Starting phenix.real_space_refine on Fri Oct 23 15:51:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vsu_65307/10_2026/9vsu_65307.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vsu_65307/10_2026/9vsu_65307.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9vsu_65307/10_2026/9vsu_65307.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vsu_65307/10_2026/9vsu_65307.map" model { file = "/net/cci-nas-00/data/ceres_data/9vsu_65307/10_2026/9vsu_65307.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vsu_65307/10_2026/9vsu_65307.cif" } resolution = 2.82 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= 0.062 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: 4 Type Number sf(0) Gaussians S 62 5.16 5 C 6553 2.51 5 N 1668 2.21 5 O 1845 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 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: 10128 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 10071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1261, 10071 Classifications: {'peptide': 1261} Link IDs: {'PTRANS': 53, 'TRANS': 1207} Chain breaks: 3 Chain: "A" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 57 Unusual residues: {'FK5': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.00, per 1000 atoms: 0.20 Number of scatterers: 10128 At special positions: 0 Unit cell: (75.331, 106.1, 144.296, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 62 16.00 O 1845 8.00 N 1668 7.00 C 6553 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: 0.84 Conformation dependent library (CDL) restraints added in 318.2 milliseconds 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2352 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 7 sheets defined 61.0% alpha, 7.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 192 through 201 Processing helix chain 'A' and resid 221 through 228 Processing helix chain 'A' and resid 247 through 258 Processing helix chain 'A' and resid 270 through 285 Processing helix chain 'A' and resid 287 through 291 removed outlier: 3.740A pdb=" N ARG A 291 " --> pdb=" O SER A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 319 Processing helix chain 'A' and resid 334 through 353 removed outlier: 3.504A pdb=" N LEU A 339 " --> pdb=" O SER A 335 " (cutoff:3.500A) removed outlier: 3.580A 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: 4.531A pdb=" N LYS A 392 " --> pdb=" O ALA A 388 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N GLU A 393 " --> pdb=" O THR A 389 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE A 395 " --> pdb=" O ALA A 391 " (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 462 removed outlier: 3.610A pdb=" N LYS A 453 " --> pdb=" O ALA A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 511 Processing helix chain 'A' and resid 512 through 533 removed outlier: 3.625A pdb=" N ILE A 516 " --> pdb=" O PRO A 512 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL A 532 " --> pdb=" O ILE A 528 " (cutoff:3.500A) removed outlier: 3.704A 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 560 Processing helix chain 'A' and resid 561 through 563 No H-bonds generated for 'chain 'A' and resid 561 through 563' Processing helix chain 'A' and resid 564 through 581 removed outlier: 3.802A pdb=" N LEU A 568 " --> pdb=" O GLU A 564 " (cutoff:3.500A) Proline residue: A 573 - end of helix Processing helix chain 'A' and resid 585 through 597 Processing helix chain 'A' and resid 597 through 617 removed outlier: 3.895A pdb=" N VAL A 611 " --> pdb=" O SER A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 648 Processing helix chain 'A' and resid 652 through 670 Proline residue: A 659 - end of helix removed outlier: 5.022A pdb=" N VAL A 662 " --> pdb=" O THR A 658 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N LEU A 663 " --> pdb=" O PRO A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 676 through 680 Processing helix chain 'A' and resid 681 through 683 No H-bonds generated for 'chain 'A' and resid 681 through 683' Processing helix chain 'A' and resid 684 through 690 removed outlier: 3.875A pdb=" N ASN A 688 " --> pdb=" O SER A 684 " (cutoff:3.500A) Processing helix chain 'A' and resid 692 through 706 removed outlier: 3.893A pdb=" N VAL A 696 " --> pdb=" O PRO A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 757 through 760 Processing helix chain 'A' and resid 761 through 784 removed outlier: 3.671A pdb=" N LEU A 765 " --> pdb=" O LYS A 761 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU A 784 " --> pdb=" O ILE A 780 " (cutoff:3.500A) Processing helix chain 'A' and resid 900 through 909 Processing helix chain 'A' and resid 932 through 936 Processing helix chain 'A' and resid 951 through 964 removed outlier: 3.612A pdb=" N SER A 959 " --> pdb=" O ALA A 955 " (cutoff:3.500A) Processing helix chain 'A' and resid 969 through 984 Processing helix chain 'A' and resid 1002 through 1016 removed outlier: 3.561A 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 removed outlier: 3.892A pdb=" N LEU A1117 " --> pdb=" O ALA A1113 " (cutoff:3.500A) Processing helix chain 'A' and resid 1131 through 1138 Processing helix chain 'A' and resid 1139 through 1156 removed outlier: 3.555A pdb=" N GLN A1143 " --> pdb=" O SER A1139 " (cutoff:3.500A) Processing helix chain 'A' and resid 1157 through 1159 No H-bonds generated for 'chain 'A' and resid 1157 through 1159' Processing helix chain 'A' and resid 1164 through 1169 removed outlier: 3.812A pdb=" N LEU A1168 " --> pdb=" O ASP A1164 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU A1169 " --> pdb=" O PRO A1165 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1164 through 1169' Processing helix chain 'A' and resid 1174 through 1193 Processing helix chain 'A' and resid 1196 through 1215 removed outlier: 3.622A pdb=" N PHE A1215 " --> pdb=" O ASN A1211 " (cutoff:3.500A) Processing helix chain 'A' and resid 1221 through 1234 removed outlier: 3.865A pdb=" N GLN A1226 " --> pdb=" O MET A1222 " (cutoff:3.500A) 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 Proline residue: A1248 - end of helix Processing helix chain 'A' and resid 1268 through 1296 removed outlier: 4.004A pdb=" N GLU A1280 " --> pdb=" O GLN A1276 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ILE A1281 " --> pdb=" O ILE A1277 " (cutoff:3.500A) Proline residue: A1282 - end of helix Processing helix chain 'A' and resid 1300 through 1304 Processing helix chain 'A' and resid 1305 through 1309 Processing helix chain 'A' and resid 1310 through 1339 removed outlier: 4.135A pdb=" N PHE A1339 " --> pdb=" O LEU A1335 " (cutoff:3.500A) Processing helix chain 'A' and resid 1342 through 1360 removed outlier: 3.597A 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 removed outlier: 3.606A pdb=" N TYR A1378 " --> pdb=" O TRP A1374 " (cutoff:3.500A) Processing helix chain 'A' and resid 1381 through 1396 removed outlier: 3.944A pdb=" N TYR A1385 " --> pdb=" O ASN A1381 " (cutoff:3.500A) Processing helix chain 'A' and resid 1403 through 1407 removed outlier: 3.572A pdb=" N TYR A1407 " --> pdb=" O GLU A1404 " (cutoff:3.500A) Processing helix chain 'A' and resid 1417 through 1421 Processing helix chain 'A' and resid 1422 through 1430 removed outlier: 3.902A pdb=" N PHE A1428 " --> pdb=" O PRO A1424 " (cutoff:3.500A) Processing helix chain 'A' and resid 1448 through 1456 removed outlier: 4.046A pdb=" N PHE A1452 " --> pdb=" O SER A1448 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER A1455 " --> pdb=" O THR A1451 " (cutoff:3.500A) Processing helix chain 'A' and resid 1459 through 1461 No H-bonds generated for 'chain 'A' and resid 1459 through 1461' Processing helix chain 'A' and resid 1462 through 1490 removed outlier: 3.535A pdb=" N VAL A1490 " --> pdb=" O TRP A1486 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 175 through 177 removed outlier: 3.531A pdb=" N THR A 216 " --> pdb=" O GLY A 124 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 130 through 131 Processing sheet with id=AA3, first strand: chain 'A' and resid 233 through 236 removed outlier: 6.139A pdb=" N GLN A 324 " --> pdb=" O LEU A 357 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N ALA A 359 " --> pdb=" O GLN A 324 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N TRP A 326 " --> pdb=" O ALA A 359 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N VAL A 374 " --> pdb=" O PHE A 385 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N PHE A 385 " --> pdb=" O VAL A 374 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N VAL A 376 " --> pdb=" O ILE A 383 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 709 through 711 Processing sheet with id=AA5, first strand: chain 'A' and resid 875 through 885 removed outlier: 5.089A pdb=" N VAL A 876 " --> pdb=" O VAL A 868 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N VAL A 868 " --> pdb=" O VAL A 876 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N LEU A 864 " --> pdb=" O HIS A 880 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ASP A 882 " --> pdb=" O ARG A 862 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ARG A 862 " --> pdb=" O ASP A 882 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N TRP A 884 " --> pdb=" O PHE A 860 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N PHE A 860 " --> pdb=" O TRP A 884 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N LEU A 864 " --> pdb=" O ASP A 919 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ASP A 919 " --> pdb=" O LEU A 864 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N TYR A 866 " --> pdb=" O ILE A 917 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ILE A 917 " --> pdb=" O TYR A 866 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N VAL A 868 " --> pdb=" O GLY A 915 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N GLY A 915 " --> pdb=" O VAL A 868 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 937 through 940 removed outlier: 6.267A pdb=" N GLY A 938 " --> pdb=" O PHE A1024 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N ASP A1026 " --> pdb=" O GLY A 938 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N VAL A 940 " --> pdb=" O ASP A1026 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N LEU A1023 " --> pdb=" O LEU A1055 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N THR A1057 " --> pdb=" O LEU A1023 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N LEU A1025 " --> pdb=" O THR A1057 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ILE A 890 " --> pdb=" O ARG A1071 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N LEU A1073 " --> pdb=" O ILE A 890 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ALA A 892 " --> pdb=" O LEU A1073 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N LEU A1075 " --> pdb=" O ALA A 892 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N MET A 894 " --> pdb=" O LEU A1075 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N LEU A1072 " --> pdb=" O PHE A1084 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N PHE A1084 " --> pdb=" O LEU A1072 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N PHE A1074 " --> pdb=" O ALA A1082 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1408 through 1410 removed outlier: 3.502A pdb=" N CYS A1441 " --> pdb=" O VAL A1410 " (cutoff:3.500A) 536 hydrogen bonds defined for protein. 1548 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: 1.82 Time building geometry restraints manager: 1.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1603 1.30 - 1.43: 2937 1.43 - 1.55: 5755 1.55 - 1.68: 0 1.68 - 1.81: 101 Bond restraints: 10396 Sorted by residual: bond pdb=" C8 FK5 A1601 " pdb=" C9 FK5 A1601 " ideal model delta sigma weight residual 1.537 1.304 0.233 2.00e-02 2.50e+03 1.36e+02 bond pdb=" C17 FK5 A1601 " pdb=" C18 FK5 A1601 " ideal model delta sigma weight residual 1.541 1.475 0.066 2.00e-02 2.50e+03 1.09e+01 bond pdb=" N ILE A1237 " pdb=" CA ILE A1237 " ideal model delta sigma weight residual 1.461 1.494 -0.032 1.23e-02 6.61e+03 6.98e+00 bond pdb=" N PHE A1236 " pdb=" CA PHE A1236 " ideal model delta sigma weight residual 1.458 1.487 -0.029 1.14e-02 7.69e+03 6.39e+00 bond pdb=" N GLU A 379 " pdb=" CA GLU A 379 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.29e-02 6.01e+03 5.75e+00 ... (remaining 10391 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.56: 13957 2.56 - 5.13: 128 5.13 - 7.69: 18 7.69 - 10.26: 1 10.26 - 12.82: 3 Bond angle restraints: 14107 Sorted by residual: angle pdb=" C10 FK5 A1601 " pdb=" O5 FK5 A1601 " pdb=" C14 FK5 A1601 " ideal model delta sigma weight residual 114.33 127.15 -12.82 3.00e+00 1.11e-01 1.83e+01 angle pdb=" C26 FK5 A1601 " pdb=" C27 FK5 A1601 " pdb=" C28 FK5 A1601 " ideal model delta sigma weight residual 118.21 129.18 -10.97 3.00e+00 1.11e-01 1.34e+01 angle pdb=" C ASN A 203 " pdb=" CA ASN A 203 " pdb=" CB ASN A 203 " ideal model delta sigma weight residual 111.83 117.57 -5.74 1.60e+00 3.91e-01 1.29e+01 angle pdb=" N GLY A 380 " pdb=" CA GLY A 380 " pdb=" C GLY A 380 " ideal model delta sigma weight residual 115.27 110.24 5.03 1.41e+00 5.03e-01 1.27e+01 angle pdb=" O5 FK5 A1601 " pdb=" C10 FK5 A1601 " pdb=" O6 FK5 A1601 " ideal model delta sigma weight residual 110.97 100.37 10.60 3.00e+00 1.11e-01 1.25e+01 ... (remaining 14102 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.95: 5960 35.95 - 71.90: 180 71.90 - 107.85: 18 107.85 - 143.80: 6 143.80 - 179.75: 12 Dihedral angle restraints: 6176 sinusoidal: 2498 harmonic: 3678 Sorted by residual: dihedral pdb=" CB CYS A1418 " pdb=" SG CYS A1418 " pdb=" SG CYS A1441 " pdb=" CB CYS A1441 " ideal model delta sinusoidal sigma weight residual -86.00 -175.33 89.33 1 1.00e+01 1.00e-02 9.49e+01 dihedral pdb=" C3 FK5 A1601 " pdb=" C1 FK5 A1601 " pdb=" C2 FK5 A1601 " pdb=" O1 FK5 A1601 " ideal model delta sinusoidal sigma weight residual 222.70 42.95 179.75 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" N7 FK5 A1601 " pdb=" C1 FK5 A1601 " pdb=" C2 FK5 A1601 " pdb=" O1 FK5 A1601 " ideal model delta sinusoidal sigma weight residual -10.67 167.48 -178.15 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 6173 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.109: 1494 0.109 - 0.217: 36 0.217 - 0.325: 2 0.325 - 0.434: 0 0.434 - 0.542: 1 Chirality restraints: 1533 Sorted by residual: chirality pdb=" C10 FK5 A1601 " pdb=" C11 FK5 A1601 " pdb=" C9 FK5 A1601 " pdb=" O5 FK5 A1601 " both_signs ideal model delta sigma weight residual False 2.69 2.15 0.54 2.00e-01 2.50e+01 7.36e+00 chirality pdb=" C29 FK5 A1601 " pdb=" C28 FK5 A1601 " pdb=" C30 FK5 A1601 " pdb=" C34 FK5 A1601 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CA ASN A 203 " pdb=" N ASN A 203 " pdb=" C ASN A 203 " pdb=" CB ASN A 203 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.26e+00 ... (remaining 1530 not shown) Planarity restraints: 1794 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C26 FK5 A1601 " 0.225 2.00e-02 2.50e+03 3.38e-01 1.43e+03 pdb=" C27 FK5 A1601 " -0.188 2.00e-02 2.50e+03 pdb=" C28 FK5 A1601 " -0.553 2.00e-02 2.50e+03 pdb=" C29 FK5 A1601 " 0.409 2.00e-02 2.50e+03 pdb=" C42 FK5 A1601 " 0.107 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 FK5 A1601 " 0.162 2.00e-02 2.50e+03 1.32e-01 2.63e+02 pdb=" C6 FK5 A1601 " -0.135 2.00e-02 2.50e+03 pdb=" C8 FK5 A1601 " -0.006 2.00e-02 2.50e+03 pdb=" C9 FK5 A1601 " 0.170 2.00e-02 2.50e+03 pdb=" N7 FK5 A1601 " -0.012 2.00e-02 2.50e+03 pdb=" O3 FK5 A1601 " -0.178 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C18 FK5 A1601 " 0.016 2.00e-02 2.50e+03 7.18e-02 6.45e+01 pdb=" C19 FK5 A1601 " 0.024 2.00e-02 2.50e+03 pdb=" C20 FK5 A1601 " 0.114 2.00e-02 2.50e+03 pdb=" C21 FK5 A1601 " -0.087 2.00e-02 2.50e+03 pdb=" C37 FK5 A1601 " -0.067 2.00e-02 2.50e+03 ... (remaining 1791 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 345 2.71 - 3.25: 10081 3.25 - 3.80: 17320 3.80 - 4.35: 23352 4.35 - 4.90: 38480 Nonbonded interactions: 89578 Sorted by model distance: nonbonded pdb=" OG SER A 247 " pdb=" O ARG A 291 " model vdw 2.157 3.040 nonbonded pdb=" O GLY A1195 " pdb=" OG SER A1199 " model vdw 2.225 3.040 nonbonded pdb=" O ALA A1389 " pdb=" OG1 THR A1393 " model vdw 2.240 3.040 nonbonded pdb=" O MET A 657 " pdb=" OG1 THR A 661 " model vdw 2.243 3.040 nonbonded pdb=" NZ LYS A 886 " pdb=" OE2 GLU A1148 " model vdw 2.246 3.120 ... (remaining 89573 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: 2.580 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.670 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 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:8.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 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 : 0.006 0.233 10399 Z= 0.262 Angle : 0.652 12.820 14113 Z= 0.335 Chirality : 0.048 0.542 1533 Planarity : 0.010 0.338 1794 Dihedral : 19.420 179.747 3815 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.95 % Allowed : 14.68 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.23), residues: 1253 helix: 0.70 (0.19), residues: 688 sheet: -0.58 (0.51), residues: 96 loop : -0.99 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 503 TYR 0.021 0.002 TYR A1297 PHE 0.019 0.002 PHE A 860 TRP 0.013 0.002 TRP A1038 HIS 0.002 0.001 HIS A 946 Details of bonding type rmsd/Z covalent geometry : bond 0.00584 / 0.26 (10396) covalent geometry : angle 0.65155 / 0.33 (14107) SS BOND : bond 0.00345 / 0.18 ( 3) SS BOND : angle 1.15233 / 0.67 ( 6) hydrogen bonds : bond 0.15886 / 9.91 ( 536) hydrogen bonds : angle 6.41508 / 4.75 ( 1548) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 133 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1086 GLU cc_start: 0.8155 (mm-30) cc_final: 0.7943 (mm-30) outliers start: 21 outliers final: 16 residues processed: 149 average time/residue: 0.5162 time to fit residues: 83.1856 Evaluate side-chains 146 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 130 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 397 LYS Chi-restraints excluded: chain A residue 567 SER Chi-restraints excluded: chain A residue 677 THR Chi-restraints excluded: chain A residue 903 THR Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 917 ILE Chi-restraints excluded: chain A residue 1022 LEU Chi-restraints excluded: chain A residue 1056 CYS Chi-restraints excluded: chain A residue 1402 CYS Chi-restraints excluded: chain A residue 1417 SER Chi-restraints excluded: chain A residue 1418 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: [108, 49, 97, 113, 53, 5, 33, 123, 65, 62, 51] chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 0.1980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 297 ASN A 417 ASN ** A 760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 867 GLN A 946 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.142441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.119611 restraints weight = 10763.228| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 1.36 r_work: 0.3266 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.0700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10399 Z= 0.190 Angle : 0.599 11.370 14113 Z= 0.300 Chirality : 0.045 0.310 1533 Planarity : 0.004 0.041 1794 Dihedral : 17.014 168.264 1519 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.79 % Allowed : 13.29 % Favored : 83.92 % 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: 0.16 (0.23), residues: 1253 helix: 0.96 (0.19), residues: 691 sheet: -0.52 (0.51), residues: 97 loop : -0.99 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 862 TYR 0.022 0.002 TYR A1297 PHE 0.021 0.002 PHE A 860 TRP 0.010 0.001 TRP A 634 HIS 0.002 0.001 HIS A 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.19 (10396) covalent geometry : angle 0.59902 / 0.30 (14107) SS BOND : bond 0.00403 / 0.20 ( 3) SS BOND : angle 0.87069 / 0.45 ( 6) hydrogen bonds : bond 0.04423 / 2.87 ( 536) hydrogen bonds : angle 4.83548 / 3.55 ( 1548) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 144 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 422 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.7284 (tt0) REVERT: A 934 GLN cc_start: 0.8389 (OUTLIER) cc_final: 0.7840 (mp10) REVERT: A 1086 GLU cc_start: 0.8260 (mm-30) cc_final: 0.7986 (mm-30) REVERT: A 1427 LYS cc_start: 0.7887 (ttpt) cc_final: 0.7671 (ttmt) REVERT: A 1434 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.7362 (mt-10) outliers start: 30 outliers final: 13 residues processed: 165 average time/residue: 0.5343 time to fit residues: 95.0226 Evaluate side-chains 148 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 132 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 422 GLU Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 677 THR Chi-restraints excluded: chain A residue 903 THR Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 934 GLN Chi-restraints excluded: chain A residue 1013 VAL Chi-restraints excluded: chain A residue 1020 LYS Chi-restraints excluded: chain A residue 1022 LEU Chi-restraints excluded: chain A residue 1056 CYS Chi-restraints excluded: chain A residue 1369 VAL Chi-restraints excluded: chain A residue 1402 CYS Chi-restraints excluded: chain A residue 1434 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: [91, 40, 99, 38, 83, 12, 46, 121, 22, 63, 4] chunk 91 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 83 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 121 optimal weight: 0.2980 chunk 22 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 4 optimal weight: 0.2980 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 297 ASN A 760 HIS A 867 GLN A 946 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.146015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.122270 restraints weight = 10756.320| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 1.44 r_work: 0.3292 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.0972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10399 Z= 0.122 Angle : 0.516 10.751 14113 Z= 0.260 Chirality : 0.042 0.338 1533 Planarity : 0.004 0.040 1794 Dihedral : 15.658 159.135 1504 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.51 % Allowed : 15.06 % Favored : 82.43 % 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: 0.51 (0.24), residues: 1253 helix: 1.32 (0.19), residues: 686 sheet: -0.36 (0.52), residues: 97 loop : -0.94 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 862 TYR 0.015 0.001 TYR A1297 PHE 0.014 0.001 PHE A 860 TRP 0.012 0.001 TRP A 634 HIS 0.003 0.000 HIS A 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (10396) covalent geometry : angle 0.51548 / 0.26 (14107) SS BOND : bond 0.00459 / 0.23 ( 3) SS BOND : angle 0.60303 / 0.29 ( 6) hydrogen bonds : bond 0.03628 / 2.36 ( 536) hydrogen bonds : angle 4.45531 / 3.27 ( 1548) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 143 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 934 GLN cc_start: 0.8343 (OUTLIER) cc_final: 0.7760 (mp10) REVERT: A 1086 GLU cc_start: 0.8231 (mm-30) cc_final: 0.7956 (mm-30) REVERT: A 1427 LYS cc_start: 0.7843 (ttpt) cc_final: 0.7618 (ttmt) REVERT: A 1434 GLU cc_start: 0.7643 (OUTLIER) cc_final: 0.7408 (mt-10) outliers start: 27 outliers final: 10 residues processed: 161 average time/residue: 0.5221 time to fit residues: 90.8730 Evaluate side-chains 142 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 130 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 353 ASP Chi-restraints excluded: chain A residue 525 MET Chi-restraints excluded: chain A residue 677 THR Chi-restraints excluded: chain A residue 903 THR Chi-restraints excluded: chain A residue 934 GLN Chi-restraints excluded: chain A residue 1020 LYS Chi-restraints excluded: chain A residue 1022 LEU Chi-restraints excluded: chain A residue 1369 VAL Chi-restraints excluded: chain A residue 1402 CYS Chi-restraints excluded: chain A residue 1434 GLU Chi-restraints excluded: chain A residue 1435 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: [11, 92, 36, 43, 6, 104, 40, 88, 109, 112, 120] chunk 11 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 36 optimal weight: 6.9990 chunk 43 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 chunk 112 optimal weight: 0.9990 chunk 120 optimal weight: 0.4980 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 297 ASN A 417 ASN A 867 GLN A 946 HIS ** A1253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.140925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.120038 restraints weight = 10861.912| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 1.20 r_work: 0.3203 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.0884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 10399 Z= 0.249 Angle : 0.618 10.379 14113 Z= 0.313 Chirality : 0.047 0.344 1533 Planarity : 0.005 0.044 1794 Dihedral : 15.591 159.915 1502 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.81 % Allowed : 14.41 % Favored : 81.78 % 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: 0.21 (0.23), residues: 1253 helix: 1.03 (0.19), residues: 685 sheet: -0.47 (0.50), residues: 97 loop : -0.99 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 227 TYR 0.024 0.002 TYR A1297 PHE 0.023 0.002 PHE A 860 TRP 0.009 0.002 TRP A1191 HIS 0.003 0.001 HIS A 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00599 / 0.25 (10396) covalent geometry : angle 0.61743 / 0.31 (14107) SS BOND : bond 0.00473 / 0.23 ( 3) SS BOND : angle 1.22633 / 0.71 ( 6) hydrogen bonds : bond 0.04460 / 2.91 ( 536) hydrogen bonds : angle 4.68258 / 3.43 ( 1548) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 138 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 273 TYR cc_start: 0.8594 (t80) cc_final: 0.8320 (t80) REVERT: A 353 ASP cc_start: 0.7645 (OUTLIER) cc_final: 0.7381 (m-30) REVERT: A 422 GLU cc_start: 0.7593 (OUTLIER) cc_final: 0.7206 (tt0) REVERT: A 471 TYR cc_start: 0.3791 (OUTLIER) cc_final: 0.2828 (t80) REVERT: A 934 GLN cc_start: 0.8368 (OUTLIER) cc_final: 0.7802 (mp10) REVERT: A 1086 GLU cc_start: 0.8202 (mm-30) cc_final: 0.7933 (mm-30) REVERT: A 1332 MET cc_start: 0.8415 (OUTLIER) cc_final: 0.7712 (tpt) REVERT: A 1411 LYS cc_start: 0.7922 (OUTLIER) cc_final: 0.7546 (tppp) REVERT: A 1427 LYS cc_start: 0.7865 (ttpt) cc_final: 0.7654 (ttmt) REVERT: A 1434 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.7398 (mt-10) outliers start: 41 outliers final: 18 residues processed: 164 average time/residue: 0.5080 time to fit residues: 89.8984 Evaluate side-chains 155 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 130 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 353 ASP Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 422 GLU Chi-restraints excluded: chain A residue 471 TYR Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 525 MET Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 677 THR Chi-restraints excluded: chain A residue 783 THR Chi-restraints excluded: chain A residue 903 THR Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 934 GLN Chi-restraints excluded: chain A residue 1013 VAL Chi-restraints excluded: chain A residue 1020 LYS Chi-restraints excluded: chain A residue 1022 LEU Chi-restraints excluded: chain A residue 1332 MET Chi-restraints excluded: chain A residue 1369 VAL Chi-restraints excluded: chain A residue 1402 CYS Chi-restraints excluded: chain A residue 1411 LYS Chi-restraints excluded: chain A residue 1434 GLU Chi-restraints excluded: chain A residue 1435 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: [81, 50, 24, 71, 58, 78, 41, 6, 75, 35, 33] chunk 81 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 35 optimal weight: 7.9990 chunk 33 optimal weight: 0.6980 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 297 ASN A 867 GLN A 946 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.142755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.119660 restraints weight = 10725.833| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 1.37 r_work: 0.3265 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.0965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10399 Z= 0.175 Angle : 0.556 9.739 14113 Z= 0.282 Chirality : 0.044 0.335 1533 Planarity : 0.004 0.041 1794 Dihedral : 15.270 158.994 1502 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.25 % Allowed : 15.61 % Favored : 81.13 % 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: 0.38 (0.23), residues: 1253 helix: 1.18 (0.19), residues: 685 sheet: -0.41 (0.50), residues: 97 loop : -0.93 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 227 TYR 0.022 0.002 TYR A1297 PHE 0.020 0.002 PHE A 860 TRP 0.011 0.001 TRP A 634 HIS 0.002 0.001 HIS A 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.18 (10396) covalent geometry : angle 0.55532 / 0.28 (14107) SS BOND : bond 0.00393 / 0.19 ( 3) SS BOND : angle 0.90436 / 0.51 ( 6) hydrogen bonds : bond 0.03929 / 2.56 ( 536) hydrogen bonds : angle 4.51918 / 3.31 ( 1548) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 141 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 273 TYR cc_start: 0.8650 (t80) cc_final: 0.8353 (t80) REVERT: A 353 ASP cc_start: 0.7725 (OUTLIER) cc_final: 0.7479 (m-30) REVERT: A 422 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.7279 (tt0) REVERT: A 471 TYR cc_start: 0.3862 (OUTLIER) cc_final: 0.3075 (t80) REVERT: A 934 GLN cc_start: 0.8362 (OUTLIER) cc_final: 0.7806 (mp10) REVERT: A 1086 GLU cc_start: 0.8252 (mm-30) cc_final: 0.7949 (mm-30) REVERT: A 1434 GLU cc_start: 0.7636 (OUTLIER) cc_final: 0.7417 (mt-10) outliers start: 35 outliers final: 18 residues processed: 164 average time/residue: 0.5182 time to fit residues: 92.0633 Evaluate side-chains 158 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 135 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 353 ASP Chi-restraints excluded: chain A residue 422 GLU Chi-restraints excluded: chain A residue 461 GLU Chi-restraints excluded: chain A residue 471 TYR Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 525 MET Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 677 THR Chi-restraints excluded: chain A residue 783 THR Chi-restraints excluded: chain A residue 903 THR Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 917 ILE Chi-restraints excluded: chain A residue 934 GLN Chi-restraints excluded: chain A residue 1013 VAL Chi-restraints excluded: chain A residue 1020 LYS Chi-restraints excluded: chain A residue 1022 LEU Chi-restraints excluded: chain A residue 1369 VAL Chi-restraints excluded: chain A residue 1402 CYS Chi-restraints excluded: chain A residue 1434 GLU Chi-restraints excluded: chain A residue 1435 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: [41, 115, 35, 82, 113, 28, 7, 86, 63, 51, 97] chunk 41 optimal weight: 1.9990 chunk 115 optimal weight: 0.9980 chunk 35 optimal weight: 7.9990 chunk 82 optimal weight: 2.9990 chunk 113 optimal weight: 0.5980 chunk 28 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 86 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 51 optimal weight: 0.1980 chunk 97 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 297 ASN A 417 ASN A 867 GLN A 946 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.144450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.123709 restraints weight = 10788.229| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 1.20 r_work: 0.3210 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 2.80 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10399 Z= 0.140 Angle : 0.525 10.496 14113 Z= 0.266 Chirality : 0.043 0.315 1533 Planarity : 0.004 0.041 1794 Dihedral : 14.857 158.720 1502 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 3.16 % Allowed : 15.99 % Favored : 80.86 % 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: 0.54 (0.23), residues: 1253 helix: 1.33 (0.19), residues: 687 sheet: -0.33 (0.50), residues: 97 loop : -0.90 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 227 TYR 0.017 0.001 TYR A1297 PHE 0.016 0.001 PHE A 860 TRP 0.012 0.001 TRP A 634 HIS 0.003 0.001 HIS A 760 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 (10396) covalent geometry : angle 0.52466 / 0.27 (14107) SS BOND : bond 0.00332 / 0.16 ( 3) SS BOND : angle 0.75620 / 0.42 ( 6) hydrogen bonds : bond 0.03611 / 2.35 ( 536) hydrogen bonds : angle 4.38237 / 3.21 ( 1548) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 142 time to evaluate : 0.365 Fit side-chains revert: symmetry clash REVERT: A 273 TYR cc_start: 0.8583 (t80) cc_final: 0.8327 (t80) REVERT: A 353 ASP cc_start: 0.7703 (OUTLIER) cc_final: 0.7421 (m-30) REVERT: A 422 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.7213 (tt0) REVERT: A 471 TYR cc_start: 0.3701 (OUTLIER) cc_final: 0.2938 (t80) REVERT: A 525 MET cc_start: 0.6981 (OUTLIER) cc_final: 0.6449 (mmt) REVERT: A 934 GLN cc_start: 0.8309 (OUTLIER) cc_final: 0.7726 (mp10) REVERT: A 1086 GLU cc_start: 0.8185 (mm-30) cc_final: 0.7903 (mm-30) REVERT: A 1434 GLU cc_start: 0.7669 (OUTLIER) cc_final: 0.7409 (mt-10) outliers start: 34 outliers final: 15 residues processed: 162 average time/residue: 0.5223 time to fit residues: 91.5581 Evaluate side-chains 156 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 135 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 353 ASP Chi-restraints excluded: chain A residue 422 GLU Chi-restraints excluded: chain A residue 461 GLU Chi-restraints excluded: chain A residue 471 TYR Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 525 MET Chi-restraints excluded: chain A residue 677 THR Chi-restraints excluded: chain A residue 783 THR Chi-restraints excluded: chain A residue 903 THR Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 917 ILE Chi-restraints excluded: chain A residue 934 GLN Chi-restraints excluded: chain A residue 996 VAL Chi-restraints excluded: chain A residue 1013 VAL Chi-restraints excluded: chain A residue 1020 LYS Chi-restraints excluded: chain A residue 1022 LEU Chi-restraints excluded: chain A residue 1369 VAL Chi-restraints excluded: chain A residue 1434 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: [108, 17, 22, 78, 6, 91, 49, 93, 25, 72, 74] chunk 108 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 22 optimal weight: 0.6980 chunk 78 optimal weight: 0.2980 chunk 6 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 93 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 72 optimal weight: 0.5980 chunk 74 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 297 ASN A 867 GLN A 946 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.146017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.121159 restraints weight = 10726.798| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 1.54 r_work: 0.3185 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.1177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10399 Z= 0.128 Angle : 0.515 11.164 14113 Z= 0.261 Chirality : 0.043 0.309 1533 Planarity : 0.004 0.041 1794 Dihedral : 14.529 158.829 1501 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.62 % Allowed : 15.43 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.24), residues: 1253 helix: 1.46 (0.19), residues: 687 sheet: -0.22 (0.50), residues: 97 loop : -0.90 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 227 TYR 0.017 0.001 TYR A1297 PHE 0.014 0.001 PHE A 860 TRP 0.011 0.001 TRP A 634 HIS 0.004 0.001 HIS A 760 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (10396) covalent geometry : angle 0.51538 / 0.26 (14107) SS BOND : bond 0.00295 / 0.14 ( 3) SS BOND : angle 0.61938 / 0.37 ( 6) hydrogen bonds : bond 0.03478 / 2.26 ( 536) hydrogen bonds : angle 4.30726 / 3.16 ( 1548) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 141 time to evaluate : 0.310 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 273 TYR cc_start: 0.8570 (t80) cc_final: 0.8284 (t80) REVERT: A 422 GLU cc_start: 0.7629 (OUTLIER) cc_final: 0.7247 (tt0) REVERT: A 457 GLU cc_start: 0.7377 (mt-10) cc_final: 0.7078 (mt-10) REVERT: A 459 PHE cc_start: 0.8147 (m-80) cc_final: 0.7867 (m-80) REVERT: A 463 GLU cc_start: 0.5883 (OUTLIER) cc_final: 0.5671 (mp0) REVERT: A 471 TYR cc_start: 0.3771 (OUTLIER) cc_final: 0.2984 (t80) REVERT: A 525 MET cc_start: 0.7070 (OUTLIER) cc_final: 0.6494 (mmt) REVERT: A 934 GLN cc_start: 0.8289 (OUTLIER) cc_final: 0.7708 (mp10) REVERT: A 1086 GLU cc_start: 0.8270 (mm-30) cc_final: 0.7999 (mm-30) REVERT: A 1434 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.7411 (mt-10) outliers start: 39 outliers final: 20 residues processed: 167 average time/residue: 0.5313 time to fit residues: 95.6741 Evaluate side-chains 162 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 136 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 353 ASP Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 422 GLU Chi-restraints excluded: chain A residue 463 GLU Chi-restraints excluded: chain A residue 471 TYR Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 525 MET Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 677 THR Chi-restraints excluded: chain A residue 783 THR Chi-restraints excluded: chain A residue 903 THR Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 917 ILE Chi-restraints excluded: chain A residue 934 GLN Chi-restraints excluded: chain A residue 996 VAL Chi-restraints excluded: chain A residue 1013 VAL Chi-restraints excluded: chain A residue 1020 LYS Chi-restraints excluded: chain A residue 1022 LEU Chi-restraints excluded: chain A residue 1369 VAL Chi-restraints excluded: chain A residue 1402 CYS Chi-restraints excluded: chain A residue 1427 LYS Chi-restraints excluded: chain A residue 1434 GLU Chi-restraints excluded: chain A residue 1435 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: [9, 45, 84, 106, 80, 59, 117, 27, 63, 102, 1] chunk 9 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 84 optimal weight: 0.9980 chunk 106 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 117 optimal weight: 0.5980 chunk 27 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 chunk 102 optimal weight: 0.5980 chunk 1 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 297 ASN A 867 GLN A 946 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.144988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.124195 restraints weight = 10662.677| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 1.20 r_work: 0.3216 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.1180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10399 Z= 0.142 Angle : 0.528 11.009 14113 Z= 0.267 Chirality : 0.043 0.301 1533 Planarity : 0.004 0.042 1794 Dihedral : 14.468 158.718 1501 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.97 % Allowed : 16.36 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.24), residues: 1253 helix: 1.47 (0.19), residues: 687 sheet: -0.16 (0.51), residues: 97 loop : -0.88 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 227 TYR 0.018 0.001 TYR A1297 PHE 0.017 0.002 PHE A 860 TRP 0.010 0.001 TRP A 634 HIS 0.003 0.001 HIS A 760 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 (10396) covalent geometry : angle 0.52804 / 0.27 (14107) SS BOND : bond 0.00321 / 0.16 ( 3) SS BOND : angle 0.68423 / 0.40 ( 6) hydrogen bonds : bond 0.03576 / 2.33 ( 536) hydrogen bonds : angle 4.31375 / 3.16 ( 1548) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 144 time to evaluate : 0.401 Fit side-chains revert: symmetry clash REVERT: A 252 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.8027 (mp) REVERT: A 273 TYR cc_start: 0.8600 (t80) cc_final: 0.8297 (t80) REVERT: A 422 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.7192 (tt0) REVERT: A 459 PHE cc_start: 0.8166 (m-80) cc_final: 0.7959 (m-80) REVERT: A 471 TYR cc_start: 0.3788 (OUTLIER) cc_final: 0.3203 (t80) REVERT: A 525 MET cc_start: 0.7026 (OUTLIER) cc_final: 0.6499 (mmt) REVERT: A 934 GLN cc_start: 0.8305 (OUTLIER) cc_final: 0.7723 (mp10) REVERT: A 1086 GLU cc_start: 0.8179 (mm-30) cc_final: 0.7875 (mm-30) REVERT: A 1434 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.7455 (mt-10) outliers start: 32 outliers final: 19 residues processed: 164 average time/residue: 0.5076 time to fit residues: 90.0876 Evaluate side-chains 162 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 137 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 353 ASP Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 422 GLU Chi-restraints excluded: chain A residue 461 GLU Chi-restraints excluded: chain A residue 471 TYR Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 525 MET Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 677 THR Chi-restraints excluded: chain A residue 783 THR Chi-restraints excluded: chain A residue 903 THR Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 917 ILE Chi-restraints excluded: chain A residue 934 GLN Chi-restraints excluded: chain A residue 996 VAL Chi-restraints excluded: chain A residue 1013 VAL Chi-restraints excluded: chain A residue 1020 LYS Chi-restraints excluded: chain A residue 1022 LEU Chi-restraints excluded: chain A residue 1369 VAL Chi-restraints excluded: chain A residue 1427 LYS Chi-restraints excluded: chain A residue 1434 GLU Chi-restraints excluded: chain A residue 1435 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: [14, 120, 103, 82, 96, 56, 94, 25, 20, 91, 65] chunk 14 optimal weight: 4.9990 chunk 120 optimal weight: 1.9990 chunk 103 optimal weight: 0.3980 chunk 82 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 94 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 91 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 297 ASN A 867 GLN A 946 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.145963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.121941 restraints weight = 10704.257| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 1.45 r_work: 0.3283 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.1217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10399 Z= 0.135 Angle : 0.522 10.520 14113 Z= 0.265 Chirality : 0.043 0.304 1533 Planarity : 0.004 0.041 1794 Dihedral : 14.347 158.410 1501 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.70 % Allowed : 16.45 % Favored : 80.86 % 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: 1253 helix: 1.52 (0.19), residues: 687 sheet: -0.14 (0.51), residues: 97 loop : -0.87 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 227 TYR 0.017 0.001 TYR A1297 PHE 0.016 0.001 PHE A 860 TRP 0.011 0.001 TRP A 634 HIS 0.003 0.001 HIS A 760 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (10396) covalent geometry : angle 0.52231 / 0.26 (14107) SS BOND : bond 0.00308 / 0.15 ( 3) SS BOND : angle 0.66850 / 0.39 ( 6) hydrogen bonds : bond 0.03513 / 2.29 ( 536) hydrogen bonds : angle 4.28843 / 3.15 ( 1548) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 135 time to evaluate : 0.370 Fit side-chains revert: symmetry clash REVERT: A 252 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8113 (mp) REVERT: A 273 TYR cc_start: 0.8646 (t80) cc_final: 0.8395 (t80) REVERT: A 422 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.7208 (tt0) REVERT: A 457 GLU cc_start: 0.7371 (mt-10) cc_final: 0.7109 (mt-10) REVERT: A 471 TYR cc_start: 0.3836 (OUTLIER) cc_final: 0.3226 (t80) REVERT: A 525 MET cc_start: 0.7187 (OUTLIER) cc_final: 0.6650 (mmt) REVERT: A 934 GLN cc_start: 0.8299 (OUTLIER) cc_final: 0.7716 (mp10) REVERT: A 1086 GLU cc_start: 0.8225 (mm-30) cc_final: 0.7926 (mm-30) outliers start: 29 outliers final: 19 residues processed: 153 average time/residue: 0.5583 time to fit residues: 92.0476 Evaluate side-chains 155 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 131 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 353 ASP Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 422 GLU Chi-restraints excluded: chain A residue 461 GLU Chi-restraints excluded: chain A residue 471 TYR Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 525 MET Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 677 THR Chi-restraints excluded: chain A residue 783 THR Chi-restraints excluded: chain A residue 903 THR Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 917 ILE Chi-restraints excluded: chain A residue 934 GLN Chi-restraints excluded: chain A residue 996 VAL Chi-restraints excluded: chain A residue 1013 VAL Chi-restraints excluded: chain A residue 1020 LYS Chi-restraints excluded: chain A residue 1022 LEU Chi-restraints excluded: chain A residue 1369 VAL Chi-restraints excluded: chain A residue 1427 LYS Chi-restraints excluded: chain A residue 1435 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: [79, 92, 108, 81, 16, 38, 51, 35, 22, 43, 1] chunk 79 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 108 optimal weight: 0.7980 chunk 81 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 35 optimal weight: 0.0050 chunk 22 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 297 ASN A 867 GLN A 946 HIS ** A1240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.147047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.122843 restraints weight = 10577.871| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 1.46 r_work: 0.3270 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.1274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10399 Z= 0.129 Angle : 0.516 9.141 14113 Z= 0.261 Chirality : 0.042 0.306 1533 Planarity : 0.004 0.041 1794 Dihedral : 14.167 158.702 1501 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.51 % Allowed : 16.64 % Favored : 80.86 % 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: 0.79 (0.23), residues: 1253 helix: 1.56 (0.19), residues: 687 sheet: -0.17 (0.51), residues: 97 loop : -0.85 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 227 TYR 0.017 0.001 TYR A1297 PHE 0.015 0.001 PHE A 860 TRP 0.011 0.001 TRP A 634 HIS 0.003 0.001 HIS A 760 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (10396) covalent geometry : angle 0.51543 / 0.26 (14107) SS BOND : bond 0.00281 / 0.14 ( 3) SS BOND : angle 0.66875 / 0.39 ( 6) hydrogen bonds : bond 0.03469 / 2.25 ( 536) hydrogen bonds : angle 4.26402 / 3.13 ( 1548) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 134 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 252 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8090 (mp) REVERT: A 422 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.7202 (tt0) REVERT: A 471 TYR cc_start: 0.3823 (OUTLIER) cc_final: 0.3226 (t80) REVERT: A 525 MET cc_start: 0.7223 (OUTLIER) cc_final: 0.6697 (mmp) REVERT: A 934 GLN cc_start: 0.8290 (OUTLIER) cc_final: 0.7707 (mp10) REVERT: A 1086 GLU cc_start: 0.8238 (mm-30) cc_final: 0.7966 (mm-30) outliers start: 27 outliers final: 18 residues processed: 152 average time/residue: 0.5542 time to fit residues: 90.7480 Evaluate side-chains 155 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 132 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 353 ASP Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 422 GLU Chi-restraints excluded: chain A residue 471 TYR Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 525 MET Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 677 THR Chi-restraints excluded: chain A residue 783 THR Chi-restraints excluded: chain A residue 903 THR Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 917 ILE Chi-restraints excluded: chain A residue 934 GLN Chi-restraints excluded: chain A residue 996 VAL Chi-restraints excluded: chain A residue 1020 LYS Chi-restraints excluded: chain A residue 1022 LEU Chi-restraints excluded: chain A residue 1369 VAL Chi-restraints excluded: chain A residue 1402 CYS Chi-restraints excluded: chain A residue 1427 LYS Chi-restraints excluded: chain A residue 1435 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: [50, 105, 75, 21, 90, 20, 67, 28, 94, 114, 53] chunk 50 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 90 optimal weight: 3.9990 chunk 20 optimal weight: 0.4980 chunk 67 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 94 optimal weight: 0.5980 chunk 114 optimal weight: 5.9990 chunk 53 optimal weight: 0.5980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 297 ASN A 867 GLN A 946 HIS ** A1240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.144559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.121335 restraints weight = 10642.324| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 1.38 r_work: 0.3284 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.1218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 10399 Z= 0.150 Angle : 0.531 7.600 14113 Z= 0.270 Chirality : 0.043 0.291 1533 Planarity : 0.004 0.041 1794 Dihedral : 13.925 158.731 1501 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.51 % Allowed : 16.54 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.23), residues: 1253 helix: 1.49 (0.19), residues: 687 sheet: -0.22 (0.51), residues: 97 loop : -0.84 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 227 TYR 0.019 0.002 TYR A1297 PHE 0.017 0.002 PHE A 860 TRP 0.010 0.001 TRP A 634 HIS 0.003 0.001 HIS A 760 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 (10396) covalent geometry : angle 0.53100 / 0.27 (14107) SS BOND : bond 0.00337 / 0.17 ( 3) SS BOND : angle 0.75265 / 0.44 ( 6) hydrogen bonds : bond 0.03644 / 2.37 ( 536) hydrogen bonds : angle 4.32583 / 3.17 ( 1548) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3299.59 seconds wall clock time: 57 minutes 2.89 seconds (3422.89 seconds total)