Starting phenix.real_space_refine on Sat Aug 23 15:50:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8as6_15607/08_2025/8as6_15607.cif Found real_map, /net/cci-nas-00/data/ceres_data/8as6_15607/08_2025/8as6_15607.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8as6_15607/08_2025/8as6_15607.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8as6_15607/08_2025/8as6_15607.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8as6_15607/08_2025/8as6_15607.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8as6_15607/08_2025/8as6_15607.map" } resolution = 3.4 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= 0.002 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 13 5.49 5 S 72 5.16 5 C 8069 2.51 5 N 2221 2.21 5 O 2409 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12784 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 12489 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1566, 12481 Classifications: {'peptide': 1566} Link IDs: {'PCIS': 2, 'PTRANS': 57, 'TRANS': 1506} Chain breaks: 6 Conformer: "B" Number of residues, atoms: 1566, 12481 Classifications: {'peptide': 1566} Link IDs: {'PCIS': 2, 'PTRANS': 57, 'TRANS': 1506} Chain breaks: 6 bond proxies already assigned to first conformer: 12732 Chain: "P" Number of atoms: 295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 295 Classifications: {'RNA': 14} Modifications used: {'5*END': 1, 'rna2p_pur': 3, 'rna3p_pur': 5, 'rna3p_pyr': 5} Link IDs: {'rna2p': 3, 'rna3p': 10} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.44, per 1000 atoms: 0.43 Number of scatterers: 12784 At special positions: 0 Unit cell: (104.55, 113.9, 129.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 72 16.00 P 13 15.00 O 2409 8.00 N 2221 7.00 C 8069 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: 1.23 Conformation dependent library (CDL) restraints added in 918.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3106 Ramachandran restraints generated. 1553 Oldfield, 0 Emsley, 1553 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2952 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 13 sheets defined 50.3% alpha, 8.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'A' and resid 2 through 10 removed outlier: 4.020A pdb=" N LEU A 6 " --> pdb=" O ASN A 2 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 84 Processing helix chain 'A' and resid 94 through 99 removed outlier: 3.960A pdb=" N VAL A 98 " --> pdb=" O ARG A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 150 removed outlier: 3.708A pdb=" N LEU A 138 " --> pdb=" O ASN A 134 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ALA A 140 " --> pdb=" O GLY A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 156 removed outlier: 3.957A pdb=" N ARG A 156 " --> pdb=" O PRO A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 209 removed outlier: 3.546A pdb=" N GLU A 190 " --> pdb=" O ASP A 186 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N MET A 208 " --> pdb=" O LYS A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 234 removed outlier: 4.483A pdb=" N GLU A 222 " --> pdb=" O GLU A 218 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ALA A 223 " --> pdb=" O GLU A 219 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N ILE A 224 " --> pdb=" O GLU A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 245 removed outlier: 4.381A pdb=" N GLY A 243 " --> pdb=" O GLU A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 258 removed outlier: 3.895A pdb=" N LEU A 253 " --> pdb=" O GLU A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 285 removed outlier: 3.990A pdb=" N ILE A 266 " --> pdb=" O ASP A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 312 removed outlier: 3.681A pdb=" N ASP A 310 " --> pdb=" O ASP A 306 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LEU A 312 " --> pdb=" O THR A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 374 Processing helix chain 'A' and resid 384 through 387 Processing helix chain 'A' and resid 388 through 393 Processing helix chain 'A' and resid 416 through 426 removed outlier: 3.890A pdb=" N GLN A 426 " --> pdb=" O GLU A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 447 removed outlier: 3.527A pdb=" N LYS A 442 " --> pdb=" O ALA A 438 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N HIS A 447 " --> pdb=" O GLU A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 463 Processing helix chain 'A' and resid 477 through 491 Processing helix chain 'A' and resid 496 through 510 Processing helix chain 'A' and resid 512 through 530 removed outlier: 3.673A pdb=" N TRP A 520 " --> pdb=" O GLN A 516 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER A 530 " --> pdb=" O GLN A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 575 No H-bonds generated for 'chain 'A' and resid 573 through 575' Processing helix chain 'A' and resid 611 through 627 Processing helix chain 'A' and resid 638 through 655 removed outlier: 3.563A pdb=" N ARG A 642 " --> pdb=" O CYS A 638 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLU A 643 " --> pdb=" O SER A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 665 removed outlier: 3.713A pdb=" N GLU A 660 " --> pdb=" O LYS A 656 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU A 661 " --> pdb=" O SER A 657 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ILE A 663 " --> pdb=" O THR A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 672 removed outlier: 3.950A pdb=" N GLU A 672 " --> pdb=" O TYR A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 716 removed outlier: 3.542A pdb=" N VAL A 700 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR A 701 " --> pdb=" O LYS A 697 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN A 716 " --> pdb=" O ARG A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 749 removed outlier: 3.533A pdb=" N MET A 746 " --> pdb=" O ASN A 742 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 756 removed outlier: 4.661A pdb=" N GLY A 753 " --> pdb=" O TRP A 750 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS A 756 " --> pdb=" O GLY A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 767 through 775 removed outlier: 4.031A pdb=" N TYR A 771 " --> pdb=" O LEU A 767 " (cutoff:3.500A) Processing helix chain 'A' and resid 777 through 781 Processing helix chain 'A' and resid 802 through 813 Processing helix chain 'A' and resid 817 through 822 Processing helix chain 'A' and resid 825 through 839 Processing helix chain 'A' and resid 841 through 845 Processing helix chain 'A' and resid 860 through 864 removed outlier: 3.646A pdb=" N GLU A 863 " --> pdb=" O LEU A 860 " (cutoff:3.500A) Processing helix chain 'A' and resid 873 through 885 removed outlier: 3.879A pdb=" N LYS A 877 " --> pdb=" O LYS A 873 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LEU A 881 " --> pdb=" O LYS A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 888 through 903 removed outlier: 3.864A pdb=" N ALA A 892 " --> pdb=" O TRP A 888 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL A 893 " --> pdb=" O TYR A 889 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N GLY A 894 " --> pdb=" O ILE A 890 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N GLN A 895 " --> pdb=" O ASP A 891 " (cutoff:3.500A) Processing helix chain 'A' and resid 926 through 945 removed outlier: 4.190A pdb=" N GLY A 935 " --> pdb=" O LEU A 931 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N VAL A 936 " --> pdb=" O VAL A 932 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL A 943 " --> pdb=" O MET A 939 " (cutoff:3.500A) Processing helix chain 'A' and resid 954 through 958 removed outlier: 3.665A pdb=" N LYS A 958 " --> pdb=" O PRO A 955 " (cutoff:3.500A) Processing helix chain 'A' and resid 964 through 973 removed outlier: 3.580A pdb=" N LEU A 973 " --> pdb=" O SER A 969 " (cutoff:3.500A) Processing helix chain 'A' and resid 994 through 1005 removed outlier: 3.908A pdb=" N LEU A 998 " --> pdb=" O TYR A 994 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N PHE A1005 " --> pdb=" O VAL A1001 " (cutoff:3.500A) Processing helix chain 'A' and resid 1011 through 1020 removed outlier: 3.533A pdb=" N MET A1020 " --> pdb=" O ALA A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1029 through 1038 removed outlier: 3.648A pdb=" N HIS A1035 " --> pdb=" O ARG A1031 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU A1036 " --> pdb=" O PHE A1032 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N SER A1038 " --> pdb=" O ALA A1034 " (cutoff:3.500A) Processing helix chain 'A' and resid 1046 through 1058 removed outlier: 3.739A pdb=" N THR A1053 " --> pdb=" O ARG A1049 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ASP A1054 " --> pdb=" O GLU A1050 " (cutoff:3.500A) Processing helix chain 'A' and resid 1084 through 1108 removed outlier: 3.537A pdb=" N SER A1088 " --> pdb=" O HIS A1084 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU A1108 " --> pdb=" O SER A1104 " (cutoff:3.500A) Processing helix chain 'A' and resid 1138 through 1160 removed outlier: 4.166A pdb=" N VAL A1156 " --> pdb=" O LEU A1152 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N LYS A1157 " --> pdb=" O LEU A1153 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N PHE A1158 " --> pdb=" O HIS A1154 " (cutoff:3.500A) Processing helix chain 'A' and resid 1161 through 1164 Processing helix chain 'A' and resid 1194 through 1200 removed outlier: 4.259A pdb=" N TRP A1198 " --> pdb=" O PRO A1194 " (cutoff:3.500A) Processing helix chain 'A' and resid 1211 through 1228 removed outlier: 4.315A pdb=" N GLN A1215 " --> pdb=" O LEU A1211 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLU A1216 " --> pdb=" O ALA A1212 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASP A1217 " --> pdb=" O SER A1213 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLN A1224 " --> pdb=" O ASN A1220 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N CYS A1225 " --> pdb=" O LEU A1221 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU A1226 " --> pdb=" O LEU A1222 " (cutoff:3.500A) Processing helix chain 'A' and resid 1231 through 1250 Processing helix chain 'A' and resid 1258 through 1267 removed outlier: 3.936A pdb=" N SER A1267 " --> pdb=" O GLY A1263 " (cutoff:3.500A) Processing helix chain 'A' and resid 1270 through 1274 Processing helix chain 'A' and resid 1288 through 1300 removed outlier: 3.578A pdb=" N ASN A1292 " --> pdb=" O GLY A1288 " (cutoff:3.500A) Processing helix chain 'A' and resid 1300 through 1307 removed outlier: 4.318A pdb=" N ARG A1304 " --> pdb=" O THR A1300 " (cutoff:3.500A) Processing helix chain 'A' and resid 1308 through 1310 No H-bonds generated for 'chain 'A' and resid 1308 through 1310' Processing helix chain 'A' and resid 1348 through 1355 Processing helix chain 'A' and resid 1362 through 1368 Processing helix chain 'A' and resid 1369 through 1374 removed outlier: 3.958A pdb=" N TYR A1373 " --> pdb=" O PRO A1369 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG A1374 " --> pdb=" O GLY A1370 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1369 through 1374' Processing helix chain 'A' and resid 1378 through 1391 Processing helix chain 'A' and resid 1392 through 1399 removed outlier: 4.100A pdb=" N THR A1396 " --> pdb=" O SER A1392 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER A1397 " --> pdb=" O PRO A1393 " (cutoff:3.500A) Processing helix chain 'A' and resid 1404 through 1411 removed outlier: 3.564A pdb=" N ALA A1411 " --> pdb=" O ARG A1407 " (cutoff:3.500A) Processing helix chain 'A' and resid 1412 through 1414 No H-bonds generated for 'chain 'A' and resid 1412 through 1414' Processing helix chain 'A' and resid 1437 through 1448 removed outlier: 3.567A pdb=" N ILE A1447 " --> pdb=" O MET A1443 " (cutoff:3.500A) Processing helix chain 'A' and resid 1460 through 1465 removed outlier: 3.712A pdb=" N LEU A1464 " --> pdb=" O GLN A1460 " (cutoff:3.500A) Processing helix chain 'A' and resid 1467 through 1479 removed outlier: 3.511A pdb=" N TYR A1471 " --> pdb=" O GLN A1467 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU A1477 " --> pdb=" O ARG A1473 " (cutoff:3.500A) Processing helix chain 'A' and resid 1506 through 1510 removed outlier: 3.700A pdb=" N LEU A1509 " --> pdb=" O PRO A1506 " (cutoff:3.500A) Processing helix chain 'A' and resid 1513 through 1523 removed outlier: 3.753A pdb=" N GLY A1523 " --> pdb=" O GLU A1519 " (cutoff:3.500A) Processing helix chain 'A' and resid 1537 through 1545 Processing helix chain 'A' and resid 1551 through 1559 removed outlier: 3.647A pdb=" N THR A1555 " --> pdb=" O ASP A1551 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLY A1559 " --> pdb=" O THR A1555 " (cutoff:3.500A) Processing helix chain 'A' and resid 1565 through 1574 removed outlier: 3.851A pdb=" N ASN A1569 " --> pdb=" O VAL A1565 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N VAL A1574 " --> pdb=" O PHE A1570 " (cutoff:3.500A) Processing helix chain 'A' and resid 1595 through 1605 removed outlier: 3.690A pdb=" N PHE A1605 " --> pdb=" O VAL A1601 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 17 removed outlier: 5.417A pdb=" N GLY A 15 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N PHE A 167 " --> pdb=" O GLY A 15 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N SER A 17 " --> pdb=" O PHE A 167 " (cutoff:3.500A) removed outlier: 9.393A pdb=" N VAL A 169 " --> pdb=" O SER A 17 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 17 removed outlier: 5.417A pdb=" N GLY A 15 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N PHE A 167 " --> pdb=" O GLY A 15 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N SER A 17 " --> pdb=" O PHE A 167 " (cutoff:3.500A) removed outlier: 9.393A pdb=" N VAL A 169 " --> pdb=" O SER A 17 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU A 126 " --> pdb=" O GLY A 168 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 36 through 37 removed outlier: 3.642A pdb=" N ILE A 49 " --> pdb=" O GLY A 66 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLY A 66 " --> pdb=" O ILE A 49 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 335 through 336 removed outlier: 3.717A pdb=" N ARG A 577 " --> pdb=" O LEU A 336 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 409 through 411 removed outlier: 4.450A pdb=" N ARG A 409 " --> pdb=" O ILE A 543 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 409 through 411 removed outlier: 4.450A pdb=" N ARG A 409 " --> pdb=" O ILE A 543 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 719 through 722 Processing sheet with id=AA8, first strand: chain 'A' and resid 923 through 925 removed outlier: 3.740A pdb=" N THR A1074 " --> pdb=" O LYS A1024 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 978 through 985 Processing sheet with id=AB1, first strand: chain 'A' and resid 1185 through 1187 removed outlier: 4.056A pdb=" N PHE A1187 " --> pdb=" O HIS A1190 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1338 through 1339 Processing sheet with id=AB3, first strand: chain 'A' and resid 1496 through 1497 Processing sheet with id=AB4, first strand: chain 'A' and resid 1500 through 1503 removed outlier: 5.660A pdb=" N ASP A1501 " --> pdb=" O VAL A1581 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N VAL A1581 " --> pdb=" O ASP A1501 " (cutoff:3.500A) 520 hydrogen bonds defined for protein. 1463 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.64 Time building geometry restraints manager: 1.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4132 1.34 - 1.46: 2823 1.46 - 1.58: 5981 1.58 - 1.69: 28 1.69 - 1.81: 118 Bond restraints: 13082 Sorted by residual: bond pdb=" CB PRO A 975 " pdb=" CG PRO A 975 " ideal model delta sigma weight residual 1.492 1.666 -0.174 5.00e-02 4.00e+02 1.21e+01 bond pdb=" CG PRO A 975 " pdb=" CD PRO A 975 " ideal model delta sigma weight residual 1.503 1.409 0.094 3.40e-02 8.65e+02 7.64e+00 bond pdb=" CB PRO A 785 " pdb=" CG PRO A 785 " ideal model delta sigma weight residual 1.492 1.578 -0.086 5.00e-02 4.00e+02 2.96e+00 bond pdb=" N PRO A 975 " pdb=" CD PRO A 975 " ideal model delta sigma weight residual 1.473 1.494 -0.021 1.40e-02 5.10e+03 2.24e+00 bond pdb=" CB PRO A 152 " pdb=" CG PRO A 152 " ideal model delta sigma weight residual 1.492 1.555 -0.063 5.00e-02 4.00e+02 1.57e+00 ... (remaining 13077 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.77: 17511 2.77 - 5.54: 190 5.54 - 8.31: 15 8.31 - 11.08: 1 11.08 - 13.85: 2 Bond angle restraints: 17719 Sorted by residual: angle pdb=" CA PRO A 975 " pdb=" N PRO A 975 " pdb=" CD PRO A 975 " ideal model delta sigma weight residual 112.00 98.15 13.85 1.40e+00 5.10e-01 9.79e+01 angle pdb=" N PRO A 975 " pdb=" CD PRO A 975 " pdb=" CG PRO A 975 " ideal model delta sigma weight residual 103.20 93.58 9.62 1.50e+00 4.44e-01 4.11e+01 angle pdb=" N GLU A 814 " pdb=" CA GLU A 814 " pdb=" C GLU A 814 " ideal model delta sigma weight residual 114.62 107.31 7.31 1.14e+00 7.69e-01 4.11e+01 angle pdb=" N GLU A 786 " pdb=" CA GLU A 786 " pdb=" C GLU A 786 " ideal model delta sigma weight residual 114.56 108.50 6.06 1.27e+00 6.20e-01 2.28e+01 angle pdb=" CA PRO A 152 " pdb=" N PRO A 152 " pdb=" CD PRO A 152 " ideal model delta sigma weight residual 112.00 105.68 6.32 1.40e+00 5.10e-01 2.04e+01 ... (remaining 17714 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 7013 17.98 - 35.96: 717 35.96 - 53.94: 146 53.94 - 71.92: 42 71.92 - 89.90: 14 Dihedral angle restraints: 7932 sinusoidal: 3376 harmonic: 4556 Sorted by residual: dihedral pdb=" CA ASN A1182 " pdb=" C ASN A1182 " pdb=" N SER A1183 " pdb=" CA SER A1183 " ideal model delta harmonic sigma weight residual 180.00 153.03 26.97 0 5.00e+00 4.00e-02 2.91e+01 dihedral pdb=" CA ILE A 293 " pdb=" C ILE A 293 " pdb=" N GLN A 294 " pdb=" CA GLN A 294 " ideal model delta harmonic sigma weight residual 180.00 156.69 23.31 0 5.00e+00 4.00e-02 2.17e+01 dihedral pdb=" CA MET A 906 " pdb=" C MET A 906 " pdb=" N ARG A 907 " pdb=" CA ARG A 907 " ideal model delta harmonic sigma weight residual -180.00 -160.21 -19.79 0 5.00e+00 4.00e-02 1.57e+01 ... (remaining 7929 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1512 0.046 - 0.091: 368 0.091 - 0.137: 85 0.137 - 0.182: 5 0.182 - 0.228: 2 Chirality restraints: 1972 Sorted by residual: chirality pdb=" CA PRO A 975 " pdb=" N PRO A 975 " pdb=" C PRO A 975 " pdb=" CB PRO A 975 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" CB ILE A 122 " pdb=" CA ILE A 122 " pdb=" CG1 ILE A 122 " pdb=" CG2 ILE A 122 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.19 2.00e-01 2.50e+01 8.72e-01 chirality pdb=" CG LEU A1234 " pdb=" CB LEU A1234 " pdb=" CD1 LEU A1234 " pdb=" CD2 LEU A1234 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.48e-01 ... (remaining 1969 not shown) Planarity restraints: 2208 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 151 " -0.079 5.00e-02 4.00e+02 1.16e-01 2.15e+01 pdb=" N PRO A 152 " 0.200 5.00e-02 4.00e+02 pdb=" CA PRO A 152 " -0.059 5.00e-02 4.00e+02 pdb=" CD PRO A 152 " -0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 974 " -0.076 5.00e-02 4.00e+02 1.05e-01 1.77e+01 pdb=" N PRO A 975 " 0.181 5.00e-02 4.00e+02 pdb=" CA PRO A 975 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO A 975 " -0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 383 " 0.064 5.00e-02 4.00e+02 9.65e-02 1.49e+01 pdb=" N PRO A 384 " -0.167 5.00e-02 4.00e+02 pdb=" CA PRO A 384 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO A 384 " 0.052 5.00e-02 4.00e+02 ... (remaining 2205 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 2090 2.77 - 3.30: 11596 3.30 - 3.83: 19882 3.83 - 4.37: 23131 4.37 - 4.90: 40912 Nonbonded interactions: 97611 Sorted by model distance: nonbonded pdb=" OG1 THR A 951 " pdb=" OH TYR A1181 " model vdw 2.232 3.040 nonbonded pdb=" O ARG A1295 " pdb=" OG1 THR A1299 " model vdw 2.272 3.040 nonbonded pdb=" OE2 GLU A 660 " pdb=" NZ LYS A 758 " model vdw 2.279 3.120 nonbonded pdb=" O PRO A 955 " pdb=" NZ LYS A 958 " model vdw 2.297 3.120 nonbonded pdb=" O ASN A 79 " pdb=" OG1 THR A 83 " model vdw 2.302 3.040 ... (remaining 97606 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.240 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: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 16.880 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.040 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:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 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 0.174 13082 Z= 0.155 Angle : 0.705 13.852 17719 Z= 0.399 Chirality : 0.042 0.228 1972 Planarity : 0.007 0.116 2208 Dihedral : 15.522 89.902 4980 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.67 (0.20), residues: 1553 helix: 0.05 (0.19), residues: 713 sheet: -0.08 (0.54), residues: 101 loop : -2.51 (0.19), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 956 TYR 0.026 0.002 TYR A 76 PHE 0.016 0.001 PHE A 649 TRP 0.021 0.002 TRP A 989 HIS 0.004 0.001 HIS A1246 Details of bonding type rmsd covalent geometry : bond 0.00369 (13082) covalent geometry : angle 0.70487 (17719) hydrogen bonds : bond 0.18601 ( 507) hydrogen bonds : angle 6.18273 ( 1463) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3106 Ramachandran restraints generated. 1553 Oldfield, 0 Emsley, 1553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3106 Ramachandran restraints generated. 1553 Oldfield, 0 Emsley, 1553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 200 time to evaluate : 0.492 Fit side-chains REVERT: A 950 GLU cc_start: 0.7121 (tm-30) cc_final: 0.6304 (tm-30) REVERT: A 1385 LYS cc_start: 0.7801 (tptt) cc_final: 0.7540 (tppt) outliers start: 0 outliers final: 0 residues processed: 200 average time/residue: 0.1301 time to fit residues: 37.1719 Evaluate side-chains 165 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.0030 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.0670 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 3.9990 overall best weight: 0.5728 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 513 ASN A 928 ASN A 990 ASN A1203 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.144915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.111672 restraints weight = 22068.444| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.27 r_work: 0.3100 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3102 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3102 r_free = 0.3102 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3102 r_free = 0.3102 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3102 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.0934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.079 13082 Z= 0.108 Angle : 0.555 11.736 17719 Z= 0.293 Chirality : 0.039 0.155 1972 Planarity : 0.005 0.078 2208 Dihedral : 8.378 81.231 1903 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 0.58 % Allowed : 6.67 % Favored : 92.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.24 (0.21), residues: 1553 helix: 0.43 (0.20), residues: 731 sheet: -0.17 (0.50), residues: 113 loop : -2.37 (0.20), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1374 TYR 0.018 0.001 TYR A 76 PHE 0.012 0.001 PHE A1310 TRP 0.014 0.001 TRP A 989 HIS 0.002 0.001 HIS A 706 Details of bonding type rmsd covalent geometry : bond 0.00237 (13082) covalent geometry : angle 0.55532 (17719) hydrogen bonds : bond 0.04088 ( 507) hydrogen bonds : angle 4.56701 ( 1463) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3106 Ramachandran restraints generated. 1553 Oldfield, 0 Emsley, 1553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3106 Ramachandran restraints generated. 1553 Oldfield, 0 Emsley, 1553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 178 time to evaluate : 0.527 Fit side-chains REVERT: A 68 ILE cc_start: 0.6903 (tt) cc_final: 0.6687 (mp) REVERT: A 950 GLU cc_start: 0.7649 (tm-30) cc_final: 0.7365 (tm-30) REVERT: A 1373 TYR cc_start: 0.6679 (m-80) cc_final: 0.6379 (m-80) REVERT: A 1461 GLU cc_start: 0.7990 (tp30) cc_final: 0.7689 (tp30) REVERT: A 1473 ARG cc_start: 0.7765 (tmm160) cc_final: 0.7452 (tmm160) outliers start: 8 outliers final: 5 residues processed: 182 average time/residue: 0.1195 time to fit residues: 31.8274 Evaluate side-chains 172 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 167 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 842 ILE Chi-restraints excluded: chain A residue 909 CYS Chi-restraints excluded: chain A residue 1006 MET Chi-restraints excluded: chain A residue 1078 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 141 optimal weight: 7.9990 chunk 88 optimal weight: 0.9980 chunk 83 optimal weight: 6.9990 chunk 151 optimal weight: 4.9990 chunk 58 optimal weight: 6.9990 chunk 17 optimal weight: 4.9990 chunk 71 optimal weight: 6.9990 chunk 79 optimal weight: 8.9990 chunk 33 optimal weight: 0.9980 chunk 0 optimal weight: 9.9990 chunk 52 optimal weight: 1.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1203 HIS A1604 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.139508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.106053 restraints weight = 19705.439| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 2.14 r_work: 0.3022 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3033 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3033 r_free = 0.3033 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3033 r_free = 0.3033 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3033 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.1372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 13082 Z= 0.206 Angle : 0.633 10.597 17719 Z= 0.331 Chirality : 0.043 0.196 1972 Planarity : 0.005 0.068 2208 Dihedral : 8.503 76.281 1903 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.38 % Favored : 91.62 % Rotamer: Outliers : 1.09 % Allowed : 8.85 % Favored : 90.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.28 (0.21), residues: 1553 helix: 0.41 (0.20), residues: 728 sheet: -0.25 (0.47), residues: 133 loop : -2.42 (0.21), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 907 TYR 0.017 0.002 TYR A 923 PHE 0.017 0.002 PHE A1097 TRP 0.012 0.002 TRP A 989 HIS 0.006 0.001 HIS A 799 Details of bonding type rmsd covalent geometry : bond 0.00490 (13082) covalent geometry : angle 0.63336 (17719) hydrogen bonds : bond 0.05024 ( 507) hydrogen bonds : angle 4.45877 ( 1463) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3106 Ramachandran restraints generated. 1553 Oldfield, 0 Emsley, 1553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3106 Ramachandran restraints generated. 1553 Oldfield, 0 Emsley, 1553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 162 time to evaluate : 0.510 Fit side-chains REVERT: A 443 GLU cc_start: 0.8202 (tp30) cc_final: 0.7519 (tp30) REVERT: A 950 GLU cc_start: 0.7882 (tm-30) cc_final: 0.7153 (tm-30) outliers start: 15 outliers final: 11 residues processed: 170 average time/residue: 0.1191 time to fit residues: 29.8220 Evaluate side-chains 166 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 155 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 728 GLU Chi-restraints excluded: chain A residue 736 ILE Chi-restraints excluded: chain A residue 770 MET Chi-restraints excluded: chain A residue 842 ILE Chi-restraints excluded: chain A residue 857 ASP Chi-restraints excluded: chain A residue 909 CYS Chi-restraints excluded: chain A residue 1110 TYR Chi-restraints excluded: chain A residue 1253 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 93 optimal weight: 3.9990 chunk 118 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 33 optimal weight: 0.3980 chunk 37 optimal weight: 9.9990 chunk 54 optimal weight: 0.6980 chunk 91 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 1 optimal weight: 0.0970 chunk 47 optimal weight: 0.1980 chunk 0 optimal weight: 10.0000 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1203 HIS A1604 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.144349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.111147 restraints weight = 19457.949| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 2.16 r_work: 0.3109 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3108 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3108 r_free = 0.3108 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3108 r_free = 0.3108 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3108 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.1427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 13082 Z= 0.093 Angle : 0.521 12.097 17719 Z= 0.270 Chirality : 0.038 0.155 1972 Planarity : 0.004 0.060 2208 Dihedral : 8.301 79.255 1903 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 0.58 % Allowed : 10.15 % Favored : 89.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.94 (0.21), residues: 1553 helix: 0.75 (0.20), residues: 727 sheet: -0.00 (0.49), residues: 118 loop : -2.30 (0.21), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1374 TYR 0.010 0.001 TYR A 923 PHE 0.011 0.001 PHE A 649 TRP 0.020 0.001 TRP A1521 HIS 0.003 0.000 HIS A 706 Details of bonding type rmsd covalent geometry : bond 0.00200 (13082) covalent geometry : angle 0.52085 (17719) hydrogen bonds : bond 0.03152 ( 507) hydrogen bonds : angle 4.10943 ( 1463) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3106 Ramachandran restraints generated. 1553 Oldfield, 0 Emsley, 1553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3106 Ramachandran restraints generated. 1553 Oldfield, 0 Emsley, 1553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 172 time to evaluate : 0.501 Fit side-chains REVERT: A 443 GLU cc_start: 0.8184 (tp30) cc_final: 0.7567 (tp30) REVERT: A 950 GLU cc_start: 0.7669 (tm-30) cc_final: 0.6991 (tm-30) REVERT: A 1308 TYR cc_start: 0.6060 (OUTLIER) cc_final: 0.5563 (m-80) REVERT: A 1373 TYR cc_start: 0.6759 (m-80) cc_final: 0.6526 (m-80) REVERT: A 1461 GLU cc_start: 0.8009 (tp30) cc_final: 0.7674 (tp30) REVERT: A 1473 ARG cc_start: 0.7528 (ttp-170) cc_final: 0.7167 (ttp-170) outliers start: 8 outliers final: 5 residues processed: 174 average time/residue: 0.1197 time to fit residues: 30.1392 Evaluate side-chains 164 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 158 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 736 ILE Chi-restraints excluded: chain A residue 770 MET Chi-restraints excluded: chain A residue 842 ILE Chi-restraints excluded: chain A residue 1006 MET Chi-restraints excluded: chain A residue 1308 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 53 optimal weight: 5.9990 chunk 102 optimal weight: 10.0000 chunk 18 optimal weight: 7.9990 chunk 92 optimal weight: 6.9990 chunk 114 optimal weight: 4.9990 chunk 110 optimal weight: 4.9990 chunk 80 optimal weight: 4.9990 chunk 26 optimal weight: 7.9990 chunk 108 optimal weight: 0.8980 chunk 119 optimal weight: 0.0020 chunk 98 optimal weight: 0.7980 overall best weight: 2.3392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 HIS A 563 HIS A1203 HIS A1604 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.140177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.106807 restraints weight = 24514.917| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 2.57 r_work: 0.2999 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2998 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2998 r_free = 0.2998 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2998 r_free = 0.2998 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2998 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13082 Z= 0.168 Angle : 0.587 10.531 17719 Z= 0.305 Chirality : 0.041 0.158 1972 Planarity : 0.005 0.059 2208 Dihedral : 8.383 76.245 1903 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.31 % Favored : 91.69 % Rotamer: Outliers : 1.09 % Allowed : 10.88 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.05 (0.21), residues: 1553 helix: 0.66 (0.20), residues: 726 sheet: -0.25 (0.46), residues: 133 loop : -2.36 (0.21), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1374 TYR 0.016 0.002 TYR A 76 PHE 0.015 0.002 PHE A 649 TRP 0.019 0.002 TRP A1521 HIS 0.005 0.001 HIS A1246 Details of bonding type rmsd covalent geometry : bond 0.00396 (13082) covalent geometry : angle 0.58686 (17719) hydrogen bonds : bond 0.04318 ( 507) hydrogen bonds : angle 4.17045 ( 1463) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3106 Ramachandran restraints generated. 1553 Oldfield, 0 Emsley, 1553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3106 Ramachandran restraints generated. 1553 Oldfield, 0 Emsley, 1553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 157 time to evaluate : 0.509 Fit side-chains REVERT: A 950 GLU cc_start: 0.7930 (tm-30) cc_final: 0.7272 (tm-30) REVERT: A 1308 TYR cc_start: 0.6099 (OUTLIER) cc_final: 0.5567 (m-80) REVERT: A 1373 TYR cc_start: 0.6922 (m-80) cc_final: 0.6675 (m-80) REVERT: A 1461 GLU cc_start: 0.8216 (tp30) cc_final: 0.7818 (tp30) REVERT: A 1473 ARG cc_start: 0.7616 (ttp-170) cc_final: 0.7350 (tmm-80) outliers start: 15 outliers final: 11 residues processed: 165 average time/residue: 0.1052 time to fit residues: 25.2618 Evaluate side-chains 165 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 153 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 368 CYS Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 728 GLU Chi-restraints excluded: chain A residue 736 ILE Chi-restraints excluded: chain A residue 770 MET Chi-restraints excluded: chain A residue 842 ILE Chi-restraints excluded: chain A residue 909 CYS Chi-restraints excluded: chain A residue 1006 MET Chi-restraints excluded: chain A residue 1110 TYR Chi-restraints excluded: chain A residue 1253 CYS Chi-restraints excluded: chain A residue 1308 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 11 optimal weight: 9.9990 chunk 69 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 144 optimal weight: 7.9990 chunk 88 optimal weight: 8.9990 chunk 96 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 105 optimal weight: 3.9990 chunk 48 optimal weight: 9.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 HIS A1203 HIS A1604 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.139260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.105612 restraints weight = 21920.332| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 2.36 r_work: 0.2970 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2960 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2960 r_free = 0.2960 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2960 r_free = 0.2960 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2960 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 13082 Z= 0.156 Angle : 0.578 10.205 17719 Z= 0.299 Chirality : 0.040 0.150 1972 Planarity : 0.005 0.057 2208 Dihedral : 8.402 75.482 1903 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.44 % Favored : 91.56 % Rotamer: Outliers : 1.45 % Allowed : 10.95 % Favored : 87.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.09 (0.21), residues: 1553 helix: 0.65 (0.20), residues: 725 sheet: -0.30 (0.45), residues: 133 loop : -2.39 (0.21), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1374 TYR 0.016 0.002 TYR A1306 PHE 0.013 0.001 PHE A 649 TRP 0.021 0.002 TRP A1521 HIS 0.004 0.001 HIS A 799 Details of bonding type rmsd covalent geometry : bond 0.00368 (13082) covalent geometry : angle 0.57827 (17719) hydrogen bonds : bond 0.04128 ( 507) hydrogen bonds : angle 4.12703 ( 1463) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3106 Ramachandran restraints generated. 1553 Oldfield, 0 Emsley, 1553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3106 Ramachandran restraints generated. 1553 Oldfield, 0 Emsley, 1553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 159 time to evaluate : 0.512 Fit side-chains REVERT: A 950 GLU cc_start: 0.8050 (tm-30) cc_final: 0.7328 (tm-30) REVERT: A 1308 TYR cc_start: 0.6087 (OUTLIER) cc_final: 0.5576 (m-80) REVERT: A 1373 TYR cc_start: 0.6892 (m-80) cc_final: 0.6611 (m-80) REVERT: A 1461 GLU cc_start: 0.8255 (tp30) cc_final: 0.7811 (tp30) REVERT: A 1473 ARG cc_start: 0.7581 (ttp-170) cc_final: 0.7354 (tmm-80) outliers start: 20 outliers final: 16 residues processed: 171 average time/residue: 0.1095 time to fit residues: 27.9483 Evaluate side-chains 170 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 153 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 368 CYS Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 493 MET Chi-restraints excluded: chain A residue 728 GLU Chi-restraints excluded: chain A residue 736 ILE Chi-restraints excluded: chain A residue 770 MET Chi-restraints excluded: chain A residue 842 ILE Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 909 CYS Chi-restraints excluded: chain A residue 1006 MET Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain A residue 1217 ASP Chi-restraints excluded: chain A residue 1253 CYS Chi-restraints excluded: chain A residue 1308 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 117 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 chunk 44 optimal weight: 6.9990 chunk 103 optimal weight: 1.9990 chunk 129 optimal weight: 6.9990 chunk 123 optimal weight: 6.9990 chunk 7 optimal weight: 5.9990 chunk 16 optimal weight: 9.9990 chunk 122 optimal weight: 0.9990 chunk 102 optimal weight: 7.9990 chunk 78 optimal weight: 0.5980 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.137706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.102826 restraints weight = 22038.478| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 2.45 r_work: 0.2949 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2958 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2958 r_free = 0.2958 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2958 r_free = 0.2958 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2958 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 13082 Z= 0.194 Angle : 0.626 15.303 17719 Z= 0.323 Chirality : 0.042 0.150 1972 Planarity : 0.005 0.056 2208 Dihedral : 8.485 73.980 1903 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.44 % Favored : 91.56 % Rotamer: Outliers : 1.45 % Allowed : 11.53 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.22 (0.21), residues: 1553 helix: 0.54 (0.20), residues: 724 sheet: -0.44 (0.45), residues: 133 loop : -2.44 (0.21), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 907 TYR 0.016 0.002 TYR A1306 PHE 0.014 0.002 PHE A 649 TRP 0.024 0.002 TRP A1521 HIS 0.005 0.001 HIS A 799 Details of bonding type rmsd covalent geometry : bond 0.00460 (13082) covalent geometry : angle 0.62599 (17719) hydrogen bonds : bond 0.04591 ( 507) hydrogen bonds : angle 4.19946 ( 1463) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3106 Ramachandran restraints generated. 1553 Oldfield, 0 Emsley, 1553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3106 Ramachandran restraints generated. 1553 Oldfield, 0 Emsley, 1553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 160 time to evaluate : 0.506 Fit side-chains REVERT: A 29 ASP cc_start: 0.7057 (p0) cc_final: 0.6262 (t0) REVERT: A 778 GLU cc_start: 0.7380 (tp30) cc_final: 0.7103 (tp30) REVERT: A 950 GLU cc_start: 0.8128 (tm-30) cc_final: 0.7405 (tm-30) REVERT: A 1308 TYR cc_start: 0.6051 (OUTLIER) cc_final: 0.5522 (m-80) REVERT: A 1373 TYR cc_start: 0.6938 (m-80) cc_final: 0.6676 (m-80) REVERT: A 1389 LYS cc_start: 0.7641 (ttpt) cc_final: 0.7286 (tmtt) REVERT: A 1473 ARG cc_start: 0.7695 (ttp-170) cc_final: 0.7462 (tmm-80) REVERT: A 1567 PHE cc_start: 0.6291 (t80) cc_final: 0.6008 (t80) outliers start: 20 outliers final: 17 residues processed: 170 average time/residue: 0.1195 time to fit residues: 29.6794 Evaluate side-chains 177 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 159 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 368 CYS Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 493 MET Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 728 GLU Chi-restraints excluded: chain A residue 736 ILE Chi-restraints excluded: chain A residue 842 ILE Chi-restraints excluded: chain A residue 857 ASP Chi-restraints excluded: chain A residue 909 CYS Chi-restraints excluded: chain A residue 1006 MET Chi-restraints excluded: chain A residue 1111 MET Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain A residue 1217 ASP Chi-restraints excluded: chain A residue 1253 CYS Chi-restraints excluded: chain A residue 1308 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 57.6892 > 50: distance: 24 - 29: 6.330 distance: 29 - 30: 27.364 distance: 29 - 35: 17.465 distance: 30 - 31: 11.560 distance: 31 - 32: 33.246 distance: 31 - 36: 35.666 distance: 34 - 35: 25.148 distance: 36 - 37: 17.613 distance: 37 - 38: 28.343 distance: 37 - 40: 22.371 distance: 38 - 39: 44.850 distance: 38 - 44: 32.759 distance: 40 - 41: 35.849 distance: 40 - 42: 39.013 distance: 41 - 43: 50.165 distance: 44 - 45: 55.923 distance: 45 - 46: 44.327 distance: 45 - 48: 31.120 distance: 46 - 47: 40.968 distance: 46 - 51: 27.613 distance: 48 - 50: 22.146 distance: 51 - 52: 5.167 distance: 52 - 53: 45.699 distance: 52 - 55: 44.894 distance: 53 - 54: 13.864 distance: 53 - 61: 42.539 distance: 55 - 56: 6.297 distance: 56 - 57: 27.322 distance: 56 - 58: 50.938 distance: 57 - 59: 9.646 distance: 58 - 60: 7.524 distance: 59 - 60: 41.405 distance: 61 - 62: 45.515 distance: 62 - 63: 36.027 distance: 62 - 65: 39.676 distance: 63 - 64: 41.662 distance: 63 - 69: 19.292 distance: 65 - 66: 16.399 distance: 66 - 67: 41.033 distance: 66 - 68: 42.829 distance: 69 - 70: 55.281 distance: 70 - 71: 45.472 distance: 71 - 72: 18.287 distance: 71 - 73: 18.295 distance: 73 - 74: 38.881 distance: 74 - 75: 22.908 distance: 74 - 77: 20.510 distance: 75 - 76: 24.703 distance: 75 - 79: 30.183 distance: 77 - 78: 31.537 distance: 79 - 80: 12.033 distance: 80 - 81: 24.771 distance: 80 - 83: 23.312 distance: 81 - 82: 5.150 distance: 81 - 87: 23.090 distance: 83 - 84: 33.580 distance: 84 - 85: 36.311 distance: 84 - 86: 5.671 distance: 87 - 88: 22.495 distance: 88 - 89: 6.129 distance: 89 - 90: 28.066 distance: 89 - 91: 28.079 distance: 91 - 92: 14.945 distance: 92 - 93: 22.731 distance: 92 - 95: 29.619 distance: 93 - 94: 3.504 distance: 93 - 99: 23.497 distance: 95 - 96: 11.219 distance: 96 - 97: 12.955 distance: 97 - 98: 10.994