Starting phenix.real_space_refine on Fri Jul 3 12:17:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7w0c_32238/07_2026/7w0c_32238.cif Found real_map, /net/cci-nas-00/data/ceres_data/7w0c_32238/07_2026/7w0c_32238.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7w0c_32238/07_2026/7w0c_32238.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7w0c_32238/07_2026/7w0c_32238.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7w0c_32238/07_2026/7w0c_32238.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7w0c_32238/07_2026/7w0c_32238.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7w0c_32238/07_2026/7w0c_32238.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7w0c_32238/07_2026/7w0c_32238.map" } resolution = 3.93 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= 0.004 sd= 0.042 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 73 5.49 5 Mg 1 5.21 5 S 63 5.16 5 C 8460 2.51 5 N 2338 2.21 5 O 2728 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13663 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 11967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1476, 11967 Classifications: {'peptide': 1476} Link IDs: {'PTRANS': 60, 'TRANS': 1415} Chain breaks: 2 Chain: "B" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 143 Classifications: {'peptide': 16} Link IDs: {'TRANS': 15} Chain: "C" Number of atoms: 748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 748 Classifications: {'RNA': 35} Modifications used: {'5*END': 1, 'rna3p_pur': 20, 'rna3p_pyr': 15} Link IDs: {'rna3p': 34} Chain: "D" Number of atoms: 777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 777 Classifications: {'RNA': 37} Modifications used: {'rna3p_pur': 15, 'rna3p_pyr': 22} Link IDs: {'rna3p': 36} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.79, per 1000 atoms: 0.20 Number of scatterers: 13663 At special positions: 0 Unit cell: (105.002, 96.3425, 185.107, 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 63 16.00 P 73 15.00 Mg 1 11.99 O 2728 8.00 N 2338 7.00 C 8460 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: 1.22 Conformation dependent library (CDL) restraints added in 551.4 milliseconds 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2852 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 9 sheets defined 55.8% alpha, 9.2% beta 25 base pairs and 56 stacking pairs defined. Time for finding SS restraints: 1.90 Creating SS restraints... Processing helix chain 'A' and resid 3 through 7 removed outlier: 3.673A pdb=" N LYS A 7 " --> pdb=" O VAL A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 9 through 22 removed outlier: 3.513A pdb=" N LYS A 21 " --> pdb=" O ASP A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 44 Processing helix chain 'A' and resid 52 through 56 Processing helix chain 'A' and resid 66 through 81 Processing helix chain 'A' and resid 98 through 109 Processing helix chain 'A' and resid 115 through 125 removed outlier: 3.717A pdb=" N PHE A 119 " --> pdb=" O THR A 115 " (cutoff:3.500A) 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: 3.610A pdb=" N LEU A 156 " --> pdb=" O GLU A 152 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N PHE A 157 " --> pdb=" O PHE A 153 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N THR A 158 " --> pdb=" O MET A 154 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE A 159 " --> pdb=" O ARG A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 195 removed outlier: 4.214A pdb=" N LYS A 187 " --> pdb=" O ASN A 183 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYR A 195 " --> pdb=" O LEU A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 213 Processing helix chain 'A' and resid 232 through 252 removed outlier: 3.700A pdb=" N ARG A 236 " --> pdb=" O LEU A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 292 removed outlier: 4.859A pdb=" N VAL A 277 " --> pdb=" O LYS A 273 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LYS A 278 " --> pdb=" O LYS A 274 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLY A 292 " --> pdb=" O MET A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 314 removed outlier: 4.011A pdb=" N ILE A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N SER A 302 " --> pdb=" O ILE A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 345 removed outlier: 3.869A pdb=" N LYS A 340 " --> pdb=" O LEU A 336 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N MET A 344 " --> pdb=" O LYS A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 362 Processing helix chain 'A' and resid 364 through 378 removed outlier: 3.817A pdb=" N PHE A 378 " --> pdb=" O LEU A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 386 removed outlier: 3.591A pdb=" N ILE A 386 " --> pdb=" O PRO A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 412 removed outlier: 3.567A pdb=" N CYS A 398 " --> pdb=" O ARG A 394 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LYS A 399 " --> pdb=" O ARG A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 418 Processing helix chain 'A' and resid 445 through 452 Processing helix chain 'A' and resid 484 through 495 removed outlier: 3.970A pdb=" N ALA A 495 " --> pdb=" O SER A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 535 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 581 removed outlier: 3.718A pdb=" N THR A 581 " --> pdb=" O ARG A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 606 Processing helix chain 'A' and resid 607 through 612 removed outlier: 4.173A pdb=" N LYS A 611 " --> pdb=" O VAL A 608 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLY A 612 " --> pdb=" O SER A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 656 Processing helix chain 'A' and resid 667 through 680 removed outlier: 3.784A pdb=" N ALA A 673 " --> pdb=" O LYS A 669 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N SER A 674 " --> pdb=" O GLU A 670 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE A 675 " --> pdb=" O ARG A 671 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N ASP A 677 " --> pdb=" O ALA A 673 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N VAL A 678 " --> pdb=" O SER A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 687 removed outlier: 3.522A pdb=" N LYS A 685 " --> pdb=" O HIS A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 692 through 699 removed outlier: 4.117A pdb=" N ASP A 698 " --> pdb=" O ASN A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 749 removed outlier: 4.295A pdb=" N ASN A 747 " --> pdb=" O HIS A 743 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLN A 749 " --> pdb=" O TYR A 745 " (cutoff:3.500A) Processing helix chain 'A' and resid 792 through 809 removed outlier: 3.658A 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 867 Processing helix chain 'A' and resid 873 through 877 Processing helix chain 'A' and resid 916 through 925 removed outlier: 3.630A pdb=" N LYS A 924 " --> pdb=" O PHE A 920 " (cutoff:3.500A) Processing helix chain 'A' and resid 925 through 930 Processing helix chain 'A' and resid 962 through 968 Processing helix chain 'A' and resid 983 through 990 Processing helix chain 'A' and resid 991 through 1016 removed outlier: 4.133A pdb=" N ARG A 998 " --> pdb=" O SER A 994 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE A1001 " --> pdb=" O ASN A 997 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N HIS A1004 " --> pdb=" O TYR A1000 " (cutoff:3.500A) Processing helix chain 'A' and resid 1024 through 1028 removed outlier: 3.775A pdb=" N ASP A1027 " --> pdb=" O ASN A1024 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TYR A1028 " --> pdb=" O GLY A1025 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1024 through 1028' Processing helix chain 'A' and resid 1174 through 1182 removed outlier: 3.559A pdb=" N SER A1182 " --> pdb=" O GLN A1178 " (cutoff:3.500A) Processing helix chain 'A' and resid 1183 through 1186 Processing helix chain 'A' and resid 1190 through 1199 Processing helix chain 'A' and resid 1200 through 1204 Processing helix chain 'A' and resid 1209 through 1232 removed outlier: 3.752A pdb=" N ILE A1214 " --> pdb=" O GLU A1210 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N LEU A1215 " --> pdb=" O ARG A1211 " (cutoff:3.500A) Processing helix chain 'A' and resid 1236 through 1248 Processing helix chain 'A' and resid 1249 through 1259 removed outlier: 4.236A pdb=" N ASP A1259 " --> pdb=" O PHE A1255 " (cutoff:3.500A) Processing helix chain 'A' and resid 1262 through 1266 Processing helix chain 'A' and resid 1285 through 1295 Processing helix chain 'A' and resid 1295 through 1300 Processing helix chain 'A' and resid 1303 through 1309 removed outlier: 3.522A pdb=" N LEU A1307 " --> pdb=" O GLY A1303 " (cutoff:3.500A) Processing helix chain 'A' and resid 1313 through 1319 Processing helix chain 'A' and resid 1324 through 1339 Processing helix chain 'A' and resid 1348 through 1353 removed outlier: 3.867A pdb=" N ASN A1353 " --> pdb=" O SER A1349 " (cutoff:3.500A) 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 1393 removed outlier: 3.770A pdb=" N ASN A1380 " --> pdb=" O VAL A1376 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N LEU A1383 " --> pdb=" O LYS A1379 " (cutoff:3.500A) removed outlier: 8.820A pdb=" N GLN A1384 " --> pdb=" O ASN A1380 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N HIS A1385 " --> pdb=" O TYR A1381 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA A1386 " --> pdb=" O GLY A1382 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N PHE A1387 " --> pdb=" O LEU A1383 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N LYS A1388 " --> pdb=" O GLN A1384 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N MET A1389 " --> pdb=" O HIS A1385 " (cutoff:3.500A) Processing helix chain 'A' and resid 1403 through 1408 removed outlier: 3.609A pdb=" N LEU A1407 " --> pdb=" O PRO A1403 " (cutoff:3.500A) Processing helix chain 'A' and resid 1408 through 1413 Processing helix chain 'A' and resid 1416 through 1421 removed outlier: 3.703A pdb=" N ALA A1419 " --> pdb=" O LYS A1416 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N VAL A1421 " --> pdb=" O ARG A1418 " (cutoff:3.500A) Processing helix chain 'A' and resid 1425 through 1430 removed outlier: 4.133A pdb=" N PHE A1429 " --> pdb=" O GLU A1425 " (cutoff:3.500A) Processing helix chain 'A' and resid 1433 through 1441 Processing helix chain 'A' and resid 1447 through 1455 Processing helix chain 'A' and resid 1468 through 1491 removed outlier: 4.876A pdb=" N ILE A1474 " --> pdb=" O GLU A1470 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ALA A1477 " --> pdb=" O PHE A1473 " (cutoff:3.500A) Processing helix chain 'A' and resid 1495 through 1507 removed outlier: 4.081A pdb=" N ASP A1501 " --> pdb=" O GLY A1497 " (cutoff:3.500A) Processing helix chain 'A' and resid 1508 through 1519 removed outlier: 3.573A pdb=" N HIS A1519 " --> pdb=" O ILE A1515 " (cutoff:3.500A) Processing helix chain 'A' and resid 1529 through 1546 removed outlier: 4.048A pdb=" N PHE A1542 " --> pdb=" O LYS A1538 " (cutoff:3.500A) Processing helix chain 'A' and resid 1609 through 1628 removed outlier: 4.093A pdb=" N GLY A1613 " --> pdb=" O PRO A1609 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU A1616 " --> pdb=" O LEU A1612 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA A1621 " --> pdb=" O GLU A1617 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N CYS A1627 " --> pdb=" O VAL A1623 " (cutoff:3.500A) Processing helix chain 'A' and resid 1629 through 1651 Proline residue: A1643 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 111 through 114 removed outlier: 3.536A pdb=" N GLY A 114 " --> pdb=" O PHE A 62 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N ARG A 59 " --> pdb=" O LEU A 133 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N VAL A 135 " --> pdb=" O ARG A 59 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASP A 139 " --> pdb=" O MET A 63 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLY A 24 " --> pdb=" O VAL A 168 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N THR A 172 " --> pdb=" O VAL A 26 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 219 through 225 removed outlier: 5.709A pdb=" N THR A 219 " --> pdb=" O PHE A 502 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N LEU A 504 " --> pdb=" O THR A 219 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N VAL A 221 " --> pdb=" O LEU A 504 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N THR A 506 " --> pdb=" O VAL A 221 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N VAL A 223 " --> pdb=" O THR A 506 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N VAL A 476 " --> pdb=" O VAL A 503 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N PHE A 505 " --> pdb=" O VAL A 476 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N ILE A 478 " --> pdb=" O PHE A 505 " (cutoff:3.500A) removed outlier: 9.369A pdb=" N ALA A 507 " --> pdb=" O ILE A 478 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N LEU A 389 " --> pdb=" O PHE A 477 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N CYS A 388 " --> pdb=" O MET A 458 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N CYS A 460 " --> pdb=" O CYS A 388 " (cutoff:3.500A) removed outlier: 5.722A 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: 3.596A pdb=" N PHE A 558 " --> pdb=" O LEU A 566 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 593 through 596 Processing sheet with id=AA5, first strand: chain 'A' and resid 703 through 706 Processing sheet with id=AA6, first strand: chain 'A' and resid 768 through 772 Processing sheet with id=AA7, first strand: chain 'A' and resid 768 through 772 removed outlier: 4.938A 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 970 through 971 removed outlier: 3.517A pdb=" N ILE A 940 " --> pdb=" O LEU A 971 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ARG A 943 " --> pdb=" O VAL A 895 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N VAL A 895 " --> pdb=" O ARG A 943 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LYS A 880 " --> pdb=" O VAL A 895 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ILE A 881 " --> pdb=" O PHE A 979 " (cutoff:3.500A) 564 hydrogen bonds defined for protein. 1581 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 59 hydrogen bonds 118 hydrogen bond angles 0 basepair planarities 25 basepair parallelities 56 stacking parallelities Total time for adding SS restraints: 3.73 Time building geometry restraints manager: 1.62 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: 4126 1.34 - 1.46: 2817 1.46 - 1.58: 6915 1.58 - 1.70: 144 1.70 - 1.82: 99 Bond restraints: 14101 Sorted by residual: bond pdb=" CB GLU A1472 " pdb=" CG GLU A1472 " ideal model delta sigma weight residual 1.520 1.466 0.054 3.00e-02 1.11e+03 3.24e+00 bond pdb=" CA ARG A 873 " pdb=" CB ARG A 873 " ideal model delta sigma weight residual 1.530 1.546 -0.016 1.58e-02 4.01e+03 1.05e+00 bond pdb=" CB LYS B 352 " pdb=" CG LYS B 352 " ideal model delta sigma weight residual 1.520 1.550 -0.030 3.00e-02 1.11e+03 1.02e+00 bond pdb=" CG GLU A1472 " pdb=" CD GLU A1472 " ideal model delta sigma weight residual 1.516 1.491 0.025 2.50e-02 1.60e+03 1.02e+00 bond pdb=" C4 ADP A1802 " pdb=" C5 ADP A1802 " ideal model delta sigma weight residual 1.490 1.471 0.019 2.00e-02 2.50e+03 9.42e-01 ... (remaining 14096 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 19012 1.55 - 3.09: 334 3.09 - 4.64: 58 4.64 - 6.18: 18 6.18 - 7.73: 3 Bond angle restraints: 19425 Sorted by residual: angle pdb=" CB LYS B 352 " pdb=" CG LYS B 352 " pdb=" CD LYS B 352 " ideal model delta sigma weight residual 111.30 119.03 -7.73 2.30e+00 1.89e-01 1.13e+01 angle pdb=" C LYS A 910 " pdb=" N ASN A 911 " pdb=" CA ASN A 911 " ideal model delta sigma weight residual 121.54 127.57 -6.03 1.91e+00 2.74e-01 9.96e+00 angle pdb=" C ASP A 350 " pdb=" N ASP A 351 " pdb=" CA ASP A 351 " ideal model delta sigma weight residual 121.54 127.49 -5.95 1.91e+00 2.74e-01 9.69e+00 angle pdb=" N GLN A 801 " pdb=" CA GLN A 801 " pdb=" CB GLN A 801 " ideal model delta sigma weight residual 110.28 114.54 -4.26 1.55e+00 4.16e-01 7.57e+00 angle pdb=" CB LYS A 441 " pdb=" CG LYS A 441 " pdb=" CD LYS A 441 " ideal model delta sigma weight residual 111.30 117.16 -5.86 2.30e+00 1.89e-01 6.50e+00 ... (remaining 19420 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.96: 7986 25.96 - 51.91: 346 51.91 - 77.87: 24 77.87 - 103.82: 6 103.82 - 129.78: 1 Dihedral angle restraints: 8363 sinusoidal: 3965 harmonic: 4398 Sorted by residual: dihedral pdb=" C5' ADP A1802 " pdb=" O5' ADP A1802 " pdb=" PA ADP A1802 " pdb=" O2A ADP A1802 " ideal model delta sinusoidal sigma weight residual 300.00 170.22 129.78 1 2.00e+01 2.50e-03 3.94e+01 dihedral pdb=" O1B ADP A1802 " pdb=" O3A ADP A1802 " pdb=" PB ADP A1802 " pdb=" PA ADP A1802 " ideal model delta sinusoidal sigma weight residual -60.00 -153.70 93.70 1 2.00e+01 2.50e-03 2.55e+01 dihedral pdb=" CA ARG A 873 " pdb=" C ARG A 873 " pdb=" N PRO A 874 " pdb=" CA PRO A 874 " ideal model delta harmonic sigma weight residual -180.00 -156.77 -23.23 0 5.00e+00 4.00e-02 2.16e+01 ... (remaining 8360 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1564 0.034 - 0.068: 471 0.068 - 0.102: 150 0.102 - 0.136: 48 0.136 - 0.170: 4 Chirality restraints: 2237 Sorted by residual: chirality pdb=" CA TYR A 519 " pdb=" N TYR A 519 " pdb=" C TYR A 519 " pdb=" CB TYR A 519 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.25e-01 chirality pdb=" CA ASP A 351 " pdb=" N ASP A 351 " pdb=" C ASP A 351 " pdb=" CB ASP A 351 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.51e-01 chirality pdb=" CA PRO A 874 " pdb=" N PRO A 874 " pdb=" C PRO A 874 " pdb=" CB PRO A 874 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.47e-01 ... (remaining 2234 not shown) Planarity restraints: 2218 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET A 768 " 0.048 5.00e-02 4.00e+02 7.33e-02 8.60e+00 pdb=" N PRO A 769 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO A 769 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 769 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A1468 " 0.018 2.00e-02 2.50e+03 1.46e-02 4.24e+00 pdb=" CG TYR A1468 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 TYR A1468 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR A1468 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR A1468 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR A1468 " 0.008 2.00e-02 2.50e+03 pdb=" CZ TYR A1468 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR A1468 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A1331 " 0.017 2.00e-02 2.50e+03 1.43e-02 3.57e+00 pdb=" CG PHE A1331 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 PHE A1331 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE A1331 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE A1331 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A1331 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A1331 " 0.003 2.00e-02 2.50e+03 ... (remaining 2215 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 308 2.66 - 3.22: 13656 3.22 - 3.78: 22865 3.78 - 4.34: 30723 4.34 - 4.90: 46438 Nonbonded interactions: 113990 Sorted by model distance: nonbonded pdb="MG MG A1801 " pdb=" O2A ADP A1802 " model vdw 2.105 2.170 nonbonded pdb=" O VAL A 608 " pdb=" NZ LYS A 611 " model vdw 2.177 3.120 nonbonded pdb=" OE1 GLN A 287 " pdb=" OG1 THR A 397 " model vdw 2.178 3.040 nonbonded pdb=" O GLU A1411 " pdb=" OH TYR A1624 " model vdw 2.194 3.040 nonbonded pdb=" O GLU A 512 " pdb=" NE2 GLN A 516 " model vdw 2.214 3.120 ... (remaining 113985 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: 0.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 15.560 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 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 : 0.002 0.054 14101 Z= 0.112 Angle : 0.547 7.726 19425 Z= 0.289 Chirality : 0.039 0.170 2237 Planarity : 0.004 0.073 2218 Dihedral : 13.504 129.779 5511 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 14.31 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.18 % Favored : 95.75 % Rotamer: Outliers : 0.07 % Allowed : 0.22 % Favored : 99.70 % 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: -0.14 (0.22), residues: 1484 helix: 0.34 (0.20), residues: 719 sheet: -0.45 (0.41), residues: 149 loop : -0.35 (0.27), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 440 TYR 0.035 0.001 TYR A1468 PHE 0.033 0.001 PHE A1331 TRP 0.008 0.001 TRP A1634 HIS 0.006 0.001 HIS A1004 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 (14101) covalent geometry : angle 0.54698 / 0.29 (19425) hydrogen bonds : bond 0.18464 / 12.54 ( 613) hydrogen bonds : angle 7.33803 / 5.24 ( 1699) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 172 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 212 MET cc_start: 0.8206 (ppp) cc_final: 0.7986 (tmm) REVERT: A 263 LYS cc_start: 0.7766 (mmmt) cc_final: 0.7443 (tptp) REVERT: A 458 MET cc_start: 0.6039 (tpt) cc_final: 0.5732 (tpt) REVERT: A 762 LEU cc_start: 0.8899 (mm) cc_final: 0.8392 (mt) REVERT: A 827 ASN cc_start: 0.8389 (m-40) cc_final: 0.7766 (m-40) REVERT: A 1029 MET cc_start: 0.6760 (mmp) cc_final: 0.6256 (ppp) REVERT: A 1209 MET cc_start: 0.8434 (ppp) cc_final: 0.7861 (ppp) REVERT: A 1408 LEU cc_start: 0.7782 (pp) cc_final: 0.7381 (mm) outliers start: 1 outliers final: 0 residues processed: 172 average time/residue: 0.1013 time to fit residues: 27.0197 Evaluate side-chains 136 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.0670 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 8.9990 overall best weight: 3.0124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 287 GLN A 354 ASN A 361 ASN A 516 GLN A 517 GLN A 562 ASN ** A 778 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 934 HIS A 954 HIS A1476 ASN A1491 ASN ** A1509 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.096230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.077004 restraints weight = 54909.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.078712 restraints weight = 33889.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.079818 restraints weight = 24667.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.080668 restraints weight = 20146.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.081060 restraints weight = 17523.674| |-----------------------------------------------------------------------------| r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 14101 Z= 0.216 Angle : 0.676 10.091 19425 Z= 0.343 Chirality : 0.043 0.173 2237 Planarity : 0.005 0.062 2218 Dihedral : 6.705 117.307 2494 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 16.04 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.26 % Favored : 94.68 % Rotamer: Outliers : 0.97 % Allowed : 9.38 % Favored : 89.65 % 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: -0.35 (0.22), residues: 1484 helix: 0.29 (0.19), residues: 707 sheet: -0.67 (0.42), residues: 150 loop : -0.58 (0.26), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 662 TYR 0.017 0.002 TYR A 917 PHE 0.026 0.002 PHE A1481 TRP 0.012 0.002 TRP A1292 HIS 0.008 0.002 HIS A 954 Details of bonding type rmsd/Z covalent geometry : bond 0.00470 / 0.22 (14101) covalent geometry : angle 0.67618 / 0.34 (19425) hydrogen bonds : bond 0.05306 / 3.48 ( 613) hydrogen bonds : angle 5.31373 / 3.73 ( 1699) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 140 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 212 MET cc_start: 0.8132 (ppp) cc_final: 0.7835 (tmm) REVERT: A 263 LYS cc_start: 0.7770 (mmmt) cc_final: 0.7350 (tptp) REVERT: A 625 MET cc_start: 0.7269 (pmm) cc_final: 0.6847 (pmm) REVERT: A 827 ASN cc_start: 0.8690 (m-40) cc_final: 0.8012 (m110) REVERT: A 908 MET cc_start: 0.6385 (ttm) cc_final: 0.6182 (ttm) REVERT: A 939 MET cc_start: 0.6289 (mmp) cc_final: 0.5957 (mmp) REVERT: A 1029 MET cc_start: 0.7371 (mmp) cc_final: 0.6513 (ppp) REVERT: A 1209 MET cc_start: 0.8401 (ppp) cc_final: 0.8096 (ppp) REVERT: A 1331 PHE cc_start: 0.6226 (m-80) cc_final: 0.5821 (m-80) REVERT: A 1456 HIS cc_start: 0.7856 (t-90) cc_final: 0.7597 (t-90) REVERT: A 1480 ASP cc_start: 0.7297 (t0) cc_final: 0.6930 (t0) REVERT: A 1607 ASP cc_start: 0.6305 (t70) cc_final: 0.6100 (t0) outliers start: 13 outliers final: 7 residues processed: 145 average time/residue: 0.0997 time to fit residues: 22.5167 Evaluate side-chains 128 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 121 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 636 ASP Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 954 HIS Chi-restraints excluded: chain A residue 1240 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 141 optimal weight: 0.0980 chunk 126 optimal weight: 0.8980 chunk 18 optimal weight: 4.9990 chunk 119 optimal weight: 0.0770 chunk 146 optimal weight: 0.8980 chunk 75 optimal weight: 8.9990 chunk 8 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 91 optimal weight: 7.9990 chunk 7 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 overall best weight: 0.5940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 227 HIS ** A 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 778 HIS ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1491 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.099604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.080092 restraints weight = 53940.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.081963 restraints weight = 32399.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.083225 restraints weight = 23161.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.084036 restraints weight = 18591.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.084463 restraints weight = 16058.930| |-----------------------------------------------------------------------------| r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14101 Z= 0.110 Angle : 0.556 8.414 19425 Z= 0.284 Chirality : 0.040 0.151 2237 Planarity : 0.004 0.053 2218 Dihedral : 6.138 98.525 2494 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.31 % Favored : 95.62 % Rotamer: Outliers : 0.97 % Allowed : 12.29 % Favored : 86.75 % 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: -0.10 (0.22), residues: 1484 helix: 0.45 (0.20), residues: 720 sheet: -0.57 (0.42), residues: 149 loop : -0.40 (0.27), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 662 TYR 0.017 0.001 TYR A 294 PHE 0.013 0.001 PHE A 378 TRP 0.008 0.001 TRP A 97 HIS 0.012 0.001 HIS A 954 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 (14101) covalent geometry : angle 0.55628 / 0.28 (19425) hydrogen bonds : bond 0.03900 / 2.57 ( 613) hydrogen bonds : angle 4.83666 / 3.39 ( 1699) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 151 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 139 ASP cc_start: 0.7058 (t0) cc_final: 0.6725 (m-30) REVERT: A 212 MET cc_start: 0.8049 (ppp) cc_final: 0.7840 (tmm) REVERT: A 243 GLU cc_start: 0.7711 (tt0) cc_final: 0.7410 (tm-30) REVERT: A 263 LYS cc_start: 0.7737 (mmmt) cc_final: 0.7278 (tptp) REVERT: A 312 ARG cc_start: 0.8488 (ttm-80) cc_final: 0.8182 (ptp-110) REVERT: A 554 ASP cc_start: 0.7197 (m-30) cc_final: 0.6975 (m-30) REVERT: A 608 VAL cc_start: 0.7698 (OUTLIER) cc_final: 0.7221 (m) REVERT: A 625 MET cc_start: 0.7660 (pmm) cc_final: 0.7232 (pmm) REVERT: A 762 LEU cc_start: 0.9002 (mm) cc_final: 0.8792 (mm) REVERT: A 827 ASN cc_start: 0.8578 (m-40) cc_final: 0.7911 (m110) REVERT: A 1029 MET cc_start: 0.7265 (mmp) cc_final: 0.6387 (ppp) REVERT: A 1209 MET cc_start: 0.8333 (ppp) cc_final: 0.8002 (ppp) REVERT: A 1331 PHE cc_start: 0.5999 (m-80) cc_final: 0.5764 (m-80) outliers start: 13 outliers final: 6 residues processed: 158 average time/residue: 0.1035 time to fit residues: 25.5236 Evaluate side-chains 135 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 128 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 636 ASP Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 1240 LEU Chi-restraints excluded: chain A residue 1374 LEU Chi-restraints excluded: chain A residue 1400 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 92 optimal weight: 10.0000 chunk 68 optimal weight: 1.9990 chunk 122 optimal weight: 7.9990 chunk 148 optimal weight: 10.9990 chunk 21 optimal weight: 6.9990 chunk 15 optimal weight: 5.9990 chunk 6 optimal weight: 0.1980 chunk 109 optimal weight: 4.9990 chunk 149 optimal weight: 7.9990 chunk 24 optimal weight: 3.9990 chunk 96 optimal weight: 8.9990 overall best weight: 3.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 257 GLN A 287 GLN ** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 HIS A1217 ASN A1491 ASN ** A1509 ASN ** 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 = 0.3883 r_free = 0.3883 target = 0.095344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.075966 restraints weight = 55166.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.077629 restraints weight = 34297.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.078825 restraints weight = 25245.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.079601 restraints weight = 20486.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.079914 restraints weight = 17872.040| |-----------------------------------------------------------------------------| r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 14101 Z= 0.235 Angle : 0.681 10.411 19425 Z= 0.343 Chirality : 0.042 0.147 2237 Planarity : 0.005 0.064 2218 Dihedral : 6.432 99.116 2494 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 16.71 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.27 % Favored : 93.67 % Rotamer: Outliers : 2.01 % Allowed : 15.19 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.22), residues: 1484 helix: 0.22 (0.20), residues: 701 sheet: -0.84 (0.40), residues: 150 loop : -0.64 (0.26), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 662 TYR 0.020 0.002 TYR A1000 PHE 0.032 0.002 PHE A 378 TRP 0.010 0.002 TRP A 593 HIS 0.007 0.002 HIS A1456 Details of bonding type rmsd/Z covalent geometry : bond 0.00519 / 0.24 (14101) covalent geometry : angle 0.68125 / 0.34 (19425) hydrogen bonds : bond 0.04721 / 3.14 ( 613) hydrogen bonds : angle 5.14815 / 3.61 ( 1699) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 130 time to evaluate : 0.538 Fit side-chains REVERT: A 263 LYS cc_start: 0.7743 (mmmt) cc_final: 0.7331 (tptp) REVERT: A 625 MET cc_start: 0.7274 (pmm) cc_final: 0.7046 (pmm) REVERT: A 939 MET cc_start: 0.6337 (mmp) cc_final: 0.5984 (mmp) REVERT: A 1029 MET cc_start: 0.7265 (mmp) cc_final: 0.6248 (ppp) REVERT: A 1209 MET cc_start: 0.8322 (ppp) cc_final: 0.8108 (ppp) REVERT: A 1480 ASP cc_start: 0.7442 (t0) cc_final: 0.7160 (t0) outliers start: 27 outliers final: 18 residues processed: 147 average time/residue: 0.1041 time to fit residues: 23.8709 Evaluate side-chains 135 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 117 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 183 ASN Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 487 MET Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 636 ASP Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 1187 THR Chi-restraints excluded: chain A residue 1206 VAL Chi-restraints excluded: chain A residue 1240 LEU Chi-restraints excluded: chain A residue 1254 LEU Chi-restraints excluded: chain A residue 1258 ILE Chi-restraints excluded: chain A residue 1376 VAL Chi-restraints excluded: chain A residue 1471 LEU Chi-restraints excluded: chain A residue 1476 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 75 optimal weight: 6.9990 chunk 26 optimal weight: 0.2980 chunk 49 optimal weight: 7.9990 chunk 128 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 35 optimal weight: 3.9990 chunk 88 optimal weight: 0.8980 chunk 150 optimal weight: 10.0000 chunk 135 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 287 GLN ** A 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 HIS ** A1267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1509 ASN ** 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 = 0.3937 r_free = 0.3937 target = 0.098439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.078919 restraints weight = 53981.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.080738 restraints weight = 32519.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.081965 restraints weight = 23340.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.082677 restraints weight = 18800.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.083250 restraints weight = 16414.566| |-----------------------------------------------------------------------------| r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14101 Z= 0.117 Angle : 0.571 10.210 19425 Z= 0.288 Chirality : 0.040 0.160 2237 Planarity : 0.004 0.082 2218 Dihedral : 6.020 87.397 2494 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.31 % Favored : 95.62 % Rotamer: Outliers : 1.56 % Allowed : 17.57 % 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: -0.19 (0.22), residues: 1484 helix: 0.41 (0.20), residues: 716 sheet: -0.65 (0.41), residues: 146 loop : -0.47 (0.27), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A1330 TYR 0.018 0.001 TYR A1000 PHE 0.017 0.001 PHE A 378 TRP 0.007 0.001 TRP A 593 HIS 0.008 0.001 HIS A 475 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (14101) covalent geometry : angle 0.57094 / 0.29 (19425) hydrogen bonds : bond 0.03670 / 2.41 ( 613) hydrogen bonds : angle 4.79675 / 3.35 ( 1699) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 139 time to evaluate : 0.522 Fit side-chains revert: symmetry clash REVERT: A 154 MET cc_start: 0.7093 (mmt) cc_final: 0.6799 (mmm) REVERT: A 212 MET cc_start: 0.8217 (ppp) cc_final: 0.7879 (tmm) REVERT: A 263 LYS cc_start: 0.7709 (mmmt) cc_final: 0.7336 (tptp) REVERT: A 762 LEU cc_start: 0.8958 (mm) cc_final: 0.8747 (mm) REVERT: A 827 ASN cc_start: 0.8340 (m-40) cc_final: 0.7738 (m110) REVERT: A 939 MET cc_start: 0.6307 (mmp) cc_final: 0.6032 (mmp) REVERT: A 967 MET cc_start: 0.0162 (mmp) cc_final: -0.0180 (mmp) REVERT: A 1029 MET cc_start: 0.7298 (mmp) cc_final: 0.6303 (ppp) REVERT: A 1209 MET cc_start: 0.8244 (ppp) cc_final: 0.7958 (ppp) outliers start: 21 outliers final: 12 residues processed: 153 average time/residue: 0.1053 time to fit residues: 25.0228 Evaluate side-chains 136 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 124 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 487 MET Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 636 ASP Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 1240 LEU Chi-restraints excluded: chain A residue 1254 LEU Chi-restraints excluded: chain A residue 1461 THR Chi-restraints excluded: chain A residue 1476 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 90 optimal weight: 7.9990 chunk 13 optimal weight: 0.9990 chunk 44 optimal weight: 0.0670 chunk 117 optimal weight: 9.9990 chunk 87 optimal weight: 7.9990 chunk 42 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 96 optimal weight: 5.9990 chunk 65 optimal weight: 0.0020 chunk 126 optimal weight: 2.9990 chunk 134 optimal weight: 0.7980 overall best weight: 0.7730 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 517 GLN ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 827 ASN A 954 HIS ** A1267 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 = 0.3950 r_free = 0.3950 target = 0.099186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.079729 restraints weight = 53495.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.081552 restraints weight = 32163.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.082801 restraints weight = 22993.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.083586 restraints weight = 18425.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.083990 restraints weight = 15983.748| |-----------------------------------------------------------------------------| r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 14101 Z= 0.111 Angle : 0.574 9.195 19425 Z= 0.289 Chirality : 0.039 0.152 2237 Planarity : 0.004 0.072 2218 Dihedral : 5.802 82.459 2494 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.58 % Favored : 95.35 % Rotamer: Outliers : 1.79 % Allowed : 17.94 % Favored : 80.27 % 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 (0.22), residues: 1484 helix: 0.59 (0.20), residues: 710 sheet: -0.90 (0.39), residues: 155 loop : -0.46 (0.27), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1330 TYR 0.019 0.001 TYR A 917 PHE 0.026 0.001 PHE A1331 TRP 0.013 0.001 TRP A 986 HIS 0.005 0.001 HIS A 475 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (14101) covalent geometry : angle 0.57423 / 0.29 (19425) hydrogen bonds : bond 0.03426 / 2.26 ( 613) hydrogen bonds : angle 4.65433 / 3.25 ( 1699) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 132 time to evaluate : 0.526 Fit side-chains revert: symmetry clash REVERT: A 263 LYS cc_start: 0.7737 (mmmt) cc_final: 0.7329 (tptp) REVERT: A 458 MET cc_start: 0.6370 (tpt) cc_final: 0.5875 (tpt) REVERT: A 625 MET cc_start: 0.7418 (pmm) cc_final: 0.6958 (pmm) REVERT: A 762 LEU cc_start: 0.8953 (mm) cc_final: 0.8728 (mm) REVERT: A 827 ASN cc_start: 0.8281 (m110) cc_final: 0.7691 (m110) REVERT: A 917 TYR cc_start: 0.7705 (m-10) cc_final: 0.7340 (m-10) REVERT: A 1029 MET cc_start: 0.7206 (mmp) cc_final: 0.6228 (ppp) REVERT: A 1209 MET cc_start: 0.8161 (ppp) cc_final: 0.7791 (ppp) outliers start: 24 outliers final: 16 residues processed: 150 average time/residue: 0.1043 time to fit residues: 24.4356 Evaluate side-chains 140 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 124 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 487 MET Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 636 ASP Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 1206 VAL Chi-restraints excluded: chain A residue 1240 LEU Chi-restraints excluded: chain A residue 1254 LEU Chi-restraints excluded: chain A residue 1374 LEU Chi-restraints excluded: chain A residue 1461 THR Chi-restraints excluded: chain A residue 1476 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 87 optimal weight: 0.0050 chunk 75 optimal weight: 4.9990 chunk 6 optimal weight: 0.0030 chunk 84 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 52 optimal weight: 7.9990 chunk 127 optimal weight: 7.9990 chunk 37 optimal weight: 0.9990 chunk 96 optimal weight: 0.3980 overall best weight: 0.8808 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 HIS ** A1267 ASN ** 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 = 0.3953 r_free = 0.3953 target = 0.099341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.079771 restraints weight = 53882.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.081600 restraints weight = 32571.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.082868 restraints weight = 23431.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.083509 restraints weight = 18794.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.084151 restraints weight = 16509.312| |-----------------------------------------------------------------------------| r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14101 Z= 0.110 Angle : 0.578 16.044 19425 Z= 0.286 Chirality : 0.039 0.150 2237 Planarity : 0.004 0.067 2218 Dihedral : 5.678 81.402 2494 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.58 % Favored : 95.35 % Rotamer: Outliers : 2.01 % Allowed : 18.24 % Favored : 79.75 % 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: -0.05 (0.22), residues: 1484 helix: 0.62 (0.20), residues: 717 sheet: -0.86 (0.39), residues: 155 loop : -0.45 (0.27), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 312 TYR 0.018 0.001 TYR A1000 PHE 0.015 0.001 PHE A1473 TRP 0.009 0.001 TRP A 986 HIS 0.005 0.001 HIS A 954 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 (14101) covalent geometry : angle 0.57755 / 0.29 (19425) hydrogen bonds : bond 0.03330 / 2.20 ( 613) hydrogen bonds : angle 4.58954 / 3.20 ( 1699) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 136 time to evaluate : 0.539 Fit side-chains revert: symmetry clash REVERT: A 263 LYS cc_start: 0.7752 (mmmt) cc_final: 0.7331 (tptp) REVERT: A 344 MET cc_start: 0.5871 (mpp) cc_final: 0.5421 (mmm) REVERT: A 458 MET cc_start: 0.6305 (tpt) cc_final: 0.5882 (tpt) REVERT: A 625 MET cc_start: 0.7350 (pmm) cc_final: 0.6911 (pmm) REVERT: A 762 LEU cc_start: 0.8957 (mm) cc_final: 0.8727 (mm) REVERT: A 827 ASN cc_start: 0.8291 (m110) cc_final: 0.7645 (m-40) REVERT: A 939 MET cc_start: 0.6128 (mmp) cc_final: 0.5763 (mmp) REVERT: A 967 MET cc_start: 0.0241 (mmp) cc_final: 0.0037 (mmp) REVERT: A 1029 MET cc_start: 0.7110 (mmp) cc_final: 0.6132 (ppp) outliers start: 27 outliers final: 18 residues processed: 154 average time/residue: 0.1052 time to fit residues: 24.9827 Evaluate side-chains 144 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 126 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 487 MET Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 636 ASP Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 1206 VAL Chi-restraints excluded: chain A residue 1240 LEU Chi-restraints excluded: chain A residue 1254 LEU Chi-restraints excluded: chain A residue 1265 THR Chi-restraints excluded: chain A residue 1374 LEU Chi-restraints excluded: chain A residue 1400 ILE Chi-restraints excluded: chain A residue 1461 THR Chi-restraints excluded: chain A residue 1476 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 132 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 47 optimal weight: 9.9990 chunk 105 optimal weight: 10.0000 chunk 23 optimal weight: 9.9990 chunk 10 optimal weight: 0.5980 chunk 143 optimal weight: 1.9990 chunk 59 optimal weight: 0.0980 chunk 16 optimal weight: 7.9990 chunk 136 optimal weight: 1.9990 chunk 111 optimal weight: 0.6980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.099641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.080062 restraints weight = 53632.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.081888 restraints weight = 32412.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.083130 restraints weight = 23308.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.083883 restraints weight = 18781.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.084441 restraints weight = 16387.204| |-----------------------------------------------------------------------------| r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14101 Z= 0.112 Angle : 0.589 11.659 19425 Z= 0.294 Chirality : 0.039 0.156 2237 Planarity : 0.004 0.062 2218 Dihedral : 5.601 80.436 2494 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.72 % Favored : 95.22 % Rotamer: Outliers : 1.64 % Allowed : 18.32 % Favored : 80.04 % 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: -0.00 (0.22), residues: 1484 helix: 0.68 (0.20), residues: 717 sheet: -0.83 (0.39), residues: 155 loop : -0.46 (0.27), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 312 TYR 0.029 0.001 TYR A 294 PHE 0.012 0.001 PHE A1331 TRP 0.009 0.001 TRP A 986 HIS 0.004 0.001 HIS A 954 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (14101) covalent geometry : angle 0.58858 / 0.29 (19425) hydrogen bonds : bond 0.03316 / 2.20 ( 613) hydrogen bonds : angle 4.54932 / 3.16 ( 1699) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 137 time to evaluate : 0.582 Fit side-chains revert: symmetry clash REVERT: A 263 LYS cc_start: 0.7640 (mmmt) cc_final: 0.7243 (tptp) REVERT: A 344 MET cc_start: 0.5915 (mpp) cc_final: 0.5475 (mmm) REVERT: A 458 MET cc_start: 0.6380 (tpt) cc_final: 0.5972 (tpt) REVERT: A 625 MET cc_start: 0.7061 (pmm) cc_final: 0.6645 (pmm) REVERT: A 762 LEU cc_start: 0.8975 (mm) cc_final: 0.8742 (mm) REVERT: A 827 ASN cc_start: 0.8303 (m110) cc_final: 0.7658 (m-40) REVERT: A 917 TYR cc_start: 0.7700 (m-10) cc_final: 0.7387 (m-10) REVERT: A 939 MET cc_start: 0.6203 (mmp) cc_final: 0.5808 (mmp) REVERT: A 1029 MET cc_start: 0.7104 (mmp) cc_final: 0.6114 (ppp) REVERT: A 1331 PHE cc_start: 0.6797 (m-10) cc_final: 0.6435 (m-80) outliers start: 22 outliers final: 18 residues processed: 152 average time/residue: 0.0973 time to fit residues: 23.4144 Evaluate side-chains 146 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 128 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 487 MET Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 589 PHE Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 636 ASP Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 1206 VAL Chi-restraints excluded: chain A residue 1240 LEU Chi-restraints excluded: chain A residue 1254 LEU Chi-restraints excluded: chain A residue 1265 THR Chi-restraints excluded: chain A residue 1374 LEU Chi-restraints excluded: chain A residue 1461 THR Chi-restraints excluded: chain A residue 1476 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 108 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 70 optimal weight: 9.9990 chunk 79 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 102 optimal weight: 0.8980 chunk 120 optimal weight: 9.9990 chunk 85 optimal weight: 0.5980 chunk 143 optimal weight: 0.9980 chunk 96 optimal weight: 0.8980 chunk 136 optimal weight: 0.1980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.099929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.080495 restraints weight = 54304.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.082307 restraints weight = 32748.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 65)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.083547 restraints weight = 23579.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.084255 restraints weight = 19049.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.084797 restraints weight = 16661.363| |-----------------------------------------------------------------------------| r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 0.2713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 14101 Z= 0.110 Angle : 0.593 14.439 19425 Z= 0.295 Chirality : 0.039 0.161 2237 Planarity : 0.004 0.059 2218 Dihedral : 5.504 78.848 2494 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.45 % Favored : 95.49 % Rotamer: Outliers : 1.41 % Allowed : 18.62 % Favored : 79.97 % 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: 1484 helix: 0.74 (0.20), residues: 717 sheet: -0.77 (0.39), residues: 155 loop : -0.40 (0.27), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 312 TYR 0.026 0.001 TYR A 294 PHE 0.029 0.001 PHE A1473 TRP 0.006 0.001 TRP A 986 HIS 0.004 0.001 HIS A 954 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (14101) covalent geometry : angle 0.59299 / 0.29 (19425) hydrogen bonds : bond 0.03277 / 2.17 ( 613) hydrogen bonds : angle 4.52319 / 3.14 ( 1699) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 136 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 263 LYS cc_start: 0.7629 (mmmt) cc_final: 0.7246 (tptp) REVERT: A 312 ARG cc_start: 0.8565 (ttm-80) cc_final: 0.8121 (ttm-80) REVERT: A 344 MET cc_start: 0.6005 (mpp) cc_final: 0.5627 (mmm) REVERT: A 458 MET cc_start: 0.6408 (tpt) cc_final: 0.6111 (tpt) REVERT: A 625 MET cc_start: 0.7046 (pmm) cc_final: 0.6660 (pmm) REVERT: A 827 ASN cc_start: 0.8301 (m110) cc_final: 0.7659 (m-40) REVERT: A 917 TYR cc_start: 0.7720 (m-10) cc_final: 0.7428 (m-10) REVERT: A 939 MET cc_start: 0.6257 (mmp) cc_final: 0.5815 (mmp) REVERT: A 995 ILE cc_start: 0.7804 (mm) cc_final: 0.7530 (mm) REVERT: A 1029 MET cc_start: 0.7094 (mmp) cc_final: 0.6123 (ppp) REVERT: A 1209 MET cc_start: 0.8628 (ppp) cc_final: 0.8290 (tmm) outliers start: 19 outliers final: 15 residues processed: 149 average time/residue: 0.1041 time to fit residues: 23.8301 Evaluate side-chains 147 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 132 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 487 MET Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 589 PHE Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 636 ASP Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 1206 VAL Chi-restraints excluded: chain A residue 1240 LEU Chi-restraints excluded: chain A residue 1254 LEU Chi-restraints excluded: chain A residue 1265 THR Chi-restraints excluded: chain A residue 1374 LEU Chi-restraints excluded: chain A residue 1461 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 47 optimal weight: 7.9990 chunk 21 optimal weight: 5.9990 chunk 62 optimal weight: 0.5980 chunk 129 optimal weight: 0.0060 chunk 61 optimal weight: 6.9990 chunk 10 optimal weight: 0.9990 chunk 111 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 97 optimal weight: 5.9990 chunk 106 optimal weight: 2.9990 chunk 151 optimal weight: 20.0000 overall best weight: 1.7202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 417 ASN ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.098375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.079194 restraints weight = 53271.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.080929 restraints weight = 32805.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.082105 restraints weight = 23773.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.082904 restraints weight = 19268.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.083275 restraints weight = 16750.490| |-----------------------------------------------------------------------------| r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14101 Z= 0.143 Angle : 0.620 14.072 19425 Z= 0.310 Chirality : 0.040 0.173 2237 Planarity : 0.004 0.062 2218 Dihedral : 5.630 81.749 2494 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.99 % Favored : 94.95 % Rotamer: Outliers : 1.49 % Allowed : 18.62 % Favored : 79.90 % 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: -0.05 (0.22), residues: 1484 helix: 0.60 (0.20), residues: 719 sheet: -0.73 (0.39), residues: 155 loop : -0.46 (0.27), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1009 TYR 0.025 0.001 TYR A 294 PHE 0.015 0.001 PHE A1473 TRP 0.009 0.001 TRP A 986 HIS 0.006 0.001 HIS A 954 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (14101) covalent geometry : angle 0.61983 / 0.31 (19425) hydrogen bonds : bond 0.03565 / 2.38 ( 613) hydrogen bonds : angle 4.64825 / 3.24 ( 1699) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 131 time to evaluate : 0.516 Fit side-chains revert: symmetry clash REVERT: A 263 LYS cc_start: 0.7762 (mmmt) cc_final: 0.7359 (tptp) REVERT: A 344 MET cc_start: 0.6114 (mpp) cc_final: 0.5710 (mmm) REVERT: A 458 MET cc_start: 0.6281 (tpt) cc_final: 0.5888 (tpt) REVERT: A 625 MET cc_start: 0.7058 (pmm) cc_final: 0.6664 (pmm) REVERT: A 827 ASN cc_start: 0.8405 (m110) cc_final: 0.7759 (m-40) REVERT: A 917 TYR cc_start: 0.7703 (m-10) cc_final: 0.7410 (m-10) REVERT: A 939 MET cc_start: 0.6311 (mmp) cc_final: 0.5782 (mmp) REVERT: A 1029 MET cc_start: 0.7123 (mmp) cc_final: 0.6137 (ppp) REVERT: A 1209 MET cc_start: 0.8682 (ppp) cc_final: 0.8402 (ppp) outliers start: 20 outliers final: 17 residues processed: 145 average time/residue: 0.1015 time to fit residues: 23.2291 Evaluate side-chains 144 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 127 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 487 MET Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 589 PHE Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 636 ASP Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 1206 VAL Chi-restraints excluded: chain A residue 1240 LEU Chi-restraints excluded: chain A residue 1254 LEU Chi-restraints excluded: chain A residue 1265 THR Chi-restraints excluded: chain A residue 1461 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 147 optimal weight: 0.9980 chunk 135 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 142 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 71 optimal weight: 6.9990 chunk 113 optimal weight: 2.9990 chunk 91 optimal weight: 6.9990 chunk 112 optimal weight: 0.9990 chunk 119 optimal weight: 8.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 HIS ** A1529 ASN ** 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 = 0.3940 r_free = 0.3940 target = 0.098641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.079619 restraints weight = 53936.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.081273 restraints weight = 33911.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.082392 restraints weight = 24988.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.083155 restraints weight = 20454.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.083554 restraints weight = 17807.469| |-----------------------------------------------------------------------------| r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 14101 Z= 0.134 Angle : 0.623 14.642 19425 Z= 0.310 Chirality : 0.040 0.187 2237 Planarity : 0.004 0.060 2218 Dihedral : 5.649 81.052 2494 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.99 % Favored : 94.95 % Rotamer: Outliers : 1.49 % Allowed : 18.84 % Favored : 79.67 % 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: -0.08 (0.22), residues: 1484 helix: 0.55 (0.20), residues: 725 sheet: -0.62 (0.40), residues: 155 loop : -0.48 (0.27), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 312 TYR 0.025 0.001 TYR A 294 PHE 0.020 0.001 PHE A1473 TRP 0.010 0.001 TRP A 986 HIS 0.007 0.001 HIS A 954 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 (14101) covalent geometry : angle 0.62285 / 0.31 (19425) hydrogen bonds : bond 0.03544 / 2.35 ( 613) hydrogen bonds : angle 4.64594 / 3.23 ( 1699) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2302.27 seconds wall clock time: 40 minutes 52.57 seconds (2452.57 seconds total)