Starting phenix.real_space_refine on Fri Oct 23 15:52:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vt2_65313/10_2026/9vt2_65313.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vt2_65313/10_2026/9vt2_65313.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9vt2_65313/10_2026/9vt2_65313.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vt2_65313/10_2026/9vt2_65313.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9vt2_65313/10_2026/9vt2_65313.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vt2_65313/10_2026/9vt2_65313.map" } resolution = 2.79 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.022 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 S 62 5.16 5 C 6469 2.51 5 N 1660 2.21 5 O 1812 1.98 5 F 2 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 64 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10005 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 9983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1251, 9983 Classifications: {'peptide': 1251} Link IDs: {'PTRANS': 53, 'TRANS': 1197} Chain breaks: 3 Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'TPF': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.02, per 1000 atoms: 0.20 Number of scatterers: 10005 At special positions: 0 Unit cell: (78.514, 105.039, 144.296, 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 62 16.00 F 2 9.00 O 1812 8.00 N 1660 7.00 C 6469 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 712 " - pdb=" SG CYS A 732 " distance=2.03 Simple disulfide: pdb=" SG CYS A1402 " - pdb=" SG CYS A1444 " distance=2.03 Simple disulfide: pdb=" SG CYS A1418 " - pdb=" SG CYS A1441 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.64 Conformation dependent library (CDL) restraints added in 354.0 milliseconds 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2330 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 6 sheets defined 61.1% alpha, 7.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 192 through 201 Processing helix chain 'A' and resid 223 through 228 removed outlier: 3.730A pdb=" N HIS A 228 " --> pdb=" O ASP A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 231 No H-bonds generated for 'chain 'A' and resid 229 through 231' Processing helix chain 'A' and resid 247 through 260 removed outlier: 4.318A pdb=" N ALA A 255 " --> pdb=" O THR A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 285 Processing helix chain 'A' and resid 287 through 291 removed outlier: 3.898A pdb=" N ARG A 291 " --> pdb=" O SER A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 319 removed outlier: 3.902A pdb=" N ARG A 310 " --> pdb=" O GLY A 306 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE A 313 " --> pdb=" O LYS A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 353 removed outlier: 3.527A pdb=" N GLU A 340 " --> pdb=" O ALA A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 369 Processing helix chain 'A' and resid 388 through 399 removed outlier: 4.435A pdb=" N LYS A 392 " --> pdb=" O ALA A 388 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N GLU A 393 " --> pdb=" O THR A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 415 Processing helix chain 'A' and resid 434 through 444 Processing helix chain 'A' and resid 445 through 461 removed outlier: 3.574A pdb=" N GLU A 450 " --> pdb=" O PRO A 446 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS A 453 " --> pdb=" O ALA A 449 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU A 457 " --> pdb=" O LYS A 453 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL A 460 " --> pdb=" O ASP A 456 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLU A 461 " --> pdb=" O GLU A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 511 Processing helix chain 'A' and resid 512 through 533 removed outlier: 3.665A pdb=" N VAL A 532 " --> pdb=" O ILE A 528 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N PHE A 533 " --> pdb=" O LEU A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 541 No H-bonds generated for 'chain 'A' and resid 539 through 541' Processing helix chain 'A' and resid 542 through 561 removed outlier: 4.649A pdb=" N SER A 561 " --> pdb=" O ASN A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 581 removed outlier: 3.544A pdb=" N LEU A 568 " --> pdb=" O GLU A 564 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE A 569 " --> pdb=" O ILE A 565 " (cutoff:3.500A) Proline residue: A 573 - end of helix removed outlier: 3.503A pdb=" N LYS A 577 " --> pdb=" O PRO A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 614 removed outlier: 3.581A pdb=" N ASP A 589 " --> pdb=" O ARG A 585 " (cutoff:3.500A) Proline residue: A 599 - end of helix removed outlier: 3.523A pdb=" N PHE A 608 " --> pdb=" O MET A 604 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N VAL A 611 " --> pdb=" O SER A 607 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N PHE A 614 " --> pdb=" O PHE A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 648 Processing helix chain 'A' and resid 652 through 658 Processing helix chain 'A' and resid 661 through 670 Processing helix chain 'A' and resid 676 through 680 Processing helix chain 'A' and resid 684 through 690 removed outlier: 4.012A pdb=" N ASN A 688 " --> pdb=" O SER A 684 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N TYR A 689 " --> pdb=" O ARG A 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 691 through 706 removed outlier: 3.669A pdb=" N TYR A 695 " --> pdb=" O ASN A 691 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL A 696 " --> pdb=" O PRO A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 726 through 730 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 757 through 761 Processing helix chain 'A' and resid 762 through 785 removed outlier: 3.539A pdb=" N GLY A 766 " --> pdb=" O TRP A 762 " (cutoff:3.500A) Processing helix chain 'A' and resid 900 through 909 removed outlier: 3.919A pdb=" N LEU A 905 " --> pdb=" O LYS A 901 " (cutoff:3.500A) Processing helix chain 'A' and resid 932 through 937 Processing helix chain 'A' and resid 951 through 964 Processing helix chain 'A' and resid 969 through 984 removed outlier: 3.528A pdb=" N VAL A 977 " --> pdb=" O LYS A 973 " (cutoff:3.500A) Processing helix chain 'A' and resid 1002 through 1016 removed outlier: 3.551A pdb=" N GLU A1014 " --> pdb=" O THR A1010 " (cutoff:3.500A) Processing helix chain 'A' and resid 1033 through 1050 Processing helix chain 'A' and resid 1062 through 1067 Processing helix chain 'A' and resid 1091 through 1101 Processing helix chain 'A' and resid 1111 through 1120 Processing helix chain 'A' and resid 1131 through 1139 Processing helix chain 'A' and resid 1139 through 1159 removed outlier: 3.715A pdb=" N GLN A1143 " --> pdb=" O SER A1139 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LYS A1158 " --> pdb=" O ALA A1154 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU A1159 " --> pdb=" O GLU A1155 " (cutoff:3.500A) Processing helix chain 'A' and resid 1174 through 1193 Processing helix chain 'A' and resid 1196 through 1215 removed outlier: 3.704A pdb=" N PHE A1215 " --> pdb=" O ASN A1211 " (cutoff:3.500A) Processing helix chain 'A' and resid 1221 through 1234 Processing helix chain 'A' and resid 1235 through 1237 No H-bonds generated for 'chain 'A' and resid 1235 through 1237' Processing helix chain 'A' and resid 1238 through 1260 removed outlier: 3.501A pdb=" N MET A1246 " --> pdb=" O LEU A1242 " (cutoff:3.500A) Proline residue: A1248 - end of helix Processing helix chain 'A' and resid 1260 through 1265 Processing helix chain 'A' and resid 1268 through 1294 removed outlier: 3.634A pdb=" N GLU A1280 " --> pdb=" O GLN A1276 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ILE A1281 " --> pdb=" O ILE A1277 " (cutoff:3.500A) Proline residue: A1282 - end of helix Processing helix chain 'A' and resid 1295 through 1300 Processing helix chain 'A' and resid 1301 through 1306 removed outlier: 3.583A pdb=" N THR A1306 " --> pdb=" O ASN A1303 " (cutoff:3.500A) Processing helix chain 'A' and resid 1310 through 1339 removed outlier: 4.415A pdb=" N PHE A1339 " --> pdb=" O LEU A1335 " (cutoff:3.500A) Processing helix chain 'A' and resid 1342 through 1360 removed outlier: 3.580A pdb=" N ALA A1346 " --> pdb=" O LEU A1342 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA A1347 " --> pdb=" O ALA A1343 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE A1360 " --> pdb=" O MET A1356 " (cutoff:3.500A) Processing helix chain 'A' and resid 1371 through 1373 No H-bonds generated for 'chain 'A' and resid 1371 through 1373' Processing helix chain 'A' and resid 1374 through 1380 Processing helix chain 'A' and resid 1381 through 1396 removed outlier: 4.243A pdb=" N TYR A1385 " --> pdb=" O ASN A1381 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU A1386 " --> pdb=" O PRO A1382 " (cutoff:3.500A) Processing helix chain 'A' and resid 1403 through 1407 Processing helix chain 'A' and resid 1417 through 1430 Proline residue: A1424 - end of helix Processing helix chain 'A' and resid 1448 through 1456 removed outlier: 4.091A pdb=" N PHE A1452 " --> pdb=" O SER A1448 " (cutoff:3.500A) Processing helix chain 'A' and resid 1462 through 1489 Processing sheet with id=AA1, first strand: chain 'A' and resid 123 through 126 removed outlier: 3.629A pdb=" N ALA A 175 " --> pdb=" O TYR A 125 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 233 through 236 removed outlier: 6.818A pdb=" N ILE A 234 " --> pdb=" O CYS A 325 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N ASP A 327 " --> pdb=" O ILE A 234 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N SER A 236 " --> pdb=" O ASP A 327 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N GLN A 324 " --> pdb=" O LEU A 357 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N ALA A 359 " --> pdb=" O GLN A 324 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N TRP A 326 " --> pdb=" O ALA A 359 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N VAL A 184 " --> pdb=" O VAL A 375 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N LEU A 377 " --> pdb=" O VAL A 184 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N LEU A 186 " --> pdb=" O LEU A 377 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N VAL A 374 " --> pdb=" O PHE A 385 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N PHE A 385 " --> pdb=" O VAL A 374 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL A 376 " --> pdb=" O ILE A 383 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 709 through 711 Processing sheet with id=AA4, first strand: chain 'A' and resid 873 through 885 removed outlier: 6.372A pdb=" N TYR A 866 " --> pdb=" O ILE A 877 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ASP A 879 " --> pdb=" O LEU A 864 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N LEU A 864 " --> pdb=" O ASP A 879 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N VAL A 881 " --> pdb=" O ARG A 862 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ARG A 862 " --> pdb=" O VAL A 881 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N GLY A 883 " --> pdb=" O PHE A 860 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N PHE A 860 " --> pdb=" O GLY A 883 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N LEU A 864 " --> pdb=" O ASP A 919 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ASP A 919 " --> pdb=" O LEU A 864 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N TYR A 866 " --> pdb=" O ILE A 917 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ILE A 917 " --> pdb=" O TYR A 866 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 939 through 940 removed outlier: 6.059A pdb=" N LEU A1023 " --> pdb=" O LEU A1055 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N THR A1057 " --> pdb=" O LEU A1023 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N LEU A1025 " --> pdb=" O THR A1057 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ILE A 890 " --> pdb=" O ARG A1071 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N LEU A1073 " --> pdb=" O ILE A 890 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ALA A 892 " --> pdb=" O LEU A1073 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N LEU A1075 " --> pdb=" O ALA A 892 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N MET A 894 " --> pdb=" O LEU A1075 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N GLN A1076 " --> pdb=" O THR A1081 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N THR A1081 " --> pdb=" O GLN A1076 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1408 through 1410 removed outlier: 3.779A pdb=" N CYS A1441 " --> pdb=" O VAL A1410 " (cutoff:3.500A) 517 hydrogen bonds defined for protein. 1500 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.61 Time building geometry restraints manager: 0.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2788 1.33 - 1.45: 1998 1.45 - 1.57: 5382 1.57 - 1.69: 0 1.69 - 1.81: 101 Bond restraints: 10269 Sorted by residual: bond pdb=" C7 TPF A1601 " pdb=" N6 TPF A1601 " ideal model delta sigma weight residual 1.311 1.391 -0.080 2.00e-02 2.50e+03 1.61e+01 bond pdb=" N ASN A1220 " pdb=" CA ASN A1220 " ideal model delta sigma weight residual 1.456 1.492 -0.036 1.18e-02 7.18e+03 9.17e+00 bond pdb=" C3 TPF A1601 " pdb=" N2 TPF A1601 " ideal model delta sigma weight residual 1.312 1.371 -0.059 2.00e-02 2.50e+03 8.80e+00 bond pdb=" N THR A1308 " pdb=" CA THR A1308 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.33e-02 5.65e+03 5.94e+00 bond pdb=" N ASN A1304 " pdb=" CA ASN A1304 " ideal model delta sigma weight residual 1.456 1.488 -0.031 1.31e-02 5.83e+03 5.74e+00 ... (remaining 10264 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.34: 13463 1.34 - 2.68: 332 2.68 - 4.02: 99 4.02 - 5.35: 24 5.35 - 6.69: 12 Bond angle restraints: 13930 Sorted by residual: angle pdb=" N ILE A1237 " pdb=" CA ILE A1237 " pdb=" CB ILE A1237 " ideal model delta sigma weight residual 111.21 106.27 4.94 1.40e+00 5.10e-01 1.24e+01 angle pdb=" N THR A 661 " pdb=" CA THR A 661 " pdb=" C THR A 661 " ideal model delta sigma weight residual 114.04 109.67 4.37 1.24e+00 6.50e-01 1.24e+01 angle pdb=" N LEU A1358 " pdb=" CA LEU A1358 " pdb=" CB LEU A1358 " ideal model delta sigma weight residual 110.28 104.87 5.41 1.55e+00 4.16e-01 1.22e+01 angle pdb=" N PHE A1235 " pdb=" CA PHE A1235 " pdb=" C PHE A1235 " ideal model delta sigma weight residual 112.89 108.65 4.24 1.24e+00 6.50e-01 1.17e+01 angle pdb=" C LEU A 664 " pdb=" N LEU A 665 " pdb=" CA LEU A 665 " ideal model delta sigma weight residual 120.31 125.32 -5.01 1.52e+00 4.33e-01 1.09e+01 ... (remaining 13925 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.55: 5064 17.55 - 35.11: 682 35.11 - 52.66: 225 52.66 - 70.22: 46 70.22 - 87.77: 7 Dihedral angle restraints: 6024 sinusoidal: 2379 harmonic: 3645 Sorted by residual: dihedral pdb=" CB CYS A 712 " pdb=" SG CYS A 712 " pdb=" SG CYS A 732 " pdb=" CB CYS A 732 " ideal model delta sinusoidal sigma weight residual -86.00 -152.39 66.39 1 1.00e+01 1.00e-02 5.76e+01 dihedral pdb=" CB CYS A1418 " pdb=" SG CYS A1418 " pdb=" SG CYS A1441 " pdb=" CB CYS A1441 " ideal model delta sinusoidal sigma weight residual 93.00 133.34 -40.34 1 1.00e+01 1.00e-02 2.28e+01 dihedral pdb=" CA LEU A 664 " pdb=" C LEU A 664 " pdb=" N LEU A 665 " pdb=" CA LEU A 665 " ideal model delta harmonic sigma weight residual 180.00 163.44 16.56 0 5.00e+00 4.00e-02 1.10e+01 ... (remaining 6021 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1222 0.050 - 0.099: 234 0.099 - 0.149: 42 0.149 - 0.198: 3 0.198 - 0.248: 4 Chirality restraints: 1505 Sorted by residual: chirality pdb=" CA THR A1241 " pdb=" N THR A1241 " pdb=" C THR A1241 " pdb=" CB THR A1241 " both_signs ideal model delta sigma weight residual False 2.53 2.28 0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" CA PHE A 552 " pdb=" N PHE A 552 " pdb=" C PHE A 552 " pdb=" CB PHE A 552 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" CA PRO A1238 " pdb=" N PRO A1238 " pdb=" C PRO A1238 " pdb=" CB PRO A1238 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.21 2.00e-01 2.50e+01 1.13e+00 ... (remaining 1502 not shown) Planarity restraints: 1775 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 TPF A1601 " -0.059 2.00e-02 2.50e+03 4.43e-02 2.95e+01 pdb=" C3 TPF A1601 " 0.037 2.00e-02 2.50e+03 pdb=" C4 TPF A1601 " -0.036 2.00e-02 2.50e+03 pdb=" N1 TPF A1601 " 0.055 2.00e-02 2.50e+03 pdb=" N2 TPF A1601 " -0.035 2.00e-02 2.50e+03 pdb=" N3 TPF A1601 " 0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 559 " -0.063 2.00e-02 2.50e+03 4.08e-02 2.92e+01 pdb=" CG PHE A 559 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 PHE A 559 " 0.047 2.00e-02 2.50e+03 pdb=" CD2 PHE A 559 " 0.039 2.00e-02 2.50e+03 pdb=" CE1 PHE A 559 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE A 559 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 559 " -0.052 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 552 " -0.054 2.00e-02 2.50e+03 3.82e-02 2.55e+01 pdb=" CG PHE A 552 " 0.018 2.00e-02 2.50e+03 pdb=" CD1 PHE A 552 " 0.033 2.00e-02 2.50e+03 pdb=" CD2 PHE A 552 " 0.057 2.00e-02 2.50e+03 pdb=" CE1 PHE A 552 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 PHE A 552 " -0.016 2.00e-02 2.50e+03 pdb=" CZ PHE A 552 " -0.047 2.00e-02 2.50e+03 ... (remaining 1772 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 784 2.74 - 3.28: 10291 3.28 - 3.82: 17387 3.82 - 4.36: 21022 4.36 - 4.90: 35667 Nonbonded interactions: 85151 Sorted by model distance: nonbonded pdb=" O PHE A1202 " pdb=" OG SER A1206 " model vdw 2.199 3.040 nonbonded pdb=" OD1 ASP A 334 " pdb=" OG1 THR A 337 " model vdw 2.199 3.040 nonbonded pdb=" O ALA A1389 " pdb=" OG1 THR A1393 " model vdw 2.212 3.040 nonbonded pdb=" O ILE A 209 " pdb=" OG SER A 213 " model vdw 2.238 3.040 nonbonded pdb=" O GLN A1388 " pdb=" OG SER A1392 " model vdw 2.248 3.040 ... (remaining 85146 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.090 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: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.510 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 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 : 0.003 0.080 10272 Z= 0.182 Angle : 0.573 6.693 13936 Z= 0.326 Chirality : 0.042 0.248 1505 Planarity : 0.004 0.048 1775 Dihedral : 17.772 87.769 3685 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.22 % Favored : 96.70 % Rotamer: Outliers : 5.63 % Allowed : 25.16 % Favored : 69.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.24), residues: 1243 helix: 0.99 (0.20), residues: 688 sheet: -0.55 (0.53), residues: 93 loop : -0.54 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 227 TYR 0.020 0.001 TYR A 125 PHE 0.063 0.002 PHE A 559 TRP 0.013 0.001 TRP A 629 HIS 0.008 0.001 HIS A 223 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.18 (10269) covalent geometry : angle 0.57267 / 0.33 (13930) SS BOND : bond 0.00156 / 0.08 ( 3) SS BOND : angle 0.39710 / 0.19 ( 6) hydrogen bonds : bond 0.20550 / 14.22 ( 517) hydrogen bonds : angle 6.73096 / 4.75 ( 1500) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 101 time to evaluate : 0.279 Fit side-chains revert: symmetry clash REVERT: A 308 ARG cc_start: 0.7491 (OUTLIER) cc_final: 0.6443 (mtm-85) REVERT: A 602 LEU cc_start: 0.7803 (tm) cc_final: 0.7118 (mp) REVERT: A 657 MET cc_start: 0.7298 (mmm) cc_final: 0.6807 (mmp) REVERT: A 1399 PHE cc_start: 0.8542 (p90) cc_final: 0.8267 (p90) outliers start: 60 outliers final: 47 residues processed: 155 average time/residue: 0.3772 time to fit residues: 64.6109 Evaluate side-chains 143 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 95 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 208 HIS Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 387 LYS Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain A residue 577 LYS Chi-restraints excluded: chain A residue 585 ARG Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain A residue 650 SER Chi-restraints excluded: chain A residue 654 SER Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 671 THR Chi-restraints excluded: chain A residue 699 SER Chi-restraints excluded: chain A residue 728 SER Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 778 ILE Chi-restraints excluded: chain A residue 914 THR Chi-restraints excluded: chain A residue 937 ILE Chi-restraints excluded: chain A residue 993 LEU Chi-restraints excluded: chain A residue 996 VAL Chi-restraints excluded: chain A residue 1007 LYS Chi-restraints excluded: chain A residue 1034 SER Chi-restraints excluded: chain A residue 1065 ILE Chi-restraints excluded: chain A residue 1129 LYS Chi-restraints excluded: chain A residue 1231 SER Chi-restraints excluded: chain A residue 1287 VAL Chi-restraints excluded: chain A residue 1311 VAL Chi-restraints excluded: chain A residue 1342 LEU Chi-restraints excluded: chain A residue 1392 SER Chi-restraints excluded: chain A residue 1402 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: [108, 49, 97, 113, 53, 5, 33, 123, 65, 62, 51] chunk 108 optimal weight: 0.9990 chunk 49 optimal weight: 0.5980 chunk 97 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 chunk 123 optimal weight: 0.7980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1228 GLN A1388 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.107600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.086104 restraints weight = 17213.326| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 2.75 r_work: 0.2974 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.1028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10272 Z= 0.173 Angle : 0.551 8.508 13936 Z= 0.287 Chirality : 0.042 0.250 1505 Planarity : 0.004 0.052 1775 Dihedral : 7.883 59.221 1464 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.30 % Favored : 96.62 % Rotamer: Outliers : 5.73 % Allowed : 23.94 % Favored : 70.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.24), residues: 1243 helix: 1.49 (0.19), residues: 691 sheet: -0.84 (0.51), residues: 93 loop : -0.50 (0.30), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 421 TYR 0.012 0.001 TYR A 670 PHE 0.014 0.001 PHE A 552 TRP 0.011 0.001 TRP A 629 HIS 0.006 0.001 HIS A 223 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.17 (10269) covalent geometry : angle 0.55105 / 0.29 (13930) SS BOND : bond 0.00371 / 0.19 ( 3) SS BOND : angle 0.72176 / 0.35 ( 6) hydrogen bonds : bond 0.04503 / 3.14 ( 517) hydrogen bonds : angle 4.45605 / 3.16 ( 1500) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 102 time to evaluate : 0.373 Fit side-chains REVERT: A 421 ARG cc_start: 0.7626 (OUTLIER) cc_final: 0.6527 (ptp-170) REVERT: A 433 ARG cc_start: 0.7767 (OUTLIER) cc_final: 0.7436 (tpp-160) REVERT: A 657 MET cc_start: 0.7695 (mmm) cc_final: 0.7464 (mmt) REVERT: A 1423 ASP cc_start: 0.8600 (m-30) cc_final: 0.8229 (m-30) outliers start: 61 outliers final: 31 residues processed: 152 average time/residue: 0.3882 time to fit residues: 65.2075 Evaluate side-chains 127 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 94 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 208 HIS Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 387 LYS Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 421 ARG Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 433 ARG Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain A residue 585 ARG Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 671 THR Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 969 SER Chi-restraints excluded: chain A residue 993 LEU Chi-restraints excluded: chain A residue 996 VAL Chi-restraints excluded: chain A residue 1007 LYS Chi-restraints excluded: chain A residue 1129 LYS Chi-restraints excluded: chain A residue 1188 VAL Chi-restraints excluded: chain A residue 1247 LEU Chi-restraints excluded: chain A residue 1287 VAL Chi-restraints excluded: chain A residue 1342 LEU Chi-restraints excluded: chain A residue 1402 CYS Chi-restraints excluded: chain A residue 1458 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: [103, 97, 76, 15, 39, 18, 49, 85, 89, 53, 84] chunk 103 optimal weight: 1.9990 chunk 97 optimal weight: 0.6980 chunk 76 optimal weight: 2.9990 chunk 15 optimal weight: 0.5980 chunk 39 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 49 optimal weight: 0.3980 chunk 85 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 223 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.108197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.086818 restraints weight = 17043.449| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 2.74 r_work: 0.2969 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.1201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10272 Z= 0.145 Angle : 0.512 7.606 13936 Z= 0.266 Chirality : 0.041 0.299 1505 Planarity : 0.004 0.051 1775 Dihedral : 6.998 56.105 1432 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.22 % Favored : 96.70 % Rotamer: Outliers : 4.32 % Allowed : 24.88 % Favored : 70.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.24), residues: 1243 helix: 1.65 (0.20), residues: 690 sheet: -0.97 (0.50), residues: 93 loop : -0.48 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 421 TYR 0.018 0.001 TYR A 125 PHE 0.014 0.001 PHE A 552 TRP 0.008 0.001 TRP A 629 HIS 0.007 0.001 HIS A 223 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 (10269) covalent geometry : angle 0.51193 / 0.27 (13930) SS BOND : bond 0.00351 / 0.18 ( 3) SS BOND : angle 0.69540 / 0.34 ( 6) hydrogen bonds : bond 0.04002 / 2.81 ( 517) hydrogen bonds : angle 4.19943 / 2.97 ( 1500) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 104 time to evaluate : 0.374 Fit side-chains REVERT: A 421 ARG cc_start: 0.7376 (OUTLIER) cc_final: 0.6306 (ptp-170) REVERT: A 433 ARG cc_start: 0.7765 (OUTLIER) cc_final: 0.7434 (tpp-160) REVERT: A 657 MET cc_start: 0.7641 (mmm) cc_final: 0.7425 (mmt) REVERT: A 871 LYS cc_start: 0.8951 (mmpt) cc_final: 0.8616 (tmmm) REVERT: A 1423 ASP cc_start: 0.8609 (m-30) cc_final: 0.8220 (m-30) REVERT: A 1459 LEU cc_start: 0.8047 (OUTLIER) cc_final: 0.7756 (mt) outliers start: 46 outliers final: 21 residues processed: 143 average time/residue: 0.4141 time to fit residues: 65.2353 Evaluate side-chains 120 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 96 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 208 HIS Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 307 GLU Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 387 LYS Chi-restraints excluded: chain A residue 421 ARG Chi-restraints excluded: chain A residue 433 ARG Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 585 ARG Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 671 THR Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 993 LEU Chi-restraints excluded: chain A residue 996 VAL Chi-restraints excluded: chain A residue 1007 LYS Chi-restraints excluded: chain A residue 1129 LYS Chi-restraints excluded: chain A residue 1188 VAL Chi-restraints excluded: chain A residue 1247 LEU Chi-restraints excluded: chain A residue 1287 VAL Chi-restraints excluded: chain A residue 1402 CYS Chi-restraints excluded: chain A residue 1458 SER Chi-restraints excluded: chain A residue 1459 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: [13, 43, 35, 42, 59, 86, 2, 71, 32, 93, 75] chunk 13 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 93 optimal weight: 0.5980 chunk 75 optimal weight: 0.1980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 263 ASN A1359 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.107834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.086494 restraints weight = 17112.164| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 2.75 r_work: 0.2968 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.1306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10272 Z= 0.150 Angle : 0.514 7.669 13936 Z= 0.266 Chirality : 0.042 0.325 1505 Planarity : 0.004 0.053 1775 Dihedral : 6.224 55.635 1417 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.38 % Favored : 96.54 % Rotamer: Outliers : 4.88 % Allowed : 24.13 % Favored : 70.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.24), residues: 1243 helix: 1.68 (0.20), residues: 693 sheet: -0.98 (0.51), residues: 93 loop : -0.48 (0.30), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 421 TYR 0.021 0.001 TYR A 125 PHE 0.023 0.001 PHE A 559 TRP 0.007 0.001 TRP A1295 HIS 0.007 0.001 HIS A 223 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 (10269) covalent geometry : angle 0.51342 / 0.27 (13930) SS BOND : bond 0.00354 / 0.18 ( 3) SS BOND : angle 0.71195 / 0.35 ( 6) hydrogen bonds : bond 0.03786 / 2.66 ( 517) hydrogen bonds : angle 4.10343 / 2.90 ( 1500) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 97 time to evaluate : 0.233 Fit side-chains REVERT: A 433 ARG cc_start: 0.7754 (OUTLIER) cc_final: 0.7406 (tpp-160) REVERT: A 657 MET cc_start: 0.7773 (mmm) cc_final: 0.7572 (mmt) REVERT: A 1423 ASP cc_start: 0.8558 (m-30) cc_final: 0.8147 (m-30) REVERT: A 1459 LEU cc_start: 0.8018 (OUTLIER) cc_final: 0.7724 (mt) outliers start: 52 outliers final: 24 residues processed: 140 average time/residue: 0.4518 time to fit residues: 68.9816 Evaluate side-chains 118 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 92 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 208 HIS Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 277 MET Chi-restraints excluded: chain A residue 307 GLU Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 387 LYS Chi-restraints excluded: chain A residue 433 ARG Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 585 ARG Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 671 THR Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 996 VAL Chi-restraints excluded: chain A residue 1007 LYS Chi-restraints excluded: chain A residue 1129 LYS Chi-restraints excluded: chain A residue 1188 VAL Chi-restraints excluded: chain A residue 1247 LEU Chi-restraints excluded: chain A residue 1287 VAL Chi-restraints excluded: chain A residue 1402 CYS Chi-restraints excluded: chain A residue 1459 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: [33, 72, 19, 54, 86, 83, 44, 25, 102, 49, 34] chunk 33 optimal weight: 0.9990 chunk 72 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 86 optimal weight: 1.9990 chunk 83 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 25 optimal weight: 0.0870 chunk 102 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 chunk 34 optimal weight: 0.5980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.108821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.087468 restraints weight = 17012.453| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 2.74 r_work: 0.2994 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10272 Z= 0.127 Angle : 0.499 7.101 13936 Z= 0.258 Chirality : 0.042 0.339 1505 Planarity : 0.004 0.051 1775 Dihedral : 6.010 55.209 1415 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.38 % Favored : 96.54 % Rotamer: Outliers : 4.13 % Allowed : 24.98 % Favored : 70.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.24), residues: 1243 helix: 1.75 (0.20), residues: 692 sheet: -1.01 (0.50), residues: 94 loop : -0.47 (0.30), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 875 TYR 0.020 0.001 TYR A 125 PHE 0.014 0.001 PHE A 552 TRP 0.008 0.001 TRP A 629 HIS 0.002 0.000 HIS A1050 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (10269) covalent geometry : angle 0.49933 / 0.26 (13930) SS BOND : bond 0.00279 / 0.14 ( 3) SS BOND : angle 0.65230 / 0.31 ( 6) hydrogen bonds : bond 0.03555 / 2.50 ( 517) hydrogen bonds : angle 4.00119 / 2.83 ( 1500) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 100 time to evaluate : 0.401 Fit side-chains revert: symmetry clash REVERT: A 421 ARG cc_start: 0.7484 (OUTLIER) cc_final: 0.6186 (ptp-170) REVERT: A 433 ARG cc_start: 0.7785 (OUTLIER) cc_final: 0.7440 (tpp-160) REVERT: A 585 ARG cc_start: 0.7611 (OUTLIER) cc_final: 0.7347 (ptp90) REVERT: A 657 MET cc_start: 0.7683 (mmm) cc_final: 0.7470 (mmt) REVERT: A 871 LYS cc_start: 0.8936 (mmpt) cc_final: 0.8569 (tmmm) REVERT: A 1423 ASP cc_start: 0.8584 (m-30) cc_final: 0.8178 (m-30) outliers start: 44 outliers final: 21 residues processed: 138 average time/residue: 0.4500 time to fit residues: 67.9767 Evaluate side-chains 115 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 91 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 208 HIS Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 277 MET Chi-restraints excluded: chain A residue 307 GLU Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 387 LYS Chi-restraints excluded: chain A residue 421 ARG Chi-restraints excluded: chain A residue 433 ARG Chi-restraints excluded: chain A residue 585 ARG Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 671 THR Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 996 VAL Chi-restraints excluded: chain A residue 1007 LYS Chi-restraints excluded: chain A residue 1188 VAL Chi-restraints excluded: chain A residue 1244 GLN Chi-restraints excluded: chain A residue 1247 LEU Chi-restraints excluded: chain A residue 1287 VAL Chi-restraints excluded: chain A residue 1402 CYS Chi-restraints excluded: chain A residue 1458 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: [12, 71, 68, 115, 99, 70, 44, 59, 89, 11, 35] chunk 12 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 263 ASN A 786 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.106264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.085352 restraints weight = 17540.518| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 2.71 r_work: 0.2955 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 10272 Z= 0.259 Angle : 0.582 7.425 13936 Z= 0.301 Chirality : 0.046 0.325 1505 Planarity : 0.004 0.053 1775 Dihedral : 6.032 56.601 1410 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.62 % Favored : 96.30 % Rotamer: Outliers : 5.73 % Allowed : 23.19 % Favored : 71.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.24), residues: 1243 helix: 1.49 (0.20), residues: 694 sheet: -1.26 (0.49), residues: 93 loop : -0.59 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1071 TYR 0.028 0.002 TYR A 125 PHE 0.024 0.002 PHE A1433 TRP 0.009 0.001 TRP A 634 HIS 0.003 0.001 HIS A1050 Details of bonding type rmsd/Z covalent geometry : bond 0.00613 / 0.26 (10269) covalent geometry : angle 0.58155 / 0.30 (13930) SS BOND : bond 0.00502 / 0.26 ( 3) SS BOND : angle 1.07167 / 0.53 ( 6) hydrogen bonds : bond 0.04251 / 2.98 ( 517) hydrogen bonds : angle 4.24135 / 3.00 ( 1500) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 88 time to evaluate : 0.291 Fit side-chains revert: symmetry clash REVERT: A 309 LYS cc_start: 0.8390 (OUTLIER) cc_final: 0.7997 (mtpp) REVERT: A 657 MET cc_start: 0.7822 (mmm) cc_final: 0.7363 (mmp) REVERT: A 667 MET cc_start: 0.9010 (ptp) cc_final: 0.8665 (ptm) REVERT: A 934 GLN cc_start: 0.8371 (OUTLIER) cc_final: 0.8094 (mp10) REVERT: A 999 GLU cc_start: 0.8180 (tp30) cc_final: 0.7905 (tp30) REVERT: A 1459 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.7993 (mt) outliers start: 61 outliers final: 28 residues processed: 139 average time/residue: 0.4500 time to fit residues: 68.3411 Evaluate side-chains 113 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 82 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 MET Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 208 HIS Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 309 LYS Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 387 LYS Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 518 SER Chi-restraints excluded: chain A residue 585 ARG Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 671 THR Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 934 GLN Chi-restraints excluded: chain A residue 969 SER Chi-restraints excluded: chain A residue 996 VAL Chi-restraints excluded: chain A residue 1007 LYS Chi-restraints excluded: chain A residue 1129 LYS Chi-restraints excluded: chain A residue 1188 VAL Chi-restraints excluded: chain A residue 1247 LEU Chi-restraints excluded: chain A residue 1287 VAL Chi-restraints excluded: chain A residue 1335 LEU Chi-restraints excluded: chain A residue 1458 SER Chi-restraints excluded: chain A residue 1459 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: [69, 67, 10, 45, 70, 41, 106, 47, 89, 108, 90] chunk 69 optimal weight: 0.9980 chunk 67 optimal weight: 5.9990 chunk 10 optimal weight: 0.7980 chunk 45 optimal weight: 0.9980 chunk 70 optimal weight: 0.0030 chunk 41 optimal weight: 0.6980 chunk 106 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 108 optimal weight: 0.2980 chunk 90 optimal weight: 0.7980 overall best weight: 0.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.108599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.087404 restraints weight = 17045.623| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 2.74 r_work: 0.2978 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10272 Z= 0.122 Angle : 0.502 7.468 13936 Z= 0.261 Chirality : 0.042 0.315 1505 Planarity : 0.004 0.051 1775 Dihedral : 5.735 53.391 1409 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.38 % Favored : 96.54 % Rotamer: Outliers : 4.04 % Allowed : 25.16 % Favored : 70.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.24), residues: 1243 helix: 1.76 (0.20), residues: 693 sheet: -1.20 (0.50), residues: 94 loop : -0.50 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 227 TYR 0.023 0.001 TYR A 125 PHE 0.017 0.001 PHE A1433 TRP 0.010 0.001 TRP A 629 HIS 0.004 0.001 HIS A 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 (10269) covalent geometry : angle 0.50241 / 0.26 (13930) SS BOND : bond 0.00284 / 0.14 ( 3) SS BOND : angle 0.58059 / 0.27 ( 6) hydrogen bonds : bond 0.03529 / 2.49 ( 517) hydrogen bonds : angle 3.98895 / 2.82 ( 1500) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 96 time to evaluate : 0.374 Fit side-chains revert: symmetry clash REVERT: A 433 ARG cc_start: 0.7744 (OUTLIER) cc_final: 0.7495 (tpp-160) REVERT: A 657 MET cc_start: 0.7658 (mmm) cc_final: 0.7199 (mmp) REVERT: A 667 MET cc_start: 0.8814 (ptp) cc_final: 0.8575 (ptm) REVERT: A 1221 ASN cc_start: 0.7617 (OUTLIER) cc_final: 0.7315 (p0) REVERT: A 1423 ASP cc_start: 0.8638 (m-30) cc_final: 0.8187 (m-30) outliers start: 43 outliers final: 23 residues processed: 134 average time/residue: 0.4218 time to fit residues: 62.4809 Evaluate side-chains 115 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 90 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 208 HIS Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 387 LYS Chi-restraints excluded: chain A residue 433 ARG Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 518 SER Chi-restraints excluded: chain A residue 585 ARG Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 671 THR Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 993 LEU Chi-restraints excluded: chain A residue 996 VAL Chi-restraints excluded: chain A residue 1007 LYS Chi-restraints excluded: chain A residue 1188 VAL Chi-restraints excluded: chain A residue 1221 ASN Chi-restraints excluded: chain A residue 1247 LEU Chi-restraints excluded: chain A residue 1287 VAL Chi-restraints excluded: chain A residue 1402 CYS Chi-restraints excluded: chain A residue 1458 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: [97, 32, 99, 94, 71, 80, 44, 115, 120, 41, 104] chunk 97 optimal weight: 0.0010 chunk 32 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 94 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 115 optimal weight: 2.9990 chunk 120 optimal weight: 0.5980 chunk 41 optimal weight: 0.6980 chunk 104 optimal weight: 1.9990 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 263 ASN A 942 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.109131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.088033 restraints weight = 17120.901| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 2.73 r_work: 0.2980 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10272 Z= 0.133 Angle : 0.506 6.936 13936 Z= 0.261 Chirality : 0.042 0.287 1505 Planarity : 0.004 0.052 1775 Dihedral : 5.644 54.221 1409 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.54 % Favored : 96.38 % Rotamer: Outliers : 3.85 % Allowed : 25.35 % Favored : 70.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.24), residues: 1243 helix: 1.84 (0.20), residues: 693 sheet: -1.11 (0.51), residues: 94 loop : -0.48 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 129 TYR 0.023 0.001 TYR A 125 PHE 0.016 0.001 PHE A 552 TRP 0.010 0.001 TRP A 629 HIS 0.001 0.000 HIS A 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 (10269) covalent geometry : angle 0.50634 / 0.26 (13930) SS BOND : bond 0.00305 / 0.15 ( 3) SS BOND : angle 0.57395 / 0.28 ( 6) hydrogen bonds : bond 0.03521 / 2.48 ( 517) hydrogen bonds : angle 3.94428 / 2.79 ( 1500) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 97 time to evaluate : 0.374 Fit side-chains REVERT: A 421 ARG cc_start: 0.7403 (OUTLIER) cc_final: 0.6237 (ptp-170) REVERT: A 433 ARG cc_start: 0.7728 (OUTLIER) cc_final: 0.7458 (tpp-160) REVERT: A 657 MET cc_start: 0.7661 (mmm) cc_final: 0.7221 (mmp) REVERT: A 667 MET cc_start: 0.8872 (ptp) cc_final: 0.8553 (ptm) REVERT: A 1331 THR cc_start: 0.8648 (m) cc_final: 0.8397 (p) REVERT: A 1423 ASP cc_start: 0.8620 (m-30) cc_final: 0.8185 (m-30) REVERT: A 1459 LEU cc_start: 0.7961 (OUTLIER) cc_final: 0.7691 (mp) outliers start: 41 outliers final: 26 residues processed: 131 average time/residue: 0.4367 time to fit residues: 62.9522 Evaluate side-chains 120 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 91 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 MET Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 208 HIS Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 387 LYS Chi-restraints excluded: chain A residue 421 ARG Chi-restraints excluded: chain A residue 433 ARG Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 518 SER Chi-restraints excluded: chain A residue 585 ARG Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 671 THR Chi-restraints excluded: chain A residue 993 LEU Chi-restraints excluded: chain A residue 996 VAL Chi-restraints excluded: chain A residue 1007 LYS Chi-restraints excluded: chain A residue 1188 VAL Chi-restraints excluded: chain A residue 1244 GLN Chi-restraints excluded: chain A residue 1247 LEU Chi-restraints excluded: chain A residue 1287 VAL Chi-restraints excluded: chain A residue 1364 LEU Chi-restraints excluded: chain A residue 1402 CYS Chi-restraints excluded: chain A residue 1458 SER Chi-restraints excluded: chain A residue 1459 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: [22, 16, 114, 104, 10, 123, 62, 67, 91, 78, 6] chunk 22 optimal weight: 0.6980 chunk 16 optimal weight: 3.9990 chunk 114 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 123 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 chunk 91 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 942 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.107747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.086581 restraints weight = 17130.478| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 2.72 r_work: 0.2967 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10272 Z= 0.157 Angle : 0.530 11.760 13936 Z= 0.271 Chirality : 0.043 0.327 1505 Planarity : 0.004 0.051 1775 Dihedral : 5.656 56.260 1408 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.46 % Favored : 96.46 % Rotamer: Outliers : 3.38 % Allowed : 25.45 % Favored : 71.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.24), residues: 1243 helix: 1.81 (0.20), residues: 693 sheet: -1.17 (0.51), residues: 94 loop : -0.49 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 421 TYR 0.025 0.001 TYR A 125 PHE 0.017 0.001 PHE A 552 TRP 0.011 0.001 TRP A 629 HIS 0.002 0.000 HIS A 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.16 (10269) covalent geometry : angle 0.53028 / 0.27 (13930) SS BOND : bond 0.00342 / 0.17 ( 3) SS BOND : angle 0.65203 / 0.32 ( 6) hydrogen bonds : bond 0.03630 / 2.56 ( 517) hydrogen bonds : angle 3.96951 / 2.81 ( 1500) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 95 time to evaluate : 0.355 Fit side-chains REVERT: A 421 ARG cc_start: 0.7478 (OUTLIER) cc_final: 0.6224 (ptp-170) REVERT: A 433 ARG cc_start: 0.7770 (OUTLIER) cc_final: 0.7452 (tpp-160) REVERT: A 657 MET cc_start: 0.7669 (mmm) cc_final: 0.7228 (mmp) REVERT: A 667 MET cc_start: 0.8912 (ptp) cc_final: 0.8590 (ptm) REVERT: A 934 GLN cc_start: 0.8256 (OUTLIER) cc_final: 0.7909 (mp10) REVERT: A 1331 THR cc_start: 0.8683 (m) cc_final: 0.8395 (p) REVERT: A 1423 ASP cc_start: 0.8629 (m-30) cc_final: 0.8193 (m-30) REVERT: A 1428 PHE cc_start: 0.8886 (t80) cc_final: 0.8504 (t80) REVERT: A 1459 LEU cc_start: 0.7987 (OUTLIER) cc_final: 0.7715 (mp) outliers start: 36 outliers final: 27 residues processed: 125 average time/residue: 0.4866 time to fit residues: 66.2944 Evaluate side-chains 124 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 93 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 MET Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 208 HIS Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 307 GLU Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 387 LYS Chi-restraints excluded: chain A residue 421 ARG Chi-restraints excluded: chain A residue 433 ARG Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 518 SER Chi-restraints excluded: chain A residue 585 ARG Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 671 THR Chi-restraints excluded: chain A residue 934 GLN Chi-restraints excluded: chain A residue 993 LEU Chi-restraints excluded: chain A residue 996 VAL Chi-restraints excluded: chain A residue 1007 LYS Chi-restraints excluded: chain A residue 1188 VAL Chi-restraints excluded: chain A residue 1244 GLN Chi-restraints excluded: chain A residue 1247 LEU Chi-restraints excluded: chain A residue 1287 VAL Chi-restraints excluded: chain A residue 1402 CYS Chi-restraints excluded: chain A residue 1427 LYS Chi-restraints excluded: chain A residue 1458 SER Chi-restraints excluded: chain A residue 1459 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: [80, 33, 54, 14, 91, 78, 46, 25, 81, 93, 92] chunk 80 optimal weight: 1.9990 chunk 33 optimal weight: 0.1980 chunk 54 optimal weight: 0.0020 chunk 14 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 78 optimal weight: 0.5980 chunk 46 optimal weight: 0.9990 chunk 25 optimal weight: 0.2980 chunk 81 optimal weight: 0.9990 chunk 93 optimal weight: 0.8980 chunk 92 optimal weight: 0.5980 overall best weight: 0.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 263 ASN A 942 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.111018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.090002 restraints weight = 16927.499| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 2.73 r_work: 0.3019 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.1734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10272 Z= 0.107 Angle : 0.502 11.169 13936 Z= 0.257 Chirality : 0.041 0.326 1505 Planarity : 0.004 0.051 1775 Dihedral : 5.519 55.339 1408 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.82 % Allowed : 26.01 % Favored : 71.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.24), residues: 1243 helix: 1.96 (0.20), residues: 695 sheet: -1.08 (0.51), residues: 94 loop : -0.48 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 331 TYR 0.022 0.001 TYR A 125 PHE 0.014 0.001 PHE A1433 TRP 0.013 0.001 TRP A 629 HIS 0.001 0.000 HIS A 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (10269) covalent geometry : angle 0.50201 / 0.26 (13930) SS BOND : bond 0.00256 / 0.13 ( 3) SS BOND : angle 0.50975 / 0.23 ( 6) hydrogen bonds : bond 0.03284 / 2.33 ( 517) hydrogen bonds : angle 3.84322 / 2.72 ( 1500) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 102 time to evaluate : 0.456 Fit side-chains revert: symmetry clash REVERT: A 421 ARG cc_start: 0.7352 (OUTLIER) cc_final: 0.6113 (ptp-170) REVERT: A 433 ARG cc_start: 0.7688 (OUTLIER) cc_final: 0.7370 (tpp-160) REVERT: A 585 ARG cc_start: 0.7533 (OUTLIER) cc_final: 0.7288 (ptp90) REVERT: A 657 MET cc_start: 0.7639 (mmm) cc_final: 0.7410 (mmt) REVERT: A 667 MET cc_start: 0.8819 (ptp) cc_final: 0.8483 (ptm) REVERT: A 1423 ASP cc_start: 0.8648 (m-30) cc_final: 0.8225 (m-30) REVERT: A 1428 PHE cc_start: 0.8925 (t80) cc_final: 0.8440 (t80) outliers start: 30 outliers final: 17 residues processed: 127 average time/residue: 0.4320 time to fit residues: 60.2687 Evaluate side-chains 111 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 91 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 HIS Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 387 LYS Chi-restraints excluded: chain A residue 421 ARG Chi-restraints excluded: chain A residue 433 ARG Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 585 ARG Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 671 THR Chi-restraints excluded: chain A residue 996 VAL Chi-restraints excluded: chain A residue 1244 GLN Chi-restraints excluded: chain A residue 1247 LEU Chi-restraints excluded: chain A residue 1287 VAL Chi-restraints excluded: chain A residue 1364 LEU Chi-restraints excluded: chain A residue 1402 CYS Chi-restraints excluded: chain A residue 1427 LYS Chi-restraints excluded: chain A residue 1458 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: [98, 49, 1, 81, 22, 6, 93, 103, 124, 78, 42] chunk 98 optimal weight: 0.5980 chunk 49 optimal weight: 0.4980 chunk 1 optimal weight: 7.9990 chunk 81 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 93 optimal weight: 0.0070 chunk 103 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 chunk 78 optimal weight: 0.9980 chunk 42 optimal weight: 0.5980 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 942 GLN A1359 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.110534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.089439 restraints weight = 17031.718| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 2.73 r_work: 0.3031 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10272 Z= 0.119 Angle : 0.505 7.563 13936 Z= 0.260 Chirality : 0.042 0.330 1505 Planarity : 0.004 0.051 1775 Dihedral : 5.311 56.445 1400 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.35 % Allowed : 26.67 % Favored : 70.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.24), residues: 1243 helix: 1.97 (0.20), residues: 695 sheet: -1.05 (0.51), residues: 94 loop : -0.45 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 685 TYR 0.022 0.001 TYR A 125 PHE 0.014 0.001 PHE A 552 TRP 0.016 0.001 TRP A1038 HIS 0.001 0.000 HIS A1050 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (10269) covalent geometry : angle 0.50528 / 0.26 (13930) SS BOND : bond 0.00276 / 0.14 ( 3) SS BOND : angle 0.55473 / 0.26 ( 6) hydrogen bonds : bond 0.03335 / 2.36 ( 517) hydrogen bonds : angle 3.85164 / 2.72 ( 1500) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2610.75 seconds wall clock time: 45 minutes 30.74 seconds (2730.74 seconds total)