Starting phenix.real_space_refine on Thu Jul 2 14:43:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8pmd_17759/07_2026/8pmd_17759.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pmd_17759/07_2026/8pmd_17759.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8pmd_17759/07_2026/8pmd_17759.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8pmd_17759/07_2026/8pmd_17759.cif" model { file = "/net/cci-nas-00/data/ceres_data/8pmd_17759/07_2026/8pmd_17759.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pmd_17759/07_2026/8pmd_17759.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8pmd_17759/07_2026/8pmd_17759.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pmd_17759/07_2026/8pmd_17759.map" } resolution = 2.95 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 52 5.16 5 C 5651 2.51 5 N 1497 2.21 5 O 1636 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8844 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 8778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1129, 8778 Classifications: {'peptide': 1129} Link IDs: {'PTRANS': 31, 'TRANS': 1097} Chain breaks: 5 Chain: "A" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 66 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4, 'water': 2} Link IDs: {None: 5} Time building chain proxies: 1.93, per 1000 atoms: 0.22 Number of scatterers: 8844 At special positions: 0 Unit cell: (89.1, 79.2, 148.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 52 16.00 P 6 15.00 Mg 2 11.99 O 1636 8.00 N 1497 7.00 C 5651 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: 0.66 Conformation dependent library (CDL) restraints added in 313.6 milliseconds 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2080 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 6 sheets defined 68.9% alpha, 7.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 46 through 50 removed outlier: 3.690A pdb=" N LEU A 50 " --> pdb=" O PHE A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 100 removed outlier: 4.312A pdb=" N GLN A 76 " --> pdb=" O HIS A 72 " (cutoff:3.500A) Proline residue: A 77 - end of helix removed outlier: 4.260A pdb=" N GLU A 96 " --> pdb=" O ASP A 92 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU A 97 " --> pdb=" O TYR A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 185 Processing helix chain 'A' and resid 186 through 193 Processing helix chain 'A' and resid 194 through 214 removed outlier: 4.949A pdb=" N ILE A 206 " --> pdb=" O PHE A 202 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ASN A 207 " --> pdb=" O SER A 203 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE A 213 " --> pdb=" O ILE A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 237 removed outlier: 4.304A pdb=" N GLY A 234 " --> pdb=" O GLY A 230 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N PHE A 235 " --> pdb=" O PHE A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 287 Proline residue: A 250 - end of helix Processing helix chain 'A' and resid 287 through 294 Processing helix chain 'A' and resid 296 through 344 removed outlier: 3.904A pdb=" N ASN A 307 " --> pdb=" O ARG A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 376 Processing helix chain 'A' and resid 376 through 398 removed outlier: 3.533A pdb=" N LEU A 380 " --> pdb=" O ALA A 376 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N SER A 392 " --> pdb=" O ALA A 388 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ILE A 393 " --> pdb=" O ALA A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 469 removed outlier: 3.719A pdb=" N ALA A 464 " --> pdb=" O GLY A 460 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLN A 469 " --> pdb=" O LEU A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 489 No H-bonds generated for 'chain 'A' and resid 487 through 489' Processing helix chain 'A' and resid 490 through 496 Processing helix chain 'A' and resid 511 through 518 Processing helix chain 'A' and resid 524 through 535 Processing helix chain 'A' and resid 537 through 543 Processing helix chain 'A' and resid 553 through 557 Processing helix chain 'A' and resid 560 through 574 Processing helix chain 'A' and resid 590 through 605 Processing helix chain 'A' and resid 616 through 621 removed outlier: 3.568A pdb=" N VAL A 620 " --> pdb=" O ARG A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 740 through 748 Processing helix chain 'A' and resid 751 through 781 removed outlier: 4.402A pdb=" N THR A 769 " --> pdb=" O ASN A 765 " (cutoff:3.500A) Proline residue: A 770 - end of helix removed outlier: 3.670A pdb=" N GLY A 781 " --> pdb=" O SER A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 793 through 841 removed outlier: 3.788A pdb=" N PHE A 811 " --> pdb=" O CYS A 807 " (cutoff:3.500A) Processing helix chain 'A' and resid 843 through 848 removed outlier: 3.505A pdb=" N PHE A 847 " --> pdb=" O ASP A 843 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 873 removed outlier: 4.211A pdb=" N ALA A 865 " --> pdb=" O LEU A 861 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N SER A 866 " --> pdb=" O ALA A 862 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA A 871 " --> pdb=" O GLN A 867 " (cutoff:3.500A) Processing helix chain 'A' and resid 874 through 895 Processing helix chain 'A' and resid 897 through 906 removed outlier: 3.625A pdb=" N SER A 901 " --> pdb=" O SER A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 907 through 946 removed outlier: 3.846A pdb=" N LEU A 911 " --> pdb=" O PHE A 907 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ARG A 928 " --> pdb=" O GLY A 924 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N GLN A 931 " --> pdb=" O SER A 927 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ASN A 946 " --> pdb=" O GLU A 942 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 954 Processing helix chain 'A' and resid 955 through 968 removed outlier: 3.994A pdb=" N PHE A 959 " --> pdb=" O LYS A 955 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE A 960 " --> pdb=" O GLU A 956 " (cutoff:3.500A) Processing helix chain 'A' and resid 968 through 1010 removed outlier: 4.416A pdb=" N LYS A 972 " --> pdb=" O GLU A 968 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N THR A 973 " --> pdb=" O LYS A 969 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ASN A 979 " --> pdb=" O ILE A 975 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE A 980 " --> pdb=" O GLN A 976 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N PHE A 993 " --> pdb=" O GLN A 989 " (cutoff:3.500A) Processing helix chain 'A' and resid 1014 through 1028 Processing helix chain 'A' and resid 1029 through 1033 removed outlier: 4.145A pdb=" N GLY A1032 " --> pdb=" O THR A1029 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ARG A1033 " --> pdb=" O ALA A1030 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1029 through 1033' Processing helix chain 'A' and resid 1037 through 1056 removed outlier: 3.615A pdb=" N ALA A1042 " --> pdb=" O THR A1038 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N LYS A1043 " --> pdb=" O PRO A1039 " (cutoff:3.500A) Processing helix chain 'A' and resid 1118 through 1127 removed outlier: 3.556A pdb=" N ILE A1123 " --> pdb=" O LYS A1119 " (cutoff:3.500A) Processing helix chain 'A' and resid 1148 through 1155 removed outlier: 3.835A pdb=" N ASN A1155 " --> pdb=" O PHE A1151 " (cutoff:3.500A) Processing helix chain 'A' and resid 1169 through 1176 Processing helix chain 'A' and resid 1184 through 1195 removed outlier: 3.543A pdb=" N VAL A1188 " --> pdb=" O PRO A1184 " (cutoff:3.500A) Processing helix chain 'A' and resid 1197 through 1203 Processing helix chain 'A' and resid 1213 through 1217 Processing helix chain 'A' and resid 1220 through 1234 Processing helix chain 'A' and resid 1256 through 1266 Processing helix chain 'A' and resid 1299 through 1307 removed outlier: 3.597A pdb=" N LYS A1307 " --> pdb=" O LEU A1303 " (cutoff:3.500A) Processing helix chain 'A' and resid 1308 through 1316 Processing sheet with id=AA1, first strand: chain 'A' and resid 438 through 441 removed outlier: 5.267A pdb=" N VAL A 425 " --> pdb=" O ASP A 440 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 438 through 441 removed outlier: 5.267A pdb=" N VAL A 425 " --> pdb=" O ASP A 440 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N PHE A 422 " --> pdb=" O THR A 480 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N THR A 480 " --> pdb=" O PHE A 422 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N ASN A 424 " --> pdb=" O MET A 478 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N MET A 478 " --> pdb=" O ASN A 424 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 498 through 501 removed outlier: 6.169A pdb=" N GLY A 499 " --> pdb=" O LEU A 581 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N ASP A 583 " --> pdb=" O GLY A 499 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N VAL A 501 " --> pdb=" O ASP A 583 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N LEU A 580 " --> pdb=" O ILE A 611 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N VAL A 613 " --> pdb=" O LEU A 580 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N LEU A 582 " --> pdb=" O VAL A 613 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N MET A 450 " --> pdb=" O THR A 625 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N ILE A 627 " --> pdb=" O MET A 450 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ALA A 452 " --> pdb=" O ILE A 627 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N PHE A 629 " --> pdb=" O ALA A 452 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N VAL A 454 " --> pdb=" O PHE A 629 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1102 through 1103 Processing sheet with id=AA5, first strand: chain 'A' and resid 1083 through 1086 removed outlier: 8.029A pdb=" N PHE A1085 " --> pdb=" O ASN A1097 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N ASN A1097 " --> pdb=" O PHE A1085 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1156 through 1159 removed outlier: 6.390A pdb=" N GLY A1157 " --> pdb=" O LEU A1241 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N ASP A1243 " --> pdb=" O GLY A1157 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N VAL A1159 " --> pdb=" O ASP A1243 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N LEU A1109 " --> pdb=" O VAL A1272 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N THR A1108 " --> pdb=" O ILE A1285 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N ALA A1287 " --> pdb=" O THR A1108 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N ALA A1110 " --> pdb=" O ALA A1287 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N MET A1289 " --> pdb=" O ALA A1110 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N VAL A1112 " --> pdb=" O MET A1289 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU A1296 " --> pdb=" O VAL A1288 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ALA A1290 " --> pdb=" O VAL A1294 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N VAL A1294 " --> pdb=" O ALA A1290 " (cutoff:3.500A) 585 hydrogen bonds defined for protein. 1713 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: 1.29 Time building geometry restraints manager: 0.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1440 1.32 - 1.44: 2403 1.44 - 1.56: 5073 1.56 - 1.69: 10 1.69 - 1.81: 85 Bond restraints: 9011 Sorted by residual: bond pdb=" C PHE A1111 " pdb=" O PHE A1111 " ideal model delta sigma weight residual 1.236 1.192 0.044 1.22e-02 6.72e+03 1.31e+01 bond pdb=" C LYS A 930 " pdb=" N GLN A 931 " ideal model delta sigma weight residual 1.335 1.297 0.037 1.36e-02 5.41e+03 7.58e+00 bond pdb=" C ALA A 773 " pdb=" N PHE A 774 " ideal model delta sigma weight residual 1.334 1.298 0.037 1.33e-02 5.65e+03 7.54e+00 bond pdb=" N ILE A1273 " pdb=" CA ILE A1273 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.20e-02 6.94e+03 7.00e+00 bond pdb=" C GLU A 504 " pdb=" N PRO A 505 " ideal model delta sigma weight residual 1.332 1.366 -0.034 1.30e-02 5.92e+03 6.81e+00 ... (remaining 9006 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.34: 11636 1.34 - 2.68: 420 2.68 - 4.02: 88 4.02 - 5.36: 31 5.36 - 6.70: 14 Bond angle restraints: 12189 Sorted by residual: angle pdb=" N LEU A 332 " pdb=" CA LEU A 332 " pdb=" C LEU A 332 " ideal model delta sigma weight residual 111.03 104.70 6.33 1.11e+00 8.12e-01 3.26e+01 angle pdb=" CA ILE A 416 " pdb=" C ILE A 416 " pdb=" O ILE A 416 " ideal model delta sigma weight residual 121.23 115.36 5.87 1.07e+00 8.73e-01 3.01e+01 angle pdb=" CA PHE A 70 " pdb=" C PHE A 70 " pdb=" O PHE A 70 " ideal model delta sigma weight residual 120.55 115.55 5.00 1.06e+00 8.90e-01 2.22e+01 angle pdb=" CA TYR A 145 " pdb=" C TYR A 145 " pdb=" N ALA A 146 " ideal model delta sigma weight residual 117.63 122.64 -5.01 1.25e+00 6.40e-01 1.61e+01 angle pdb=" CA ILE A 416 " pdb=" C ILE A 416 " pdb=" N LYS A 417 " ideal model delta sigma weight residual 116.10 120.87 -4.77 1.20e+00 6.94e-01 1.58e+01 ... (remaining 12184 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.11: 4523 17.11 - 34.21: 548 34.21 - 51.32: 203 51.32 - 68.42: 40 68.42 - 85.53: 13 Dihedral angle restraints: 5327 sinusoidal: 2091 harmonic: 3236 Sorted by residual: dihedral pdb=" CA ASP A 404 " pdb=" CB ASP A 404 " pdb=" CG ASP A 404 " pdb=" OD1 ASP A 404 " ideal model delta sinusoidal sigma weight residual -30.00 -89.80 59.80 1 2.00e+01 2.50e-03 1.19e+01 dihedral pdb=" CG ARG A 575 " pdb=" CD ARG A 575 " pdb=" NE ARG A 575 " pdb=" CZ ARG A 575 " ideal model delta sinusoidal sigma weight residual -90.00 -134.34 44.34 2 1.50e+01 4.44e-03 1.04e+01 dihedral pdb=" CG ARG A 487 " pdb=" CD ARG A 487 " pdb=" NE ARG A 487 " pdb=" CZ ARG A 487 " ideal model delta sinusoidal sigma weight residual 90.00 131.92 -41.92 2 1.50e+01 4.44e-03 9.52e+00 ... (remaining 5324 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1095 0.051 - 0.102: 234 0.102 - 0.153: 48 0.153 - 0.204: 4 0.204 - 0.255: 1 Chirality restraints: 1382 Sorted by residual: chirality pdb=" CA ILE A 416 " pdb=" N ILE A 416 " pdb=" C ILE A 416 " pdb=" CB ILE A 416 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.26 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" CA LEU A 332 " pdb=" N LEU A 332 " pdb=" C LEU A 332 " pdb=" CB LEU A 332 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.97e-01 chirality pdb=" CG LEU A 827 " pdb=" CB LEU A 827 " pdb=" CD1 LEU A 827 " pdb=" CD2 LEU A 827 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 7.77e-01 ... (remaining 1379 not shown) Planarity restraints: 1544 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 416 " 0.015 2.00e-02 2.50e+03 2.99e-02 8.94e+00 pdb=" C ILE A 416 " -0.052 2.00e-02 2.50e+03 pdb=" O ILE A 416 " 0.019 2.00e-02 2.50e+03 pdb=" N LYS A 417 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 332 " -0.014 2.00e-02 2.50e+03 2.82e-02 7.98e+00 pdb=" C LEU A 332 " 0.049 2.00e-02 2.50e+03 pdb=" O LEU A 332 " -0.018 2.00e-02 2.50e+03 pdb=" N ILE A 333 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 216 " -0.013 2.00e-02 2.50e+03 2.68e-02 7.18e+00 pdb=" C GLN A 216 " 0.046 2.00e-02 2.50e+03 pdb=" O GLN A 216 " -0.018 2.00e-02 2.50e+03 pdb=" N MET A 217 " -0.016 2.00e-02 2.50e+03 ... (remaining 1541 not shown) Histogram of nonbonded interaction distances: 1.35 - 2.06: 7 2.06 - 2.77: 1751 2.77 - 3.48: 13046 3.48 - 4.19: 20598 4.19 - 4.90: 37436 Nonbonded interactions: 72838 Sorted by model distance: nonbonded pdb=" OE2 GLU A1127 " pdb=" CD1 ILE A1158 " model vdw 1.353 3.460 nonbonded pdb="MG MG A1503 " pdb=" O HOH A1601 " model vdw 1.962 2.170 nonbonded pdb=" OE1 GLN A1161 " pdb="MG MG A1503 " model vdw 1.981 2.170 nonbonded pdb=" OG SER A1120 " pdb="MG MG A1503 " model vdw 2.018 2.170 nonbonded pdb=" O3G ATP A1502 " pdb="MG MG A1504 " model vdw 2.027 2.170 ... (remaining 72833 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=0.00 max=1.00 mean=0.93 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: 4.110 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.010 Process input model: 8.730 Find NCS groups from input model: 0.020 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:5.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 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 : 0.004 0.044 9011 Z= 0.210 Angle : 0.658 6.699 12189 Z= 0.384 Chirality : 0.044 0.255 1382 Planarity : 0.004 0.054 1544 Dihedral : 17.667 85.530 3247 Min Nonbonded Distance : 1.353 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.21 % Allowed : 28.83 % Favored : 70.95 % 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: 1.07 (0.24), residues: 1117 helix: 1.42 (0.18), residues: 736 sheet: 0.56 (0.54), residues: 77 loop : -0.94 (0.32), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 184 TYR 0.025 0.002 TYR A 337 PHE 0.018 0.002 PHE A 747 TRP 0.012 0.001 TRP A1071 HIS 0.003 0.001 HIS A 428 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.21 ( 9011) covalent geometry : angle 0.65822 / 0.38 (12189) hydrogen bonds : bond 0.11521 / 7.70 ( 582) hydrogen bonds : angle 4.80207 / 3.57 ( 1713) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 207 time to evaluate : 0.265 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 207 average time/residue: 0.4733 time to fit residues: 105.0103 Evaluate side-chains 187 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 186 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 776 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.0030 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 0.0870 overall best weight: 0.5368 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 361 GLN A 372 ASN A 598 GLN A 989 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.150065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.138595 restraints weight = 10739.787| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 1.12 r_work: 0.3482 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.3385 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3381 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3381 r_free = 0.3381 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 317 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3372 r_free = 0.3372 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 328 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (11 function evaluations) r_final: 0.3372 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.0967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9011 Z= 0.136 Angle : 0.538 7.234 12189 Z= 0.292 Chirality : 0.041 0.142 1382 Planarity : 0.004 0.052 1544 Dihedral : 5.566 72.657 1223 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 5.57 % Allowed : 26.26 % Favored : 68.17 % 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: 1.49 (0.24), residues: 1117 helix: 1.76 (0.19), residues: 744 sheet: 0.62 (0.53), residues: 77 loop : -0.88 (0.32), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 184 TYR 0.021 0.001 TYR A 337 PHE 0.023 0.001 PHE A 383 TRP 0.011 0.001 TRP A1071 HIS 0.003 0.001 HIS A 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.14 ( 9011) covalent geometry : angle 0.53838 / 0.29 (12189) hydrogen bonds : bond 0.06190 / 4.04 ( 582) hydrogen bonds : angle 4.17926 / 3.11 ( 1713) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 212 time to evaluate : 0.289 Fit side-chains REVERT: A 224 MET cc_start: 0.8335 (OUTLIER) cc_final: 0.8132 (mmp) REVERT: A 268 ASP cc_start: 0.8125 (t0) cc_final: 0.7869 (t0) REVERT: A 428 HIS cc_start: 0.7782 (OUTLIER) cc_final: 0.6718 (p90) REVERT: A 573 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7873 (mp) REVERT: A 591 ASN cc_start: 0.7575 (m-40) cc_final: 0.7362 (m110) REVERT: A 611 ILE cc_start: 0.8791 (mt) cc_final: 0.8531 (tt) REVERT: A 956 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7327 (mm-30) REVERT: A 1238 LYS cc_start: 0.7582 (mtpm) cc_final: 0.7334 (ttmt) outliers start: 52 outliers final: 18 residues processed: 241 average time/residue: 0.5035 time to fit residues: 129.9627 Evaluate side-chains 212 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 190 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 224 MET Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 428 HIS Chi-restraints excluded: chain A residue 431 SER Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 625 THR Chi-restraints excluded: chain A residue 776 PHE Chi-restraints excluded: chain A residue 827 LEU Chi-restraints excluded: chain A residue 956 GLU Chi-restraints excluded: chain A residue 999 SER Chi-restraints excluded: chain A residue 1008 SER Chi-restraints excluded: chain A residue 1072 ASP Chi-restraints excluded: chain A residue 1122 SER Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1304 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 4.9990 chunk 52 optimal weight: 7.9990 chunk 94 optimal weight: 0.0770 chunk 96 optimal weight: 0.0870 chunk 46 optimal weight: 4.9990 chunk 93 optimal weight: 0.9980 chunk 48 optimal weight: 0.7980 chunk 92 optimal weight: 5.9990 chunk 77 optimal weight: 6.9990 chunk 106 optimal weight: 6.9990 chunk 107 optimal weight: 0.7980 overall best weight: 0.5516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 466 GLN A 598 GLN A 813 GLN ** A 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1124 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.151060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.139176 restraints weight = 10499.512| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 1.08 r_work: 0.3491 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3395 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3390 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3390 r_free = 0.3390 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 328 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3389 r_free = 0.3389 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 337 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.3389 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.1263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9011 Z= 0.131 Angle : 0.526 7.346 12189 Z= 0.283 Chirality : 0.040 0.138 1382 Planarity : 0.003 0.053 1544 Dihedral : 5.580 78.264 1223 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 4.61 % Allowed : 26.58 % Favored : 68.81 % 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: 1.59 (0.24), residues: 1117 helix: 1.85 (0.19), residues: 742 sheet: 0.64 (0.53), residues: 77 loop : -0.87 (0.32), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1265 TYR 0.023 0.001 TYR A 337 PHE 0.013 0.001 PHE A 540 TRP 0.013 0.001 TRP A1071 HIS 0.003 0.001 HIS A 428 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.13 ( 9011) covalent geometry : angle 0.52649 / 0.28 (12189) hydrogen bonds : bond 0.05950 / 3.86 ( 582) hydrogen bonds : angle 4.08542 / 3.04 ( 1713) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 193 time to evaluate : 0.279 Fit side-chains REVERT: A 181 ARG cc_start: 0.7913 (mpt180) cc_final: 0.7189 (mmm160) REVERT: A 224 MET cc_start: 0.8392 (OUTLIER) cc_final: 0.8192 (mmp) REVERT: A 254 ILE cc_start: 0.7395 (mm) cc_final: 0.7116 (tp) REVERT: A 268 ASP cc_start: 0.8126 (t0) cc_final: 0.7854 (t0) REVERT: A 428 HIS cc_start: 0.7832 (OUTLIER) cc_final: 0.6850 (p90) REVERT: A 573 LEU cc_start: 0.8079 (OUTLIER) cc_final: 0.7863 (mp) REVERT: A 591 ASN cc_start: 0.7626 (m-40) cc_final: 0.7388 (m110) REVERT: A 611 ILE cc_start: 0.8817 (mt) cc_final: 0.8575 (tt) REVERT: A 956 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7256 (mm-30) REVERT: A 1171 MET cc_start: 0.7887 (tpp) cc_final: 0.7660 (tpt) REVERT: A 1302 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7728 (mp0) outliers start: 43 outliers final: 19 residues processed: 219 average time/residue: 0.4812 time to fit residues: 112.8503 Evaluate side-chains 204 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 180 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 224 MET Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 428 HIS Chi-restraints excluded: chain A residue 431 SER Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 776 PHE Chi-restraints excluded: chain A residue 956 GLU Chi-restraints excluded: chain A residue 999 SER Chi-restraints excluded: chain A residue 1008 SER Chi-restraints excluded: chain A residue 1093 SER Chi-restraints excluded: chain A residue 1122 SER Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1164 VAL Chi-restraints excluded: chain A residue 1302 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 82 optimal weight: 6.9990 chunk 81 optimal weight: 3.9990 chunk 16 optimal weight: 0.4980 chunk 70 optimal weight: 0.8980 chunk 97 optimal weight: 8.9990 chunk 12 optimal weight: 4.9990 chunk 96 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 361 GLN A 372 ASN A 466 GLN A 598 GLN ** A 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.144741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.132690 restraints weight = 10772.072| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 1.08 r_work: 0.3414 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3317 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3339 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3339 r_free = 0.3339 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 337 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3337 r_free = 0.3337 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 331 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3337 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.1357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 9011 Z= 0.218 Angle : 0.610 8.709 12189 Z= 0.333 Chirality : 0.045 0.138 1382 Planarity : 0.004 0.052 1544 Dihedral : 5.854 74.378 1223 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 6.43 % Allowed : 24.76 % Favored : 68.81 % 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: 1.08 (0.24), residues: 1117 helix: 1.46 (0.18), residues: 741 sheet: 0.40 (0.50), residues: 77 loop : -1.04 (0.31), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 184 TYR 0.023 0.002 TYR A 337 PHE 0.028 0.002 PHE A 383 TRP 0.012 0.002 TRP A 163 HIS 0.004 0.001 HIS A 428 Details of bonding type rmsd/Z covalent geometry : bond 0.00482 / 0.22 ( 9011) covalent geometry : angle 0.61047 / 0.33 (12189) hydrogen bonds : bond 0.07387 / 4.79 ( 582) hydrogen bonds : angle 4.26833 / 3.14 ( 1713) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 200 time to evaluate : 0.366 Fit side-chains REVERT: A 70 PHE cc_start: 0.8363 (t80) cc_final: 0.8136 (t80) REVERT: A 80 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.8060 (mt) REVERT: A 181 ARG cc_start: 0.7996 (mpt180) cc_final: 0.7282 (mmm160) REVERT: A 268 ASP cc_start: 0.8157 (t0) cc_final: 0.7889 (t0) REVERT: A 321 VAL cc_start: 0.7826 (OUTLIER) cc_final: 0.7565 (m) REVERT: A 342 TRP cc_start: 0.6435 (t60) cc_final: 0.5875 (t-100) REVERT: A 428 HIS cc_start: 0.7840 (OUTLIER) cc_final: 0.6935 (p-80) REVERT: A 465 LEU cc_start: 0.8412 (mt) cc_final: 0.7787 (tp) REVERT: A 591 ASN cc_start: 0.7767 (m-40) cc_final: 0.7559 (m110) REVERT: A 790 GLU cc_start: 0.3805 (OUTLIER) cc_final: 0.3590 (pp20) REVERT: A 930 LYS cc_start: 0.7784 (OUTLIER) cc_final: 0.7576 (mttp) REVERT: A 956 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7318 (mm-30) REVERT: A 1296 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7192 (mt-10) outliers start: 60 outliers final: 25 residues processed: 237 average time/residue: 0.4304 time to fit residues: 110.0647 Evaluate side-chains 220 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 188 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 428 HIS Chi-restraints excluded: chain A residue 431 SER Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 625 THR Chi-restraints excluded: chain A residue 760 VAL Chi-restraints excluded: chain A residue 790 GLU Chi-restraints excluded: chain A residue 930 LYS Chi-restraints excluded: chain A residue 940 THR Chi-restraints excluded: chain A residue 956 GLU Chi-restraints excluded: chain A residue 999 SER Chi-restraints excluded: chain A residue 1008 SER Chi-restraints excluded: chain A residue 1093 SER Chi-restraints excluded: chain A residue 1122 SER Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1164 VAL Chi-restraints excluded: chain A residue 1235 ARG Chi-restraints excluded: chain A residue 1296 GLU Chi-restraints excluded: chain A residue 1316 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 81 optimal weight: 5.9990 chunk 111 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 68 optimal weight: 7.9990 chunk 63 optimal weight: 0.7980 chunk 55 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 74 optimal weight: 0.5980 chunk 101 optimal weight: 0.7980 chunk 78 optimal weight: 6.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 361 GLN A 530 GLN A 598 GLN ** A 918 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.147883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.135926 restraints weight = 10619.030| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 1.08 r_work: 0.3456 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.3360 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3358 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3358 r_free = 0.3358 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 331 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3357 r_free = 0.3357 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 337 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3357 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.1404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9011 Z= 0.140 Angle : 0.548 6.447 12189 Z= 0.296 Chirality : 0.041 0.179 1382 Planarity : 0.003 0.053 1544 Dihedral : 5.529 76.644 1221 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 5.36 % Allowed : 26.80 % Favored : 67.85 % 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: 1.33 (0.24), residues: 1117 helix: 1.63 (0.19), residues: 742 sheet: 0.72 (0.53), residues: 77 loop : -0.96 (0.31), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1001 TYR 0.021 0.001 TYR A 337 PHE 0.020 0.001 PHE A 774 TRP 0.012 0.001 TRP A 163 HIS 0.003 0.001 HIS A 428 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.14 ( 9011) covalent geometry : angle 0.54827 / 0.30 (12189) hydrogen bonds : bond 0.06451 / 4.18 ( 582) hydrogen bonds : angle 4.15726 / 3.08 ( 1713) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 194 time to evaluate : 0.310 Fit side-chains REVERT: A 70 PHE cc_start: 0.8321 (t80) cc_final: 0.8085 (t80) REVERT: A 268 ASP cc_start: 0.8108 (t0) cc_final: 0.7859 (t0) REVERT: A 300 GLU cc_start: 0.8223 (mm-30) cc_final: 0.8003 (mm-30) REVERT: A 428 HIS cc_start: 0.7844 (OUTLIER) cc_final: 0.6890 (p90) REVERT: A 591 ASN cc_start: 0.7646 (m-40) cc_final: 0.7402 (m110) REVERT: A 930 LYS cc_start: 0.7685 (OUTLIER) cc_final: 0.7201 (mttp) REVERT: A 934 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.7307 (mp0) REVERT: A 956 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7275 (mm-30) REVERT: A 1226 ARG cc_start: 0.8502 (mtp180) cc_final: 0.8232 (mtm-85) REVERT: A 1296 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.7158 (mt-10) outliers start: 50 outliers final: 18 residues processed: 220 average time/residue: 0.4646 time to fit residues: 109.6668 Evaluate side-chains 209 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 186 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 428 HIS Chi-restraints excluded: chain A residue 431 SER Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 625 THR Chi-restraints excluded: chain A residue 776 PHE Chi-restraints excluded: chain A residue 899 LYS Chi-restraints excluded: chain A residue 930 LYS Chi-restraints excluded: chain A residue 934 GLU Chi-restraints excluded: chain A residue 956 GLU Chi-restraints excluded: chain A residue 999 SER Chi-restraints excluded: chain A residue 1008 SER Chi-restraints excluded: chain A residue 1093 SER Chi-restraints excluded: chain A residue 1122 SER Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1164 VAL Chi-restraints excluded: chain A residue 1296 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 95 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 110 optimal weight: 0.9980 chunk 108 optimal weight: 6.9990 chunk 79 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 69 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 361 GLN A 598 GLN ** A 918 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.146469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.134456 restraints weight = 10697.926| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 1.08 r_work: 0.3435 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3339 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3369 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3369 r_free = 0.3369 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 337 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3368 r_free = 0.3368 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 341 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3368 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9011 Z= 0.166 Angle : 0.563 6.557 12189 Z= 0.309 Chirality : 0.043 0.155 1382 Planarity : 0.004 0.054 1544 Dihedral : 5.572 75.219 1221 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 5.36 % Allowed : 27.12 % Favored : 67.52 % 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: 1.20 (0.24), residues: 1117 helix: 1.54 (0.18), residues: 742 sheet: 0.65 (0.52), residues: 77 loop : -1.01 (0.31), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1001 TYR 0.024 0.002 TYR A 145 PHE 0.024 0.002 PHE A 774 TRP 0.013 0.001 TRP A 163 HIS 0.003 0.001 HIS A 428 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.17 ( 9011) covalent geometry : angle 0.56345 / 0.31 (12189) hydrogen bonds : bond 0.06764 / 4.37 ( 582) hydrogen bonds : angle 4.19270 / 3.09 ( 1713) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 192 time to evaluate : 0.329 Fit side-chains REVERT: A 70 PHE cc_start: 0.8359 (t80) cc_final: 0.8075 (t80) REVERT: A 181 ARG cc_start: 0.7948 (mpt180) cc_final: 0.7213 (mmm160) REVERT: A 268 ASP cc_start: 0.8170 (t0) cc_final: 0.7908 (t0) REVERT: A 269 TYR cc_start: 0.7332 (m-10) cc_final: 0.7125 (m-10) REVERT: A 300 GLU cc_start: 0.8268 (mm-30) cc_final: 0.8030 (mm-30) REVERT: A 428 HIS cc_start: 0.7727 (OUTLIER) cc_final: 0.6839 (p-80) REVERT: A 438 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8021 (tt) REVERT: A 591 ASN cc_start: 0.7691 (m-40) cc_final: 0.7484 (m110) REVERT: A 930 LYS cc_start: 0.7748 (OUTLIER) cc_final: 0.7227 (mttp) REVERT: A 934 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.7291 (mp0) REVERT: A 956 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7264 (mm-30) REVERT: A 1221 ARG cc_start: 0.7826 (mpt90) cc_final: 0.7483 (mmt180) REVERT: A 1296 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.7187 (mt-10) outliers start: 50 outliers final: 20 residues processed: 223 average time/residue: 0.4392 time to fit residues: 105.7644 Evaluate side-chains 212 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 186 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 428 HIS Chi-restraints excluded: chain A residue 431 SER Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 625 THR Chi-restraints excluded: chain A residue 760 VAL Chi-restraints excluded: chain A residue 930 LYS Chi-restraints excluded: chain A residue 934 GLU Chi-restraints excluded: chain A residue 956 GLU Chi-restraints excluded: chain A residue 999 SER Chi-restraints excluded: chain A residue 1093 SER Chi-restraints excluded: chain A residue 1122 SER Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1164 VAL Chi-restraints excluded: chain A residue 1296 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 82 optimal weight: 8.9990 chunk 67 optimal weight: 0.9990 chunk 80 optimal weight: 0.6980 chunk 43 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 361 GLN A 598 GLN ** A 918 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.148039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.136056 restraints weight = 10718.018| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 1.08 r_work: 0.3455 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.3359 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3353 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3353 r_free = 0.3353 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 341 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3351 r_free = 0.3351 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 338 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3351 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9011 Z= 0.142 Angle : 0.551 6.472 12189 Z= 0.299 Chirality : 0.042 0.154 1382 Planarity : 0.004 0.054 1544 Dihedral : 5.457 75.725 1221 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 4.39 % Allowed : 28.51 % Favored : 67.10 % 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: 1.36 (0.24), residues: 1117 helix: 1.66 (0.19), residues: 741 sheet: 0.58 (0.52), residues: 78 loop : -0.91 (0.32), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 184 TYR 0.019 0.001 TYR A 337 PHE 0.024 0.001 PHE A 774 TRP 0.013 0.001 TRP A 163 HIS 0.003 0.001 HIS A 428 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.14 ( 9011) covalent geometry : angle 0.55071 / 0.30 (12189) hydrogen bonds : bond 0.06393 / 4.12 ( 582) hydrogen bonds : angle 4.11303 / 3.04 ( 1713) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 190 time to evaluate : 0.223 Fit side-chains REVERT: A 70 PHE cc_start: 0.8338 (t80) cc_final: 0.8053 (t80) REVERT: A 181 ARG cc_start: 0.7907 (mpt180) cc_final: 0.7189 (mmm160) REVERT: A 197 GLU cc_start: 0.7858 (mm-30) cc_final: 0.7439 (tm-30) REVERT: A 268 ASP cc_start: 0.8147 (t0) cc_final: 0.7886 (t0) REVERT: A 269 TYR cc_start: 0.7279 (m-10) cc_final: 0.7051 (m-10) REVERT: A 300 GLU cc_start: 0.8218 (mm-30) cc_final: 0.8005 (mm-30) REVERT: A 428 HIS cc_start: 0.7753 (OUTLIER) cc_final: 0.6803 (p90) REVERT: A 438 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.8038 (tt) REVERT: A 591 ASN cc_start: 0.7614 (m-40) cc_final: 0.7399 (m110) REVERT: A 930 LYS cc_start: 0.7705 (OUTLIER) cc_final: 0.7224 (mttp) REVERT: A 934 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.7283 (mp0) REVERT: A 956 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7239 (mm-30) REVERT: A 1221 ARG cc_start: 0.7803 (mpt90) cc_final: 0.7470 (mmt180) REVERT: A 1284 ASP cc_start: 0.8565 (m-30) cc_final: 0.7838 (m-30) REVERT: A 1296 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7162 (mt-10) outliers start: 41 outliers final: 20 residues processed: 213 average time/residue: 0.4910 time to fit residues: 111.9788 Evaluate side-chains 210 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 184 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 428 HIS Chi-restraints excluded: chain A residue 431 SER Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 625 THR Chi-restraints excluded: chain A residue 899 LYS Chi-restraints excluded: chain A residue 930 LYS Chi-restraints excluded: chain A residue 934 GLU Chi-restraints excluded: chain A residue 956 GLU Chi-restraints excluded: chain A residue 999 SER Chi-restraints excluded: chain A residue 1008 SER Chi-restraints excluded: chain A residue 1093 SER Chi-restraints excluded: chain A residue 1122 SER Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1164 VAL Chi-restraints excluded: chain A residue 1296 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 82 optimal weight: 7.9990 chunk 26 optimal weight: 7.9990 chunk 104 optimal weight: 0.9980 chunk 89 optimal weight: 0.6980 chunk 43 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 chunk 36 optimal weight: 6.9990 chunk 50 optimal weight: 0.6980 chunk 94 optimal weight: 8.9990 chunk 40 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 193 ASN ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 598 GLN ** A 918 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1124 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.148980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.136992 restraints weight = 10551.386| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 1.08 r_work: 0.3463 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3368 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3367 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3367 r_free = 0.3367 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 338 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3366 r_free = 0.3366 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 340 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.3366 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9011 Z= 0.141 Angle : 0.555 6.467 12189 Z= 0.300 Chirality : 0.042 0.147 1382 Planarity : 0.004 0.055 1544 Dihedral : 5.389 75.008 1221 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 4.29 % Allowed : 28.72 % Favored : 66.99 % 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: 1.42 (0.24), residues: 1117 helix: 1.71 (0.19), residues: 741 sheet: 0.64 (0.53), residues: 78 loop : -0.91 (0.32), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 184 TYR 0.019 0.001 TYR A 337 PHE 0.024 0.001 PHE A 774 TRP 0.014 0.001 TRP A 163 HIS 0.003 0.001 HIS A 428 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.14 ( 9011) covalent geometry : angle 0.55483 / 0.30 (12189) hydrogen bonds : bond 0.06243 / 4.03 ( 582) hydrogen bonds : angle 4.08562 / 3.02 ( 1713) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 189 time to evaluate : 0.334 Fit side-chains REVERT: A 70 PHE cc_start: 0.8349 (t80) cc_final: 0.8059 (t80) REVERT: A 268 ASP cc_start: 0.8135 (t0) cc_final: 0.7867 (t0) REVERT: A 269 TYR cc_start: 0.7269 (m-10) cc_final: 0.7061 (m-10) REVERT: A 428 HIS cc_start: 0.7720 (OUTLIER) cc_final: 0.6802 (p90) REVERT: A 438 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.8013 (tt) REVERT: A 591 ASN cc_start: 0.7671 (m-40) cc_final: 0.7468 (m110) REVERT: A 930 LYS cc_start: 0.7691 (OUTLIER) cc_final: 0.7217 (mttp) REVERT: A 934 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.7272 (mp0) REVERT: A 956 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7221 (mm-30) REVERT: A 1209 GLU cc_start: 0.8428 (mm-30) cc_final: 0.8212 (mm-30) REVERT: A 1221 ARG cc_start: 0.7813 (mpt90) cc_final: 0.7463 (mmt180) REVERT: A 1276 ARG cc_start: 0.7012 (OUTLIER) cc_final: 0.5614 (mpp-170) REVERT: A 1296 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7144 (mt-10) outliers start: 40 outliers final: 18 residues processed: 214 average time/residue: 0.5097 time to fit residues: 117.0052 Evaluate side-chains 208 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 183 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 428 HIS Chi-restraints excluded: chain A residue 431 SER Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 625 THR Chi-restraints excluded: chain A residue 930 LYS Chi-restraints excluded: chain A residue 934 GLU Chi-restraints excluded: chain A residue 956 GLU Chi-restraints excluded: chain A residue 999 SER Chi-restraints excluded: chain A residue 1008 SER Chi-restraints excluded: chain A residue 1093 SER Chi-restraints excluded: chain A residue 1122 SER Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1164 VAL Chi-restraints excluded: chain A residue 1276 ARG Chi-restraints excluded: chain A residue 1296 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 58 optimal weight: 5.9990 chunk 93 optimal weight: 0.7980 chunk 103 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 72 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 78 optimal weight: 0.0270 overall best weight: 0.9040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 598 GLN ** A 918 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.149077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.137129 restraints weight = 10555.066| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 1.07 r_work: 0.3477 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3382 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3367 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3367 r_free = 0.3367 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 340 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3366 r_free = 0.3366 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 342 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3366 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9011 Z= 0.144 Angle : 0.574 6.483 12189 Z= 0.307 Chirality : 0.042 0.144 1382 Planarity : 0.004 0.055 1544 Dihedral : 5.383 74.628 1221 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 3.64 % Allowed : 29.69 % Favored : 66.67 % 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: 1.41 (0.24), residues: 1117 helix: 1.69 (0.19), residues: 741 sheet: 0.76 (0.55), residues: 78 loop : -0.94 (0.32), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 184 TYR 0.019 0.001 TYR A 337 PHE 0.026 0.001 PHE A 774 TRP 0.012 0.001 TRP A 163 HIS 0.003 0.001 HIS A 428 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.14 ( 9011) covalent geometry : angle 0.57378 / 0.31 (12189) hydrogen bonds : bond 0.06230 / 4.02 ( 582) hydrogen bonds : angle 4.10717 / 3.04 ( 1713) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 188 time to evaluate : 0.211 Fit side-chains REVERT: A 70 PHE cc_start: 0.8350 (t80) cc_final: 0.8046 (t80) REVERT: A 268 ASP cc_start: 0.8115 (t0) cc_final: 0.7846 (t0) REVERT: A 269 TYR cc_start: 0.7271 (m-10) cc_final: 0.7071 (m-10) REVERT: A 428 HIS cc_start: 0.7692 (OUTLIER) cc_final: 0.6849 (p90) REVERT: A 438 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.8013 (tt) REVERT: A 930 LYS cc_start: 0.7695 (OUTLIER) cc_final: 0.7221 (mttp) REVERT: A 934 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.7292 (mp0) REVERT: A 956 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.7209 (mm-30) REVERT: A 1209 GLU cc_start: 0.8415 (mm-30) cc_final: 0.8159 (mm-30) REVERT: A 1221 ARG cc_start: 0.7812 (mpt90) cc_final: 0.7453 (mmt180) REVERT: A 1276 ARG cc_start: 0.7018 (OUTLIER) cc_final: 0.5609 (mpp-170) REVERT: A 1284 ASP cc_start: 0.8451 (m-30) cc_final: 0.7705 (m-30) REVERT: A 1296 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7163 (mt-10) outliers start: 34 outliers final: 20 residues processed: 206 average time/residue: 0.4727 time to fit residues: 104.1219 Evaluate side-chains 208 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 181 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 428 HIS Chi-restraints excluded: chain A residue 431 SER Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 625 THR Chi-restraints excluded: chain A residue 899 LYS Chi-restraints excluded: chain A residue 930 LYS Chi-restraints excluded: chain A residue 934 GLU Chi-restraints excluded: chain A residue 956 GLU Chi-restraints excluded: chain A residue 999 SER Chi-restraints excluded: chain A residue 1008 SER Chi-restraints excluded: chain A residue 1093 SER Chi-restraints excluded: chain A residue 1115 SER Chi-restraints excluded: chain A residue 1122 SER Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1164 VAL Chi-restraints excluded: chain A residue 1276 ARG Chi-restraints excluded: chain A residue 1296 GLU Chi-restraints excluded: chain A residue 1304 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- 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: 63.2671 > 50: distance: 45 - 193: 21.813 distance: 48 - 190: 14.795 distance: 114 - 120: 5.141 distance: 120 - 121: 3.681 distance: 121 - 122: 16.461 distance: 122 - 123: 7.204 distance: 122 - 131: 6.977 distance: 124 - 125: 8.781 distance: 125 - 126: 12.284 distance: 126 - 127: 6.977 distance: 127 - 128: 7.241 distance: 128 - 129: 10.197 distance: 128 - 130: 6.549 distance: 131 - 132: 4.871 distance: 132 - 133: 10.047 distance: 132 - 135: 11.881 distance: 133 - 134: 15.800 distance: 133 - 142: 7.354 distance: 135 - 136: 13.437 distance: 136 - 137: 20.961 distance: 136 - 138: 12.411 distance: 137 - 139: 16.113 distance: 138 - 140: 3.472 distance: 142 - 143: 35.126 distance: 143 - 144: 49.226 distance: 143 - 146: 40.367 distance: 144 - 145: 22.461 distance: 144 - 154: 63.267 distance: 146 - 147: 21.443 distance: 147 - 148: 9.153 distance: 147 - 149: 10.857 distance: 148 - 150: 12.552 distance: 150 - 152: 8.692 distance: 151 - 152: 7.297 distance: 152 - 153: 4.759 distance: 154 - 155: 17.876 distance: 155 - 156: 44.736 distance: 155 - 158: 29.625 distance: 156 - 157: 35.937 distance: 156 - 162: 21.457 distance: 158 - 159: 12.609 distance: 159 - 160: 26.609 distance: 159 - 161: 14.108 distance: 162 - 163: 15.564 distance: 162 - 168: 17.200 distance: 163 - 164: 8.685 distance: 163 - 166: 8.434 distance: 164 - 165: 7.543 distance: 164 - 169: 7.318 distance: 166 - 167: 25.829 distance: 167 - 168: 11.949 distance: 169 - 170: 13.569 distance: 170 - 171: 6.388 distance: 170 - 173: 8.626 distance: 171 - 172: 9.387 distance: 171 - 177: 8.634 distance: 173 - 174: 15.515 distance: 174 - 175: 11.206 distance: 174 - 176: 3.469 distance: 177 - 178: 12.614 distance: 178 - 179: 4.194 distance: 178 - 181: 16.954 distance: 179 - 180: 7.054 distance: 179 - 186: 8.144 distance: 181 - 182: 13.356 distance: 182 - 183: 3.053 distance: 183 - 184: 7.294 distance: 183 - 185: 9.313 distance: 186 - 187: 4.338 distance: 187 - 188: 11.238 distance: 188 - 189: 13.621 distance: 188 - 190: 6.662 distance: 190 - 191: 9.880 distance: 191 - 192: 18.370 distance: 191 - 194: 10.412 distance: 192 - 193: 29.875 distance: 192 - 199: 7.420 distance: 194 - 195: 14.728 distance: 195 - 196: 15.381 distance: 196 - 197: 10.868 distance: 197 - 198: 4.924 distance: 199 - 200: 19.294 distance: 200 - 201: 9.362 distance: 200 - 203: 5.266 distance: 201 - 202: 7.810 distance: 201 - 206: 11.186 distance: 203 - 204: 22.601 distance: 203 - 205: 28.056