Starting phenix.real_space_refine on Tue Nov 18 12:28:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7w0c_32238/11_2025/7w0c_32238.cif Found real_map, /net/cci-nas-00/data/ceres_data/7w0c_32238/11_2025/7w0c_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_32238/11_2025/7w0c_32238.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7w0c_32238/11_2025/7w0c_32238.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7w0c_32238/11_2025/7w0c_32238.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7w0c_32238/11_2025/7w0c_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-2.0-5881/lib/python3.9/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: 3.35, per 1000 atoms: 0.25 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: 1.04 Conformation dependent library (CDL) restraints added in 614.7 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: 1.99 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: 3.68 Time building geometry restraints manager: 1.34 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: 1.350 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 16.520 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.590 ------------------------------------------------------------------------------- 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= 0.112 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 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 covalent geometry : bond 0.00234 (14101) covalent geometry : angle 0.54698 (19425) hydrogen bonds : bond 0.18464 ( 613) hydrogen bonds : angle 7.33803 ( 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 : 0.530 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: 0.1093 time to fit residues: 29.0780 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 : 0.521 ------------------------------------------------------------------------------- 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: 7.9990 overall best weight: 3.0124 ------------------------------------------------------------------------------- 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 ** 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 A1217 ASN A1476 ASN A1491 ASN ** A1509 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.096423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.076941 restraints weight = 55108.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.078721 restraints weight = 33518.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.079947 restraints weight = 24175.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.080747 restraints weight = 19509.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.081246 restraints weight = 16993.834| |-----------------------------------------------------------------------------| r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 14101 Z= 0.216 Angle : 0.674 9.772 19425 Z= 0.341 Chirality : 0.043 0.172 2237 Planarity : 0.005 0.060 2218 Dihedral : 14.613 118.411 2748 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 15.70 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.19 % Favored : 94.74 % Rotamer: Outliers : 0.97 % Allowed : 8.94 % Favored : 90.10 % 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: -0.34 (0.22), residues: 1484 helix: 0.31 (0.19), residues: 705 sheet: -0.66 (0.42), residues: 150 loop : -0.58 (0.26), residues: 629 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 0.013 0.002 TRP A1292 HIS 0.008 0.002 HIS A 954 Details of bonding type rmsd covalent geometry : bond 0.00471 (14101) covalent geometry : angle 0.67378 (19425) hydrogen bonds : bond 0.05353 ( 613) hydrogen bonds : angle 5.33484 ( 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 152 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 139 time to evaluate : 0.510 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 212 MET cc_start: 0.8155 (ppp) cc_final: 0.7867 (tmm) REVERT: A 263 LYS cc_start: 0.7788 (mmmt) cc_final: 0.7350 (tptp) REVERT: A 625 MET cc_start: 0.7264 (pmm) cc_final: 0.6843 (pmm) REVERT: A 827 ASN cc_start: 0.8674 (m-40) cc_final: 0.7983 (m110) REVERT: A 939 MET cc_start: 0.6333 (mmp) cc_final: 0.6029 (mmp) REVERT: A 1029 MET cc_start: 0.7211 (mmp) cc_final: 0.6426 (ppp) REVERT: A 1209 MET cc_start: 0.8396 (ppp) cc_final: 0.8112 (ppp) REVERT: A 1331 PHE cc_start: 0.6201 (m-80) cc_final: 0.5813 (m-80) REVERT: A 1456 HIS cc_start: 0.7836 (t-90) cc_final: 0.7563 (t-90) REVERT: A 1494 MET cc_start: 0.6174 (ppp) cc_final: 0.5969 (ppp) outliers start: 13 outliers final: 7 residues processed: 144 average time/residue: 0.1109 time to fit residues: 24.6426 Evaluate side-chains 129 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 122 time to evaluate : 0.516 ------------------------------------------------------------------------------- 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: 0.7980 chunk 126 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 119 optimal weight: 10.0000 chunk 146 optimal weight: 0.8980 chunk 75 optimal weight: 8.9990 chunk 8 optimal weight: 4.9990 chunk 101 optimal weight: 0.7980 chunk 91 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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** A1491 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.098629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.079091 restraints weight = 54486.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.080933 restraints weight = 32741.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.082203 restraints weight = 23500.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.082955 restraints weight = 18917.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.083319 restraints weight = 16467.828| |-----------------------------------------------------------------------------| r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14101 Z= 0.124 Angle : 0.570 7.743 19425 Z= 0.290 Chirality : 0.040 0.151 2237 Planarity : 0.004 0.054 2218 Dihedral : 14.482 103.334 2748 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.72 % Favored : 95.22 % Rotamer: Outliers : 1.27 % Allowed : 11.99 % 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: -0.20 (0.22), residues: 1484 helix: 0.38 (0.19), residues: 719 sheet: -0.61 (0.42), residues: 149 loop : -0.46 (0.26), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 662 TYR 0.017 0.001 TYR A 294 PHE 0.012 0.001 PHE A1648 TRP 0.007 0.001 TRP A 97 HIS 0.013 0.001 HIS A 954 Details of bonding type rmsd covalent geometry : bond 0.00266 (14101) covalent geometry : angle 0.57016 (19425) hydrogen bonds : bond 0.04093 ( 613) hydrogen bonds : angle 4.92602 ( 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 163 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 146 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 MET cc_start: 0.8083 (ppp) cc_final: 0.7875 (tmm) REVERT: A 263 LYS cc_start: 0.7742 (mmmt) cc_final: 0.7336 (tptp) REVERT: A 608 VAL cc_start: 0.7710 (OUTLIER) cc_final: 0.6881 (p) REVERT: A 625 MET cc_start: 0.7628 (pmm) cc_final: 0.7171 (pmm) REVERT: A 762 LEU cc_start: 0.8953 (mm) cc_final: 0.8736 (mm) REVERT: A 827 ASN cc_start: 0.8602 (m-40) cc_final: 0.7936 (m110) REVERT: A 1029 MET cc_start: 0.7287 (mmp) cc_final: 0.6389 (ppp) REVERT: A 1209 MET cc_start: 0.8318 (ppp) cc_final: 0.8033 (ppp) REVERT: A 1331 PHE cc_start: 0.6025 (m-80) cc_final: 0.5783 (m-80) REVERT: A 1480 ASP cc_start: 0.7239 (t0) cc_final: 0.6936 (t0) REVERT: A 1494 MET cc_start: 0.6477 (ppp) cc_final: 0.6266 (ppp) outliers start: 17 outliers final: 9 residues processed: 157 average time/residue: 0.1063 time to fit residues: 25.7869 Evaluate side-chains 135 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 125 time to evaluate : 0.497 ------------------------------------------------------------------------------- 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 590 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 758 LEU Chi-restraints excluded: chain A residue 796 LEU 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 92 optimal weight: 7.9990 chunk 68 optimal weight: 0.9990 chunk 122 optimal weight: 7.9990 chunk 148 optimal weight: 10.0000 chunk 21 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 6 optimal weight: 7.9990 chunk 109 optimal weight: 0.7980 chunk 149 optimal weight: 7.9990 chunk 24 optimal weight: 3.9990 chunk 96 optimal weight: 8.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 257 GLN ** A 417 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.095582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.076235 restraints weight = 55059.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.077956 restraints weight = 34184.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.079122 restraints weight = 24918.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.079899 restraints weight = 20271.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.080134 restraints weight = 17637.157| |-----------------------------------------------------------------------------| r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 14101 Z= 0.220 Angle : 0.661 10.363 19425 Z= 0.333 Chirality : 0.042 0.145 2237 Planarity : 0.005 0.058 2218 Dihedral : 14.436 100.129 2748 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 15.92 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.93 % Favored : 94.00 % Rotamer: Outliers : 2.16 % Allowed : 14.89 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.22), residues: 1484 helix: 0.21 (0.19), residues: 703 sheet: -0.82 (0.41), residues: 150 loop : -0.67 (0.26), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 662 TYR 0.018 0.002 TYR A 917 PHE 0.030 0.002 PHE A 378 TRP 0.010 0.002 TRP A 593 HIS 0.006 0.002 HIS A1456 Details of bonding type rmsd covalent geometry : bond 0.00484 (14101) covalent geometry : angle 0.66081 (19425) hydrogen bonds : bond 0.04597 ( 613) hydrogen bonds : angle 5.13137 ( 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 161 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 132 time to evaluate : 0.510 Fit side-chains revert: symmetry clash REVERT: A 263 LYS cc_start: 0.7754 (mmmt) cc_final: 0.7295 (tptp) REVERT: A 625 MET cc_start: 0.7406 (pmm) cc_final: 0.7170 (pmm) REVERT: A 939 MET cc_start: 0.6399 (mmp) cc_final: 0.6067 (mmp) REVERT: A 1029 MET cc_start: 0.7292 (mmp) cc_final: 0.6287 (ppp) REVERT: A 1480 ASP cc_start: 0.7323 (t0) cc_final: 0.7014 (t0) REVERT: A 1607 ASP cc_start: 0.6849 (t70) cc_final: 0.6464 (t0) REVERT: A 1610 LYS cc_start: 0.7424 (tppt) cc_final: 0.7174 (tppt) outliers start: 29 outliers final: 19 residues processed: 151 average time/residue: 0.1091 time to fit residues: 25.4426 Evaluate side-chains 139 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 120 time to evaluate : 0.490 ------------------------------------------------------------------------------- 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 243 GLU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 574 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 1220 LEU Chi-restraints excluded: chain A residue 1240 LEU Chi-restraints excluded: chain A residue 1254 LEU 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: 0.7980 chunk 49 optimal weight: 7.9990 chunk 128 optimal weight: 0.2980 chunk 27 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 88 optimal weight: 0.6980 chunk 150 optimal weight: 10.0000 chunk 135 optimal weight: 0.8980 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 ** 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** A1329 ASN ** 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 = 0.3945 r_free = 0.3945 target = 0.098831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.079336 restraints weight = 54014.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.081168 restraints weight = 32406.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.082433 restraints weight = 23180.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.083083 restraints weight = 18615.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.083697 restraints weight = 16308.259| |-----------------------------------------------------------------------------| r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 14101 Z= 0.112 Angle : 0.568 9.478 19425 Z= 0.288 Chirality : 0.040 0.152 2237 Planarity : 0.004 0.056 2218 Dihedral : 14.313 86.603 2748 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.38 % Favored : 95.55 % Rotamer: Outliers : 1.49 % Allowed : 16.98 % Favored : 81.53 % 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: 0.40 (0.20), residues: 717 sheet: -0.64 (0.41), residues: 147 loop : -0.46 (0.27), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1330 TYR 0.015 0.001 TYR A 294 PHE 0.018 0.001 PHE A 378 TRP 0.007 0.001 TRP A1634 HIS 0.008 0.001 HIS A 475 Details of bonding type rmsd covalent geometry : bond 0.00242 (14101) covalent geometry : angle 0.56805 (19425) hydrogen bonds : bond 0.03614 ( 613) hydrogen bonds : angle 4.76621 ( 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 163 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 143 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 212 MET cc_start: 0.8170 (ppp) cc_final: 0.7843 (tmm) REVERT: A 243 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.7354 (tm-30) REVERT: A 263 LYS cc_start: 0.7714 (mmmt) cc_final: 0.7330 (tptp) REVERT: A 762 LEU cc_start: 0.8966 (mm) cc_final: 0.8733 (mm) REVERT: A 827 ASN cc_start: 0.8407 (m-40) cc_final: 0.7832 (m110) REVERT: A 939 MET cc_start: 0.6020 (mmp) cc_final: 0.5785 (mmp) REVERT: A 967 MET cc_start: 0.0166 (mmp) cc_final: -0.0175 (mmp) REVERT: A 1029 MET cc_start: 0.7211 (mmp) cc_final: 0.6209 (ppp) REVERT: A 1209 MET cc_start: 0.8519 (ppp) cc_final: 0.8220 (ppp) REVERT: A 1610 LYS cc_start: 0.7424 (tppt) cc_final: 0.7179 (tppt) outliers start: 20 outliers final: 9 residues processed: 158 average time/residue: 0.1077 time to fit residues: 26.1627 Evaluate side-chains 136 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 126 time to evaluate : 0.519 ------------------------------------------------------------------------------- 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 574 ILE Chi-restraints excluded: chain A residue 590 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 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: 0.3980 chunk 13 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 117 optimal weight: 7.9990 chunk 87 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 96 optimal weight: 0.0570 chunk 65 optimal weight: 0.2980 chunk 126 optimal weight: 3.9990 chunk 134 optimal weight: 0.7980 overall best weight: 0.4898 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 227 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 827 ASN 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 = 0.3966 r_free = 0.3966 target = 0.100068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.080564 restraints weight = 53419.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.082405 restraints weight = 32138.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.083688 restraints weight = 23003.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.084481 restraints weight = 18413.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 58)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.085014 restraints weight = 15953.633| |-----------------------------------------------------------------------------| r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 14101 Z= 0.107 Angle : 0.574 13.930 19425 Z= 0.285 Chirality : 0.039 0.155 2237 Planarity : 0.004 0.054 2218 Dihedral : 14.137 79.692 2748 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.65 % Favored : 95.28 % Rotamer: Outliers : 1.34 % Allowed : 17.42 % Favored : 81.24 % 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: -0.04 (0.23), residues: 1484 helix: 0.58 (0.20), residues: 713 sheet: -0.75 (0.40), residues: 155 loop : -0.40 (0.27), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 312 TYR 0.020 0.001 TYR A 917 PHE 0.022 0.001 PHE A1331 TRP 0.011 0.001 TRP A 986 HIS 0.005 0.001 HIS A 475 Details of bonding type rmsd covalent geometry : bond 0.00234 (14101) covalent geometry : angle 0.57430 (19425) hydrogen bonds : bond 0.03339 ( 613) hydrogen bonds : angle 4.58889 ( 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 155 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 137 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.7312 (tm-30) REVERT: A 263 LYS cc_start: 0.7737 (mmmt) cc_final: 0.7328 (tptp) REVERT: A 312 ARG cc_start: 0.8571 (ttm-80) cc_final: 0.8240 (ptp-110) REVERT: A 458 MET cc_start: 0.6165 (tpt) cc_final: 0.5817 (tpt) REVERT: A 625 MET cc_start: 0.7403 (pmm) cc_final: 0.6962 (pmm) REVERT: A 762 LEU cc_start: 0.8990 (mm) cc_final: 0.8761 (mm) REVERT: A 827 ASN cc_start: 0.8268 (m110) cc_final: 0.7685 (m110) REVERT: A 917 TYR cc_start: 0.7698 (m-10) cc_final: 0.7338 (m-10) REVERT: A 967 MET cc_start: 0.0399 (mmp) cc_final: 0.0162 (mmp) REVERT: A 1029 MET cc_start: 0.7220 (mmp) cc_final: 0.6230 (ppp) REVERT: A 1209 MET cc_start: 0.8525 (ppp) cc_final: 0.8204 (ppp) REVERT: A 1331 PHE cc_start: 0.6632 (m-10) cc_final: 0.6116 (m-80) REVERT: A 1389 MET cc_start: 0.7414 (mmp) cc_final: 0.7179 (mmm) REVERT: A 1610 LYS cc_start: 0.7450 (tppt) cc_final: 0.7231 (tptt) outliers start: 18 outliers final: 10 residues processed: 149 average time/residue: 0.1061 time to fit residues: 24.5949 Evaluate side-chains 139 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 128 time to evaluate : 0.509 ------------------------------------------------------------------------------- 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 536 VAL Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 636 ASP 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 1400 ILE 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: 8.9990 chunk 75 optimal weight: 4.9990 chunk 6 optimal weight: 0.7980 chunk 84 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 79 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 52 optimal weight: 4.9990 chunk 127 optimal weight: 7.9990 chunk 37 optimal weight: 8.9990 chunk 96 optimal weight: 0.9980 overall best weight: 2.9586 ------------------------------------------------------------------------------- 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 ** 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 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 HIS A1409 ASN A1491 ASN ** A1509 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 = 0.3898 r_free = 0.3898 target = 0.096317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.076816 restraints weight = 54653.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.078509 restraints weight = 33994.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.079681 restraints weight = 24992.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.080450 restraints weight = 20298.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.080843 restraints weight = 17696.334| |-----------------------------------------------------------------------------| r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.2566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 14101 Z= 0.205 Angle : 0.657 13.547 19425 Z= 0.330 Chirality : 0.041 0.147 2237 Planarity : 0.005 0.061 2218 Dihedral : 14.204 88.931 2748 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.80 % Favored : 94.14 % Rotamer: Outliers : 2.08 % Allowed : 18.39 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.22), residues: 1484 helix: 0.35 (0.20), residues: 709 sheet: -0.97 (0.38), residues: 157 loop : -0.62 (0.26), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 662 TYR 0.021 0.002 TYR A1000 PHE 0.021 0.002 PHE A1481 TRP 0.016 0.002 TRP A 986 HIS 0.006 0.001 HIS A 954 Details of bonding type rmsd covalent geometry : bond 0.00457 (14101) covalent geometry : angle 0.65733 (19425) hydrogen bonds : bond 0.04185 ( 613) hydrogen bonds : angle 4.88965 ( 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 155 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 127 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 243 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7300 (tm-30) REVERT: A 263 LYS cc_start: 0.7744 (mmmt) cc_final: 0.7337 (tptp) REVERT: A 312 ARG cc_start: 0.8587 (ttm-80) cc_final: 0.8011 (ttm-80) REVERT: A 625 MET cc_start: 0.7098 (pmm) cc_final: 0.6590 (pmm) REVERT: A 827 ASN cc_start: 0.8486 (m110) cc_final: 0.7858 (m-40) REVERT: A 917 TYR cc_start: 0.7707 (m-10) cc_final: 0.7446 (m-10) REVERT: A 939 MET cc_start: 0.6197 (mmp) cc_final: 0.5904 (mmp) REVERT: A 1029 MET cc_start: 0.7112 (mmp) cc_final: 0.6155 (ppp) REVERT: A 1209 MET cc_start: 0.8530 (ppp) cc_final: 0.8191 (ppp) REVERT: A 1331 PHE cc_start: 0.6845 (m-80) cc_final: 0.6491 (m-80) REVERT: A 1480 ASP cc_start: 0.7352 (t0) cc_final: 0.7026 (t0) REVERT: A 1610 LYS cc_start: 0.7643 (tppt) cc_final: 0.7389 (tppt) outliers start: 28 outliers final: 19 residues processed: 147 average time/residue: 0.1142 time to fit residues: 25.3924 Evaluate side-chains 140 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 120 time to evaluate : 0.496 ------------------------------------------------------------------------------- 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 191 LEU Chi-restraints excluded: chain A residue 243 GLU 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 1376 VAL 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 ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 54.1668 > 50: distance: 30 - 195: 16.561 distance: 39 - 198: 36.600 distance: 69 - 170: 8.330 distance: 76 - 173: 32.105 distance: 79 - 188: 8.652 distance: 91 - 191: 16.994 distance: 119 - 122: 18.420 distance: 122 - 123: 8.794 distance: 123 - 124: 15.036 distance: 123 - 126: 9.346 distance: 124 - 125: 30.299 distance: 124 - 130: 13.047 distance: 126 - 127: 18.366 distance: 127 - 128: 16.755 distance: 127 - 129: 14.112 distance: 131 - 134: 7.803 distance: 132 - 133: 7.854 distance: 132 - 139: 8.918 distance: 134 - 135: 3.256 distance: 139 - 140: 12.932 distance: 140 - 141: 5.238 distance: 140 - 143: 8.297 distance: 141 - 142: 34.440 distance: 141 - 146: 14.499 distance: 143 - 144: 5.203 distance: 143 - 145: 11.293 distance: 146 - 147: 7.137 distance: 147 - 148: 35.879 distance: 147 - 150: 28.299 distance: 148 - 149: 39.650 distance: 148 - 155: 34.841 distance: 150 - 151: 26.013 distance: 151 - 152: 18.425 distance: 152 - 153: 8.878 distance: 153 - 154: 3.031 distance: 155 - 156: 18.431 distance: 156 - 157: 30.504 distance: 156 - 159: 49.328 distance: 157 - 158: 22.868 distance: 157 - 163: 20.195 distance: 159 - 160: 9.382 distance: 160 - 161: 20.109 distance: 160 - 162: 26.625 distance: 163 - 164: 11.369 distance: 163 - 169: 17.121 distance: 164 - 165: 8.182 distance: 164 - 167: 9.070 distance: 165 - 166: 9.681 distance: 165 - 170: 7.296 distance: 167 - 168: 15.613 distance: 168 - 169: 9.931 distance: 170 - 171: 13.204 distance: 171 - 172: 10.798 distance: 171 - 174: 16.472 distance: 172 - 173: 39.351 distance: 172 - 181: 20.314 distance: 174 - 175: 25.574 distance: 181 - 182: 13.632 distance: 182 - 183: 18.857 distance: 182 - 185: 19.943 distance: 183 - 184: 7.758 distance: 183 - 188: 11.453 distance: 185 - 186: 22.055 distance: 185 - 187: 15.430 distance: 188 - 189: 9.361 distance: 189 - 190: 4.983 distance: 189 - 192: 9.347 distance: 190 - 191: 14.193 distance: 190 - 195: 7.414 distance: 192 - 193: 14.462 distance: 192 - 194: 9.103 distance: 195 - 196: 17.358 distance: 196 - 197: 22.397 distance: 197 - 198: 28.526 distance: 197 - 199: 9.731