Starting phenix.real_space_refine on Mon Dec 30 12:26:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8as6_15607/12_2024/8as6_15607.cif Found real_map, /net/cci-nas-00/data/ceres_data/8as6_15607/12_2024/8as6_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8as6_15607/12_2024/8as6_15607.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8as6_15607/12_2024/8as6_15607.map" model { file = "/net/cci-nas-00/data/ceres_data/8as6_15607/12_2024/8as6_15607.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8as6_15607/12_2024/8as6_15607.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: 13.03, per 1000 atoms: 1.02 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: 3.21 Conformation dependent library (CDL) restraints added in 2.9 seconds 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: 1.86 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: 5.00 Time building geometry restraints manager: 3.73 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: 2.790 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: 0.590 Check model and map are aligned: 0.110 Set scattering table: 0.120 Process input model: 39.090 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.070 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: 0.010 Load rotamer database and sin/cos tables:2.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.390 ------------------------------------------------------------------------------- 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= 0.241 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 : 4.32 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.021 0.002 TRP A 989 HIS 0.004 0.001 HIS A1246 PHE 0.016 0.001 PHE A 649 TYR 0.026 0.002 TYR A 76 ARG 0.012 0.001 ARG A 956 *********************** 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 : 1.526 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: 0.2817 time to fit residues: 80.4010 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 : 1.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 132 optimal weight: 2.9990 chunk 118 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 40 optimal weight: 10.0000 chunk 80 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 chunk 123 optimal weight: 7.9990 chunk 47 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 chunk 91 optimal weight: 0.9980 chunk 142 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- 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 A1604 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.0960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 13082 Z= 0.217 Angle : 0.587 11.344 17719 Z= 0.310 Chirality : 0.041 0.160 1972 Planarity : 0.005 0.078 2208 Dihedral : 8.440 79.553 1903 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 0.58 % Allowed : 6.89 % Favored : 92.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.21), residues: 1553 helix: 0.34 (0.20), residues: 730 sheet: -0.18 (0.48), residues: 128 loop : -2.43 (0.21), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 989 HIS 0.004 0.001 HIS A 799 PHE 0.013 0.001 PHE A1310 TYR 0.018 0.002 TYR A 76 ARG 0.006 0.000 ARG A1374 *********************** 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 182 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 174 time to evaluate : 1.479 Fit side-chains REVERT: A 429 GLU cc_start: 0.7605 (tm-30) cc_final: 0.7235 (tm-30) REVERT: A 950 GLU cc_start: 0.7136 (tm-30) cc_final: 0.6405 (tm-30) REVERT: A 1027 MET cc_start: 0.7751 (ttt) cc_final: 0.7546 (ttt) REVERT: A 1473 ARG cc_start: 0.7743 (tmm160) cc_final: 0.7462 (tmm160) outliers start: 8 outliers final: 7 residues processed: 179 average time/residue: 0.2778 time to fit residues: 71.9806 Evaluate side-chains 173 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 166 time to evaluate : 1.598 ------------------------------------------------------------------------------- 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 857 ASP Chi-restraints excluded: chain A residue 909 CYS Chi-restraints excluded: chain A residue 1006 MET Chi-restraints excluded: chain A residue 1078 MET Chi-restraints excluded: chain A residue 1253 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 79 optimal weight: 6.9990 chunk 44 optimal weight: 7.9990 chunk 118 optimal weight: 2.9990 chunk 97 optimal weight: 0.3980 chunk 39 optimal weight: 0.8980 chunk 142 optimal weight: 2.9990 chunk 154 optimal weight: 4.9990 chunk 127 optimal weight: 7.9990 chunk 141 optimal weight: 0.6980 chunk 48 optimal weight: 9.9990 chunk 114 optimal weight: 0.1980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 447 HIS A1203 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.1200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 13082 Z= 0.162 Angle : 0.536 11.416 17719 Z= 0.278 Chirality : 0.039 0.167 1972 Planarity : 0.005 0.066 2208 Dihedral : 8.337 79.317 1903 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 0.73 % Allowed : 8.70 % Favored : 90.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.21), residues: 1553 helix: 0.61 (0.20), residues: 729 sheet: 0.06 (0.49), residues: 123 loop : -2.32 (0.21), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 520 HIS 0.003 0.001 HIS A 799 PHE 0.012 0.001 PHE A 649 TYR 0.014 0.001 TYR A 923 ARG 0.006 0.000 ARG A1374 *********************** 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 183 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 173 time to evaluate : 1.374 Fit side-chains REVERT: A 950 GLU cc_start: 0.7119 (tm-30) cc_final: 0.6447 (tm-30) REVERT: A 1027 MET cc_start: 0.7638 (ttt) cc_final: 0.7394 (ttt) REVERT: A 1473 ARG cc_start: 0.7667 (tmm160) cc_final: 0.7221 (ttp-170) outliers start: 10 outliers final: 8 residues processed: 175 average time/residue: 0.2637 time to fit residues: 67.1132 Evaluate side-chains 170 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 162 time to evaluate : 1.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 728 GLU 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 1078 MET 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 141 optimal weight: 2.9990 chunk 107 optimal weight: 7.9990 chunk 74 optimal weight: 0.0470 chunk 15 optimal weight: 6.9990 chunk 68 optimal weight: 5.9990 chunk 95 optimal weight: 0.8980 chunk 143 optimal weight: 0.8980 chunk 151 optimal weight: 9.9990 chunk 135 optimal weight: 0.9990 chunk 40 optimal weight: 10.0000 chunk 126 optimal weight: 2.9990 overall best weight: 1.1682 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 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 : 0.003 0.045 13082 Z= 0.169 Angle : 0.529 11.704 17719 Z= 0.275 Chirality : 0.039 0.151 1972 Planarity : 0.004 0.059 2208 Dihedral : 8.281 78.665 1903 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 1.16 % Allowed : 10.01 % Favored : 88.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.21), residues: 1553 helix: 0.75 (0.20), residues: 727 sheet: 0.03 (0.47), residues: 128 loop : -2.32 (0.21), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 520 HIS 0.003 0.001 HIS A 799 PHE 0.013 0.001 PHE A 649 TYR 0.017 0.001 TYR A 76 ARG 0.005 0.000 ARG A1374 *********************** 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 182 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 166 time to evaluate : 1.644 Fit side-chains REVERT: A 950 GLU cc_start: 0.7119 (tm-30) cc_final: 0.6482 (tm-30) REVERT: A 1308 TYR cc_start: 0.6046 (OUTLIER) cc_final: 0.5562 (m-80) REVERT: A 1473 ARG cc_start: 0.7588 (tmm160) cc_final: 0.7103 (ttp-170) outliers start: 16 outliers final: 12 residues processed: 173 average time/residue: 0.2867 time to fit residues: 71.1540 Evaluate side-chains 173 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 160 time to evaluate : 1.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU 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 741 THR 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 86 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 112 optimal weight: 8.9990 chunk 62 optimal weight: 0.6980 chunk 129 optimal weight: 6.9990 chunk 104 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 chunk 77 optimal weight: 8.9990 chunk 136 optimal weight: 8.9990 chunk 38 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 563 HIS A1203 HIS A1604 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 13082 Z= 0.380 Angle : 0.670 9.892 17719 Z= 0.349 Chirality : 0.044 0.178 1972 Planarity : 0.005 0.059 2208 Dihedral : 8.582 73.617 1903 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.83 % Favored : 91.17 % Rotamer: Outliers : 1.60 % Allowed : 10.37 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.21), residues: 1553 helix: 0.38 (0.20), residues: 724 sheet: -0.37 (0.45), residues: 133 loop : -2.45 (0.21), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A1521 HIS 0.008 0.001 HIS A1190 PHE 0.017 0.002 PHE A1097 TYR 0.018 0.002 TYR A1306 ARG 0.007 0.001 ARG A 907 *********************** 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 183 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 161 time to evaluate : 1.632 Fit side-chains REVERT: A 29 ASP cc_start: 0.6721 (p0) cc_final: 0.6217 (t0) REVERT: A 950 GLU cc_start: 0.7520 (tm-30) cc_final: 0.6945 (tm-30) REVERT: A 1308 TYR cc_start: 0.6068 (OUTLIER) cc_final: 0.5608 (m-80) REVERT: A 1389 LYS cc_start: 0.7658 (ttpt) cc_final: 0.7110 (tmtt) REVERT: A 1473 ARG cc_start: 0.7608 (tmm160) cc_final: 0.7218 (ttp-170) REVERT: A 1567 PHE cc_start: 0.6247 (t80) cc_final: 0.5999 (t80) outliers start: 22 outliers final: 16 residues processed: 172 average time/residue: 0.2822 time to fit residues: 69.9672 Evaluate side-chains 174 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 157 time to evaluate : 1.516 ------------------------------------------------------------------------------- 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 389 ASP Chi-restraints excluded: chain A residue 493 MET Chi-restraints excluded: chain A residue 633 LEU 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 1110 TYR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 136 optimal weight: 0.0040 chunk 29 optimal weight: 0.0470 chunk 89 optimal weight: 3.9990 chunk 37 optimal weight: 0.3980 chunk 151 optimal weight: 8.9990 chunk 126 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 146 optimal weight: 10.0000 overall best weight: 0.6894 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 13082 Z= 0.143 Angle : 0.538 10.985 17719 Z= 0.278 Chirality : 0.039 0.146 1972 Planarity : 0.004 0.054 2208 Dihedral : 8.369 76.792 1903 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 0.73 % Allowed : 12.33 % Favored : 86.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.21), residues: 1553 helix: 0.75 (0.20), residues: 724 sheet: -0.16 (0.48), residues: 118 loop : -2.35 (0.21), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A1521 HIS 0.003 0.001 HIS A 993 PHE 0.012 0.001 PHE A 649 TYR 0.013 0.001 TYR A1306 ARG 0.005 0.000 ARG A1374 *********************** 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 186 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 176 time to evaluate : 1.622 Fit side-chains REVERT: A 29 ASP cc_start: 0.6584 (p0) cc_final: 0.6200 (t0) REVERT: A 950 GLU cc_start: 0.7240 (tm-30) cc_final: 0.6646 (tm-30) REVERT: A 1308 TYR cc_start: 0.6037 (OUTLIER) cc_final: 0.5583 (m-80) REVERT: A 1352 LEU cc_start: 0.7239 (mt) cc_final: 0.7038 (tp) REVERT: A 1473 ARG cc_start: 0.7581 (tmm160) cc_final: 0.7228 (ttp-170) outliers start: 10 outliers final: 6 residues processed: 181 average time/residue: 0.2641 time to fit residues: 69.5297 Evaluate side-chains 178 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 171 time to evaluate : 1.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 736 ILE 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 1308 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 17 optimal weight: 7.9990 chunk 86 optimal weight: 4.9990 chunk 110 optimal weight: 0.7980 chunk 85 optimal weight: 0.8980 chunk 127 optimal weight: 8.9990 chunk 84 optimal weight: 9.9990 chunk 151 optimal weight: 0.9980 chunk 94 optimal weight: 0.9980 chunk 92 optimal weight: 5.9990 chunk 69 optimal weight: 0.5980 chunk 93 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 13082 Z= 0.147 Angle : 0.532 14.963 17719 Z= 0.272 Chirality : 0.038 0.146 1972 Planarity : 0.004 0.062 2208 Dihedral : 8.261 77.511 1903 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 0.65 % Allowed : 12.98 % Favored : 86.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.21), residues: 1553 helix: 0.86 (0.20), residues: 728 sheet: -0.09 (0.46), residues: 128 loop : -2.33 (0.21), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A1521 HIS 0.003 0.001 HIS A1246 PHE 0.013 0.001 PHE A 649 TYR 0.019 0.001 TYR A 76 ARG 0.005 0.000 ARG A1374 *********************** 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 184 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 175 time to evaluate : 1.425 Fit side-chains revert: symmetry clash REVERT: A 29 ASP cc_start: 0.6601 (p0) cc_final: 0.6191 (t0) REVERT: A 778 GLU cc_start: 0.7046 (tp30) cc_final: 0.6807 (tp30) REVERT: A 950 GLU cc_start: 0.7191 (tm-30) cc_final: 0.6618 (tm-30) REVERT: A 1308 TYR cc_start: 0.5968 (OUTLIER) cc_final: 0.5563 (m-80) REVERT: A 1348 TYR cc_start: 0.6000 (t80) cc_final: 0.5786 (t80) REVERT: A 1352 LEU cc_start: 0.7196 (mt) cc_final: 0.6976 (tp) REVERT: A 1473 ARG cc_start: 0.7594 (tmm160) cc_final: 0.7225 (ttp-170) outliers start: 9 outliers final: 8 residues processed: 180 average time/residue: 0.2804 time to fit residues: 73.7858 Evaluate side-chains 176 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 167 time to evaluate : 1.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU 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 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 1308 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 60 optimal weight: 0.6980 chunk 90 optimal weight: 6.9990 chunk 45 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 96 optimal weight: 6.9990 chunk 103 optimal weight: 0.9980 chunk 74 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 137 optimal weight: 5.9990 chunk 144 optimal weight: 8.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 13082 Z= 0.161 Angle : 0.536 13.770 17719 Z= 0.273 Chirality : 0.039 0.147 1972 Planarity : 0.004 0.068 2208 Dihedral : 8.236 77.102 1903 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 0.73 % Allowed : 13.13 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.21), residues: 1553 helix: 0.93 (0.20), residues: 726 sheet: -0.01 (0.46), residues: 128 loop : -2.31 (0.21), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A1521 HIS 0.003 0.001 HIS A1246 PHE 0.013 0.001 PHE A 649 TYR 0.013 0.001 TYR A1306 ARG 0.005 0.000 ARG A1374 *********************** REFINEMENT MACRO_CYCLE 8 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 178 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 168 time to evaluate : 1.534 Fit side-chains revert: symmetry clash REVERT: A 778 GLU cc_start: 0.6996 (tp30) cc_final: 0.6769 (tp30) REVERT: A 950 GLU cc_start: 0.7212 (tm-30) cc_final: 0.6622 (tm-30) REVERT: A 1308 TYR cc_start: 0.6001 (OUTLIER) cc_final: 0.5600 (m-80) REVERT: A 1473 ARG cc_start: 0.7603 (tmm160) cc_final: 0.7225 (ttp-170) outliers start: 10 outliers final: 9 residues processed: 174 average time/residue: 0.2830 time to fit residues: 71.2967 Evaluate side-chains 178 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 168 time to evaluate : 1.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU 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 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 1115 ILE Chi-restraints excluded: chain A residue 1308 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 132 optimal weight: 4.9990 chunk 141 optimal weight: 1.9990 chunk 144 optimal weight: 7.9990 chunk 84 optimal weight: 8.9990 chunk 61 optimal weight: 0.9980 chunk 110 optimal weight: 6.9990 chunk 43 optimal weight: 3.9990 chunk 127 optimal weight: 7.9990 chunk 133 optimal weight: 6.9990 chunk 140 optimal weight: 8.9990 chunk 92 optimal weight: 5.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 13082 Z= 0.361 Angle : 0.657 14.005 17719 Z= 0.340 Chirality : 0.044 0.182 1972 Planarity : 0.005 0.065 2208 Dihedral : 8.494 73.620 1903 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.89 % Favored : 91.11 % Rotamer: Outliers : 1.23 % Allowed : 12.76 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.21), residues: 1553 helix: 0.57 (0.20), residues: 724 sheet: -0.37 (0.44), residues: 133 loop : -2.42 (0.21), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A1521 HIS 0.006 0.001 HIS A1190 PHE 0.019 0.002 PHE A1503 TYR 0.018 0.002 TYR A 76 ARG 0.005 0.001 ARG A1374 *********************** REFINEMENT MACRO_CYCLE 9 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 183 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 166 time to evaluate : 1.460 Fit side-chains REVERT: A 29 ASP cc_start: 0.6746 (p0) cc_final: 0.6128 (t0) REVERT: A 778 GLU cc_start: 0.7116 (tp30) cc_final: 0.6914 (tp30) REVERT: A 950 GLU cc_start: 0.7495 (tm-30) cc_final: 0.6939 (tm-30) REVERT: A 1308 TYR cc_start: 0.6132 (OUTLIER) cc_final: 0.5681 (m-80) REVERT: A 1374 ARG cc_start: 0.7153 (ttp-110) cc_final: 0.6932 (ptm160) REVERT: A 1389 LYS cc_start: 0.7574 (ttpt) cc_final: 0.7251 (tmtt) REVERT: A 1473 ARG cc_start: 0.7639 (tmm160) cc_final: 0.7402 (ttp-170) REVERT: A 1567 PHE cc_start: 0.6317 (t80) cc_final: 0.6007 (t80) outliers start: 17 outliers final: 14 residues processed: 172 average time/residue: 0.2884 time to fit residues: 70.9844 Evaluate side-chains 174 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 159 time to evaluate : 1.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 389 ASP 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 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 1076 THR Chi-restraints excluded: chain A residue 1110 TYR Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain A residue 1217 ASP Chi-restraints excluded: chain A residue 1308 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 149 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 chunk 70 optimal weight: 0.7980 chunk 103 optimal weight: 0.8980 chunk 156 optimal weight: 5.9990 chunk 143 optimal weight: 9.9990 chunk 124 optimal weight: 8.9990 chunk 12 optimal weight: 9.9990 chunk 96 optimal weight: 0.3980 chunk 76 optimal weight: 0.9990 chunk 98 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 13082 Z= 0.157 Angle : 0.543 13.596 17719 Z= 0.278 Chirality : 0.039 0.146 1972 Planarity : 0.004 0.065 2208 Dihedral : 8.316 76.216 1903 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 0.73 % Allowed : 13.34 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.21), residues: 1553 helix: 0.86 (0.20), residues: 726 sheet: -0.15 (0.45), residues: 131 loop : -2.33 (0.21), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 520 HIS 0.003 0.001 HIS A 706 PHE 0.017 0.001 PHE A1503 TYR 0.017 0.001 TYR A 76 ARG 0.005 0.000 ARG A1374 ********************** REFINEMENT MACRO_CYCLE 10 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 176 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 166 time to evaluate : 1.518 Fit side-chains revert: symmetry clash REVERT: A 778 GLU cc_start: 0.6912 (tp30) cc_final: 0.6658 (tp30) REVERT: A 950 GLU cc_start: 0.7264 (tm-30) cc_final: 0.6662 (tm-30) REVERT: A 1006 MET cc_start: 0.8694 (OUTLIER) cc_final: 0.8421 (mmp) REVERT: A 1308 TYR cc_start: 0.6041 (OUTLIER) cc_final: 0.5669 (m-80) REVERT: A 1473 ARG cc_start: 0.7514 (tmm160) cc_final: 0.7164 (ttp-170) outliers start: 10 outliers final: 7 residues processed: 171 average time/residue: 0.2850 time to fit residues: 70.9721 Evaluate side-chains 172 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 163 time to evaluate : 1.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 389 ASP 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 1006 MET Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain A residue 1308 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 132 optimal weight: 9.9990 chunk 38 optimal weight: 6.9990 chunk 114 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 34 optimal weight: 7.9990 chunk 124 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 128 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 22 optimal weight: 9.9990 chunk 109 optimal weight: 2.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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 = 0.3679 r_free = 0.3679 target = 0.139689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.105705 restraints weight = 31150.367| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 3.43 r_work: 0.2962 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2965 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2965 r_free = 0.2965 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2965 r_free = 0.2965 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2965 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.1927 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= 0.233 Angle : 0.583 13.728 17719 Z= 0.299 Chirality : 0.040 0.149 1972 Planarity : 0.005 0.064 2208 Dihedral : 8.342 75.202 1903 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 0.80 % Allowed : 13.56 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.21), residues: 1553 helix: 0.80 (0.20), residues: 729 sheet: -0.25 (0.45), residues: 131 loop : -2.36 (0.21), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A1521 HIS 0.004 0.001 HIS A1246 PHE 0.020 0.001 PHE A1503 TYR 0.015 0.002 TYR A1306 ARG 0.005 0.000 ARG A1374 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2769.70 seconds wall clock time: 52 minutes 14.29 seconds (3134.29 seconds total)