Starting phenix.real_space_refine on Sat Jul 4 08:04:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7pw8_13678/07_2026/7pw8_13678.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pw8_13678/07_2026/7pw8_13678.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7pw8_13678/07_2026/7pw8_13678.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pw8_13678/07_2026/7pw8_13678.map" model { file = "/net/cci-nas-00/data/ceres_data/7pw8_13678/07_2026/7pw8_13678.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pw8_13678/07_2026/7pw8_13678.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7pw8_13678/07_2026/7pw8_13678.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7pw8_13678/07_2026/7pw8_13678.cif" } resolution = 2.82 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.159 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 12 5.49 5 Mg 1 5.21 5 S 93 5.16 5 C 12179 2.51 5 N 3357 2.21 5 O 3318 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 18960 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 9176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1295, 9176 Classifications: {'peptide': 1295} Incomplete info: {'truncation_to_alanine': 337} Link IDs: {'PTRANS': 35, 'TRANS': 1259} Chain breaks: 25 Unresolved non-hydrogen bonds: 926 Unresolved non-hydrogen angles: 1214 Unresolved non-hydrogen dihedrals: 672 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'UNK:plan-1': 121, 'PHE:plan': 5, 'ASN:plan1': 13, 'ARG:plan': 4, 'ASP:plan': 32, 'GLN:plan1': 9, 'TRP:plan': 2, 'GLU:plan': 44, 'TYR:plan': 2, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 560 Chain: "A" Number of atoms: 1428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1428 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 98} Link IDs: {'PTRANS': 7, 'TRANS': 208} Chain breaks: 6 Unresolved non-hydrogen bonds: 279 Unresolved non-hydrogen angles: 371 Unresolved non-hydrogen dihedrals: 199 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'UNK:plan-1': 42, 'GLU:plan': 7, 'ARG:plan': 3, 'ASP:plan': 6, 'GLN:plan1': 8, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 159 Chain: "A" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 196 Classifications: {'peptide': 38} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain breaks: 1 Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'UNK:plan-1': 16, 'GLU:plan': 3, 'TRP:plan': 1, 'PHE:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 2, 'ASN:plan1': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 66 Chain: "A" Number of atoms: 2920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 2920 Classifications: {'peptide': 394} Incomplete info: {'truncation_to_alanine': 73} Link IDs: {'PTRANS': 18, 'TRANS': 375} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 217 Unresolved non-hydrogen angles: 279 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'UNK:plan-1': 16, 'ARG:plan': 3, 'GLU:plan': 16, 'ASN:plan1': 1, 'ASP:plan': 9, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 133 Chain: "B" Number of atoms: 2718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2718 Classifications: {'peptide': 376} Incomplete info: {'truncation_to_alanine': 102} Link IDs: {'PTRANS': 19, 'TRANS': 356} Chain breaks: 8 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 366 Unresolved non-hydrogen angles: 459 Unresolved non-hydrogen dihedrals: 305 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'ARG:plan': 7, 'ASP:plan': 13, 'GLU:plan': 15, 'ASN:plan1': 5, 'GLN:plan1': 8, 'PHE:plan': 3, 'HIS:plan': 4, 'TYR:plan': 3, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 249 Chain: "C" Number of atoms: 2423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2423 Classifications: {'peptide': 310} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 17, 'TRANS': 292} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 117 Unresolved non-hydrogen dihedrals: 74 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 8, 'ARG:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 70 Chain: "A" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'ANP': 1, 'IHP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.72, per 1000 atoms: 0.20 Number of scatterers: 18960 At special positions: 0 Unit cell: (130.234, 123.424, 178.752, 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 93 16.00 P 12 15.00 Mg 1 11.99 O 3318 8.00 N 3357 7.00 C 12179 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: 1.71 Conformation dependent library (CDL) restraints added in 853.2 milliseconds 4708 Ramachandran restraints generated. 2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5074 Finding SS restraints... Secondary structure from input PDB file: 140 helices and 5 sheets defined 75.1% alpha, 4.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.73 Creating SS restraints... Processing helix chain 'A' and resid 147 through 156 removed outlier: 3.900A pdb=" N UNK A 154 " --> pdb=" O UNK A 150 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N UNK A 155 " --> pdb=" O UNK A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 175 removed outlier: 3.928A pdb=" N UNK A 172 " --> pdb=" O UNK A 168 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N UNK A 173 " --> pdb=" O UNK A 169 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N UNK A 175 " --> pdb=" O UNK A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 198 Processing helix chain 'A' and resid 199 through 201 No H-bonds generated for 'chain 'A' and resid 199 through 201' Processing helix chain 'A' and resid 208 through 219 Processing helix chain 'A' and resid 230 through 244 removed outlier: 3.558A pdb=" N UNK A 234 " --> pdb=" O UNK A 230 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N UNK A 244 " --> pdb=" O UNK A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 265 removed outlier: 4.076A pdb=" N UNK A 265 " --> pdb=" O UNK A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 283 Processing helix chain 'A' and resid 291 through 302 Processing helix chain 'A' and resid 313 through 322 removed outlier: 4.233A pdb=" N ASP A 317 " --> pdb=" O THR A 313 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N THR A 318 " --> pdb=" O ASN A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 347 removed outlier: 3.804A pdb=" N GLU A 347 " --> pdb=" O LEU A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 374 removed outlier: 3.778A pdb=" N GLY A 362 " --> pdb=" O THR A 358 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLN A 363 " --> pdb=" O THR A 359 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N PHE A 364 " --> pdb=" O LEU A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 412 removed outlier: 4.059A pdb=" N ILE A 412 " --> pdb=" O VAL A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 444 removed outlier: 4.151A pdb=" N VAL A 432 " --> pdb=" O TYR A 428 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ASN A 444 " --> pdb=" O VAL A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 467 removed outlier: 4.354A pdb=" N LEU A 467 " --> pdb=" O LEU A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 487 removed outlier: 4.047A pdb=" N VAL A 478 " --> pdb=" O HIS A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 511 removed outlier: 3.681A pdb=" N SER A 499 " --> pdb=" O ASP A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 524 removed outlier: 4.036A pdb=" N VAL A 520 " --> pdb=" O PRO A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 528 through 533 removed outlier: 4.040A pdb=" N PHE A 532 " --> pdb=" O SER A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 536 No H-bonds generated for 'chain 'A' and resid 534 through 536' Processing helix chain 'A' and resid 538 through 553 removed outlier: 3.690A pdb=" N VAL A 542 " --> pdb=" O GLU A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 583 removed outlier: 4.069A pdb=" N THR A 563 " --> pdb=" O PRO A 559 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA A 564 " --> pdb=" O VAL A 560 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU A 583 " --> pdb=" O LEU A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 598 removed outlier: 3.567A pdb=" N PHE A 597 " --> pdb=" O HIS A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 623 removed outlier: 3.693A pdb=" N ILE A 612 " --> pdb=" O LYS A 608 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N THR A 620 " --> pdb=" O SER A 616 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N ILE A 621 " --> pdb=" O ALA A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 645 Processing helix chain 'A' and resid 646 through 651 Processing helix chain 'A' and resid 652 through 657 removed outlier: 3.743A pdb=" N HIS A 656 " --> pdb=" O ASP A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 657 through 674 removed outlier: 3.922A pdb=" N GLN A 661 " --> pdb=" O PHE A 657 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ARG A 674 " --> pdb=" O SER A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 675 through 679 Processing helix chain 'A' and resid 705 through 719 removed outlier: 3.863A pdb=" N ILE A 709 " --> pdb=" O LYS A 705 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 742 Processing helix chain 'A' and resid 743 through 744 No H-bonds generated for 'chain 'A' and resid 743 through 744' Processing helix chain 'A' and resid 745 through 753 removed outlier: 3.734A pdb=" N TYR A 748 " --> pdb=" O SER A 745 " (cutoff:3.500A) Proline residue: A 750 - end of helix removed outlier: 3.786A pdb=" N SER A 753 " --> pdb=" O PRO A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 754 through 767 removed outlier: 3.570A pdb=" N HIS A 758 " --> pdb=" O LEU A 754 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 786 Processing helix chain 'A' and resid 791 through 806 removed outlier: 3.693A pdb=" N ARG A 797 " --> pdb=" O ASP A 793 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASP A 800 " --> pdb=" O GLN A 796 " (cutoff:3.500A) Processing helix chain 'A' and resid 810 through 822 removed outlier: 3.682A pdb=" N ARG A 814 " --> pdb=" O GLY A 810 " (cutoff:3.500A) Processing helix chain 'A' and resid 825 through 830 Processing helix chain 'A' and resid 835 through 851 removed outlier: 3.531A pdb=" N GLU A 840 " --> pdb=" O THR A 836 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE A 841 " --> pdb=" O GLU A 837 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER A 842 " --> pdb=" O ILE A 838 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS A 851 " --> pdb=" O SER A 847 " (cutoff:3.500A) Processing helix chain 'A' and resid 858 through 871 Processing helix chain 'A' and resid 882 through 890 Processing helix chain 'A' and resid 902 through 906 Processing helix chain 'A' and resid 908 through 927 Processing helix chain 'A' and resid 935 through 956 removed outlier: 3.687A pdb=" N PHE A 940 " --> pdb=" O ALA A 936 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU A 955 " --> pdb=" O ALA A 951 " (cutoff:3.500A) Processing helix chain 'A' and resid 969 through 999 removed outlier: 3.847A pdb=" N HIS A 973 " --> pdb=" O ASN A 969 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLY A 974 " --> pdb=" O ASP A 970 " (cutoff:3.500A) Processing helix chain 'A' and resid 1009 through 1019 Processing helix chain 'A' and resid 1019 through 1041 removed outlier: 4.700A pdb=" N LEU A1032 " --> pdb=" O THR A1028 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N SER A1033 " --> pdb=" O ARG A1029 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ARG A1036 " --> pdb=" O LEU A1032 " (cutoff:3.500A) Processing helix chain 'A' and resid 1043 through 1058 removed outlier: 3.755A pdb=" N THR A1047 " --> pdb=" O GLN A1043 " (cutoff:3.500A) Processing helix chain 'A' and resid 1068 through 1083 removed outlier: 3.500A pdb=" N THR A1072 " --> pdb=" O GLU A1068 " (cutoff:3.500A) Processing helix chain 'A' and resid 1085 through 1097 removed outlier: 3.518A pdb=" N ILE A1089 " --> pdb=" O CYS A1085 " (cutoff:3.500A) Processing helix chain 'A' and resid 1106 through 1115 removed outlier: 3.554A pdb=" N GLU A1115 " --> pdb=" O ALA A1111 " (cutoff:3.500A) Processing helix chain 'A' and resid 1117 through 1134 removed outlier: 3.738A pdb=" N VAL A1123 " --> pdb=" O GLU A1119 " (cutoff:3.500A) Processing helix chain 'A' and resid 1143 through 1151 removed outlier: 3.954A pdb=" N LEU A1149 " --> pdb=" O SER A1145 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASN A1151 " --> pdb=" O LEU A1147 " (cutoff:3.500A) Processing helix chain 'A' and resid 1179 through 1197 removed outlier: 3.667A pdb=" N ILE A1197 " --> pdb=" O CYS A1193 " (cutoff:3.500A) Processing helix chain 'A' and resid 1199 through 1216 Processing helix chain 'A' and resid 1227 through 1240 Processing helix chain 'A' and resid 1241 through 1250 removed outlier: 3.721A pdb=" N GLU A1250 " --> pdb=" O THR A1246 " (cutoff:3.500A) Processing helix chain 'A' and resid 1281 through 1305 removed outlier: 3.749A pdb=" N ASN A1305 " --> pdb=" O ALA A1301 " (cutoff:3.500A) Processing helix chain 'A' and resid 1317 through 1332 removed outlier: 3.614A pdb=" N VAL A1321 " --> pdb=" O THR A1317 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LYS A1322 " --> pdb=" O GLU A1318 " (cutoff:3.500A) Processing helix chain 'A' and resid 1332 through 1341 removed outlier: 3.764A pdb=" N THR A1339 " --> pdb=" O LEU A1335 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU A1340 " --> pdb=" O ARG A1336 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N THR A1341 " --> pdb=" O LEU A1337 " (cutoff:3.500A) Processing helix chain 'A' and resid 1347 through 1367 removed outlier: 3.514A pdb=" N THR A1351 " --> pdb=" O PRO A1347 " (cutoff:3.500A) Processing helix chain 'A' and resid 1370 through 1374 removed outlier: 3.629A pdb=" N LEU A1374 " --> pdb=" O GLU A1371 " (cutoff:3.500A) Processing helix chain 'A' and resid 1378 through 1383 removed outlier: 3.584A pdb=" N ARG A1383 " --> pdb=" O GLU A1380 " (cutoff:3.500A) Processing helix chain 'A' and resid 1390 through 1407 removed outlier: 3.697A pdb=" N TYR A1402 " --> pdb=" O ARG A1398 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLN A1403 " --> pdb=" O TYR A1399 " (cutoff:3.500A) Processing helix chain 'A' and resid 1408 through 1410 No H-bonds generated for 'chain 'A' and resid 1408 through 1410' Processing helix chain 'A' and resid 1417 through 1434 Processing helix chain 'A' and resid 1437 through 1450 Processing helix chain 'A' and resid 1458 through 1467 Processing helix chain 'A' and resid 1479 through 1495 Processing helix chain 'A' and resid 1496 through 1512 Processing helix chain 'A' and resid 1517 through 1535 removed outlier: 3.913A pdb=" N VAL A1521 " --> pdb=" O ALA A1517 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ALA A1522 " --> pdb=" O GLU A1518 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA A1534 " --> pdb=" O LYS A1530 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLU A1535 " --> pdb=" O TRP A1531 " (cutoff:3.500A) Processing helix chain 'A' and resid 1535 through 1551 removed outlier: 5.135A pdb=" N GLY A1541 " --> pdb=" O LYS A1537 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N GLN A1542 " --> pdb=" O GLU A1538 " (cutoff:3.500A) Processing helix chain 'A' and resid 1559 through 1570 Processing helix chain 'A' and resid 1595 through 1612 removed outlier: 3.517A pdb=" N PHE A1599 " --> pdb=" O GLY A1595 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ILE A1600 " --> pdb=" O GLU A1596 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU A1601 " --> pdb=" O PRO A1597 " (cutoff:3.500A) Processing helix chain 'A' and resid 1615 through 1637 removed outlier: 3.850A pdb=" N TRP A1619 " --> pdb=" O VAL A1615 " (cutoff:3.500A) Processing helix chain 'A' and resid 1647 through 1656 Processing helix chain 'A' and resid 1664 through 1674 removed outlier: 3.749A pdb=" N UNK A1674 " --> pdb=" O UNK A1670 " (cutoff:3.500A) Processing helix chain 'A' and resid 1704 through 1716 Processing helix chain 'A' and resid 1728 through 1741 removed outlier: 3.878A pdb=" N VAL A1732 " --> pdb=" O GLY A1728 " (cutoff:3.500A) Processing helix chain 'A' and resid 1741 through 1757 Processing helix chain 'A' and resid 1781 through 1799 Processing helix chain 'A' and resid 1803 through 1814 removed outlier: 3.547A pdb=" N LEU A1807 " --> pdb=" O LEU A1803 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N HIS A1809 " --> pdb=" O GLN A1805 " (cutoff:3.500A) Processing helix chain 'A' and resid 1822 through 1829 Processing helix chain 'A' and resid 1830 through 1832 No H-bonds generated for 'chain 'A' and resid 1830 through 1832' Processing helix chain 'A' and resid 1835 through 1850 removed outlier: 3.518A pdb=" N GLN A1850 " --> pdb=" O CYS A1846 " (cutoff:3.500A) Processing helix chain 'A' and resid 1852 through 1855 removed outlier: 4.077A pdb=" N LEU A1855 " --> pdb=" O SER A1852 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1852 through 1855' Processing helix chain 'A' and resid 1856 through 1865 Processing helix chain 'A' and resid 1924 through 1939 removed outlier: 3.933A pdb=" N CYS A1929 " --> pdb=" O MET A1925 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N TYR A1930 " --> pdb=" O MET A1926 " (cutoff:3.500A) Processing helix chain 'A' and resid 1941 through 1958 Processing helix chain 'A' and resid 1963 through 1978 removed outlier: 4.636A pdb=" N LEU A1978 " --> pdb=" O HIS A1974 " (cutoff:3.500A) Processing helix chain 'A' and resid 2007 through 2020 Processing helix chain 'A' and resid 2036 through 2045 Processing helix chain 'A' and resid 2046 through 2055 Processing helix chain 'A' and resid 2069 through 2083 removed outlier: 3.888A pdb=" N UNK A2083 " --> pdb=" O UNK A2079 " (cutoff:3.500A) Processing helix chain 'A' and resid 2160 through 2176 removed outlier: 3.688A pdb=" N ARG A2165 " --> pdb=" O HIS A2161 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N MET A2176 " --> pdb=" O ILE A2172 " (cutoff:3.500A) Processing helix chain 'A' and resid 2177 through 2178 No H-bonds generated for 'chain 'A' and resid 2177 through 2178' Processing helix chain 'A' and resid 2179 through 2183 Processing helix chain 'A' and resid 2214 through 2232 removed outlier: 3.763A pdb=" N TYR A2218 " --> pdb=" O LEU A2214 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLN A2231 " --> pdb=" O ALA A2227 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LYS A2232 " --> pdb=" O LEU A2228 " (cutoff:3.500A) Processing helix chain 'A' and resid 2248 through 2263 removed outlier: 3.661A pdb=" N LYS A2256 " --> pdb=" O LEU A2252 " (cutoff:3.500A) Proline residue: A2259 - end of helix Processing helix chain 'A' and resid 2276 through 2291 removed outlier: 3.527A pdb=" N MET A2280 " --> pdb=" O PRO A2276 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA A2290 " --> pdb=" O GLU A2286 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR A2291 " --> pdb=" O LEU A2287 " (cutoff:3.500A) Processing helix chain 'A' and resid 2294 through 2304 Processing helix chain 'A' and resid 2306 through 2332 Processing helix chain 'A' and resid 2360 through 2364 removed outlier: 3.502A pdb=" N SER A2364 " --> pdb=" O LYS A2361 " (cutoff:3.500A) Processing helix chain 'A' and resid 2376 through 2382 removed outlier: 3.507A pdb=" N ALA A2382 " --> pdb=" O ASN A2378 " (cutoff:3.500A) Processing helix chain 'A' and resid 2390 through 2406 Processing helix chain 'A' and resid 2406 through 2419 removed outlier: 3.639A pdb=" N LEU A2410 " --> pdb=" O GLY A2406 " (cutoff:3.500A) Processing helix chain 'A' and resid 3608 through 3621 Processing helix chain 'A' and resid 3632 through 3646 Processing helix chain 'A' and resid 3646 through 3652 removed outlier: 3.512A pdb=" N LEU A3650 " --> pdb=" O ASN A3646 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLN A3652 " --> pdb=" O ASP A3648 " (cutoff:3.500A) Processing helix chain 'A' and resid 3654 through 3658 Processing helix chain 'B' and resid 7 through 12 removed outlier: 3.887A pdb=" N MET B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 43 removed outlier: 3.557A pdb=" N ARG B 43 " --> pdb=" O PRO B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 72 removed outlier: 3.525A pdb=" N SER B 66 " --> pdb=" O SER B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 172 removed outlier: 3.683A pdb=" N ARG B 164 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER B 171 " --> pdb=" O ARG B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 204 removed outlier: 3.878A pdb=" N HIS B 186 " --> pdb=" O HIS B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 235 removed outlier: 4.138A pdb=" N ARG B 225 " --> pdb=" O ILE B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 245 Processing helix chain 'B' and resid 251 through 258 removed outlier: 3.748A pdb=" N LYS B 255 " --> pdb=" O GLY B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 315 Processing helix chain 'B' and resid 346 through 359 Processing helix chain 'B' and resid 409 through 423 removed outlier: 4.373A pdb=" N HIS B 417 " --> pdb=" O PHE B 413 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N LEU B 420 " --> pdb=" O GLN B 416 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N VAL B 421 " --> pdb=" O HIS B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 458 removed outlier: 3.672A pdb=" N ALA B 451 " --> pdb=" O LYS B 447 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LYS B 454 " --> pdb=" O SER B 450 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL B 458 " --> pdb=" O LYS B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 483 Processing helix chain 'B' and resid 489 through 509 Proline residue: B 505 - end of helix Processing helix chain 'B' and resid 524 through 539 Processing helix chain 'B' and resid 543 through 558 removed outlier: 3.847A pdb=" N TYR B 547 " --> pdb=" O ALA B 543 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 198 Processing helix chain 'C' and resid 216 through 226 Processing helix chain 'C' and resid 232 through 236 removed outlier: 3.561A pdb=" N TYR C 236 " --> pdb=" O GLN C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 248 removed outlier: 3.844A pdb=" N GLU C 247 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ARG C 248 " --> pdb=" O GLU C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 284 removed outlier: 3.560A pdb=" N ASN C 284 " --> pdb=" O ASP C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 315 removed outlier: 3.647A pdb=" N TYR C 299 " --> pdb=" O LEU C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 340 removed outlier: 3.600A pdb=" N VAL C 340 " --> pdb=" O THR C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 375 through 379 Processing helix chain 'C' and resid 380 through 395 Processing helix chain 'C' and resid 418 through 422 Processing helix chain 'C' and resid 453 through 457 Processing helix chain 'C' and resid 465 through 479 removed outlier: 3.682A pdb=" N SER C 479 " --> pdb=" O SER C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 491 through 508 removed outlier: 3.791A pdb=" N PHE C 496 " --> pdb=" O GLU C 492 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N HIS C 497 " --> pdb=" O LYS C 493 " (cutoff:3.500A) Processing helix chain 'C' and resid 510 through 518 Processing sheet with id=AA1, first strand: chain 'A' and resid 2090 through 2091 removed outlier: 7.705A pdb=" N THR A2127 " --> pdb=" O LEU A2141 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N LEU A2141 " --> pdb=" O THR A2127 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR A2129 " --> pdb=" O LYS A2139 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N LEU A2141 " --> pdb=" O VAL A2124 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N VAL A2124 " --> pdb=" O LEU A2141 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LEU A2143 " --> pdb=" O HIS A2122 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 2090 through 2091 removed outlier: 7.705A pdb=" N THR A2127 " --> pdb=" O LEU A2141 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N LEU A2141 " --> pdb=" O THR A2127 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR A2129 " --> pdb=" O LYS A2139 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 2212 through 2213 Processing sheet with id=AA4, first strand: chain 'B' and resid 5 through 6 removed outlier: 3.503A pdb=" N VAL B 148 " --> pdb=" O SER B 143 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N GLY B 54 " --> pdb=" O LEU B 153 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LEU B 210 " --> pdb=" O LEU B 266 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N LEU B 268 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N LEU B 212 " --> pdb=" O LEU B 268 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N GLN B 270 " --> pdb=" O LEU B 212 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N HIS B 214 " --> pdb=" O GLN B 270 " (cutoff:3.500A) removed outlier: 8.769A pdb=" N TYR B 337 " --> pdb=" O LEU B 265 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N PHE B 267 " --> pdb=" O TYR B 337 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N VAL B 339 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N PHE B 269 " --> pdb=" O VAL B 339 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 181 through 184 removed outlier: 6.437A pdb=" N ILE C 256 " --> pdb=" O LEU C 183 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LEU C 205 " --> pdb=" O VAL C 266 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N LEU C 268 " --> pdb=" O LEU C 205 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N VAL C 207 " --> pdb=" O LEU C 268 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N THR C 270 " --> pdb=" O VAL C 207 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N VAL C 209 " --> pdb=" O THR C 270 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N VAL C 206 " --> pdb=" O VAL C 317 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N ILE C 319 " --> pdb=" O VAL C 206 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N GLY C 208 " --> pdb=" O ILE C 319 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N VAL C 321 " --> pdb=" O GLY C 208 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N LEU C 210 " --> pdb=" O VAL C 321 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N PHE C 429 " --> pdb=" O LEU C 370 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N ASN C 372 " --> pdb=" O PHE C 429 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N VAL C 431 " --> pdb=" O ASN C 372 " (cutoff:3.500A) 1211 hydrogen bonds defined for protein. 3525 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.52 Time building geometry restraints manager: 2.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.06 - 1.21: 15 1.21 - 1.36: 6186 1.36 - 1.51: 5220 1.51 - 1.66: 7742 1.66 - 1.81: 142 Bond restraints: 19305 Sorted by residual: bond pdb=" C ILE A 838 " pdb=" O ILE A 838 " ideal model delta sigma weight residual 1.237 1.068 0.169 1.19e-02 7.06e+03 2.03e+02 bond pdb=" C LEU A 830 " pdb=" O LEU A 830 " ideal model delta sigma weight residual 1.235 1.058 0.177 1.32e-02 5.74e+03 1.80e+02 bond pdb=" C HIS A 835 " pdb=" O HIS A 835 " ideal model delta sigma weight residual 1.234 1.082 0.152 1.19e-02 7.06e+03 1.63e+02 bond pdb=" CE1 HIS A 835 " pdb=" NE2 HIS A 835 " ideal model delta sigma weight residual 1.321 1.194 0.127 1.00e-02 1.00e+04 1.62e+02 bond pdb=" C GLN A 839 " pdb=" O GLN A 839 " ideal model delta sigma weight residual 1.236 1.078 0.159 1.26e-02 6.30e+03 1.59e+02 ... (remaining 19300 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.35: 26178 3.35 - 6.71: 162 6.71 - 10.06: 24 10.06 - 13.41: 2 13.41 - 16.77: 1 Bond angle restraints: 26367 Sorted by residual: angle pdb=" CA HIS A 835 " pdb=" CB HIS A 835 " pdb=" CG HIS A 835 " ideal model delta sigma weight residual 113.80 121.00 -7.20 1.00e+00 1.00e+00 5.18e+01 angle pdb=" CA ASN A 833 " pdb=" CB ASN A 833 " pdb=" CG ASN A 833 " ideal model delta sigma weight residual 112.60 106.08 6.52 1.00e+00 1.00e+00 4.25e+01 angle pdb=" C ASN A 834 " pdb=" CA ASN A 834 " pdb=" CB ASN A 834 " ideal model delta sigma weight residual 109.51 120.49 -10.98 1.71e+00 3.42e-01 4.12e+01 angle pdb=" N THR C 326 " pdb=" CA THR C 326 " pdb=" C THR C 326 " ideal model delta sigma weight residual 110.91 118.36 -7.45 1.17e+00 7.31e-01 4.05e+01 angle pdb=" C GLN A 839 " pdb=" N GLU A 840 " pdb=" CA GLU A 840 " ideal model delta sigma weight residual 120.28 128.53 -8.25 1.34e+00 5.57e-01 3.79e+01 ... (remaining 26362 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.65: 10880 21.65 - 43.30: 472 43.30 - 64.96: 50 64.96 - 86.61: 19 86.61 - 108.26: 2 Dihedral angle restraints: 11423 sinusoidal: 3702 harmonic: 7721 Sorted by residual: dihedral pdb=" C ASN A 834 " pdb=" N ASN A 834 " pdb=" CA ASN A 834 " pdb=" CB ASN A 834 " ideal model delta harmonic sigma weight residual -122.60 -145.53 22.93 0 2.50e+00 1.60e-01 8.41e+01 dihedral pdb=" N ASN A 834 " pdb=" C ASN A 834 " pdb=" CA ASN A 834 " pdb=" CB ASN A 834 " ideal model delta harmonic sigma weight residual 122.80 144.05 -21.25 0 2.50e+00 1.60e-01 7.23e+01 dihedral pdb=" N ASN A 832 " pdb=" C ASN A 832 " pdb=" CA ASN A 832 " pdb=" CB ASN A 832 " ideal model delta harmonic sigma weight residual 122.80 139.94 -17.14 0 2.50e+00 1.60e-01 4.70e+01 ... (remaining 11420 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.006: 3244 1.006 - 2.012: 0 2.012 - 3.019: 0 3.019 - 4.025: 0 4.025 - 5.031: 3 Chirality restraints: 3247 Sorted by residual: chirality pdb=" C2 IHP A3701 " pdb=" C1 IHP A3701 " pdb=" C3 IHP A3701 " pdb=" O12 IHP A3701 " both_signs ideal model delta sigma weight residual False -2.52 2.51 -5.03 2.00e-01 2.50e+01 6.33e+02 chirality pdb=" C4 IHP A3701 " pdb=" C3 IHP A3701 " pdb=" C5 IHP A3701 " pdb=" O14 IHP A3701 " both_signs ideal model delta sigma weight residual False 2.48 -2.36 4.84 2.00e-01 2.50e+01 5.86e+02 chirality pdb=" C1 IHP A3701 " pdb=" C2 IHP A3701 " pdb=" C6 IHP A3701 " pdb=" O11 IHP A3701 " both_signs ideal model delta sigma weight residual False 2.32 -2.49 4.80 2.00e-01 2.50e+01 5.77e+02 ... (remaining 3244 not shown) Planarity restraints: 3274 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 836 " 0.022 2.00e-02 2.50e+03 4.56e-02 2.08e+01 pdb=" C THR A 836 " -0.079 2.00e-02 2.50e+03 pdb=" O THR A 836 " 0.030 2.00e-02 2.50e+03 pdb=" N GLU A 837 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 839 " 0.010 2.00e-02 2.50e+03 2.09e-02 4.35e+00 pdb=" C GLN A 839 " -0.036 2.00e-02 2.50e+03 pdb=" O GLN A 839 " 0.014 2.00e-02 2.50e+03 pdb=" N GLU A 840 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 833 " -0.009 2.00e-02 2.50e+03 1.83e-02 3.36e+00 pdb=" CG ASN A 833 " 0.032 2.00e-02 2.50e+03 pdb=" OD1 ASN A 833 " -0.012 2.00e-02 2.50e+03 pdb=" ND2 ASN A 833 " -0.011 2.00e-02 2.50e+03 ... (remaining 3271 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 121 2.65 - 3.21: 17006 3.21 - 3.77: 28323 3.77 - 4.34: 37395 4.34 - 4.90: 63300 Nonbonded interactions: 146145 Sorted by model distance: nonbonded pdb=" OG SER C 218 " pdb="MG MG C 602 " model vdw 2.086 2.170 nonbonded pdb=" OG1 THR C 253 " pdb="MG MG C 602 " model vdw 2.128 2.170 nonbonded pdb=" O SER A 616 " pdb=" OG1 THR A 619 " model vdw 2.227 3.040 nonbonded pdb=" OH TYR A2193 " pdb=" O ILE A2353 " model vdw 2.233 3.040 nonbonded pdb=" O1G ANP A3702 " pdb=" O2B ANP A3702 " model vdw 2.239 3.040 ... (remaining 146140 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 17.400 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 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:6.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 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 : 0.005 0.177 19305 Z= 0.337 Angle : 0.749 16.767 26367 Z= 0.433 Chirality : 0.156 5.031 3247 Planarity : 0.004 0.046 3274 Dihedral : 12.384 108.262 6349 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.18 % Allowed : 0.24 % Favored : 99.59 % Cbeta Deviations : 0.16 % 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: 1.21 (0.18), residues: 2354 helix: 1.87 (0.14), residues: 1493 sheet: 0.19 (0.43), residues: 129 loop : -1.38 (0.23), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1820 TYR 0.015 0.001 TYR A1185 PHE 0.018 0.001 PHE A 817 TRP 0.016 0.001 TRP A2221 HIS 0.012 0.001 HIS A 706 Details of bonding type rmsd/Z covalent geometry : bond 0.00498 / 0.34 (19305) covalent geometry : angle 0.74941 / 0.43 (26367) hydrogen bonds : bond 0.17093 / 10.69 ( 1208) hydrogen bonds : angle 4.66778 / 3.14 ( 3525) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4708 Ramachandran restraints generated. 2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4708 Ramachandran restraints generated. 2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 288 time to evaluate : 0.643 Fit side-chains REVERT: A 1547 TYR cc_start: 0.8444 (t80) cc_final: 0.8220 (t80) REVERT: A 2122 HIS cc_start: 0.7356 (t70) cc_final: 0.7098 (t70) REVERT: A 2326 MET cc_start: 0.8635 (mmt) cc_final: 0.8357 (mmt) REVERT: A 3631 MET cc_start: 0.8140 (mtm) cc_final: 0.7895 (mtm) REVERT: C 219 MET cc_start: 0.8536 (ttp) cc_final: 0.8265 (ttm) REVERT: C 221 MET cc_start: 0.8823 (mmm) cc_final: 0.8532 (mmm) outliers start: 3 outliers final: 0 residues processed: 291 average time/residue: 0.6245 time to fit residues: 203.1682 Evaluate side-chains 195 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 30.0000 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 20.0000 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 600 HIS A 881 ASN A1276 ASN A1344 GLN B 159 ASN ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.156402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.118035 restraints weight = 22343.707| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 1.67 r_work: 0.3010 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8924 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 19305 Z= 0.177 Angle : 0.598 9.978 26367 Z= 0.300 Chirality : 0.042 0.495 3247 Planarity : 0.005 0.057 3274 Dihedral : 4.648 116.545 2761 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.94 % Allowed : 7.94 % Favored : 90.12 % 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: 1.23 (0.18), residues: 2354 helix: 1.80 (0.14), residues: 1533 sheet: 0.56 (0.45), residues: 129 loop : -1.44 (0.23), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A2336 TYR 0.022 0.002 TYR A 998 PHE 0.016 0.002 PHE A 609 TRP 0.017 0.002 TRP A1393 HIS 0.012 0.001 HIS A 706 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.18 (19305) covalent geometry : angle 0.59812 / 0.30 (26367) hydrogen bonds : bond 0.05771 / 3.55 ( 1208) hydrogen bonds : angle 3.68213 / 2.49 ( 3525) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4708 Ramachandran restraints generated. 2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4708 Ramachandran restraints generated. 2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 198 time to evaluate : 0.712 Fit side-chains REVERT: A 566 LYS cc_start: 0.8359 (mmtm) cc_final: 0.8011 (mttp) REVERT: A 1078 GLU cc_start: 0.8672 (tp30) cc_final: 0.8284 (tp30) REVERT: A 1132 MET cc_start: 0.8874 (mtm) cc_final: 0.8666 (mtp) REVERT: A 1283 ARG cc_start: 0.8715 (mtt90) cc_final: 0.8480 (mtt90) REVERT: A 1794 ARG cc_start: 0.8541 (ttt180) cc_final: 0.8316 (ttt-90) REVERT: A 2122 HIS cc_start: 0.7758 (t70) cc_final: 0.7241 (t70) REVERT: A 2183 GLN cc_start: 0.8138 (OUTLIER) cc_final: 0.7755 (pt0) REVERT: A 2326 MET cc_start: 0.8963 (mmt) cc_final: 0.8725 (mmt) REVERT: C 231 GLU cc_start: 0.9014 (mt-10) cc_final: 0.8741 (mt-10) REVERT: C 335 GLN cc_start: 0.8824 (OUTLIER) cc_final: 0.8174 (mt0) REVERT: C 383 LYS cc_start: 0.8738 (OUTLIER) cc_final: 0.8500 (tttt) REVERT: C 461 ARG cc_start: 0.8917 (OUTLIER) cc_final: 0.8600 (ptt180) outliers start: 33 outliers final: 13 residues processed: 217 average time/residue: 0.7022 time to fit residues: 169.4136 Evaluate side-chains 202 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 185 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 900 THR Chi-restraints excluded: chain A residue 1352 LEU Chi-restraints excluded: chain A residue 1439 SER Chi-restraints excluded: chain A residue 1519 TYR Chi-restraints excluded: chain A residue 2090 LEU Chi-restraints excluded: chain A residue 2183 GLN Chi-restraints excluded: chain A residue 3607 SER Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain C residue 335 GLN Chi-restraints excluded: chain C residue 383 LYS Chi-restraints excluded: chain C residue 461 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 105 optimal weight: 0.8980 chunk 73 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 79 optimal weight: 0.0050 chunk 256 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 199 optimal weight: 0.9980 chunk 219 optimal weight: 10.0000 chunk 152 optimal weight: 2.9990 chunk 125 optimal weight: 6.9990 chunk 30 optimal weight: 0.4980 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 881 ASN A1551 HIS ** C 297 HIS ** 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 = 0.3818 r_free = 0.3818 target = 0.159927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.121583 restraints weight = 22537.148| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 1.66 r_work: 0.3062 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8885 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 19305 Z= 0.099 Angle : 0.461 9.615 26367 Z= 0.231 Chirality : 0.036 0.287 3247 Planarity : 0.004 0.041 3274 Dihedral : 4.310 110.520 2761 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.82 % Allowed : 10.47 % Favored : 87.71 % 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: 1.67 (0.18), residues: 2354 helix: 2.18 (0.14), residues: 1538 sheet: 0.74 (0.45), residues: 129 loop : -1.39 (0.23), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 930 TYR 0.017 0.001 TYR A 998 PHE 0.010 0.001 PHE A 609 TRP 0.014 0.001 TRP A2221 HIS 0.006 0.001 HIS A 706 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.10 (19305) covalent geometry : angle 0.46061 / 0.23 (26367) hydrogen bonds : bond 0.03942 / 2.42 ( 1208) hydrogen bonds : angle 3.34122 / 2.25 ( 3525) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4708 Ramachandran restraints generated. 2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4708 Ramachandran restraints generated. 2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 194 time to evaluate : 0.722 Fit side-chains REVERT: A 566 LYS cc_start: 0.8346 (mmtm) cc_final: 0.8005 (mttp) REVERT: A 786 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.7849 (mt) REVERT: A 1078 GLU cc_start: 0.8692 (tp30) cc_final: 0.8342 (tp30) REVERT: A 1389 ASP cc_start: 0.7768 (p0) cc_final: 0.7503 (p0) REVERT: A 1501 MET cc_start: 0.8431 (mtt) cc_final: 0.8145 (mtt) REVERT: A 1548 ARG cc_start: 0.7792 (mtm110) cc_final: 0.7379 (ttp80) REVERT: A 1782 ASP cc_start: 0.7882 (OUTLIER) cc_final: 0.7532 (t0) REVERT: A 2122 HIS cc_start: 0.7758 (t70) cc_final: 0.7226 (t70) REVERT: A 2159 ASP cc_start: 0.8086 (t70) cc_final: 0.7881 (t70) REVERT: B 257 ASN cc_start: 0.8346 (m-40) cc_final: 0.8020 (m110) REVERT: C 231 GLU cc_start: 0.9017 (mt-10) cc_final: 0.8766 (mt-10) REVERT: C 247 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7845 (mt-10) REVERT: C 294 ASN cc_start: 0.7578 (OUTLIER) cc_final: 0.7374 (m-40) REVERT: C 335 GLN cc_start: 0.8659 (OUTLIER) cc_final: 0.8428 (mt0) REVERT: C 383 LYS cc_start: 0.8554 (OUTLIER) cc_final: 0.8315 (tttt) REVERT: C 461 ARG cc_start: 0.8809 (OUTLIER) cc_final: 0.8508 (ptt180) outliers start: 31 outliers final: 12 residues processed: 209 average time/residue: 0.6670 time to fit residues: 156.0525 Evaluate side-chains 204 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 185 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 725 GLN Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 834 ASN Chi-restraints excluded: chain A residue 900 THR Chi-restraints excluded: chain A residue 941 GLN Chi-restraints excluded: chain A residue 1047 THR Chi-restraints excluded: chain A residue 1592 ILE Chi-restraints excluded: chain A residue 1782 ASP Chi-restraints excluded: chain A residue 1829 ARG Chi-restraints excluded: chain A residue 3607 SER Chi-restraints excluded: chain A residue 3625 VAL Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain C residue 247 GLU Chi-restraints excluded: chain C residue 294 ASN Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 335 GLN Chi-restraints excluded: chain C residue 383 LYS Chi-restraints excluded: chain C residue 461 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 153 optimal weight: 0.5980 chunk 242 optimal weight: 0.0770 chunk 103 optimal weight: 0.1980 chunk 35 optimal weight: 0.8980 chunk 70 optimal weight: 0.0370 chunk 31 optimal weight: 0.4980 chunk 170 optimal weight: 1.9990 chunk 234 optimal weight: 5.9990 chunk 193 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 overall best weight: 0.2816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 600 HIS A 767 ASN A 881 ASN A1533 GLN A1551 HIS ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.163056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.125325 restraints weight = 22618.314| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 1.66 r_work: 0.3127 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 19305 Z= 0.082 Angle : 0.422 9.132 26367 Z= 0.210 Chirality : 0.035 0.250 3247 Planarity : 0.003 0.040 3274 Dihedral : 3.957 101.107 2761 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.41 % Allowed : 10.76 % Favored : 86.82 % 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: 2.07 (0.18), residues: 2354 helix: 2.48 (0.14), residues: 1542 sheet: 0.94 (0.45), residues: 129 loop : -1.24 (0.24), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 375 TYR 0.018 0.001 TYR A 998 PHE 0.009 0.001 PHE A 609 TRP 0.013 0.001 TRP A2221 HIS 0.005 0.000 HIS A2278 Details of bonding type rmsd/Z covalent geometry : bond 0.00170 / 0.08 (19305) covalent geometry : angle 0.42237 / 0.21 (26367) hydrogen bonds : bond 0.02962 / 1.82 ( 1208) hydrogen bonds : angle 3.09991 / 2.08 ( 3525) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4708 Ramachandran restraints generated. 2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4708 Ramachandran restraints generated. 2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 208 time to evaluate : 0.514 Fit side-chains REVERT: A 566 LYS cc_start: 0.8280 (mmtm) cc_final: 0.7997 (mttt) REVERT: A 786 LEU cc_start: 0.8163 (OUTLIER) cc_final: 0.7928 (mt) REVERT: A 937 GLN cc_start: 0.8335 (mp10) cc_final: 0.8108 (mp10) REVERT: A 1078 GLU cc_start: 0.8624 (tp30) cc_final: 0.8280 (tp30) REVERT: A 1501 MET cc_start: 0.8259 (mtt) cc_final: 0.7974 (mtt) REVERT: A 1548 ARG cc_start: 0.7658 (mtm110) cc_final: 0.7265 (ttp80) REVERT: A 1782 ASP cc_start: 0.7674 (OUTLIER) cc_final: 0.7314 (t0) REVERT: A 2122 HIS cc_start: 0.7723 (t70) cc_final: 0.7189 (t70) REVERT: A 2167 MET cc_start: 0.8905 (mmt) cc_final: 0.8513 (mmt) REVERT: B 408 PHE cc_start: 0.6755 (m-10) cc_final: 0.6533 (m-10) REVERT: B 415 TRP cc_start: 0.8300 (OUTLIER) cc_final: 0.6810 (m-90) REVERT: C 171 LEU cc_start: 0.6786 (OUTLIER) cc_final: 0.6358 (pp) REVERT: C 231 GLU cc_start: 0.8975 (mt-10) cc_final: 0.8744 (mt-10) REVERT: C 247 GLU cc_start: 0.7987 (mt-10) cc_final: 0.7676 (mt-10) REVERT: C 383 LYS cc_start: 0.8486 (OUTLIER) cc_final: 0.8252 (tttt) REVERT: C 461 ARG cc_start: 0.8733 (OUTLIER) cc_final: 0.8432 (ptt180) outliers start: 41 outliers final: 10 residues processed: 228 average time/residue: 0.5921 time to fit residues: 151.8751 Evaluate side-chains 204 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 188 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 834 ASN Chi-restraints excluded: chain A residue 941 GLN Chi-restraints excluded: chain A residue 1352 LEU Chi-restraints excluded: chain A residue 1782 ASP Chi-restraints excluded: chain A residue 1803 LEU Chi-restraints excluded: chain A residue 1829 ARG Chi-restraints excluded: chain A residue 2149 SER Chi-restraints excluded: chain A residue 3607 SER Chi-restraints excluded: chain A residue 3657 TRP Chi-restraints excluded: chain B residue 316 ARG Chi-restraints excluded: chain B residue 415 TRP Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 383 LYS Chi-restraints excluded: chain C residue 461 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 61 optimal weight: 2.9990 chunk 151 optimal weight: 0.7980 chunk 68 optimal weight: 0.6980 chunk 240 optimal weight: 0.8980 chunk 108 optimal weight: 0.7980 chunk 99 optimal weight: 3.9990 chunk 117 optimal weight: 0.9990 chunk 100 optimal weight: 0.0020 chunk 98 optimal weight: 0.9980 chunk 134 optimal weight: 5.9990 chunk 84 optimal weight: 0.9980 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 881 ASN A1533 GLN B 159 ASN ** C 297 HIS ** 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 = 0.3829 r_free = 0.3829 target = 0.160927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.122415 restraints weight = 22481.199| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 1.76 r_work: 0.3090 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 19305 Z= 0.091 Angle : 0.438 8.763 26367 Z= 0.218 Chirality : 0.036 0.281 3247 Planarity : 0.003 0.039 3274 Dihedral : 3.928 98.089 2761 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.71 % Allowed : 12.35 % Favored : 85.94 % 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: 2.18 (0.18), residues: 2354 helix: 2.57 (0.14), residues: 1541 sheet: 0.97 (0.45), residues: 129 loop : -1.22 (0.24), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 375 TYR 0.019 0.001 TYR A 998 PHE 0.010 0.001 PHE A 817 TRP 0.010 0.001 TRP A2221 HIS 0.006 0.001 HIS A2278 Details of bonding type rmsd/Z covalent geometry : bond 0.00197 / 0.09 (19305) covalent geometry : angle 0.43831 / 0.22 (26367) hydrogen bonds : bond 0.03471 / 2.13 ( 1208) hydrogen bonds : angle 3.10888 / 2.09 ( 3525) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4708 Ramachandran restraints generated. 2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4708 Ramachandran restraints generated. 2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 202 time to evaluate : 0.804 Fit side-chains REVERT: A 566 LYS cc_start: 0.8251 (mmtm) cc_final: 0.7977 (mttt) REVERT: A 1078 GLU cc_start: 0.8684 (tp30) cc_final: 0.8330 (tp30) REVERT: A 1501 MET cc_start: 0.8310 (mtt) cc_final: 0.8100 (mtt) REVERT: A 1548 ARG cc_start: 0.7638 (mtm110) cc_final: 0.7250 (ttp80) REVERT: A 2122 HIS cc_start: 0.7633 (t70) cc_final: 0.7069 (t70) REVERT: A 2167 MET cc_start: 0.8948 (mmt) cc_final: 0.8524 (mmt) REVERT: B 257 ASN cc_start: 0.8250 (m-40) cc_final: 0.7946 (m110) REVERT: C 171 LEU cc_start: 0.6801 (OUTLIER) cc_final: 0.6409 (pp) REVERT: C 231 GLU cc_start: 0.9004 (mt-10) cc_final: 0.8747 (mt-10) REVERT: C 247 GLU cc_start: 0.7980 (mt-10) cc_final: 0.7650 (mt-10) REVERT: C 383 LYS cc_start: 0.8560 (OUTLIER) cc_final: 0.8277 (tttt) REVERT: C 461 ARG cc_start: 0.8792 (OUTLIER) cc_final: 0.8498 (ptt180) outliers start: 29 outliers final: 13 residues processed: 221 average time/residue: 0.6332 time to fit residues: 157.1350 Evaluate side-chains 206 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 190 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 719 LYS Chi-restraints excluded: chain A residue 834 ASN Chi-restraints excluded: chain A residue 900 THR Chi-restraints excluded: chain A residue 941 GLN Chi-restraints excluded: chain A residue 1047 THR Chi-restraints excluded: chain A residue 1317 THR Chi-restraints excluded: chain A residue 1352 LEU Chi-restraints excluded: chain A residue 1803 LEU Chi-restraints excluded: chain A residue 1829 ARG Chi-restraints excluded: chain A residue 2149 SER Chi-restraints excluded: chain A residue 3657 TRP Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 383 LYS Chi-restraints excluded: chain C residue 461 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 226 optimal weight: 6.9990 chunk 170 optimal weight: 0.0040 chunk 187 optimal weight: 0.7980 chunk 202 optimal weight: 4.9990 chunk 107 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 2 optimal weight: 50.0000 chunk 232 optimal weight: 0.6980 chunk 106 optimal weight: 0.6980 chunk 152 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 881 ASN A1533 GLN ** C 297 HIS ** 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 = 0.3830 r_free = 0.3830 target = 0.161102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.122887 restraints weight = 22370.153| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 1.80 r_work: 0.3094 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8837 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 19305 Z= 0.089 Angle : 0.430 7.340 26367 Z= 0.216 Chirality : 0.036 0.264 3247 Planarity : 0.003 0.039 3274 Dihedral : 3.825 92.217 2761 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.76 % Allowed : 12.82 % Favored : 85.41 % 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: 2.28 (0.18), residues: 2354 helix: 2.65 (0.13), residues: 1543 sheet: 1.01 (0.45), residues: 124 loop : -1.17 (0.23), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 375 TYR 0.017 0.001 TYR A 998 PHE 0.009 0.001 PHE A 817 TRP 0.011 0.001 TRP A1629 HIS 0.005 0.001 HIS A2278 Details of bonding type rmsd/Z covalent geometry : bond 0.00194 / 0.09 (19305) covalent geometry : angle 0.43009 / 0.22 (26367) hydrogen bonds : bond 0.03337 / 2.04 ( 1208) hydrogen bonds : angle 3.06812 / 2.06 ( 3525) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4708 Ramachandran restraints generated. 2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4708 Ramachandran restraints generated. 2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 198 time to evaluate : 0.582 Fit side-chains REVERT: A 522 LYS cc_start: 0.8403 (mtmt) cc_final: 0.8107 (mtpt) REVERT: A 566 LYS cc_start: 0.8244 (mmtm) cc_final: 0.7969 (mttt) REVERT: A 1078 GLU cc_start: 0.8713 (tp30) cc_final: 0.8352 (tp30) REVERT: A 1548 ARG cc_start: 0.7651 (mtm110) cc_final: 0.7260 (ttp80) REVERT: A 2167 MET cc_start: 0.8941 (mmt) cc_final: 0.8519 (mmt) REVERT: B 257 ASN cc_start: 0.8213 (m-40) cc_final: 0.7915 (m110) REVERT: C 171 LEU cc_start: 0.6855 (OUTLIER) cc_final: 0.6463 (pp) REVERT: C 231 GLU cc_start: 0.8999 (mt-10) cc_final: 0.8755 (mt-10) REVERT: C 247 GLU cc_start: 0.7941 (mt-10) cc_final: 0.7631 (mt-10) REVERT: C 383 LYS cc_start: 0.8546 (OUTLIER) cc_final: 0.8270 (tttt) REVERT: C 461 ARG cc_start: 0.8786 (OUTLIER) cc_final: 0.8494 (ptt180) outliers start: 30 outliers final: 16 residues processed: 219 average time/residue: 0.5995 time to fit residues: 147.8943 Evaluate side-chains 210 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 191 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 719 LYS Chi-restraints excluded: chain A residue 834 ASN Chi-restraints excluded: chain A residue 900 THR Chi-restraints excluded: chain A residue 941 GLN Chi-restraints excluded: chain A residue 1047 THR Chi-restraints excluded: chain A residue 1352 LEU Chi-restraints excluded: chain A residue 1439 SER Chi-restraints excluded: chain A residue 1803 LEU Chi-restraints excluded: chain A residue 1829 ARG Chi-restraints excluded: chain A residue 3607 SER Chi-restraints excluded: chain A residue 3657 TRP Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 383 LYS Chi-restraints excluded: chain C residue 461 ARG Chi-restraints excluded: chain C residue 488 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 157 optimal weight: 6.9990 chunk 233 optimal weight: 8.9990 chunk 100 optimal weight: 0.2980 chunk 229 optimal weight: 0.0020 chunk 21 optimal weight: 9.9990 chunk 102 optimal weight: 0.6980 chunk 126 optimal weight: 0.7980 chunk 234 optimal weight: 0.9990 chunk 110 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 overall best weight: 0.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 881 ASN A1533 GLN ** C 297 HIS ** 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 = 0.3835 r_free = 0.3835 target = 0.161636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.123855 restraints weight = 22460.209| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 1.66 r_work: 0.3102 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8831 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 19305 Z= 0.085 Angle : 0.419 8.281 26367 Z= 0.211 Chirality : 0.036 0.284 3247 Planarity : 0.003 0.039 3274 Dihedral : 3.701 85.206 2761 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.88 % Allowed : 13.06 % Favored : 85.06 % 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: 2.37 (0.18), residues: 2354 helix: 2.72 (0.13), residues: 1543 sheet: 1.05 (0.45), residues: 124 loop : -1.14 (0.23), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 375 TYR 0.017 0.001 TYR A 998 PHE 0.009 0.001 PHE A 817 TRP 0.010 0.001 TRP A2221 HIS 0.005 0.001 HIS A2278 Details of bonding type rmsd/Z covalent geometry : bond 0.00181 / 0.08 (19305) covalent geometry : angle 0.41903 / 0.21 (26367) hydrogen bonds : bond 0.03143 / 1.93 ( 1208) hydrogen bonds : angle 3.02350 / 2.03 ( 3525) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4708 Ramachandran restraints generated. 2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4708 Ramachandran restraints generated. 2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 201 time to evaluate : 0.744 Fit side-chains REVERT: A 522 LYS cc_start: 0.8308 (mtmt) cc_final: 0.8014 (mtpt) REVERT: A 566 LYS cc_start: 0.8232 (mmtm) cc_final: 0.7956 (mttt) REVERT: A 1078 GLU cc_start: 0.8733 (tp30) cc_final: 0.8368 (tp30) REVERT: A 1367 ARG cc_start: 0.8283 (mtp-110) cc_final: 0.7987 (mtt-85) REVERT: A 1548 ARG cc_start: 0.7632 (mtm110) cc_final: 0.7239 (ttp80) REVERT: A 2167 MET cc_start: 0.8945 (mmt) cc_final: 0.8531 (mmt) REVERT: A 2324 MET cc_start: 0.8727 (OUTLIER) cc_final: 0.8155 (tpt) REVERT: B 257 ASN cc_start: 0.8191 (m-40) cc_final: 0.7893 (m110) REVERT: C 171 LEU cc_start: 0.6858 (OUTLIER) cc_final: 0.6533 (pp) REVERT: C 231 GLU cc_start: 0.8992 (mt-10) cc_final: 0.8760 (mt-10) REVERT: C 247 GLU cc_start: 0.7961 (mt-10) cc_final: 0.7672 (mt-10) REVERT: C 383 LYS cc_start: 0.8541 (OUTLIER) cc_final: 0.8290 (tttt) REVERT: C 461 ARG cc_start: 0.8769 (OUTLIER) cc_final: 0.8473 (ptt180) outliers start: 32 outliers final: 19 residues processed: 221 average time/residue: 0.6188 time to fit residues: 154.5191 Evaluate side-chains 217 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 194 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 719 LYS Chi-restraints excluded: chain A residue 834 ASN Chi-restraints excluded: chain A residue 900 THR Chi-restraints excluded: chain A residue 941 GLN Chi-restraints excluded: chain A residue 1047 THR Chi-restraints excluded: chain A residue 1352 LEU Chi-restraints excluded: chain A residue 1439 SER Chi-restraints excluded: chain A residue 1803 LEU Chi-restraints excluded: chain A residue 1829 ARG Chi-restraints excluded: chain A residue 2105 THR Chi-restraints excluded: chain A residue 2324 MET Chi-restraints excluded: chain A residue 3607 SER Chi-restraints excluded: chain A residue 3625 VAL Chi-restraints excluded: chain A residue 3657 TRP Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 383 LYS Chi-restraints excluded: chain C residue 461 ARG Chi-restraints excluded: chain C residue 488 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 235 optimal weight: 0.8980 chunk 152 optimal weight: 10.0000 chunk 6 optimal weight: 20.0000 chunk 27 optimal weight: 5.9990 chunk 197 optimal weight: 2.9990 chunk 9 optimal weight: 50.0000 chunk 93 optimal weight: 0.6980 chunk 108 optimal weight: 0.6980 chunk 80 optimal weight: 0.8980 chunk 183 optimal weight: 0.6980 chunk 114 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 767 ASN A 881 ASN A1533 GLN ** C 297 HIS ** 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 = 0.3822 r_free = 0.3822 target = 0.160441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.122577 restraints weight = 22383.736| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 1.69 r_work: 0.3078 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8874 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 19305 Z= 0.096 Angle : 0.443 9.089 26367 Z= 0.222 Chirality : 0.036 0.250 3247 Planarity : 0.003 0.040 3274 Dihedral : 3.731 78.870 2761 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.88 % Allowed : 13.24 % Favored : 84.88 % 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: 2.33 (0.18), residues: 2354 helix: 2.67 (0.13), residues: 1544 sheet: 1.05 (0.46), residues: 124 loop : -1.11 (0.23), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 375 TYR 0.018 0.001 TYR A 998 PHE 0.011 0.001 PHE A 817 TRP 0.010 0.001 TRP A1629 HIS 0.005 0.001 HIS A2278 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.10 (19305) covalent geometry : angle 0.44304 / 0.22 (26367) hydrogen bonds : bond 0.03627 / 2.22 ( 1208) hydrogen bonds : angle 3.07197 / 2.06 ( 3525) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4708 Ramachandran restraints generated. 2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4708 Ramachandran restraints generated. 2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 195 time to evaluate : 0.718 Fit side-chains REVERT: A 522 LYS cc_start: 0.8381 (mtmt) cc_final: 0.8103 (mtpt) REVERT: A 558 ILE cc_start: 0.7613 (OUTLIER) cc_final: 0.7408 (mp) REVERT: A 566 LYS cc_start: 0.8263 (mmtm) cc_final: 0.7958 (mttp) REVERT: A 937 GLN cc_start: 0.8394 (mp10) cc_final: 0.8098 (mp10) REVERT: A 1078 GLU cc_start: 0.8742 (tp30) cc_final: 0.8383 (tp30) REVERT: A 1548 ARG cc_start: 0.7720 (mtm110) cc_final: 0.7374 (ttp80) REVERT: A 2167 MET cc_start: 0.8931 (mmt) cc_final: 0.8148 (mmt) REVERT: C 171 LEU cc_start: 0.6958 (OUTLIER) cc_final: 0.6622 (pp) REVERT: C 231 GLU cc_start: 0.8995 (mt-10) cc_final: 0.8757 (mt-10) REVERT: C 239 ARG cc_start: 0.8167 (ttm110) cc_final: 0.7959 (ttp-110) REVERT: C 247 GLU cc_start: 0.7965 (mt-10) cc_final: 0.7676 (mt-10) REVERT: C 383 LYS cc_start: 0.8607 (OUTLIER) cc_final: 0.8315 (tttt) REVERT: C 461 ARG cc_start: 0.8812 (OUTLIER) cc_final: 0.8478 (ptt180) outliers start: 32 outliers final: 18 residues processed: 215 average time/residue: 0.6335 time to fit residues: 153.4528 Evaluate side-chains 206 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 184 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 558 ILE Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 719 LYS Chi-restraints excluded: chain A residue 834 ASN Chi-restraints excluded: chain A residue 900 THR Chi-restraints excluded: chain A residue 941 GLN Chi-restraints excluded: chain A residue 1047 THR Chi-restraints excluded: chain A residue 1352 LEU Chi-restraints excluded: chain A residue 1439 SER Chi-restraints excluded: chain A residue 1803 LEU Chi-restraints excluded: chain A residue 1829 ARG Chi-restraints excluded: chain A residue 2202 SER Chi-restraints excluded: chain A residue 3607 SER Chi-restraints excluded: chain A residue 3625 VAL Chi-restraints excluded: chain A residue 3657 TRP Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 383 LYS Chi-restraints excluded: chain C residue 461 ARG Chi-restraints excluded: chain C residue 488 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 80 optimal weight: 0.7980 chunk 153 optimal weight: 6.9990 chunk 32 optimal weight: 0.5980 chunk 201 optimal weight: 0.5980 chunk 160 optimal weight: 3.9990 chunk 113 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 185 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 247 optimal weight: 3.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 881 ASN A1533 GLN ** C 297 HIS ** 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 = 0.3823 r_free = 0.3823 target = 0.160558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.122801 restraints weight = 22340.760| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 1.68 r_work: 0.3083 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8872 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 19305 Z= 0.095 Angle : 0.439 9.286 26367 Z= 0.221 Chirality : 0.036 0.247 3247 Planarity : 0.004 0.041 3274 Dihedral : 3.685 71.573 2761 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.59 % Allowed : 13.76 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.37 (0.18), residues: 2354 helix: 2.68 (0.13), residues: 1542 sheet: 1.06 (0.46), residues: 124 loop : -1.05 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1283 TYR 0.017 0.001 TYR A 998 PHE 0.010 0.001 PHE A 817 TRP 0.010 0.001 TRP A1629 HIS 0.006 0.001 HIS A2278 Details of bonding type rmsd/Z covalent geometry : bond 0.00209 / 0.09 (19305) covalent geometry : angle 0.43939 / 0.22 (26367) hydrogen bonds : bond 0.03537 / 2.16 ( 1208) hydrogen bonds : angle 3.07402 / 2.06 ( 3525) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4708 Ramachandran restraints generated. 2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4708 Ramachandran restraints generated. 2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 184 time to evaluate : 0.765 Fit side-chains REVERT: A 522 LYS cc_start: 0.8342 (mtmt) cc_final: 0.8062 (mtpp) REVERT: A 558 ILE cc_start: 0.7606 (OUTLIER) cc_final: 0.7406 (mp) REVERT: A 566 LYS cc_start: 0.8252 (mmtm) cc_final: 0.7944 (mttp) REVERT: A 937 GLN cc_start: 0.8394 (mp10) cc_final: 0.8080 (mp10) REVERT: A 1548 ARG cc_start: 0.7736 (mtm110) cc_final: 0.7438 (ttp80) REVERT: B 257 ASN cc_start: 0.8235 (m-40) cc_final: 0.7979 (m110) REVERT: C 171 LEU cc_start: 0.6946 (OUTLIER) cc_final: 0.6640 (pp) REVERT: C 231 GLU cc_start: 0.9023 (mt-10) cc_final: 0.8791 (mt-10) REVERT: C 239 ARG cc_start: 0.8190 (ttm110) cc_final: 0.7976 (ttp-110) REVERT: C 247 GLU cc_start: 0.7929 (mt-10) cc_final: 0.7637 (mt-10) REVERT: C 383 LYS cc_start: 0.8604 (OUTLIER) cc_final: 0.8325 (tttt) REVERT: C 461 ARG cc_start: 0.8783 (OUTLIER) cc_final: 0.8486 (ptt180) outliers start: 27 outliers final: 18 residues processed: 204 average time/residue: 0.6546 time to fit residues: 150.5800 Evaluate side-chains 204 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 182 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 558 ILE Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 719 LYS Chi-restraints excluded: chain A residue 834 ASN Chi-restraints excluded: chain A residue 900 THR Chi-restraints excluded: chain A residue 941 GLN Chi-restraints excluded: chain A residue 1047 THR Chi-restraints excluded: chain A residue 1352 LEU Chi-restraints excluded: chain A residue 1439 SER Chi-restraints excluded: chain A residue 1803 LEU Chi-restraints excluded: chain A residue 1829 ARG Chi-restraints excluded: chain A residue 2202 SER Chi-restraints excluded: chain A residue 3607 SER Chi-restraints excluded: chain A residue 3625 VAL Chi-restraints excluded: chain A residue 3657 TRP Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 383 LYS Chi-restraints excluded: chain C residue 461 ARG Chi-restraints excluded: chain C residue 488 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 237 optimal weight: 6.9990 chunk 239 optimal weight: 0.8980 chunk 136 optimal weight: 0.8980 chunk 175 optimal weight: 0.9980 chunk 244 optimal weight: 0.0060 chunk 95 optimal weight: 0.9980 chunk 5 optimal weight: 40.0000 chunk 110 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 236 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 overall best weight: 0.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 881 ASN A1533 GLN ** C 297 HIS ** 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 = 0.3823 r_free = 0.3823 target = 0.160421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.123041 restraints weight = 22272.381| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 1.70 r_work: 0.3073 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8878 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 19305 Z= 0.094 Angle : 0.439 9.253 26367 Z= 0.221 Chirality : 0.036 0.246 3247 Planarity : 0.003 0.041 3274 Dihedral : 3.629 63.040 2761 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.53 % Allowed : 13.88 % Favored : 84.59 % 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: 2.39 (0.18), residues: 2354 helix: 2.70 (0.13), residues: 1541 sheet: 1.09 (0.46), residues: 124 loop : -1.05 (0.24), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 375 TYR 0.018 0.001 TYR A 998 PHE 0.010 0.001 PHE A 817 TRP 0.010 0.001 TRP A2221 HIS 0.005 0.001 HIS A2278 Details of bonding type rmsd/Z covalent geometry : bond 0.00208 / 0.09 (19305) covalent geometry : angle 0.43881 / 0.22 (26367) hydrogen bonds : bond 0.03531 / 2.16 ( 1208) hydrogen bonds : angle 3.06490 / 2.06 ( 3525) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4708 Ramachandran restraints generated. 2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4708 Ramachandran restraints generated. 2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 187 time to evaluate : 0.858 Fit side-chains REVERT: A 522 LYS cc_start: 0.8341 (mtmt) cc_final: 0.8057 (mtpp) REVERT: A 566 LYS cc_start: 0.8263 (mmtm) cc_final: 0.7944 (mttp) REVERT: A 937 GLN cc_start: 0.8400 (mp10) cc_final: 0.8077 (mp10) REVERT: A 1548 ARG cc_start: 0.7712 (mtm110) cc_final: 0.7455 (ttp80) REVERT: A 2167 MET cc_start: 0.8894 (mmt) cc_final: 0.8143 (mmt) REVERT: B 257 ASN cc_start: 0.8198 (m-40) cc_final: 0.7905 (m110) REVERT: C 171 LEU cc_start: 0.6862 (OUTLIER) cc_final: 0.6552 (pp) REVERT: C 231 GLU cc_start: 0.9029 (mt-10) cc_final: 0.8799 (mt-10) REVERT: C 239 ARG cc_start: 0.8185 (ttm110) cc_final: 0.7971 (ttp-110) REVERT: C 247 GLU cc_start: 0.7939 (mt-10) cc_final: 0.7649 (mt-10) REVERT: C 383 LYS cc_start: 0.8617 (OUTLIER) cc_final: 0.8333 (tttt) REVERT: C 461 ARG cc_start: 0.8783 (OUTLIER) cc_final: 0.8486 (ptt180) outliers start: 26 outliers final: 18 residues processed: 205 average time/residue: 0.6621 time to fit residues: 153.2788 Evaluate side-chains 202 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 181 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 719 LYS Chi-restraints excluded: chain A residue 834 ASN Chi-restraints excluded: chain A residue 900 THR Chi-restraints excluded: chain A residue 941 GLN Chi-restraints excluded: chain A residue 1047 THR Chi-restraints excluded: chain A residue 1352 LEU Chi-restraints excluded: chain A residue 1439 SER Chi-restraints excluded: chain A residue 1803 LEU Chi-restraints excluded: chain A residue 1829 ARG Chi-restraints excluded: chain A residue 2202 SER Chi-restraints excluded: chain A residue 3607 SER Chi-restraints excluded: chain A residue 3625 VAL Chi-restraints excluded: chain A residue 3657 TRP Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 383 LYS Chi-restraints excluded: chain C residue 461 ARG Chi-restraints excluded: chain C residue 488 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 243 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 4 optimal weight: 50.0000 chunk 8 optimal weight: 50.0000 chunk 102 optimal weight: 0.5980 chunk 193 optimal weight: 6.9990 chunk 83 optimal weight: 0.0270 chunk 109 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 63 optimal weight: 0.4980 overall best weight: 0.6040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 881 ASN A1533 GLN ** C 297 HIS ** 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 = 0.3831 r_free = 0.3831 target = 0.161146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.123487 restraints weight = 22318.288| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 1.73 r_work: 0.3094 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8843 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 19305 Z= 0.089 Angle : 0.432 9.123 26367 Z= 0.217 Chirality : 0.036 0.243 3247 Planarity : 0.003 0.041 3274 Dihedral : 3.547 55.445 2761 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.65 % Allowed : 13.59 % Favored : 84.76 % 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: 2.44 (0.18), residues: 2354 helix: 2.74 (0.13), residues: 1542 sheet: 1.10 (0.46), residues: 124 loop : -1.04 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 375 TYR 0.017 0.001 TYR A 998 PHE 0.009 0.001 PHE A 817 TRP 0.011 0.001 TRP A1629 HIS 0.006 0.001 HIS A2278 Details of bonding type rmsd/Z covalent geometry : bond 0.00192 / 0.09 (19305) covalent geometry : angle 0.43231 / 0.22 (26367) hydrogen bonds : bond 0.03306 / 2.02 ( 1208) hydrogen bonds : angle 3.04143 / 2.04 ( 3525) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6995.95 seconds wall clock time: 119 minutes 42.80 seconds (7182.80 seconds total)