Starting phenix.real_space_refine on Thu Sep 18 06:42:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yih_39319/09_2025/8yih_39319.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yih_39319/09_2025/8yih_39319.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yih_39319/09_2025/8yih_39319.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yih_39319/09_2025/8yih_39319.map" model { file = "/net/cci-nas-00/data/ceres_data/8yih_39319/09_2025/8yih_39319.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yih_39319/09_2025/8yih_39319.cif" } resolution = 4.08 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= 0.003 sd= 0.049 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 98 5.49 5 Mg 2 5.21 5 S 68 5.16 5 C 9018 2.51 5 N 2510 2.21 5 O 2996 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14692 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 144 Classifications: {'peptide': 16} Modifications used: {'COO': 1} Link IDs: {'TRANS': 15} Chain: "A" Number of atoms: 12490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1544, 12490 Classifications: {'peptide': 1544} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 63, 'TRANS': 1480} Chain breaks: 2 Chain: "C" Number of atoms: 2029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 2029 Classifications: {'RNA': 96} Modifications used: {'rna2p_pyr': 2, 'rna3p_pur': 46, 'rna3p_pyr': 48} Link IDs: {'rna2p': 2, 'rna3p': 93} Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' MG': 2, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 3.41, per 1000 atoms: 0.23 Number of scatterers: 14692 At special positions: 0 Unit cell: (97.7522, 95.6038, 172.946, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 68 16.00 P 98 15.00 Mg 2 11.99 O 2996 8.00 N 2510 7.00 C 9018 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.34 Conformation dependent library (CDL) restraints added in 574.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2982 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 11 sheets defined 55.1% alpha, 8.8% beta 35 base pairs and 58 stacking pairs defined. Time for finding SS restraints: 2.11 Creating SS restraints... Processing helix chain 'A' and resid 9 through 22 removed outlier: 3.610A pdb=" N LEU A 13 " --> pdb=" O ARG A 9 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ARG A 14 " --> pdb=" O GLY A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 44 removed outlier: 3.525A pdb=" N ARG A 44 " --> pdb=" O LEU A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 81 Processing helix chain 'A' and resid 93 through 97 removed outlier: 3.997A pdb=" N ASP A 96 " --> pdb=" O GLY A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 108 removed outlier: 3.912A pdb=" N GLU A 105 " --> pdb=" O MET A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 125 Processing helix chain 'A' and resid 129 through 131 No H-bonds generated for 'chain 'A' and resid 129 through 131' Processing helix chain 'A' and resid 141 through 144 Processing helix chain 'A' and resid 148 through 160 removed outlier: 3.559A pdb=" N LEU A 156 " --> pdb=" O GLU A 152 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N PHE A 157 " --> pdb=" O PHE A 153 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N THR A 158 " --> pdb=" O MET A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 195 removed outlier: 4.047A pdb=" N LYS A 187 " --> pdb=" O ASN A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 213 removed outlier: 3.587A pdb=" N MET A 208 " --> pdb=" O ASP A 204 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N ASN A 210 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N VAL A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 252 removed outlier: 3.519A pdb=" N ARG A 236 " --> pdb=" O LEU A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 292 Processing helix chain 'A' and resid 293 through 314 removed outlier: 4.280A pdb=" N ILE A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N SER A 302 " --> pdb=" O ILE A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 343 Processing helix chain 'A' and resid 350 through 362 Processing helix chain 'A' and resid 364 through 379 Processing helix chain 'A' and resid 394 through 412 removed outlier: 3.790A pdb=" N CYS A 398 " --> pdb=" O ARG A 394 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS A 399 " --> pdb=" O ARG A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 452 Processing helix chain 'A' and resid 462 through 465 Processing helix chain 'A' and resid 484 through 495 removed outlier: 3.648A pdb=" N ALA A 495 " --> pdb=" O SER A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 534 removed outlier: 3.603A pdb=" N ILE A 528 " --> pdb=" O ALA A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 550 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 567 through 569 No H-bonds generated for 'chain 'A' and resid 567 through 569' Processing helix chain 'A' and resid 570 through 582 Processing helix chain 'A' and resid 598 through 606 Processing helix chain 'A' and resid 607 through 612 Processing helix chain 'A' and resid 637 through 656 Processing helix chain 'A' and resid 667 through 680 removed outlier: 3.628A pdb=" N ARG A 671 " --> pdb=" O THR A 667 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ASP A 677 " --> pdb=" O ALA A 673 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N VAL A 678 " --> pdb=" O SER A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 687 Processing helix chain 'A' and resid 692 through 697 Processing helix chain 'A' and resid 741 through 748 Processing helix chain 'A' and resid 792 through 810 removed outlier: 3.679A pdb=" N PHE A 807 " --> pdb=" O HIS A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 845 through 852 Processing helix chain 'A' and resid 862 through 869 removed outlier: 4.332A pdb=" N GLN A 868 " --> pdb=" O GLN A 864 " (cutoff:3.500A) Processing helix chain 'A' and resid 873 through 878 Processing helix chain 'A' and resid 916 through 930 removed outlier: 7.087A pdb=" N ASN A 927 " --> pdb=" O SER A 923 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ARG A 928 " --> pdb=" O LYS A 924 " (cutoff:3.500A) Processing helix chain 'A' and resid 960 through 965 removed outlier: 4.041A pdb=" N ALA A 965 " --> pdb=" O ALA A 961 " (cutoff:3.500A) Processing helix chain 'A' and resid 972 through 976 Processing helix chain 'A' and resid 982 through 990 Processing helix chain 'A' and resid 991 through 1016 removed outlier: 3.644A pdb=" N HIS A1004 " --> pdb=" O TYR A1000 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU A1016 " --> pdb=" O PHE A1012 " (cutoff:3.500A) Processing helix chain 'A' and resid 1020 through 1024 removed outlier: 3.687A pdb=" N ASN A1024 " --> pdb=" O LEU A1021 " (cutoff:3.500A) Processing helix chain 'A' and resid 1174 through 1182 Processing helix chain 'A' and resid 1183 through 1186 Processing helix chain 'A' and resid 1190 through 1199 removed outlier: 3.639A pdb=" N PHE A1194 " --> pdb=" O GLU A1190 " (cutoff:3.500A) Processing helix chain 'A' and resid 1209 through 1232 removed outlier: 4.157A pdb=" N ILE A1214 " --> pdb=" O GLU A1210 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N LEU A1215 " --> pdb=" O ARG A1211 " (cutoff:3.500A) Processing helix chain 'A' and resid 1236 through 1248 removed outlier: 3.534A pdb=" N LEU A1240 " --> pdb=" O ASN A1236 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL A1248 " --> pdb=" O LYS A1244 " (cutoff:3.500A) Processing helix chain 'A' and resid 1249 through 1259 removed outlier: 3.880A pdb=" N ASP A1259 " --> pdb=" O PHE A1255 " (cutoff:3.500A) Processing helix chain 'A' and resid 1260 through 1261 No H-bonds generated for 'chain 'A' and resid 1260 through 1261' Processing helix chain 'A' and resid 1262 through 1266 Processing helix chain 'A' and resid 1272 through 1277 removed outlier: 3.588A pdb=" N TRP A1277 " --> pdb=" O PRO A1273 " (cutoff:3.500A) Processing helix chain 'A' and resid 1285 through 1293 Processing helix chain 'A' and resid 1295 through 1300 removed outlier: 3.730A pdb=" N LYS A1300 " --> pdb=" O PRO A1296 " (cutoff:3.500A) Processing helix chain 'A' and resid 1303 through 1310 removed outlier: 3.762A pdb=" N LEU A1310 " --> pdb=" O ASN A1306 " (cutoff:3.500A) Processing helix chain 'A' and resid 1313 through 1319 Processing helix chain 'A' and resid 1324 through 1337 Processing helix chain 'A' and resid 1338 through 1341 Processing helix chain 'A' and resid 1348 through 1353 Processing helix chain 'A' and resid 1354 through 1356 No H-bonds generated for 'chain 'A' and resid 1354 through 1356' Processing helix chain 'A' and resid 1362 through 1382 removed outlier: 3.737A pdb=" N ILE A1366 " --> pdb=" O PRO A1362 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLU A1371 " --> pdb=" O ALA A1367 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N TYR A1381 " --> pdb=" O ILE A1377 " (cutoff:3.500A) Processing helix chain 'A' and resid 1382 through 1393 removed outlier: 4.101A pdb=" N LYS A1388 " --> pdb=" O GLN A1384 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N MET A1389 " --> pdb=" O HIS A1385 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEU A1390 " --> pdb=" O ALA A1386 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLU A1391 " --> pdb=" O PHE A1387 " (cutoff:3.500A) Processing helix chain 'A' and resid 1408 through 1412 Processing helix chain 'A' and resid 1416 through 1420 Processing helix chain 'A' and resid 1425 through 1430 removed outlier: 3.623A pdb=" N PHE A1429 " --> pdb=" O GLU A1425 " (cutoff:3.500A) Processing helix chain 'A' and resid 1432 through 1441 removed outlier: 3.653A pdb=" N LEU A1436 " --> pdb=" O ASN A1432 " (cutoff:3.500A) Processing helix chain 'A' and resid 1446 through 1455 removed outlier: 4.456A pdb=" N LEU A1450 " --> pdb=" O ASP A1446 " (cutoff:3.500A) Processing helix chain 'A' and resid 1468 through 1491 removed outlier: 4.104A pdb=" N ILE A1474 " --> pdb=" O GLU A1470 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALA A1477 " --> pdb=" O PHE A1473 " (cutoff:3.500A) Processing helix chain 'A' and resid 1495 through 1507 removed outlier: 4.385A pdb=" N ASP A1501 " --> pdb=" O GLY A1497 " (cutoff:3.500A) Processing helix chain 'A' and resid 1508 through 1519 Processing helix chain 'A' and resid 1520 through 1525 removed outlier: 3.643A pdb=" N PHE A1523 " --> pdb=" O ARG A1520 " (cutoff:3.500A) Processing helix chain 'A' and resid 1529 through 1546 Processing helix chain 'A' and resid 1609 through 1628 removed outlier: 3.874A pdb=" N GLY A1613 " --> pdb=" O PRO A1609 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA A1621 " --> pdb=" O GLU A1617 " (cutoff:3.500A) Processing helix chain 'A' and resid 1629 through 1651 Proline residue: A1643 - end of helix Processing helix chain 'A' and resid 1657 through 1662 Processing helix chain 'A' and resid 1701 through 1722 Processing sheet with id=AA1, first strand: chain 'A' and resid 24 through 27 removed outlier: 3.732A pdb=" N GLY A 24 " --> pdb=" O VAL A 168 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY A 170 " --> pdb=" O GLY A 24 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N THR A 172 " --> pdb=" O VAL A 26 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N ARG A 59 " --> pdb=" O VAL A 135 " (cutoff:3.500A) removed outlier: 8.662A pdb=" N ILE A 137 " --> pdb=" O ARG A 59 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N LEU A 61 " --> pdb=" O ILE A 137 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N ASP A 139 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N MET A 63 " --> pdb=" O ASP A 139 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLY A 114 " --> pdb=" O PHE A 62 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 219 through 225 removed outlier: 5.758A pdb=" N THR A 219 " --> pdb=" O PHE A 502 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N LEU A 504 " --> pdb=" O THR A 219 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N VAL A 221 " --> pdb=" O LEU A 504 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N THR A 506 " --> pdb=" O VAL A 221 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N VAL A 223 " --> pdb=" O THR A 506 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N VAL A 476 " --> pdb=" O VAL A 503 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N PHE A 505 " --> pdb=" O VAL A 476 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ILE A 478 " --> pdb=" O PHE A 505 " (cutoff:3.500A) removed outlier: 8.862A pdb=" N ALA A 507 " --> pdb=" O ILE A 478 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N LEU A 389 " --> pdb=" O PHE A 477 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N CYS A 388 " --> pdb=" O MET A 458 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N CYS A 460 " --> pdb=" O CYS A 388 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N VAL A 390 " --> pdb=" O CYS A 460 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 558 through 559 removed outlier: 3.668A pdb=" N PHE A 558 " --> pdb=" O LEU A 566 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 594 through 596 Processing sheet with id=AA5, first strand: chain 'A' and resid 704 through 706 Processing sheet with id=AA6, first strand: chain 'A' and resid 768 through 771 removed outlier: 3.581A pdb=" N ARG A 780 " --> pdb=" O PHE A 730 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 768 through 771 removed outlier: 3.581A pdb=" N ARG A 780 " --> pdb=" O PHE A 730 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N TYR A 754 " --> pdb=" O ILE A 729 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 819 through 820 Processing sheet with id=AA9, first strand: chain 'A' and resid 969 through 971 removed outlier: 4.739A pdb=" N VAL A 969 " --> pdb=" O VAL A 942 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N MET A 939 " --> pdb=" O VAL A 898 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N VAL A 898 " --> pdb=" O MET A 939 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N GLU A 941 " --> pdb=" O THR A 896 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU A 894 " --> pdb=" O ARG A 943 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR A 883 " --> pdb=" O PHE A 977 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1669 through 1670 removed outlier: 3.964A pdb=" N CYS A1684 " --> pdb=" O VAL A1695 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N VAL A1695 " --> pdb=" O CYS A1684 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1674 through 1676 removed outlier: 3.760A pdb=" N ILE A1674 " --> pdb=" O MET A1681 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N MET A1681 " --> pdb=" O ILE A1674 " (cutoff:3.500A) 583 hydrogen bonds defined for protein. 1638 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 82 hydrogen bonds 164 hydrogen bond angles 0 basepair planarities 35 basepair parallelities 58 stacking parallelities Total time for adding SS restraints: 3.79 Time building geometry restraints manager: 1.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4438 1.34 - 1.46: 3908 1.46 - 1.58: 6554 1.58 - 1.70: 194 1.70 - 1.83: 106 Bond restraints: 15200 Sorted by residual: bond pdb=" CG PRO A 872 " pdb=" CD PRO A 872 " ideal model delta sigma weight residual 1.503 1.363 0.140 3.40e-02 8.65e+02 1.69e+01 bond pdb=" CB PRO A 872 " pdb=" CG PRO A 872 " ideal model delta sigma weight residual 1.492 1.563 -0.071 5.00e-02 4.00e+02 2.00e+00 bond pdb=" CA GLU A 541 " pdb=" CB GLU A 541 " ideal model delta sigma weight residual 1.522 1.532 -0.010 7.00e-03 2.04e+04 1.97e+00 bond pdb=" C4 ADP A1802 " pdb=" C5 ADP A1802 " ideal model delta sigma weight residual 1.490 1.468 0.022 2.00e-02 2.50e+03 1.23e+00 bond pdb=" C1' U C 46 " pdb=" N1 U C 46 " ideal model delta sigma weight residual 1.470 1.486 -0.016 1.50e-02 4.44e+03 1.16e+00 ... (remaining 15195 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.69: 20839 2.69 - 5.39: 156 5.39 - 8.08: 17 8.08 - 10.77: 8 10.77 - 13.47: 4 Bond angle restraints: 21024 Sorted by residual: angle pdb=" N PRO A 872 " pdb=" CD PRO A 872 " pdb=" CG PRO A 872 " ideal model delta sigma weight residual 103.20 89.73 13.47 1.50e+00 4.44e-01 8.06e+01 angle pdb=" CA PRO A 872 " pdb=" N PRO A 872 " pdb=" CD PRO A 872 " ideal model delta sigma weight residual 112.00 102.73 9.27 1.40e+00 5.10e-01 4.38e+01 angle pdb=" CA PRO A 872 " pdb=" CB PRO A 872 " pdb=" CG PRO A 872 " ideal model delta sigma weight residual 104.50 95.82 8.68 1.90e+00 2.77e-01 2.09e+01 angle pdb=" CB MET A 344 " pdb=" CG MET A 344 " pdb=" SD MET A 344 " ideal model delta sigma weight residual 112.70 125.02 -12.32 3.00e+00 1.11e-01 1.69e+01 angle pdb=" CB MET A 288 " pdb=" CG MET A 288 " pdb=" SD MET A 288 " ideal model delta sigma weight residual 112.70 124.96 -12.26 3.00e+00 1.11e-01 1.67e+01 ... (remaining 21019 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.70: 8656 29.70 - 59.39: 534 59.39 - 89.09: 94 89.09 - 118.79: 3 118.79 - 148.48: 1 Dihedral angle restraints: 9288 sinusoidal: 4691 harmonic: 4597 Sorted by residual: dihedral pdb=" C5' U C 46 " pdb=" C4' U C 46 " pdb=" C3' U C 46 " pdb=" O3' U C 46 " ideal model delta sinusoidal sigma weight residual 147.00 82.64 64.36 1 8.00e+00 1.56e-02 8.51e+01 dihedral pdb=" C4' U C 46 " pdb=" C3' U C 46 " pdb=" C2' U C 46 " pdb=" C1' U C 46 " ideal model delta sinusoidal sigma weight residual -35.00 25.21 -60.21 1 8.00e+00 1.56e-02 7.55e+01 dihedral pdb=" O4' U C 46 " pdb=" C4' U C 46 " pdb=" C3' U C 46 " pdb=" C2' U C 46 " ideal model delta sinusoidal sigma weight residual 24.00 -32.57 56.57 1 8.00e+00 1.56e-02 6.74e+01 ... (remaining 9285 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 2110 0.057 - 0.114: 301 0.114 - 0.171: 26 0.171 - 0.228: 2 0.228 - 0.285: 1 Chirality restraints: 2440 Sorted by residual: chirality pdb=" C3' U C 46 " pdb=" C4' U C 46 " pdb=" O3' U C 46 " pdb=" C2' U C 46 " both_signs ideal model delta sigma weight residual False -2.74 -2.46 -0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" C2' U C 46 " pdb=" C3' U C 46 " pdb=" O2' U C 46 " pdb=" C1' U C 46 " both_signs ideal model delta sigma weight residual False -2.52 -2.72 0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" C1' U C 46 " pdb=" O4' U C 46 " pdb=" C2' U C 46 " pdb=" N1 U C 46 " both_signs ideal model delta sigma weight residual False 2.45 2.27 0.17 2.00e-01 2.50e+01 7.53e-01 ... (remaining 2437 not shown) Planarity restraints: 2335 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 370 " 0.014 2.00e-02 2.50e+03 1.78e-02 5.57e+00 pdb=" CG PHE A 370 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 PHE A 370 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE A 370 " 0.015 2.00e-02 2.50e+03 pdb=" CE1 PHE A 370 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE A 370 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 370 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 582 " -0.031 5.00e-02 4.00e+02 4.72e-02 3.57e+00 pdb=" N PRO A 583 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 583 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 583 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 903 " -0.029 5.00e-02 4.00e+02 4.44e-02 3.15e+00 pdb=" N PRO A 904 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 904 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 904 " -0.025 5.00e-02 4.00e+02 ... (remaining 2332 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 169 2.51 - 3.11: 11311 3.11 - 3.70: 26054 3.70 - 4.30: 34304 4.30 - 4.90: 51635 Nonbonded interactions: 123473 Sorted by model distance: nonbonded pdb="MG MG A1801 " pdb=" O3B ADP A1802 " model vdw 1.910 2.170 nonbonded pdb=" O2' U C 46 " pdb=" O5' U C 47 " model vdw 2.133 3.040 nonbonded pdb=" O LYS A1402 " pdb=" OG1 THR A1405 " model vdw 2.143 3.040 nonbonded pdb=" O PHE A 370 " pdb=" OG SER A 373 " model vdw 2.150 3.040 nonbonded pdb=" O LYS A 696 " pdb=" O2' G C 75 " model vdw 2.188 3.040 ... (remaining 123468 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.910 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: 0.210 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 17.310 Find NCS groups from input model: 0.090 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 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 0.140 15200 Z= 0.143 Angle : 0.643 13.468 21024 Z= 0.326 Chirality : 0.039 0.285 2440 Planarity : 0.004 0.047 2335 Dihedral : 18.401 148.482 6306 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 18.39 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.57 % Favored : 95.23 % Rotamer: Outliers : 0.07 % Allowed : 21.75 % Favored : 78.17 % 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 aren not related in a simple way. whole: -0.09 (0.22), residues: 1552 helix: 0.90 (0.20), residues: 712 sheet: -1.24 (0.37), residues: 167 loop : -0.69 (0.26), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1658 TYR 0.010 0.001 TYR A 286 PHE 0.041 0.001 PHE A 370 TRP 0.020 0.001 TRP A1634 HIS 0.004 0.001 HIS A1522 Details of bonding type rmsd covalent geometry : bond 0.00319 (15200) covalent geometry : angle 0.64331 (21024) hydrogen bonds : bond 0.15128 ( 658) hydrogen bonds : angle 6.21107 ( 1802) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 76 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1389 MET cc_start: 0.9342 (tpp) cc_final: 0.9047 (mmm) REVERT: A 1479 LEU cc_start: 0.9147 (tp) cc_final: 0.8811 (pp) outliers start: 1 outliers final: 0 residues processed: 77 average time/residue: 0.1185 time to fit residues: 14.7313 Evaluate side-chains 71 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 20.0000 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 0.0000 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 7.9990 chunk 149 optimal weight: 30.0000 overall best weight: 4.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 GLN A 335 HIS A 407 ASN A 490 GLN A 569 ASN ** A 773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1217 ASN ** A1353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1548 HIS ** A1659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.065250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.046565 restraints weight = 90766.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.048040 restraints weight = 50938.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.048989 restraints weight = 35398.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.049585 restraints weight = 28345.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.049899 restraints weight = 24788.788| |-----------------------------------------------------------------------------| r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 15200 Z= 0.224 Angle : 0.677 8.897 21024 Z= 0.345 Chirality : 0.043 0.206 2440 Planarity : 0.005 0.060 2335 Dihedral : 16.458 134.342 3159 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 16.95 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.28 % Favored : 94.52 % Rotamer: Outliers : 0.14 % Allowed : 6.49 % Favored : 93.37 % 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 aren not related in a simple way. whole: -0.33 (0.21), residues: 1552 helix: 0.63 (0.19), residues: 718 sheet: -1.36 (0.37), residues: 156 loop : -0.77 (0.25), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 511 TYR 0.019 0.002 TYR A1624 PHE 0.014 0.002 PHE A 62 TRP 0.011 0.002 TRP A1634 HIS 0.010 0.002 HIS A1522 Details of bonding type rmsd covalent geometry : bond 0.00479 (15200) covalent geometry : angle 0.67652 (21024) hydrogen bonds : bond 0.04627 ( 658) hydrogen bonds : angle 4.94339 ( 1802) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 92 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 458 MET cc_start: 0.8829 (tpp) cc_final: 0.8604 (tpp) REVERT: A 893 MET cc_start: 0.8056 (tpp) cc_final: 0.7585 (tpp) REVERT: A 914 ASP cc_start: 0.7632 (t70) cc_final: 0.7296 (m-30) outliers start: 2 outliers final: 0 residues processed: 94 average time/residue: 0.1179 time to fit residues: 17.1390 Evaluate side-chains 68 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 101 optimal weight: 6.9990 chunk 9 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 144 optimal weight: 0.9990 chunk 103 optimal weight: 10.0000 chunk 64 optimal weight: 4.9990 chunk 118 optimal weight: 8.9990 chunk 60 optimal weight: 0.9990 chunk 105 optimal weight: 0.8980 chunk 113 optimal weight: 0.7980 chunk 14 optimal weight: 4.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 HIS A 266 GLN A 323 HIS A 449 GLN ** A 773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 948 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1270 GLN ** A1384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1456 HIS ** A1656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.067804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.048954 restraints weight = 88908.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.050510 restraints weight = 49833.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.051549 restraints weight = 34432.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.052175 restraints weight = 27265.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.052576 restraints weight = 23674.295| |-----------------------------------------------------------------------------| r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 15200 Z= 0.111 Angle : 0.559 8.506 21024 Z= 0.281 Chirality : 0.039 0.199 2440 Planarity : 0.004 0.045 2335 Dihedral : 16.167 131.401 3159 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.99 % Favored : 95.88 % Rotamer: Outliers : 0.07 % Allowed : 3.99 % Favored : 95.93 % 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 aren not related in a simple way. whole: -0.20 (0.21), residues: 1552 helix: 0.64 (0.19), residues: 736 sheet: -1.17 (0.37), residues: 161 loop : -0.62 (0.25), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 998 TYR 0.012 0.001 TYR A1624 PHE 0.011 0.001 PHE A1194 TRP 0.011 0.001 TRP A 102 HIS 0.006 0.001 HIS A 323 Details of bonding type rmsd covalent geometry : bond 0.00237 (15200) covalent geometry : angle 0.55946 (21024) hydrogen bonds : bond 0.03776 ( 658) hydrogen bonds : angle 4.55820 ( 1802) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 110 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 MET cc_start: 0.8490 (tmm) cc_final: 0.8176 (tmm) REVERT: A 322 MET cc_start: 0.8144 (ppp) cc_final: 0.7829 (ppp) REVERT: A 458 MET cc_start: 0.8846 (tpp) cc_final: 0.8545 (tpp) REVERT: A 543 GLU cc_start: 0.7308 (mp0) cc_final: 0.6954 (mp0) REVERT: A 625 MET cc_start: 0.8218 (ptp) cc_final: 0.7990 (mtm) REVERT: A 893 MET cc_start: 0.8163 (tpp) cc_final: 0.7663 (tpp) REVERT: A 999 MET cc_start: 0.9089 (ptm) cc_final: 0.8678 (ppp) outliers start: 1 outliers final: 0 residues processed: 110 average time/residue: 0.1117 time to fit residues: 19.2803 Evaluate side-chains 79 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 44 optimal weight: 10.0000 chunk 58 optimal weight: 2.9990 chunk 110 optimal weight: 7.9990 chunk 13 optimal weight: 0.8980 chunk 141 optimal weight: 9.9990 chunk 71 optimal weight: 5.9990 chunk 39 optimal weight: 10.0000 chunk 54 optimal weight: 8.9990 chunk 56 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 chunk 63 optimal weight: 6.9990 overall best weight: 2.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 GLN ** A 773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 948 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.066848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.047951 restraints weight = 90205.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.049472 restraints weight = 50974.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.050471 restraints weight = 35340.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.051096 restraints weight = 28165.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.051404 restraints weight = 24608.055| |-----------------------------------------------------------------------------| r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15200 Z= 0.139 Angle : 0.564 8.111 21024 Z= 0.285 Chirality : 0.039 0.205 2440 Planarity : 0.004 0.046 2335 Dihedral : 16.072 130.830 3159 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.77 % Favored : 95.17 % Rotamer: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % 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 aren not related in a simple way. whole: -0.17 (0.21), residues: 1552 helix: 0.65 (0.19), residues: 737 sheet: -0.92 (0.39), residues: 149 loop : -0.68 (0.25), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 44 TYR 0.012 0.001 TYR A1624 PHE 0.010 0.001 PHE A1194 TRP 0.009 0.001 TRP A1634 HIS 0.006 0.001 HIS A1522 Details of bonding type rmsd covalent geometry : bond 0.00306 (15200) covalent geometry : angle 0.56417 (21024) hydrogen bonds : bond 0.03726 ( 658) hydrogen bonds : angle 4.48229 ( 1802) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 322 MET cc_start: 0.8240 (ppp) cc_final: 0.7942 (ppp) REVERT: A 458 MET cc_start: 0.8836 (tpp) cc_final: 0.8542 (tpp) REVERT: A 543 GLU cc_start: 0.7445 (mp0) cc_final: 0.7104 (mp0) REVERT: A 620 MET cc_start: 0.8727 (tpt) cc_final: 0.8505 (mmm) REVERT: A 625 MET cc_start: 0.8317 (ptp) cc_final: 0.7965 (mtm) REVERT: A 893 MET cc_start: 0.8002 (tpp) cc_final: 0.7524 (tpp) REVERT: A 914 ASP cc_start: 0.7607 (t70) cc_final: 0.7218 (m-30) REVERT: A 999 MET cc_start: 0.9019 (ptm) cc_final: 0.8723 (ppp) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.1060 time to fit residues: 15.7543 Evaluate side-chains 76 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 162 optimal weight: 20.0000 chunk 126 optimal weight: 10.0000 chunk 91 optimal weight: 3.9990 chunk 51 optimal weight: 8.9990 chunk 34 optimal weight: 7.9990 chunk 41 optimal weight: 7.9990 chunk 81 optimal weight: 10.0000 chunk 119 optimal weight: 0.5980 chunk 151 optimal weight: 10.0000 chunk 5 optimal weight: 9.9990 chunk 61 optimal weight: 10.0000 overall best weight: 5.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 GLN A 734 GLN A 773 ASN A 948 GLN ** A1267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1286 HIS ** A1384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.063209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.044882 restraints weight = 91689.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.046291 restraints weight = 51713.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.047201 restraints weight = 35952.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.047693 restraints weight = 28753.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.048079 restraints weight = 25340.559| |-----------------------------------------------------------------------------| r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 15200 Z= 0.286 Angle : 0.742 10.903 21024 Z= 0.378 Chirality : 0.044 0.212 2440 Planarity : 0.005 0.073 2335 Dihedral : 16.461 127.299 3159 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 20.40 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.19 % Favored : 93.62 % Rotamer: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % 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 aren not related in a simple way. whole: -0.55 (0.21), residues: 1552 helix: 0.39 (0.19), residues: 729 sheet: -1.20 (0.40), residues: 143 loop : -0.90 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 167 TYR 0.024 0.002 TYR A1434 PHE 0.023 0.002 PHE A1219 TRP 0.009 0.002 TRP A 102 HIS 0.009 0.002 HIS A1522 Details of bonding type rmsd covalent geometry : bond 0.00611 (15200) covalent geometry : angle 0.74160 (21024) hydrogen bonds : bond 0.05082 ( 658) hydrogen bonds : angle 4.96143 ( 1802) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 MET cc_start: 0.9081 (tpp) cc_final: 0.8660 (mmt) REVERT: A 620 MET cc_start: 0.8879 (tpt) cc_final: 0.8476 (mmm) REVERT: A 768 MET cc_start: 0.8878 (tpp) cc_final: 0.8590 (tpp) REVERT: A 893 MET cc_start: 0.7946 (tpp) cc_final: 0.7538 (tpp) REVERT: A 1389 MET cc_start: 0.9414 (mmp) cc_final: 0.9062 (mmm) outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.1150 time to fit residues: 14.4616 Evaluate side-chains 67 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 155 optimal weight: 30.0000 chunk 89 optimal weight: 9.9990 chunk 125 optimal weight: 0.7980 chunk 41 optimal weight: 0.7980 chunk 149 optimal weight: 30.0000 chunk 62 optimal weight: 9.9990 chunk 91 optimal weight: 10.0000 chunk 3 optimal weight: 2.9990 chunk 17 optimal weight: 7.9990 chunk 142 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 overall best weight: 3.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 GLN A 695 ASN ** A 792 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.064396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.045932 restraints weight = 88620.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.047370 restraints weight = 49785.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.048300 restraints weight = 34457.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.048896 restraints weight = 27485.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.049192 restraints weight = 23934.713| |-----------------------------------------------------------------------------| r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 15200 Z= 0.188 Angle : 0.618 6.969 21024 Z= 0.315 Chirality : 0.041 0.203 2440 Planarity : 0.005 0.047 2335 Dihedral : 16.421 118.063 3159 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 16.04 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.54 % Favored : 94.33 % Rotamer: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % 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 aren not related in a simple way. whole: -0.38 (0.21), residues: 1552 helix: 0.57 (0.19), residues: 727 sheet: -1.27 (0.39), residues: 145 loop : -0.84 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 9 TYR 0.014 0.002 TYR A1624 PHE 0.014 0.001 PHE A1219 TRP 0.013 0.001 TRP A1634 HIS 0.008 0.002 HIS A1522 Details of bonding type rmsd covalent geometry : bond 0.00408 (15200) covalent geometry : angle 0.61781 (21024) hydrogen bonds : bond 0.04118 ( 658) hydrogen bonds : angle 4.69881 ( 1802) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 MET cc_start: 0.9245 (tpp) cc_final: 0.8508 (mmt) REVERT: A 222 MET cc_start: 0.8522 (tmm) cc_final: 0.7947 (tmm) REVERT: A 458 MET cc_start: 0.8798 (tpp) cc_final: 0.8594 (tpp) REVERT: A 543 GLU cc_start: 0.7478 (mp0) cc_final: 0.7138 (mp0) REVERT: A 620 MET cc_start: 0.8664 (tpt) cc_final: 0.8247 (mmm) REVERT: A 862 ASN cc_start: 0.8536 (t0) cc_final: 0.8147 (t0) REVERT: A 893 MET cc_start: 0.7997 (tpp) cc_final: 0.7638 (tpp) REVERT: A 922 MET cc_start: 0.8165 (mmp) cc_final: 0.7897 (mmm) REVERT: A 1389 MET cc_start: 0.9363 (mmp) cc_final: 0.8998 (mmm) outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.1097 time to fit residues: 15.4164 Evaluate side-chains 67 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 33 optimal weight: 10.0000 chunk 63 optimal weight: 9.9990 chunk 95 optimal weight: 5.9990 chunk 162 optimal weight: 20.0000 chunk 48 optimal weight: 7.9990 chunk 73 optimal weight: 9.9990 chunk 13 optimal weight: 7.9990 chunk 72 optimal weight: 7.9990 chunk 40 optimal weight: 8.9990 chunk 138 optimal weight: 9.9990 chunk 112 optimal weight: 5.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 GLN ** A 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 695 ASN A 815 HIS ** A1656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.062598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.044198 restraints weight = 92589.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.045506 restraints weight = 54599.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.046324 restraints weight = 39201.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.046848 restraints weight = 32214.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.047116 restraints weight = 28552.362| |-----------------------------------------------------------------------------| r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.3389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 15200 Z= 0.339 Angle : 0.809 11.665 21024 Z= 0.413 Chirality : 0.046 0.210 2440 Planarity : 0.006 0.069 2335 Dihedral : 16.751 112.333 3159 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 22.86 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.80 % Favored : 92.07 % Rotamer: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % 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 aren not related in a simple way. whole: -1.00 (0.21), residues: 1552 helix: 0.13 (0.19), residues: 735 sheet: -1.79 (0.37), residues: 147 loop : -1.20 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 167 TYR 0.027 0.003 TYR A 402 PHE 0.024 0.002 PHE A 423 TRP 0.011 0.002 TRP A 102 HIS 0.012 0.003 HIS A1305 Details of bonding type rmsd covalent geometry : bond 0.00723 (15200) covalent geometry : angle 0.80924 (21024) hydrogen bonds : bond 0.05549 ( 658) hydrogen bonds : angle 5.27160 ( 1802) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 MET cc_start: 0.9297 (tpp) cc_final: 0.8793 (mmp) REVERT: A 458 MET cc_start: 0.8780 (tpp) cc_final: 0.8566 (tpp) REVERT: A 620 MET cc_start: 0.9003 (tpt) cc_final: 0.8497 (tmm) REVERT: A 768 MET cc_start: 0.8644 (tpp) cc_final: 0.8291 (tpp) REVERT: A 922 MET cc_start: 0.8033 (mmp) cc_final: 0.7771 (mmm) outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.1170 time to fit residues: 13.7775 Evaluate side-chains 61 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 59 optimal weight: 5.9990 chunk 101 optimal weight: 2.9990 chunk 146 optimal weight: 0.8980 chunk 79 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 163 optimal weight: 20.0000 chunk 6 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 132 optimal weight: 8.9990 chunk 111 optimal weight: 8.9990 chunk 3 optimal weight: 0.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 266 GLN ** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 695 ASN ** A1267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.064992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.046309 restraints weight = 90690.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.047684 restraints weight = 52683.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.048583 restraints weight = 37405.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.049136 restraints weight = 30312.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.049479 restraints weight = 26719.784| |-----------------------------------------------------------------------------| r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.3363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 15200 Z= 0.141 Angle : 0.603 8.022 21024 Z= 0.306 Chirality : 0.040 0.224 2440 Planarity : 0.004 0.046 2335 Dihedral : 16.523 110.572 3159 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 14.91 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.03 % Favored : 94.85 % Rotamer: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % 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 aren not related in a simple way. whole: -0.46 (0.21), residues: 1552 helix: 0.54 (0.19), residues: 725 sheet: -1.46 (0.38), residues: 145 loop : -0.89 (0.25), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 928 TYR 0.014 0.002 TYR A1000 PHE 0.023 0.001 PHE A1387 TRP 0.016 0.001 TRP A1634 HIS 0.006 0.001 HIS A1522 Details of bonding type rmsd covalent geometry : bond 0.00311 (15200) covalent geometry : angle 0.60254 (21024) hydrogen bonds : bond 0.03998 ( 658) hydrogen bonds : angle 4.68855 ( 1802) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 MET cc_start: 0.9378 (tpp) cc_final: 0.8870 (mmp) REVERT: A 222 MET cc_start: 0.8498 (tmm) cc_final: 0.8243 (tmm) REVERT: A 458 MET cc_start: 0.8781 (tpp) cc_final: 0.8519 (tpp) REVERT: A 543 GLU cc_start: 0.7422 (mp0) cc_final: 0.7140 (mp0) REVERT: A 620 MET cc_start: 0.8777 (tpt) cc_final: 0.8267 (tmm) REVERT: A 768 MET cc_start: 0.8850 (tpp) cc_final: 0.8308 (tpp) REVERT: A 922 MET cc_start: 0.8063 (mmp) cc_final: 0.7853 (mmm) REVERT: A 1198 ILE cc_start: 0.9096 (mt) cc_final: 0.8872 (tp) outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.1073 time to fit residues: 15.2186 Evaluate side-chains 64 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 1 optimal weight: 0.8980 chunk 112 optimal weight: 0.6980 chunk 108 optimal weight: 0.0270 chunk 126 optimal weight: 3.9990 chunk 21 optimal weight: 10.0000 chunk 88 optimal weight: 10.0000 chunk 115 optimal weight: 0.9990 chunk 71 optimal weight: 7.9990 chunk 111 optimal weight: 5.9990 chunk 65 optimal weight: 7.9990 chunk 152 optimal weight: 10.0000 overall best weight: 1.3242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 266 GLN A 695 ASN ** A 792 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.065833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.047099 restraints weight = 89812.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.048592 restraints weight = 50753.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.049562 restraints weight = 35307.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.050152 restraints weight = 28301.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.050462 restraints weight = 24753.142| |-----------------------------------------------------------------------------| r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.3445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 15200 Z= 0.116 Angle : 0.578 7.819 21024 Z= 0.292 Chirality : 0.040 0.237 2440 Planarity : 0.004 0.048 2335 Dihedral : 16.200 106.052 3159 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.35 % Favored : 94.59 % Rotamer: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % 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 aren not related in a simple way. whole: -0.25 (0.21), residues: 1552 helix: 0.64 (0.19), residues: 731 sheet: -1.22 (0.39), residues: 146 loop : -0.72 (0.25), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 928 TYR 0.013 0.001 TYR A1000 PHE 0.026 0.001 PHE A1387 TRP 0.020 0.001 TRP A1634 HIS 0.004 0.001 HIS A1456 Details of bonding type rmsd covalent geometry : bond 0.00255 (15200) covalent geometry : angle 0.57841 (21024) hydrogen bonds : bond 0.03763 ( 658) hydrogen bonds : angle 4.51023 ( 1802) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 TYR cc_start: 0.8524 (t80) cc_final: 0.7746 (t80) REVERT: A 63 MET cc_start: 0.9414 (tpp) cc_final: 0.8984 (mmp) REVERT: A 162 GLN cc_start: 0.8817 (mm110) cc_final: 0.8320 (mp10) REVERT: A 222 MET cc_start: 0.8530 (tmm) cc_final: 0.8254 (tmm) REVERT: A 458 MET cc_start: 0.8795 (tpp) cc_final: 0.8505 (tpp) REVERT: A 543 GLU cc_start: 0.7555 (mp0) cc_final: 0.7272 (mp0) REVERT: A 620 MET cc_start: 0.8824 (tpt) cc_final: 0.8321 (tmm) REVERT: A 768 MET cc_start: 0.8849 (tpp) cc_final: 0.8612 (tpp) REVERT: A 922 MET cc_start: 0.8053 (mmp) cc_final: 0.7816 (mmm) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.1057 time to fit residues: 14.9766 Evaluate side-chains 68 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 81 optimal weight: 9.9990 chunk 42 optimal weight: 2.9990 chunk 101 optimal weight: 7.9990 chunk 146 optimal weight: 3.9990 chunk 105 optimal weight: 0.9980 chunk 46 optimal weight: 9.9990 chunk 126 optimal weight: 0.5980 chunk 50 optimal weight: 9.9990 chunk 15 optimal weight: 10.0000 chunk 60 optimal weight: 7.9990 chunk 110 optimal weight: 2.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 GLN A 695 ASN ** A 792 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.065220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.046534 restraints weight = 89770.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.048006 restraints weight = 50236.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.048970 restraints weight = 34940.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.049575 restraints weight = 27850.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.049938 restraints weight = 24311.141| |-----------------------------------------------------------------------------| r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.3528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 15200 Z= 0.138 Angle : 0.582 8.150 21024 Z= 0.295 Chirality : 0.040 0.218 2440 Planarity : 0.004 0.048 2335 Dihedral : 16.165 109.887 3159 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.41 % Favored : 94.52 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % 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 aren not related in a simple way. whole: -0.24 (0.21), residues: 1552 helix: 0.68 (0.19), residues: 731 sheet: -1.23 (0.38), residues: 156 loop : -0.73 (0.25), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 928 TYR 0.019 0.001 TYR A 402 PHE 0.024 0.001 PHE A1387 TRP 0.015 0.001 TRP A1634 HIS 0.006 0.001 HIS A1522 Details of bonding type rmsd covalent geometry : bond 0.00306 (15200) covalent geometry : angle 0.58186 (21024) hydrogen bonds : bond 0.03800 ( 658) hydrogen bonds : angle 4.49893 ( 1802) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 MET cc_start: 0.9364 (tpp) cc_final: 0.8889 (mmp) REVERT: A 162 GLN cc_start: 0.8840 (mm110) cc_final: 0.8319 (mp10) REVERT: A 543 GLU cc_start: 0.7514 (mp0) cc_final: 0.7159 (mp0) REVERT: A 620 MET cc_start: 0.8894 (tpt) cc_final: 0.8387 (tmm) REVERT: A 768 MET cc_start: 0.8835 (tpp) cc_final: 0.8540 (tpp) REVERT: A 922 MET cc_start: 0.8044 (mmp) cc_final: 0.7805 (mmm) outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.1096 time to fit residues: 14.3463 Evaluate side-chains 67 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 117 optimal weight: 6.9990 chunk 63 optimal weight: 7.9990 chunk 41 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 139 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 chunk 145 optimal weight: 4.9990 chunk 89 optimal weight: 20.0000 chunk 120 optimal weight: 9.9990 chunk 160 optimal weight: 20.0000 chunk 125 optimal weight: 0.8980 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 GLN A 695 ASN ** A 792 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.065577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.046775 restraints weight = 89304.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.048246 restraints weight = 50461.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.049229 restraints weight = 35180.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.049832 restraints weight = 28041.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.050220 restraints weight = 24483.171| |-----------------------------------------------------------------------------| r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.3624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 15200 Z= 0.125 Angle : 0.572 8.266 21024 Z= 0.288 Chirality : 0.039 0.217 2440 Planarity : 0.004 0.048 2335 Dihedral : 16.101 108.998 3159 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.41 % Favored : 94.52 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % 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 aren not related in a simple way. whole: -0.17 (0.21), residues: 1552 helix: 0.75 (0.19), residues: 728 sheet: -1.21 (0.38), residues: 156 loop : -0.71 (0.25), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 928 TYR 0.018 0.001 TYR A 402 PHE 0.024 0.001 PHE A1387 TRP 0.017 0.001 TRP A1634 HIS 0.005 0.001 HIS A1522 Details of bonding type rmsd covalent geometry : bond 0.00278 (15200) covalent geometry : angle 0.57158 (21024) hydrogen bonds : bond 0.03696 ( 658) hydrogen bonds : angle 4.43611 ( 1802) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2430.16 seconds wall clock time: 43 minutes 9.98 seconds (2589.98 seconds total)