Starting phenix.real_space_refine on Thu Sep 26 20:59:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w0c_32238/09_2024/7w0c_32238.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w0c_32238/09_2024/7w0c_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w0c_32238/09_2024/7w0c_32238.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w0c_32238/09_2024/7w0c_32238.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w0c_32238/09_2024/7w0c_32238.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w0c_32238/09_2024/7w0c_32238.cif" } resolution = 3.93 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/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: 8.01, per 1000 atoms: 0.59 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: 3.19 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 5.14 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: 7.07 Time building geometry restraints manager: 3.71 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: 8062 25.96 - 51.91: 428 51.91 - 77.87: 120 77.87 - 103.82: 6 103.82 - 129.78: 1 Dihedral angle restraints: 8617 sinusoidal: 4219 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 8614 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: 3.110 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: 0.340 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 36.370 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 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= 0.153 Angle : 0.547 7.726 19425 Z= 0.289 Chirality : 0.039 0.170 2237 Planarity : 0.004 0.073 2218 Dihedral : 16.220 129.779 5765 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (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 TRP 0.008 0.001 TRP A1634 HIS 0.006 0.001 HIS A1004 PHE 0.033 0.001 PHE A1331 TYR 0.035 0.001 TYR A1468 ARG 0.009 0.001 ARG A 440 *********************** 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 fitting. rotamer outliers: 1 poor density : 172 time to evaluate : 1.373 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: 0.2386 time to fit residues: 62.2833 Evaluate side-chains 136 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 1.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 5.9990 chunk 116 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 39 optimal weight: 4.9990 chunk 78 optimal weight: 9.9990 chunk 62 optimal weight: 7.9990 chunk 120 optimal weight: 5.9990 chunk 46 optimal weight: 0.9990 chunk 73 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 chunk 139 optimal weight: 0.4980 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 148 HIS ** A 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 287 GLN A 354 ASN A 361 ASN A 516 GLN ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 778 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 934 HIS A 954 HIS A1476 ASN ** A1509 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14101 Z= 0.214 Angle : 0.619 9.820 19425 Z= 0.312 Chirality : 0.042 0.175 2237 Planarity : 0.004 0.059 2218 Dihedral : 14.543 111.968 2748 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.85 % Favored : 95.08 % Rotamer: Outliers : 0.74 % Allowed : 8.34 % Favored : 90.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.22), residues: 1484 helix: 0.46 (0.20), residues: 719 sheet: -0.43 (0.42), residues: 148 loop : -0.41 (0.27), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1292 HIS 0.007 0.001 HIS A 954 PHE 0.016 0.002 PHE A1481 TYR 0.018 0.002 TYR A 917 ARG 0.005 0.001 ARG A 269 *********************** 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 159 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 149 time to evaluate : 1.395 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 263 LYS cc_start: 0.7719 (mmmt) cc_final: 0.7390 (tptp) REVERT: A 625 MET cc_start: 0.7787 (pmm) cc_final: 0.7436 (pmm) REVERT: A 827 ASN cc_start: 0.8548 (m-40) cc_final: 0.7918 (m-40) REVERT: A 939 MET cc_start: 0.6250 (mmp) cc_final: 0.5919 (mmp) REVERT: A 1029 MET cc_start: 0.7025 (mmp) cc_final: 0.6363 (ppp) REVERT: A 1209 MET cc_start: 0.8384 (ppp) cc_final: 0.8129 (ppp) REVERT: A 1331 PHE cc_start: 0.6276 (m-80) cc_final: 0.5875 (m-80) REVERT: A 1456 HIS cc_start: 0.7599 (t-90) cc_final: 0.7357 (t-90) REVERT: A 1607 ASP cc_start: 0.6049 (t70) cc_final: 0.5845 (t0) outliers start: 10 outliers final: 6 residues processed: 152 average time/residue: 0.2366 time to fit residues: 54.8385 Evaluate side-chains 134 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 128 time to evaluate : 1.456 ------------------------------------------------------------------------------- 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 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 77 optimal weight: 5.9990 chunk 43 optimal weight: 0.0970 chunk 116 optimal weight: 0.8980 chunk 95 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 140 optimal weight: 0.6980 chunk 151 optimal weight: 10.0000 chunk 124 optimal weight: 0.9990 chunk 138 optimal weight: 1.9990 chunk 47 optimal weight: 7.9990 chunk 112 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 562 ASN A 623 ASN A 778 HIS A 954 HIS ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1476 ASN A1491 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 14101 Z= 0.152 Angle : 0.559 7.831 19425 Z= 0.283 Chirality : 0.039 0.152 2237 Planarity : 0.004 0.053 2218 Dihedral : 14.379 97.877 2748 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.38 % Favored : 95.55 % Rotamer: Outliers : 0.97 % Allowed : 10.95 % Favored : 88.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.22), residues: 1484 helix: 0.61 (0.20), residues: 720 sheet: -0.46 (0.42), residues: 149 loop : -0.36 (0.26), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 97 HIS 0.008 0.001 HIS A 954 PHE 0.023 0.001 PHE A1481 TYR 0.015 0.001 TYR A 88 ARG 0.004 0.000 ARG A 269 *********************** 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 162 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 149 time to evaluate : 1.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 263 LYS cc_start: 0.7748 (mmmt) cc_final: 0.7358 (tptp) REVERT: A 312 ARG cc_start: 0.8414 (ttm-80) cc_final: 0.8141 (ptp-110) REVERT: A 458 MET cc_start: 0.6335 (tpt) cc_final: 0.5842 (tpt) REVERT: A 608 VAL cc_start: 0.7723 (OUTLIER) cc_final: 0.7331 (m) REVERT: A 625 MET cc_start: 0.7608 (pmm) cc_final: 0.7175 (pmm) REVERT: A 827 ASN cc_start: 0.8561 (m-40) cc_final: 0.7937 (m110) REVERT: A 1029 MET cc_start: 0.7101 (mmp) cc_final: 0.6396 (ppp) REVERT: A 1209 MET cc_start: 0.8295 (ppp) cc_final: 0.7986 (ppp) REVERT: A 1331 PHE cc_start: 0.5973 (m-80) cc_final: 0.5728 (m-80) outliers start: 13 outliers final: 5 residues processed: 158 average time/residue: 0.2305 time to fit residues: 55.9900 Evaluate side-chains 131 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 125 time to evaluate : 1.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 GLU Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 636 ASP Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 1240 LEU Chi-restraints excluded: chain A residue 1374 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 138 optimal weight: 1.9990 chunk 105 optimal weight: 0.0370 chunk 72 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 94 optimal weight: 8.9990 chunk 140 optimal weight: 5.9990 chunk 148 optimal weight: 10.0000 chunk 73 optimal weight: 10.0000 chunk 133 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 overall best weight: 1.5464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 227 HIS ** 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** A1491 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 14101 Z= 0.195 Angle : 0.574 8.839 19425 Z= 0.288 Chirality : 0.039 0.144 2237 Planarity : 0.004 0.056 2218 Dihedral : 14.253 91.076 2748 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.85 % Favored : 95.08 % Rotamer: Outliers : 1.41 % Allowed : 13.25 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.22), residues: 1484 helix: 0.62 (0.20), residues: 719 sheet: -0.58 (0.42), residues: 149 loop : -0.44 (0.26), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1292 HIS 0.005 0.001 HIS A1004 PHE 0.033 0.001 PHE A 378 TYR 0.017 0.001 TYR A1000 ARG 0.004 0.000 ARG A 662 *********************** 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 149 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 130 time to evaluate : 1.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 263 LYS cc_start: 0.7683 (mmmt) cc_final: 0.7352 (tptp) REVERT: A 608 VAL cc_start: 0.7970 (OUTLIER) cc_final: 0.7654 (m) REVERT: A 827 ASN cc_start: 0.8498 (m-40) cc_final: 0.7812 (m110) REVERT: A 917 TYR cc_start: 0.7669 (m-10) cc_final: 0.7288 (m-10) REVERT: A 939 MET cc_start: 0.6264 (mmp) cc_final: 0.5941 (mmp) REVERT: A 1029 MET cc_start: 0.7324 (mmp) cc_final: 0.6446 (ppp) REVERT: A 1209 MET cc_start: 0.8248 (ppp) cc_final: 0.7885 (ppp) outliers start: 19 outliers final: 11 residues processed: 145 average time/residue: 0.2382 time to fit residues: 52.8519 Evaluate side-chains 133 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 121 time to evaluate : 1.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 183 ASN Chi-restraints excluded: chain A residue 243 GLU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 608 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 1240 LEU Chi-restraints excluded: chain A residue 1374 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 123 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 110 optimal weight: 4.9990 chunk 61 optimal weight: 5.9990 chunk 127 optimal weight: 0.8980 chunk 102 optimal weight: 0.2980 chunk 0 optimal weight: 10.0000 chunk 76 optimal weight: 3.9990 chunk 133 optimal weight: 5.9990 chunk 37 optimal weight: 0.0570 overall best weight: 1.0500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 227 HIS ** 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** A1491 ASN ** A1509 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 14101 Z= 0.160 Angle : 0.544 9.946 19425 Z= 0.276 Chirality : 0.039 0.146 2237 Planarity : 0.004 0.053 2218 Dihedral : 14.158 82.841 2748 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.78 % Favored : 95.15 % Rotamer: Outliers : 1.86 % Allowed : 14.30 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.22), residues: 1484 helix: 0.65 (0.20), residues: 720 sheet: -0.61 (0.41), residues: 149 loop : -0.42 (0.27), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1292 HIS 0.005 0.001 HIS A1004 PHE 0.040 0.001 PHE A1331 TYR 0.017 0.001 TYR A 917 ARG 0.003 0.000 ARG A 662 *********************** 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 158 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 133 time to evaluate : 1.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.7274 (tm-30) REVERT: A 263 LYS cc_start: 0.7717 (mmmt) cc_final: 0.7373 (tptp) REVERT: A 312 ARG cc_start: 0.8495 (ttm-80) cc_final: 0.8217 (ptp-110) REVERT: A 458 MET cc_start: 0.6198 (tpt) cc_final: 0.5721 (tpt) REVERT: A 625 MET cc_start: 0.7247 (pmm) cc_final: 0.6801 (pmm) REVERT: A 827 ASN cc_start: 0.8486 (m-40) cc_final: 0.7900 (m110) REVERT: A 917 TYR cc_start: 0.7735 (m-10) cc_final: 0.7375 (m-10) REVERT: A 939 MET cc_start: 0.6235 (mmp) cc_final: 0.6012 (mmp) REVERT: A 967 MET cc_start: -0.0074 (mmp) cc_final: -0.0427 (mmp) REVERT: A 1029 MET cc_start: 0.7356 (mmp) cc_final: 0.6445 (ppp) REVERT: A 1209 MET cc_start: 0.8153 (ppp) cc_final: 0.7771 (ppp) REVERT: A 1389 MET cc_start: 0.7106 (mmp) cc_final: 0.6812 (mmm) REVERT: A 1607 ASP cc_start: 0.6629 (t70) cc_final: 0.6336 (t0) outliers start: 25 outliers final: 13 residues processed: 154 average time/residue: 0.2342 time to fit residues: 55.4844 Evaluate side-chains 138 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 124 time to evaluate : 1.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 243 GLU Chi-restraints excluded: chain A residue 316 THR 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 1206 VAL Chi-restraints excluded: chain A residue 1240 LEU Chi-restraints excluded: chain A residue 1265 THR Chi-restraints excluded: chain A residue 1374 LEU 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 50 optimal weight: 7.9990 chunk 134 optimal weight: 0.0970 chunk 29 optimal weight: 4.9990 chunk 87 optimal weight: 0.8980 chunk 36 optimal weight: 0.3980 chunk 149 optimal weight: 8.9990 chunk 123 optimal weight: 0.5980 chunk 68 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 49 optimal weight: 5.9990 chunk 78 optimal weight: 8.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 HIS ** A1509 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 14101 Z= 0.143 Angle : 0.543 9.507 19425 Z= 0.273 Chirality : 0.039 0.147 2237 Planarity : 0.004 0.052 2218 Dihedral : 14.057 77.815 2748 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.38 % Favored : 95.55 % Rotamer: Outliers : 1.49 % Allowed : 15.79 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.23), residues: 1484 helix: 0.78 (0.20), residues: 716 sheet: -0.54 (0.40), residues: 149 loop : -0.39 (0.27), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 986 HIS 0.004 0.001 HIS A 323 PHE 0.027 0.001 PHE A1481 TYR 0.017 0.001 TYR A1000 ARG 0.004 0.000 ARG A 998 *********************** 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 165 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 145 time to evaluate : 1.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7213 (tm-30) REVERT: A 263 LYS cc_start: 0.7600 (mmmt) cc_final: 0.7279 (tptp) REVERT: A 312 ARG cc_start: 0.8491 (ttm-80) cc_final: 0.8283 (ptp-110) REVERT: A 331 GLU cc_start: 0.7380 (pp20) cc_final: 0.7082 (pp20) REVERT: A 458 MET cc_start: 0.6163 (tpt) cc_final: 0.5852 (tpt) REVERT: A 554 ASP cc_start: 0.7062 (m-30) cc_final: 0.6759 (m-30) REVERT: A 625 MET cc_start: 0.7266 (pmm) cc_final: 0.6840 (pmm) REVERT: A 827 ASN cc_start: 0.8416 (m-40) cc_final: 0.7843 (m110) REVERT: A 939 MET cc_start: 0.5955 (mmp) cc_final: 0.5727 (mmp) REVERT: A 967 MET cc_start: 0.0013 (mmp) cc_final: -0.0305 (mmp) REVERT: A 1029 MET cc_start: 0.7359 (mmp) cc_final: 0.6441 (ppp) REVERT: A 1209 MET cc_start: 0.8078 (ppp) cc_final: 0.7687 (ppp) REVERT: A 1389 MET cc_start: 0.7024 (mmp) cc_final: 0.6748 (mmp) outliers start: 20 outliers final: 17 residues processed: 159 average time/residue: 0.2372 time to fit residues: 57.6452 Evaluate side-chains 141 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 123 time to evaluate : 1.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 243 GLU Chi-restraints excluded: chain A residue 316 THR 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 869 GLN Chi-restraints excluded: chain A residue 999 MET Chi-restraints excluded: chain A residue 1206 VAL 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 1476 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 143 optimal weight: 5.9990 chunk 16 optimal weight: 7.9990 chunk 84 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 148 optimal weight: 10.0000 chunk 92 optimal weight: 4.9990 chunk 90 optimal weight: 7.9990 chunk 68 optimal weight: 0.9980 chunk 91 optimal weight: 9.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 14101 Z= 0.321 Angle : 0.650 7.438 19425 Z= 0.333 Chirality : 0.042 0.149 2237 Planarity : 0.005 0.054 2218 Dihedral : 14.171 88.091 2748 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.93 % Favored : 94.00 % Rotamer: Outliers : 2.38 % Allowed : 16.75 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.22), residues: 1484 helix: 0.44 (0.20), residues: 707 sheet: -0.73 (0.39), residues: 151 loop : -0.52 (0.26), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 986 HIS 0.007 0.001 HIS A 954 PHE 0.029 0.002 PHE A1481 TYR 0.022 0.002 TYR A1000 ARG 0.006 0.001 ARG A 662 *********************** 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 154 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 122 time to evaluate : 1.465 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 243 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7390 (tm-30) REVERT: A 263 LYS cc_start: 0.7713 (mmmt) cc_final: 0.7375 (tptp) REVERT: A 331 GLU cc_start: 0.7544 (pp20) cc_final: 0.7306 (pp20) REVERT: A 625 MET cc_start: 0.6964 (pmm) cc_final: 0.6479 (pmm) REVERT: A 827 ASN cc_start: 0.8607 (m-40) cc_final: 0.8000 (m110) REVERT: A 1029 MET cc_start: 0.7290 (mmp) cc_final: 0.6262 (ppp) REVERT: A 1209 MET cc_start: 0.8132 (ppp) cc_final: 0.7789 (ppp) REVERT: A 1480 ASP cc_start: 0.7345 (t0) cc_final: 0.7004 (t0) outliers start: 32 outliers final: 20 residues processed: 144 average time/residue: 0.2397 time to fit residues: 52.3965 Evaluate side-chains 135 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 114 time to evaluate : 1.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 243 GLU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 404 LEU 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 1376 VAL Chi-restraints excluded: chain A residue 1444 PHE Chi-restraints excluded: chain A residue 1471 LEU 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 59 optimal weight: 3.9990 chunk 88 optimal weight: 0.2980 chunk 44 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 chunk 94 optimal weight: 5.9990 chunk 101 optimal weight: 5.9990 chunk 73 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 116 optimal weight: 0.8980 chunk 135 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 HIS A1491 ASN ** A1529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 14101 Z= 0.163 Angle : 0.569 9.153 19425 Z= 0.288 Chirality : 0.039 0.147 2237 Planarity : 0.004 0.053 2218 Dihedral : 14.129 82.518 2748 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.65 % Favored : 95.28 % Rotamer: Outliers : 2.08 % Allowed : 17.72 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.22), residues: 1484 helix: 0.61 (0.20), residues: 712 sheet: -0.76 (0.38), residues: 155 loop : -0.34 (0.27), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 986 HIS 0.006 0.001 HIS A 954 PHE 0.027 0.001 PHE A1481 TYR 0.019 0.001 TYR A 917 ARG 0.006 0.000 ARG A 312 *********************** 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 fitting. rotamer outliers: 28 poor density : 131 time to evaluate : 1.494 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 243 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.7310 (tm-30) REVERT: A 263 LYS cc_start: 0.7715 (mmmt) cc_final: 0.7356 (tptp) REVERT: A 360 MET cc_start: 0.8550 (mmm) cc_final: 0.8145 (tpp) REVERT: A 458 MET cc_start: 0.6260 (tpt) cc_final: 0.5883 (tpt) REVERT: A 625 MET cc_start: 0.6977 (pmm) cc_final: 0.6578 (pmm) REVERT: A 827 ASN cc_start: 0.8488 (m-40) cc_final: 0.7940 (m110) REVERT: A 917 TYR cc_start: 0.7390 (m-10) cc_final: 0.7136 (m-10) REVERT: A 939 MET cc_start: 0.5954 (mmp) cc_final: 0.5692 (mmp) REVERT: A 967 MET cc_start: -0.0410 (mmp) cc_final: -0.0677 (mmp) REVERT: A 1029 MET cc_start: 0.7229 (mmp) cc_final: 0.6294 (ppp) REVERT: A 1209 MET cc_start: 0.8074 (ppp) cc_final: 0.7785 (ppp) REVERT: A 1389 MET cc_start: 0.7055 (mmp) cc_final: 0.6814 (mmp) outliers start: 28 outliers final: 17 residues processed: 147 average time/residue: 0.2552 time to fit residues: 55.8012 Evaluate side-chains 141 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 123 time to evaluate : 1.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 243 GLU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 404 LEU 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 1240 LEU Chi-restraints excluded: chain A residue 1254 LEU Chi-restraints excluded: chain A residue 1265 THR Chi-restraints excluded: chain A residue 1291 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 142 optimal weight: 0.0270 chunk 129 optimal weight: 10.0000 chunk 138 optimal weight: 0.8980 chunk 83 optimal weight: 0.0170 chunk 60 optimal weight: 0.4980 chunk 108 optimal weight: 1.9990 chunk 42 optimal weight: 6.9990 chunk 124 optimal weight: 2.9990 chunk 130 optimal weight: 6.9990 chunk 137 optimal weight: 0.8980 chunk 90 optimal weight: 8.9990 overall best weight: 0.4676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1529 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.2682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 14101 Z= 0.149 Angle : 0.565 9.460 19425 Z= 0.284 Chirality : 0.039 0.151 2237 Planarity : 0.004 0.051 2218 Dihedral : 13.997 77.812 2748 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.58 % Favored : 95.35 % Rotamer: Outliers : 1.64 % Allowed : 17.80 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.23), residues: 1484 helix: 0.80 (0.20), residues: 714 sheet: -0.67 (0.39), residues: 155 loop : -0.32 (0.27), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 986 HIS 0.005 0.001 HIS A1004 PHE 0.022 0.001 PHE A1481 TYR 0.020 0.001 TYR A1000 ARG 0.005 0.000 ARG A1041 *********************** 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 158 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 136 time to evaluate : 1.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7383 (tm-30) REVERT: A 263 LYS cc_start: 0.7597 (mmmt) cc_final: 0.7292 (tptp) REVERT: A 344 MET cc_start: 0.5746 (mpp) cc_final: 0.5542 (mpp) REVERT: A 458 MET cc_start: 0.6155 (tpt) cc_final: 0.5877 (tpt) REVERT: A 625 MET cc_start: 0.6977 (pmm) cc_final: 0.6636 (pmm) REVERT: A 827 ASN cc_start: 0.8515 (m-40) cc_final: 0.7965 (m110) REVERT: A 939 MET cc_start: 0.6035 (mmp) cc_final: 0.5642 (mmp) REVERT: A 1029 MET cc_start: 0.7185 (mmp) cc_final: 0.6189 (ppp) REVERT: A 1389 MET cc_start: 0.6932 (mmp) cc_final: 0.6416 (mmp) outliers start: 22 outliers final: 17 residues processed: 150 average time/residue: 0.2398 time to fit residues: 55.2906 Evaluate side-chains 145 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 127 time to evaluate : 1.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 GLU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 404 LEU 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 758 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 1291 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 146 optimal weight: 0.3980 chunk 89 optimal weight: 0.6980 chunk 69 optimal weight: 0.8980 chunk 101 optimal weight: 3.9990 chunk 153 optimal weight: 8.9990 chunk 141 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 12 optimal weight: 0.4980 chunk 94 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 227 HIS ** 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** A1529 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14101 Z= 0.166 Angle : 0.593 8.792 19425 Z= 0.300 Chirality : 0.040 0.282 2237 Planarity : 0.004 0.052 2218 Dihedral : 13.965 77.440 2748 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.65 % Favored : 95.28 % Rotamer: Outliers : 1.49 % Allowed : 18.17 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.23), residues: 1484 helix: 0.78 (0.20), residues: 712 sheet: -0.59 (0.39), residues: 155 loop : -0.30 (0.27), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 986 HIS 0.006 0.001 HIS A 954 PHE 0.022 0.001 PHE A1001 TYR 0.030 0.001 TYR A1000 ARG 0.003 0.000 ARG A 998 ********************** 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 155 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 135 time to evaluate : 1.550 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 243 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.7405 (tm-30) REVERT: A 263 LYS cc_start: 0.7600 (mmmt) cc_final: 0.7300 (tptp) REVERT: A 458 MET cc_start: 0.6229 (tpt) cc_final: 0.5942 (tpt) REVERT: A 625 MET cc_start: 0.7051 (pmm) cc_final: 0.6701 (pmm) REVERT: A 827 ASN cc_start: 0.8349 (m110) cc_final: 0.7765 (m110) REVERT: A 939 MET cc_start: 0.6046 (mmp) cc_final: 0.5539 (mmp) REVERT: A 1029 MET cc_start: 0.7212 (mmp) cc_final: 0.6229 (ppp) REVERT: A 1389 MET cc_start: 0.6889 (mmp) cc_final: 0.6433 (mmp) outliers start: 20 outliers final: 16 residues processed: 145 average time/residue: 0.2492 time to fit residues: 55.1840 Evaluate side-chains 143 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 126 time to evaluate : 1.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 243 GLU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 404 LEU 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 758 LEU Chi-restraints excluded: chain A residue 954 HIS Chi-restraints excluded: chain A residue 1240 LEU Chi-restraints excluded: chain A residue 1254 LEU Chi-restraints excluded: chain A residue 1291 LEU Chi-restraints excluded: chain A residue 1461 THR Chi-restraints excluded: chain A residue 1529 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 chunk 18 optimal weight: 0.4980 chunk 33 optimal weight: 0.9990 chunk 122 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 125 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 22 optimal weight: 6.9990 chunk 107 optimal weight: 4.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 GLN ** 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** A1491 ASN ** A1529 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 = 0.3973 r_free = 0.3973 target = 0.100286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.080966 restraints weight = 53142.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.082797 restraints weight = 32066.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.084070 restraints weight = 22970.152| |-----------------------------------------------------------------------------| r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14101 Z= 0.172 Angle : 0.606 10.187 19425 Z= 0.304 Chirality : 0.040 0.289 2237 Planarity : 0.004 0.051 2218 Dihedral : 13.953 77.222 2748 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.92 % Favored : 95.01 % Rotamer: Outliers : 1.71 % Allowed : 18.32 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.23), residues: 1484 helix: 0.81 (0.20), residues: 714 sheet: -0.39 (0.40), residues: 147 loop : -0.34 (0.27), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 986 HIS 0.004 0.001 HIS A1004 PHE 0.032 0.001 PHE A1473 TYR 0.026 0.001 TYR A1000 ARG 0.004 0.000 ARG A 943 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2508.10 seconds wall clock time: 48 minutes 15.29 seconds (2895.29 seconds total)