 through 945 removed outlier: 3.603A pdb=" N SER A1363 " --> pdb=" O SER A1455 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 976 through 978 Processing sheet with id=AB5, first strand: chain 'A' and resid 991 through 993 removed outlier: 4.035A pdb=" N VAL A1275 " --> pdb=" O GLY A 993 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N TYR A1276 " --> pdb=" O ILE A1287 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N ILE A1287 " --> pdb=" O TYR A1276 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N LYS A1278 " --> pdb=" O GLU A1285 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1001 through 1011 removed outlier: 8.390A pdb=" N ALA A1129 " --> pdb=" O THR A1008 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ARG A1010 " --> pdb=" O ALA A1129 " (cutoff:3.500A) removed outlier: 19.405A pdb=" N CYS A1143 " --> pdb=" O LYS A1223 " (cutoff:3.500A) removed outlier: 14.370A pdb=" N LYS A1223 " --> pdb=" O CYS A1143 " (cutoff:3.500A) removed outlier: 9.178A pdb=" N GLU A1145 " --> pdb=" O ASP A1221 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASP A1221 " --> pdb=" O GLU A1145 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N PHE A1220 " --> pdb=" O GLU A1007 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N GLU A1007 " --> pdb=" O PHE A1220 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LEU A1222 " --> pdb=" O PHE A1005 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N PHE A1005 " --> pdb=" O LEU A1222 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N GLU A1224 " --> pdb=" O GLN A1003 " (cutoff:3.500A) removed outlier: 8.512A pdb=" N GLN A1003 " --> pdb=" O GLU A1224 " (cutoff:3.500A) removed outlier: 10.121A pdb=" N GLU A1226 " --> pdb=" O HIS A1001 " (cutoff:3.500A) removed outlier: 8.960A pdb=" N HIS A1001 " --> pdb=" O GLU A1226 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1044 through 1047 Processing sheet with id=AB8, first strand: chain 'A' and resid 1070 through 1071 Processing sheet with id=AB9, first strand: chain 'A' and resid 1081 through 1086 removed outlier: 3.670A pdb=" N LEU A1096 " --> pdb=" O PHE A1083 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL A1085 " --> pdb=" O PHE A1094 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1200 through 1202 Processing sheet with id=AC2, first strand: chain 'A' and resid 1385 through 1387 307 hydrogen bonds defined for protein. 825 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 40 hydrogen bonds 80 hydrogen bond angles 0 basepair planarities 16 basepair parallelities 23 stacking parallelities Total time for adding SS restraints: 3.22 Time building geometry restraints manager: 1.78 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: 3596 1.33 - 1.45: 2944 1.45 - 1.57: 7491 1.57 - 1.69: 124 1.69 - 1.81: 82 Bond restraints: 14237 Sorted by residual: bond pdb=" C CYS A1560 " pdb=" N TYR A1561 " ideal model delta sigma weight residual 1.331 1.267 0.064 2.07e-02 2.33e+03 9.42e+00 bond pdb=" N CYS A 965 " pdb=" CA CYS A 965 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.22e-02 6.72e+03 7.06e+00 bond pdb=" N CYS A 706 " pdb=" CA CYS A 706 " ideal model delta sigma weight residual 1.455 1.489 -0.034 1.30e-02 5.92e+03 6.87e+00 bond pdb=" N CYS A 711 " pdb=" CA CYS A 711 " ideal model delta sigma weight residual 1.457 1.491 -0.033 1.29e-02 6.01e+03 6.68e+00 bond pdb=" N CYS A 708 " pdb=" CA CYS A 708 " ideal model delta sigma weight residual 1.456 1.487 -0.031 1.25e-02 6.40e+03 6.19e+00 ... (remaining 14232 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.23: 19113 2.23 - 4.45: 342 4.45 - 6.68: 25 6.68 - 8.91: 3 8.91 - 11.13: 1 Bond angle restraints: 19484 Sorted by residual: angle pdb=" N SER A1080 " pdb=" CA SER A1080 " pdb=" C SER A1080 " ideal model delta sigma weight residual 108.34 113.35 -5.01 1.31e+00 5.83e-01 1.46e+01 angle pdb=" N LYS A1586 " pdb=" CA LYS A1586 " pdb=" C LYS A1586 " ideal model delta sigma weight residual 114.75 110.41 4.34 1.26e+00 6.30e-01 1.18e+01 angle pdb=" CA CYS A 708 " pdb=" C CYS A 708 " pdb=" O CYS A 708 " ideal model delta sigma weight residual 121.55 118.02 3.53 1.06e+00 8.90e-01 1.11e+01 angle pdb=" N GLN A 884 " pdb=" CA GLN A 884 " pdb=" C GLN A 884 " ideal model delta sigma weight residual 110.80 103.99 6.81 2.13e+00 2.20e-01 1.02e+01 angle pdb=" C SER A1403 " pdb=" N ASP A1404 " pdb=" CA ASP A1404 " ideal model delta sigma weight residual 121.54 115.60 5.94 1.91e+00 2.74e-01 9.69e+00 ... (remaining 19479 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.14: 8272 34.14 - 68.28: 203 68.28 - 102.42: 23 102.42 - 136.56: 2 136.56 - 170.70: 1 Dihedral angle restraints: 8501 sinusoidal: 4070 harmonic: 4431 Sorted by residual: dihedral pdb=" CA HIS A 383 " pdb=" C HIS A 383 " pdb=" N GLY A 384 " pdb=" CA GLY A 384 " ideal model delta harmonic sigma weight residual -180.00 -156.48 -23.52 0 5.00e+00 4.00e-02 2.21e+01 dihedral pdb=" CA LEU A 173 " pdb=" C LEU A 173 " pdb=" N ASN A 174 " pdb=" CA ASN A 174 " ideal model delta harmonic sigma weight residual -180.00 -159.20 -20.80 0 5.00e+00 4.00e-02 1.73e+01 dihedral pdb=" C4' U B -14 " pdb=" C3' U B -14 " pdb=" O3' U B -14 " pdb=" P G B -13 " ideal model delta sinusoidal sigma weight residual -110.00 60.70 -170.70 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 8498 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1524 0.048 - 0.097: 440 0.097 - 0.145: 103 0.145 - 0.193: 13 0.193 - 0.241: 4 Chirality restraints: 2084 Sorted by residual: chirality pdb=" C3' U B -14 " pdb=" C4' U B -14 " pdb=" O3' U B -14 " pdb=" C2' U B -14 " both_signs ideal model delta sigma weight residual False -2.74 -2.50 -0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" C1' A B 13 " pdb=" O4' A B 13 " pdb=" C2' A B 13 " pdb=" N9 A B 13 " both_signs ideal model delta sigma weight residual False 2.46 2.25 0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CA CYS A1342 " pdb=" N CYS A1342 " pdb=" C CYS A1342 " pdb=" CB CYS A1342 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 1.00e+00 ... (remaining 2081 not shown) Planarity restraints: 2315 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A 863 " -0.052 5.00e-02 4.00e+02 7.89e-02 9.96e+00 pdb=" N PRO A 864 " 0.137 5.00e-02 4.00e+02 pdb=" CA PRO A 864 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO A 864 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' G B 9 " -0.037 2.00e-02 2.50e+03 1.69e-02 8.56e+00 pdb=" N9 G B 9 " 0.043 2.00e-02 2.50e+03 pdb=" C8 G B 9 " 0.001 2.00e-02 2.50e+03 pdb=" N7 G B 9 " 0.000 2.00e-02 2.50e+03 pdb=" C5 G B 9 " -0.001 2.00e-02 2.50e+03 pdb=" C6 G B 9 " -0.006 2.00e-02 2.50e+03 pdb=" O6 G B 9 " -0.007 2.00e-02 2.50e+03 pdb=" N1 G B 9 " -0.005 2.00e-02 2.50e+03 pdb=" C2 G B 9 " 0.005 2.00e-02 2.50e+03 pdb=" N2 G B 9 " 0.001 2.00e-02 2.50e+03 pdb=" N3 G B 9 " 0.004 2.00e-02 2.50e+03 pdb=" C4 G B 9 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A1311 " -0.013 2.00e-02 2.50e+03 2.62e-02 6.87e+00 pdb=" C PRO A1311 " 0.045 2.00e-02 2.50e+03 pdb=" O PRO A1311 " -0.017 2.00e-02 2.50e+03 pdb=" N CYS A1312 " -0.015 2.00e-02 2.50e+03 ... (remaining 2312 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 609 2.69 - 3.25: 13133 3.25 - 3.80: 20329 3.80 - 4.35: 25821 4.35 - 4.90: 44074 Nonbonded interactions: 103966 Sorted by model distance: nonbonded pdb=" O2' A B 11 " pdb=" O4' C B 12 " model vdw 2.143 3.040 nonbonded pdb=" OG SER A 445 " pdb=" OP1 A B -2 " model vdw 2.186 3.040 nonbonded pdb=" NZ LYS A1004 " pdb=" O PHE A1005 " model vdw 2.229 3.120 nonbonded pdb=" NE2 HIS A 931 " pdb=" OG1 THR A1444 " model vdw 2.241 3.120 nonbonded pdb=" NH1 ARG A 974 " pdb=" O ASP A1298 " model vdw 2.241 3.120 ... (remaining 103961 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.020 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: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.560 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 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 0.064 14237 Z= 0.293 Angle : 0.729 11.132 19484 Z= 0.406 Chirality : 0.048 0.241 2084 Planarity : 0.005 0.079 2315 Dihedral : 15.368 170.704 5643 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.13 % Allowed : 16.06 % Favored : 83.81 % Rotamer: Outliers : 0.60 % Allowed : 7.22 % Favored : 92.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.75 (0.17), residues: 1526 helix: -1.14 (0.28), residues: 300 sheet: -3.22 (0.26), residues: 281 loop : -4.07 (0.15), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 444 TYR 0.021 0.002 TYR A 863 PHE 0.015 0.002 PHE A 528 TRP 0.015 0.002 TRP A1600 HIS 0.005 0.002 HIS A1473 Details of bonding type rmsd/Z covalent geometry : bond 0.00655 / 0.29 (14237) covalent geometry : angle 0.72934 / 0.41 (19484) hydrogen bonds : bond 0.21404 / 12.94 ( 342) hydrogen bonds : angle 6.95324 / 4.99 ( 905) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 time to evaluate : 0.526 Fit side-chains REVERT: A 311 ASP cc_start: 0.8125 (t0) cc_final: 0.7676 (t70) REVERT: A 1065 ARG cc_start: 0.8012 (mmm160) cc_final: 0.7252 (ttm170) REVERT: A 1211 MET cc_start: 0.7960 (tmm) cc_final: 0.7124 (tmm) REVERT: A 1270 LYS cc_start: 0.7649 (mmmt) cc_final: 0.7340 (mttm) REVERT: A 1342 CYS cc_start: 0.8291 (OUTLIER) cc_final: 0.7846 (p) outliers start: 8 outliers final: 3 residues processed: 74 average time/residue: 0.1643 time to fit residues: 16.8613 Evaluate side-chains 48 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 44 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 CYS Chi-restraints excluded: chain A residue 708 CYS Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 1342 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.5980 chunk 149 optimal weight: 3.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 118 ASN A 306 HIS A 456 GLN A 586 ASN A1027 GLN A1095 HIS A1136 ASN A1207 ASN A1417 HIS A1419 HIS A1452 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.081495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.061364 restraints weight = 36623.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.063423 restraints weight = 19902.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.064747 restraints weight = 13927.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.065545 restraints weight = 11181.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.065979 restraints weight = 9804.308| |-----------------------------------------------------------------------------| r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.1112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14237 Z= 0.134 Angle : 0.614 12.069 19484 Z= 0.319 Chirality : 0.044 0.212 2084 Planarity : 0.005 0.066 2315 Dihedral : 12.139 164.434 2437 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.29 % Favored : 89.71 % Rotamer: Outliers : 0.37 % Allowed : 10.27 % Favored : 89.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.77 (0.19), residues: 1526 helix: 0.27 (0.31), residues: 311 sheet: -2.51 (0.28), residues: 275 loop : -3.72 (0.16), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 393 TYR 0.011 0.001 TYR A 863 PHE 0.011 0.001 PHE A 776 TRP 0.011 0.001 TRP A1600 HIS 0.004 0.001 HIS A1473 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (14237) covalent geometry : angle 0.61407 / 0.32 (19484) hydrogen bonds : bond 0.04744 / 2.94 ( 342) hydrogen bonds : angle 4.71905 / 3.35 ( 905) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 65 time to evaluate : 0.506 Fit side-chains REVERT: A 305 ASP cc_start: 0.7313 (t0) cc_final: 0.6854 (t0) REVERT: A 410 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.7754 (pp) REVERT: A 989 ASP cc_start: 0.8142 (t70) cc_final: 0.7919 (t0) REVERT: A 1065 ARG cc_start: 0.7847 (mmm160) cc_final: 0.7203 (ttm170) REVERT: A 1211 MET cc_start: 0.7972 (tmm) cc_final: 0.7211 (tmm) REVERT: A 1270 LYS cc_start: 0.7631 (mmmt) cc_final: 0.7376 (mttm) outliers start: 5 outliers final: 3 residues processed: 70 average time/residue: 0.1377 time to fit residues: 14.1829 Evaluate side-chains 55 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 51 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 CYS Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 1479 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 83 optimal weight: 7.9990 chunk 9 optimal weight: 9.9990 chunk 5 optimal weight: 5.9990 chunk 122 optimal weight: 10.0000 chunk 100 optimal weight: 10.0000 chunk 102 optimal weight: 6.9990 chunk 56 optimal weight: 6.9990 chunk 104 optimal weight: 9.9990 chunk 156 optimal weight: 10.0000 chunk 94 optimal weight: 10.0000 chunk 36 optimal weight: 5.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 100 GLN A 208 ASN ** A1020 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1246 ASN A1483 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.075777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.055760 restraints weight = 38335.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.057544 restraints weight = 22225.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.058644 restraints weight = 16120.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.059346 restraints weight = 13346.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.059744 restraints weight = 11877.940| |-----------------------------------------------------------------------------| r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8812 moved from start: 0.1247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.080 14237 Z= 0.523 Angle : 0.919 10.371 19484 Z= 0.475 Chirality : 0.056 0.303 2084 Planarity : 0.007 0.094 2315 Dihedral : 12.556 167.849 2435 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.64 % Favored : 83.36 % Rotamer: Outliers : 2.60 % Allowed : 14.96 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.02 (0.19), residues: 1526 helix: -0.02 (0.30), residues: 303 sheet: -2.81 (0.27), residues: 280 loop : -3.78 (0.16), residues: 943 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 444 TYR 0.034 0.003 TYR A 863 PHE 0.025 0.003 PHE A 418 TRP 0.020 0.003 TRP A1597 HIS 0.010 0.002 HIS A1149 Details of bonding type rmsd/Z covalent geometry : bond 0.01209 / 0.52 (14237) covalent geometry : angle 0.91910 / 0.48 (19484) hydrogen bonds : bond 0.07513 / 4.82 ( 342) hydrogen bonds : angle 5.39719 / 3.84 ( 905) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 38 time to evaluate : 0.516 Fit side-chains REVERT: A 1013 PHE cc_start: 0.8391 (OUTLIER) cc_final: 0.7998 (m-80) REVERT: A 1037 MET cc_start: 0.7908 (mmt) cc_final: 0.7650 (mmt) REVERT: A 1065 ARG cc_start: 0.8013 (mmm160) cc_final: 0.7257 (ttm170) REVERT: A 1211 MET cc_start: 0.8192 (tmm) cc_final: 0.7088 (tmm) REVERT: A 1270 LYS cc_start: 0.7706 (mmmt) cc_final: 0.7444 (mttm) REVERT: A 1533 TRP cc_start: 0.8569 (OUTLIER) cc_final: 0.8063 (m-10) outliers start: 35 outliers final: 22 residues processed: 73 average time/residue: 0.1206 time to fit residues: 13.5493 Evaluate side-chains 61 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 37 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 CYS Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 731 GLU Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 900 ILE Chi-restraints excluded: chain A residue 903 THR Chi-restraints excluded: chain A residue 968 ILE Chi-restraints excluded: chain A residue 1008 THR Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1013 PHE Chi-restraints excluded: chain A residue 1087 THR Chi-restraints excluded: chain A residue 1367 ASP Chi-restraints excluded: chain A residue 1386 VAL Chi-restraints excluded: chain A residue 1397 THR Chi-restraints excluded: chain A residue 1436 ILE Chi-restraints excluded: chain A residue 1479 LYS Chi-restraints excluded: chain A residue 1500 VAL Chi-restraints excluded: chain A residue 1533 TRP Chi-restraints excluded: chain A residue 1600 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 108 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 104 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 95 optimal weight: 8.9990 chunk 114 optimal weight: 9.9990 chunk 36 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 chunk 134 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 100 GLN A1105 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.080632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.060515 restraints weight = 37187.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.062555 restraints weight = 20237.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.063839 restraints weight = 14155.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.064642 restraints weight = 11452.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.065086 restraints weight = 10037.739| |-----------------------------------------------------------------------------| r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.1383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14237 Z= 0.135 Angle : 0.612 11.377 19484 Z= 0.317 Chirality : 0.044 0.198 2084 Planarity : 0.005 0.072 2315 Dihedral : 12.125 163.900 2435 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.22 % Favored : 89.78 % Rotamer: Outliers : 1.19 % Allowed : 17.04 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.30 (0.20), residues: 1526 helix: 0.72 (0.31), residues: 310 sheet: -2.19 (0.29), residues: 277 loop : -3.45 (0.16), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 393 TYR 0.011 0.001 TYR A 313 PHE 0.011 0.001 PHE A 15 TRP 0.012 0.001 TRP A1600 HIS 0.004 0.001 HIS A1473 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (14237) covalent geometry : angle 0.61200 / 0.32 (19484) hydrogen bonds : bond 0.04314 / 2.71 ( 342) hydrogen bonds : angle 4.34506 / 3.09 ( 905) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 49 time to evaluate : 0.597 Fit side-chains REVERT: A 410 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.7658 (pp) REVERT: A 989 ASP cc_start: 0.8198 (t70) cc_final: 0.7935 (t0) REVERT: A 1065 ARG cc_start: 0.7945 (mmm160) cc_final: 0.7268 (ttm170) REVERT: A 1211 MET cc_start: 0.8024 (tmm) cc_final: 0.7058 (tmm) REVERT: A 1270 LYS cc_start: 0.7608 (mmmt) cc_final: 0.7251 (mttm) outliers start: 16 outliers final: 8 residues processed: 64 average time/residue: 0.1273 time to fit residues: 12.4597 Evaluate side-chains 56 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 47 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 CYS Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 731 GLU Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 1446 GLU Chi-restraints excluded: chain A residue 1479 LYS Chi-restraints excluded: chain A residue 1491 MET Chi-restraints excluded: chain A residue 1600 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 67 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 33 optimal weight: 0.4980 chunk 82 optimal weight: 0.1980 chunk 48 optimal weight: 0.9980 chunk 103 optimal weight: 4.9990 chunk 152 optimal weight: 0.9980 chunk 150 optimal weight: 9.9990 chunk 147 optimal weight: 3.9990 chunk 143 optimal weight: 1.9990 chunk 129 optimal weight: 4.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 100 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.082196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.062229 restraints weight = 36807.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.064307 restraints weight = 19942.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.065614 restraints weight = 13906.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.066438 restraints weight = 11169.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.066901 restraints weight = 9765.463| |-----------------------------------------------------------------------------| r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14237 Z= 0.114 Angle : 0.561 12.175 19484 Z= 0.289 Chirality : 0.042 0.194 2084 Planarity : 0.005 0.064 2315 Dihedral : 11.901 163.091 2435 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.62 % Favored : 89.38 % Rotamer: Outliers : 1.93 % Allowed : 16.67 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.80 (0.20), residues: 1526 helix: 1.22 (0.32), residues: 311 sheet: -1.65 (0.30), residues: 277 loop : -3.23 (0.17), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 393 TYR 0.010 0.001 TYR A 313 PHE 0.011 0.001 PHE A 747 TRP 0.010 0.001 TRP A1600 HIS 0.005 0.001 HIS A1473 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 (14237) covalent geometry : angle 0.56082 / 0.29 (19484) hydrogen bonds : bond 0.03599 / 2.28 ( 342) hydrogen bonds : angle 3.99639 / 2.84 ( 905) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 51 time to evaluate : 0.560 Fit side-chains REVERT: A 410 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.7953 (pt) REVERT: A 989 ASP cc_start: 0.8163 (t70) cc_final: 0.7955 (t0) REVERT: A 1065 ARG cc_start: 0.7887 (mmm160) cc_final: 0.7299 (ttm170) REVERT: A 1211 MET cc_start: 0.7957 (tmm) cc_final: 0.7256 (tmm) REVERT: A 1270 LYS cc_start: 0.7615 (mmmt) cc_final: 0.7381 (mttm) REVERT: A 1444 THR cc_start: 0.9496 (OUTLIER) cc_final: 0.9232 (m) REVERT: A 1473 HIS cc_start: 0.8281 (OUTLIER) cc_final: 0.7888 (t-90) outliers start: 26 outliers final: 16 residues processed: 73 average time/residue: 0.1294 time to fit residues: 14.2627 Evaluate side-chains 63 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 44 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 731 GLU Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 861 VAL Chi-restraints excluded: chain A residue 968 ILE Chi-restraints excluded: chain A residue 1087 THR Chi-restraints excluded: chain A residue 1103 PHE Chi-restraints excluded: chain A residue 1156 VAL Chi-restraints excluded: chain A residue 1305 MET Chi-restraints excluded: chain A residue 1444 THR Chi-restraints excluded: chain A residue 1446 GLU Chi-restraints excluded: chain A residue 1473 HIS Chi-restraints excluded: chain A residue 1479 LYS Chi-restraints excluded: chain A residue 1491 MET Chi-restraints excluded: chain A residue 1600 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 7 optimal weight: 7.9990 chunk 14 optimal weight: 1.9990 chunk 110 optimal weight: 5.9990 chunk 107 optimal weight: 20.0000 chunk 78 optimal weight: 0.1980 chunk 17 optimal weight: 6.9990 chunk 72 optimal weight: 8.9990 chunk 44 optimal weight: 0.9980 chunk 73 optimal weight: 5.9990 chunk 129 optimal weight: 4.9990 chunk 153 optimal weight: 10.0000 overall best weight: 2.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 306 HIS A 865 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.079443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.059312 restraints weight = 37163.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.061295 restraints weight = 20398.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.062578 restraints weight = 14375.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.063344 restraints weight = 11604.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.063833 restraints weight = 10211.547| |-----------------------------------------------------------------------------| r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 14237 Z= 0.230 Angle : 0.647 11.206 19484 Z= 0.333 Chirality : 0.045 0.228 2084 Planarity : 0.005 0.072 2315 Dihedral : 11.970 165.416 2434 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.58 % Favored : 87.42 % Rotamer: Outliers : 2.46 % Allowed : 17.56 % Favored : 79.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.87 (0.20), residues: 1526 helix: 1.13 (0.32), residues: 310 sheet: -1.77 (0.30), residues: 293 loop : -3.25 (0.17), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 393 TYR 0.017 0.001 TYR A 863 PHE 0.015 0.002 PHE A 528 TRP 0.013 0.001 TRP A1600 HIS 0.005 0.001 HIS A1473 Details of bonding type rmsd/Z covalent geometry : bond 0.00531 / 0.23 (14237) covalent geometry : angle 0.64696 / 0.33 (19484) hydrogen bonds : bond 0.04779 / 3.05 ( 342) hydrogen bonds : angle 4.30394 / 3.06 ( 905) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 43 time to evaluate : 0.599 Fit side-chains REVERT: A 410 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.7657 (pp) REVERT: A 989 ASP cc_start: 0.8173 (t70) cc_final: 0.7944 (t0) REVERT: A 1065 ARG cc_start: 0.7926 (mmm160) cc_final: 0.7337 (ttm170) REVERT: A 1211 MET cc_start: 0.8015 (tmm) cc_final: 0.7172 (tmm) REVERT: A 1270 LYS cc_start: 0.7671 (mmmt) cc_final: 0.7372 (mttm) REVERT: A 1283 TYR cc_start: 0.7798 (OUTLIER) cc_final: 0.7246 (m-10) REVERT: A 1473 HIS cc_start: 0.8401 (OUTLIER) cc_final: 0.7936 (t-90) REVERT: A 1533 TRP cc_start: 0.8288 (OUTLIER) cc_final: 0.7820 (m-10) outliers start: 33 outliers final: 23 residues processed: 72 average time/residue: 0.1200 time to fit residues: 13.4806 Evaluate side-chains 70 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 43 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 731 GLU Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 861 VAL Chi-restraints excluded: chain A residue 900 ILE Chi-restraints excluded: chain A residue 968 ILE Chi-restraints excluded: chain A residue 1008 THR Chi-restraints excluded: chain A residue 1087 THR Chi-restraints excluded: chain A residue 1103 PHE Chi-restraints excluded: chain A residue 1156 VAL Chi-restraints excluded: chain A residue 1201 CYS Chi-restraints excluded: chain A residue 1283 TYR Chi-restraints excluded: chain A residue 1305 MET Chi-restraints excluded: chain A residue 1446 GLU Chi-restraints excluded: chain A residue 1473 HIS Chi-restraints excluded: chain A residue 1479 LYS Chi-restraints excluded: chain A residue 1500 VAL Chi-restraints excluded: chain A residue 1533 TRP Chi-restraints excluded: chain A residue 1600 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 63 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 chunk 129 optimal weight: 1.9990 chunk 103 optimal weight: 10.0000 chunk 37 optimal weight: 0.1980 chunk 36 optimal weight: 0.9980 chunk 127 optimal weight: 0.8980 chunk 113 optimal weight: 0.5980 chunk 154 optimal weight: 4.9990 chunk 91 optimal weight: 0.9990 chunk 137 optimal weight: 6.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.083092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.063039 restraints weight = 36838.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.065177 restraints weight = 19594.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.066511 restraints weight = 13510.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.067349 restraints weight = 10812.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.067890 restraints weight = 9419.086| |-----------------------------------------------------------------------------| r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14237 Z= 0.103 Angle : 0.549 12.341 19484 Z= 0.281 Chirality : 0.041 0.187 2084 Planarity : 0.005 0.059 2315 Dihedral : 11.817 162.831 2434 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.17 % Favored : 90.83 % Rotamer: Outliers : 2.01 % Allowed : 17.93 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.47 (0.21), residues: 1526 helix: 1.48 (0.32), residues: 311 sheet: -1.41 (0.31), residues: 275 loop : -3.02 (0.17), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 393 TYR 0.010 0.001 TYR A 313 PHE 0.010 0.001 PHE A1407 TRP 0.009 0.001 TRP A1600 HIS 0.005 0.001 HIS A1473 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.10 (14237) covalent geometry : angle 0.54900 / 0.28 (19484) hydrogen bonds : bond 0.03341 / 2.11 ( 342) hydrogen bonds : angle 3.83089 / 2.73 ( 905) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 49 time to evaluate : 0.975 Fit side-chains revert: symmetry clash REVERT: A 410 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7941 (pt) REVERT: A 989 ASP cc_start: 0.8147 (t70) cc_final: 0.7886 (t0) REVERT: A 1211 MET cc_start: 0.7901 (tmm) cc_final: 0.7296 (tmm) REVERT: A 1270 LYS cc_start: 0.7610 (mmmt) cc_final: 0.7297 (mttm) REVERT: A 1473 HIS cc_start: 0.8312 (OUTLIER) cc_final: 0.7884 (t-90) outliers start: 27 outliers final: 21 residues processed: 73 average time/residue: 0.1234 time to fit residues: 13.7904 Evaluate side-chains 69 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 46 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 731 GLU Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 861 VAL Chi-restraints excluded: chain A residue 900 ILE Chi-restraints excluded: chain A residue 968 ILE Chi-restraints excluded: chain A residue 1087 THR Chi-restraints excluded: chain A residue 1103 PHE Chi-restraints excluded: chain A residue 1156 VAL Chi-restraints excluded: chain A residue 1305 MET Chi-restraints excluded: chain A residue 1390 LEU Chi-restraints excluded: chain A residue 1446 GLU Chi-restraints excluded: chain A residue 1473 HIS Chi-restraints excluded: chain A residue 1479 LYS Chi-restraints excluded: chain A residue 1491 MET Chi-restraints excluded: chain A residue 1600 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( ^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( ^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 53.096 > 50: distance: 11 - 60: 9.412 distance: 14 - 57: 17.604 distance: 53 - 57: 14.489 distance: 57 - 58: 36.845 distance: 58 - 59: 13.627 distance: 59 - 60: 14.970 distance: 59 - 61: 13.367 distance: 61 - 62: 8.714 distance: 62 - 63: 6.157 distance: 62 - 65: 10.196 distance: 63 - 64: 9.149 distance: 63 - 67: 5.950 distance: 65 - 66: 14.720 distance: 67 - 68: 8.836 distance: 68 - 69: 3.972 distance: 68 - 71: 4.589 distance: 69 - 70: 14.208 distance: 69 - 76: 14.832 distance: 71 - 72: 4.307 distance: 72 - 73: 11.561 distance: 73 - 74: 5.168 distance: 76 - 77: 18.797 distance: 77 - 78: 14.081 distance: 77 - 80: 7.656 distance: 78 - 79: 21.828 distance: 78 - 84: 27.956 distance: 80 - 81: 23.486 distance: 81 - 82: 17.113 distance: 81 - 83: 10.938 distance: 84 - 85: 36.678 distance: 85 - 86: 49.585 distance: 86 - 87: 27.292 distance: 86 - 88: 34.265 distance: 88 - 89: 26.714 distance: 89 - 90: 25.002 distance: 89 - 92: 24.652 distance: 90 - 91: 31.747 distance: 90 - 96: 20.515 distance: 92 - 93: 11.967 distance: 93 - 94: 18.034 distance: 93 - 95: 29.859 distance: 96 - 97: 21.441 distance: 96 - 102: 29.474 distance: 97 - 98: 20.222 distance: 97 - 100: 22.619 distance: 98 - 99: 10.113 distance: 98 - 103: 16.729 distance: 99 - 124: 11.113 distance: 100 - 101: 17.453 distance: 101 - 102: 16.225 distance: 103 - 104: 10.422 distance: 104 - 105: 37.822 distance: 104 - 107: 10.836 distance: 105 - 106: 50.472 distance: 105 - 111: 34.597 distance: 106 - 133: 22.422 distance: 107 - 108: 44.663 distance: 108 - 109: 49.642 distance: 108 - 110: 51.553 distance: 111 - 112: 13.052 distance: 112 - 113: 19.534 distance: 112 - 115: 22.756 distance: 113 - 114: 9.904 distance: 113 - 116: 13.700 distance: 114 - 140: 13.015 distance: 116 - 117: 10.530 distance: 117 - 118: 8.401 distance: 117 - 120: 12.265 distance: 118 - 119: 13.008 distance: 118 - 124: 10.580 distance: 119 - 147: 7.730 distance: 120 - 121: 16.550 distance: 121 - 122: 6.033 distance: 121 - 123: 4.932