Starting phenix.real_space_refine on Tue Oct 27 21:20:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9utw_64502/10_2026/9utw_64502.cif Found real_map, /net/cci-nas-00/data/ceres_data/9utw_64502/10_2026/9utw_64502.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9utw_64502/10_2026/9utw_64502.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9utw_64502/10_2026/9utw_64502.map" model { file = "/net/cci-nas-00/data/ceres_data/9utw_64502/10_2026/9utw_64502.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9utw_64502/10_2026/9utw_64502.cif" } resolution = 2.96 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= -0.001 sd= 0.038 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 66 5.49 5 Mg 2 5.21 5 S 148 5.16 5 C 16467 2.51 5 N 4144 2.21 5 O 4581 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 57 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 25408 Number of models: 1 Model: "" Number of chains: 10 Chain: "C" Number of atoms: 203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 203 Classifications: {'peptide': 25} Link IDs: {'PTRANS': 2, 'TRANS': 22} Chain: "G" Number of atoms: 203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 203 Classifications: {'peptide': 25} Link IDs: {'PTRANS': 2, 'TRANS': 22} Chain: "H" Number of atoms: 11499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1409, 11499 Classifications: {'peptide': 1409} Link IDs: {'PTRANS': 64, 'TRANS': 1344} Chain breaks: 10 Chain: "B" Number of atoms: 11499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1409, 11499 Classifications: {'peptide': 1409} Link IDs: {'PTRANS': 64, 'TRANS': 1344} Chain breaks: 10 Chain: "A" Number of atoms: 571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 571 Classifications: {'RNA': 27} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 2, 'rna3p_pur': 9, 'rna3p_pyr': 14} Link IDs: {'rna2p': 4, 'rna3p': 22} Chain breaks: 1 Chain: "A" Number of atoms: 748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 748 Classifications: {'RNA': 35} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 3, 'rna3p': 1, 'rna3p_pur': 15, 'rna3p_pyr': 14} Link IDs: {'rna2p': 5, 'rna3p': 29} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "J" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 34 Unusual residues: {'BGC': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {'BGC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 289 Unusual residues: {' MG': 1, 'D10': 1, 'DCR': 1, 'DD9': 4, 'HP6': 2, 'PEF': 1, 'PLM': 7, 'XKP': 1} Classifications: {'undetermined': 18} Link IDs: {None: 17} Chain: "B" Number of atoms: 339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 339 Unusual residues: {' MG': 1, 'D10': 1, 'DCR': 1, 'DD9': 4, 'HP6': 4, 'PEF': 1, 'PLM': 9, 'XKP': 1} Classifications: {'undetermined': 22} Link IDs: {None: 21} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 8365 SG CYS H1244 128.829 62.582 49.427 1.00 40.73 S ATOM 19864 SG CYS B1244 37.153 115.686 49.992 1.00 9.74 S Time building chain proxies: 6.25, per 1000 atoms: 0.25 Number of scatterers: 25408 At special positions: 0 Unit cell: (168.3, 179.3, 136.4, 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 148 16.00 P 66 15.00 Mg 2 11.99 O 4581 8.00 N 4144 7.00 C 16467 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS H1328 " - pdb=" SG CYS H1345 " distance=2.03 Simple disulfide: pdb=" SG CYS B1328 " - pdb=" SG CYS B1345 " distance=2.02 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=4, symmetry=0 Links applied BETA1-3 " BGC D 1 " - " BGC D 2 " " BGC J 1 " - " BGC J 2 " " BGC J 2 " - " BGC J 3 " Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.50 Conformation dependent library (CDL) restraints added in 895.1 milliseconds 5640 Ramachandran restraints generated. 2820 Oldfield, 0 Emsley, 2820 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5468 Finding SS restraints... Secondary structure from input PDB file: 148 helices and 7 sheets defined 68.6% alpha, 3.6% beta 10 base pairs and 28 stacking pairs defined. Time for finding SS restraints: 3.04 Creating SS restraints... Processing helix chain 'C' and resid 104 through 116 removed outlier: 3.620A pdb=" N VAL C 116 " --> pdb=" O PHE C 112 " (cutoff:3.500A) Processing helix chain 'G' and resid 104 through 116 removed outlier: 3.714A pdb=" N VAL G 116 " --> pdb=" O PHE G 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 161 through 176 removed outlier: 3.729A pdb=" N ASP H 166 " --> pdb=" O GLU H 162 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N ILE H 167 " --> pdb=" O GLN H 163 " (cutoff:3.500A) Processing helix chain 'H' and resid 178 through 197 Processing helix chain 'H' and resid 201 through 214 Processing helix chain 'H' and resid 219 through 229 removed outlier: 3.717A pdb=" N LYS H 223 " --> pdb=" O ALA H 219 " (cutoff:3.500A) Processing helix chain 'H' and resid 232 through 247 removed outlier: 5.104A pdb=" N GLY H 244 " --> pdb=" O ASN H 240 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N LYS H 245 " --> pdb=" O MET H 241 " (cutoff:3.500A) Processing helix chain 'H' and resid 281 through 294 Processing helix chain 'H' and resid 297 through 313 Processing helix chain 'H' and resid 315 through 320 removed outlier: 3.699A pdb=" N PHE H 320 " --> pdb=" O GLN H 317 " (cutoff:3.500A) Processing helix chain 'H' and resid 321 through 337 Processing helix chain 'H' and resid 338 through 343 removed outlier: 3.603A pdb=" N GLN H 342 " --> pdb=" O SER H 338 " (cutoff:3.500A) Processing helix chain 'H' and resid 351 through 356 Processing helix chain 'H' and resid 357 through 369 removed outlier: 4.424A pdb=" N ILE H 361 " --> pdb=" O VAL H 357 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLN H 368 " --> pdb=" O PHE H 364 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N VAL H 369 " --> pdb=" O ILE H 365 " (cutoff:3.500A) Processing helix chain 'H' and resid 383 through 387 Processing helix chain 'H' and resid 389 through 396 Processing helix chain 'H' and resid 399 through 404 Processing helix chain 'H' and resid 418 through 422 Processing helix chain 'H' and resid 425 through 429 removed outlier: 3.638A pdb=" N VAL H 429 " --> pdb=" O LEU H 426 " (cutoff:3.500A) Processing helix chain 'H' and resid 443 through 452 removed outlier: 3.844A pdb=" N HIS H 447 " --> pdb=" O ARG H 443 " (cutoff:3.500A) Processing helix chain 'H' and resid 452 through 470 removed outlier: 4.136A pdb=" N TRP H 456 " --> pdb=" O PHE H 452 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER H 461 " --> pdb=" O VAL H 457 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE H 462 " --> pdb=" O MET H 458 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASN H 470 " --> pdb=" O TYR H 466 " (cutoff:3.500A) Processing helix chain 'H' and resid 471 through 476 removed outlier: 3.975A pdb=" N PHE H 474 " --> pdb=" O SER H 471 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N THR H 476 " --> pdb=" O THR H 473 " (cutoff:3.500A) Processing helix chain 'H' and resid 488 through 497 removed outlier: 3.636A pdb=" N LYS H 492 " --> pdb=" O LEU H 488 " (cutoff:3.500A) Processing helix chain 'H' and resid 498 through 516 removed outlier: 4.117A pdb=" N SER H 516 " --> pdb=" O LEU H 512 " (cutoff:3.500A) Processing helix chain 'H' and resid 525 through 551 removed outlier: 4.290A pdb=" N SER H 529 " --> pdb=" O ALA H 525 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N PHE H 534 " --> pdb=" O ARG H 530 " (cutoff:3.500A) Proline residue: H 545 - end of helix removed outlier: 3.583A pdb=" N PHE H 548 " --> pdb=" O GLY H 544 " (cutoff:3.500A) Processing helix chain 'H' and resid 559 through 583 removed outlier: 3.748A pdb=" N HIS H 563 " --> pdb=" O SER H 559 " (cutoff:3.500A) Processing helix chain 'H' and resid 603 through 608 Processing helix chain 'H' and resid 616 through 654 removed outlier: 3.823A pdb=" N TRP H 625 " --> pdb=" O SER H 621 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N LEU H 642 " --> pdb=" O TYR H 638 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER H 643 " --> pdb=" O PHE H 639 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU H 644 " --> pdb=" O LEU H 640 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ARG H 645 " --> pdb=" O VAL H 641 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ASP H 646 " --> pdb=" O LEU H 642 " (cutoff:3.500A) Proline residue: H 647 - end of helix removed outlier: 3.674A pdb=" N THR H 653 " --> pdb=" O ARG H 649 " (cutoff:3.500A) Processing helix chain 'H' and resid 665 through 669 removed outlier: 3.957A pdb=" N LEU H 668 " --> pdb=" O GLY H 665 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N CYS H 669 " --> pdb=" O ALA H 666 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 665 through 669' Processing helix chain 'H' and resid 671 through 688 Processing helix chain 'H' and resid 690 through 712 removed outlier: 4.116A pdb=" N LEU H 694 " --> pdb=" O LEU H 690 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER H 708 " --> pdb=" O SER H 704 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N PHE H 709 " --> pdb=" O VAL H 705 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N TYR H 710 " --> pdb=" O GLY H 706 " (cutoff:3.500A) Processing helix chain 'H' and resid 719 through 724 removed outlier: 3.590A pdb=" N PHE H 723 " --> pdb=" O TRP H 719 " (cutoff:3.500A) Processing helix chain 'H' and resid 725 through 734 Processing helix chain 'H' and resid 745 through 764 removed outlier: 3.785A pdb=" N LEU H 749 " --> pdb=" O LYS H 745 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLN H 752 " --> pdb=" O VAL H 748 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL H 753 " --> pdb=" O LEU H 749 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ALA H 756 " --> pdb=" O GLN H 752 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLU H 764 " --> pdb=" O SER H 760 " (cutoff:3.500A) Processing helix chain 'H' and resid 768 through 773 removed outlier: 3.985A pdb=" N GLN H 773 " --> pdb=" O ILE H 769 " (cutoff:3.500A) Processing helix chain 'H' and resid 785 through 789 Processing helix chain 'H' and resid 815 through 827 Processing helix chain 'H' and resid 835 through 839 Processing helix chain 'H' and resid 856 through 862 Processing helix chain 'H' and resid 872 through 880 Processing helix chain 'H' and resid 880 through 895 Processing helix chain 'H' and resid 932 through 946 Processing helix chain 'H' and resid 949 through 958 removed outlier: 3.601A pdb=" N THR H 953 " --> pdb=" O THR H 949 " (cutoff:3.500A) Processing helix chain 'H' and resid 958 through 972 removed outlier: 4.410A pdb=" N ARG H 962 " --> pdb=" O MET H 958 " (cutoff:3.500A) Processing helix chain 'H' and resid 972 through 980 removed outlier: 4.596A pdb=" N VAL H 976 " --> pdb=" O ASN H 972 " (cutoff:3.500A) Processing helix chain 'H' and resid 982 through 996 removed outlier: 4.032A pdb=" N ARG H 996 " --> pdb=" O LYS H 992 " (cutoff:3.500A) Processing helix chain 'H' and resid 1006 through 1010 removed outlier: 3.859A pdb=" N PHE H1010 " --> pdb=" O LEU H1007 " (cutoff:3.500A) Processing helix chain 'H' and resid 1011 through 1025 Processing helix chain 'H' and resid 1082 through 1090 removed outlier: 3.783A pdb=" N HIS H1088 " --> pdb=" O ASP H1084 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ALA H1089 " --> pdb=" O ASN H1085 " (cutoff:3.500A) Processing helix chain 'H' and resid 1108 through 1113 Processing helix chain 'H' and resid 1114 through 1120 Processing helix chain 'H' and resid 1121 through 1123 No H-bonds generated for 'chain 'H' and resid 1121 through 1123' Processing helix chain 'H' and resid 1201 through 1205 Processing helix chain 'H' and resid 1222 through 1233 Processing helix chain 'H' and resid 1268 through 1271 removed outlier: 3.666A pdb=" N LEU H1271 " --> pdb=" O GLU H1268 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 1268 through 1271' Processing helix chain 'H' and resid 1272 through 1280 removed outlier: 3.529A pdb=" N TYR H1276 " --> pdb=" O SER H1272 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N THR H1280 " --> pdb=" O TYR H1276 " (cutoff:3.500A) Processing helix chain 'H' and resid 1283 through 1292 Processing helix chain 'H' and resid 1295 through 1325 removed outlier: 3.594A pdb=" N GLN H1305 " --> pdb=" O ASN H1301 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER H1325 " --> pdb=" O LEU H1321 " (cutoff:3.500A) Processing helix chain 'H' and resid 1348 through 1378 Proline residue: H1372 - end of helix Processing helix chain 'H' and resid 1437 through 1446 removed outlier: 3.557A pdb=" N PHE H1445 " --> pdb=" O LEU H1441 " (cutoff:3.500A) Processing helix chain 'H' and resid 1450 through 1467 Processing helix chain 'H' and resid 1471 through 1489 removed outlier: 3.665A pdb=" N PHE H1475 " --> pdb=" O PRO H1471 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA H1477 " --> pdb=" O LEU H1473 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N SER H1480 " --> pdb=" O TRP H1476 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N LEU H1482 " --> pdb=" O SER H1478 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE H1483 " --> pdb=" O LEU H1479 " (cutoff:3.500A) Proline residue: H1486 - end of helix removed outlier: 3.627A pdb=" N PHE H1489 " --> pdb=" O ALA H1485 " (cutoff:3.500A) Processing helix chain 'H' and resid 1495 through 1511 Processing helix chain 'H' and resid 1556 through 1562 removed outlier: 3.997A pdb=" N MET H1562 " --> pdb=" O THR H1558 " (cutoff:3.500A) Processing helix chain 'H' and resid 1564 through 1584 removed outlier: 4.757A pdb=" N CYS H1568 " --> pdb=" O GLU H1564 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE H1570 " --> pdb=" O ILE H1566 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR H1571 " --> pdb=" O PRO H1567 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA H1572 " --> pdb=" O CYS H1568 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ALA H1578 " --> pdb=" O GLY H1574 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ILE H1582 " --> pdb=" O ALA H1578 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ASN H1583 " --> pdb=" O PHE H1579 " (cutoff:3.500A) Processing helix chain 'H' and resid 1598 through 1622 Proline residue: H1609 - end of helix Processing helix chain 'H' and resid 1627 through 1635 removed outlier: 3.893A pdb=" N PHE H1631 " --> pdb=" O SER H1627 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY H1632 " --> pdb=" O GLY H1628 " (cutoff:3.500A) Processing helix chain 'H' and resid 1637 through 1662 removed outlier: 4.012A pdb=" N VAL H1641 " --> pdb=" O LYS H1637 " (cutoff:3.500A) Processing helix chain 'H' and resid 1670 through 1696 removed outlier: 4.350A pdb=" N ILE H1674 " --> pdb=" O VAL H1670 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLY H1675 " --> pdb=" O ARG H1671 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR H1696 " --> pdb=" O ALA H1692 " (cutoff:3.500A) Processing helix chain 'H' and resid 1723 through 1753 removed outlier: 3.821A pdb=" N ILE H1735 " --> pdb=" O THR H1731 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N CYS H1753 " --> pdb=" O VAL H1749 " (cutoff:3.500A) Processing helix chain 'H' and resid 1754 through 1760 removed outlier: 4.000A pdb=" N ILE H1760 " --> pdb=" O PRO H1756 " (cutoff:3.500A) Processing helix chain 'H' and resid 1762 through 1774 removed outlier: 3.857A pdb=" N PHE H1766 " --> pdb=" O LYS H1762 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N MET H1770 " --> pdb=" O PHE H1766 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LEU H1771 " --> pdb=" O HIS H1767 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N PHE H1772 " --> pdb=" O SER H1768 " (cutoff:3.500A) Processing helix chain 'H' and resid 1786 through 1825 removed outlier: 3.696A pdb=" N LEU H1792 " --> pdb=" O LYS H1788 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG H1793 " --> pdb=" O GLN H1789 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ILE H1815 " --> pdb=" O PHE H1811 " (cutoff:3.500A) Proline residue: H1818 - end of helix removed outlier: 3.790A pdb=" N ALA H1823 " --> pdb=" O ALA H1819 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 176 removed outlier: 4.202A pdb=" N ASP B 166 " --> pdb=" O GLU B 162 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ILE B 167 " --> pdb=" O GLN B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 198 removed outlier: 4.400A pdb=" N ASN B 184 " --> pdb=" O ASP B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 214 Processing helix chain 'B' and resid 219 through 229 removed outlier: 4.049A pdb=" N LYS B 223 " --> pdb=" O ALA B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 247 removed outlier: 3.792A pdb=" N ILE B 236 " --> pdb=" O MET B 232 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N GLY B 244 " --> pdb=" O ASN B 240 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N LYS B 245 " --> pdb=" O MET B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 294 Processing helix chain 'B' and resid 297 through 315 removed outlier: 3.650A pdb=" N TYR B 308 " --> pdb=" O HIS B 304 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLU B 314 " --> pdb=" O LEU B 310 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA B 315 " --> pdb=" O CYS B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 320 Processing helix chain 'B' and resid 321 through 337 removed outlier: 3.617A pdb=" N LEU B 325 " --> pdb=" O THR B 321 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASP B 337 " --> pdb=" O LEU B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 357 Processing helix chain 'B' and resid 357 through 367 removed outlier: 4.588A pdb=" N ILE B 361 " --> pdb=" O VAL B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 389 through 395 Processing helix chain 'B' and resid 396 through 398 No H-bonds generated for 'chain 'B' and resid 396 through 398' Processing helix chain 'B' and resid 399 through 404 Processing helix chain 'B' and resid 413 through 417 removed outlier: 3.629A pdb=" N GLU B 416 " --> pdb=" O LYS B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 420 No H-bonds generated for 'chain 'B' and resid 418 through 420' Processing helix chain 'B' and resid 421 through 426 removed outlier: 3.736A pdb=" N ARG B 425 " --> pdb=" O GLU B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 452 removed outlier: 3.770A pdb=" N HIS B 447 " --> pdb=" O ARG B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 470 removed outlier: 4.048A pdb=" N TRP B 456 " --> pdb=" O PHE B 452 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N MET B 458 " --> pdb=" O ARG B 454 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SER B 461 " --> pdb=" O VAL B 457 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ILE B 462 " --> pdb=" O MET B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 476 removed outlier: 4.076A pdb=" N PHE B 474 " --> pdb=" O SER B 471 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N THR B 476 " --> pdb=" O THR B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 497 Processing helix chain 'B' and resid 498 through 515 Processing helix chain 'B' and resid 524 through 542 removed outlier: 4.552A pdb=" N LEU B 528 " --> pdb=" O GLY B 524 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N SER B 529 " --> pdb=" O ALA B 525 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 551 removed outlier: 3.585A pdb=" N ILE B 547 " --> pdb=" O LEU B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 556 Processing helix chain 'B' and resid 559 through 583 removed outlier: 3.692A pdb=" N HIS B 563 " --> pdb=" O SER B 559 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE B 571 " --> pdb=" O ALA B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 589 through 594 removed outlier: 4.014A pdb=" N MET B 593 " --> pdb=" O PHE B 589 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N LYS B 594 " --> pdb=" O THR B 590 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 589 through 594' Processing helix chain 'B' and resid 603 through 608 Processing helix chain 'B' and resid 615 through 641 removed outlier: 4.005A pdb=" N TRP B 619 " --> pdb=" O GLY B 615 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR B 622 " --> pdb=" O ARG B 618 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TRP B 625 " --> pdb=" O SER B 621 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N TYR B 638 " --> pdb=" O SER B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 644 through 652 Processing helix chain 'B' and resid 671 through 688 Processing helix chain 'B' and resid 690 through 712 removed outlier: 3.948A pdb=" N LEU B 694 " --> pdb=" O LEU B 690 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER B 708 " --> pdb=" O SER B 704 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N PHE B 709 " --> pdb=" O VAL B 705 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N TYR B 710 " --> pdb=" O GLY B 706 " (cutoff:3.500A) Processing helix chain 'B' and resid 719 through 724 removed outlier: 3.507A pdb=" N THR B 724 " --> pdb=" O ARG B 720 " (cutoff:3.500A) Processing helix chain 'B' and resid 725 through 734 removed outlier: 3.505A pdb=" N ARG B 729 " --> pdb=" O ARG B 725 " (cutoff:3.500A) Processing helix chain 'B' and resid 745 through 764 removed outlier: 3.594A pdb=" N LEU B 749 " --> pdb=" O LYS B 745 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N GLN B 752 " --> pdb=" O VAL B 748 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL B 753 " --> pdb=" O LEU B 749 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ALA B 756 " --> pdb=" O GLN B 752 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU B 764 " --> pdb=" O SER B 760 " (cutoff:3.500A) Processing helix chain 'B' and resid 768 through 773 removed outlier: 3.503A pdb=" N VAL B 772 " --> pdb=" O ALA B 768 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLN B 773 " --> pdb=" O ILE B 769 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 768 through 773' Processing helix chain 'B' and resid 785 through 790 removed outlier: 3.915A pdb=" N LEU B 790 " --> pdb=" O LYS B 787 " (cutoff:3.500A) Processing helix chain 'B' and resid 815 through 826 Processing helix chain 'B' and resid 857 through 862 Processing helix chain 'B' and resid 872 through 880 Processing helix chain 'B' and resid 880 through 895 Processing helix chain 'B' and resid 932 through 945 Processing helix chain 'B' and resid 949 through 958 removed outlier: 3.798A pdb=" N THR B 953 " --> pdb=" O THR B 949 " (cutoff:3.500A) Processing helix chain 'B' and resid 958 through 972 removed outlier: 4.297A pdb=" N ARG B 962 " --> pdb=" O MET B 958 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ASN B 972 " --> pdb=" O TYR B 968 " (cutoff:3.500A) Processing helix chain 'B' and resid 972 through 980 removed outlier: 4.488A pdb=" N VAL B 976 " --> pdb=" O ASN B 972 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLY B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 982 through 996 removed outlier: 3.795A pdb=" N ARG B 996 " --> pdb=" O LYS B 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 1006 through 1010 removed outlier: 3.983A pdb=" N PHE B1010 " --> pdb=" O LEU B1007 " (cutoff:3.500A) Processing helix chain 'B' and resid 1011 through 1025 Processing helix chain 'B' and resid 1082 through 1090 removed outlier: 3.546A pdb=" N HIS B1088 " --> pdb=" O ASP B1084 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ALA B1089 " --> pdb=" O ASN B1085 " (cutoff:3.500A) Processing helix chain 'B' and resid 1091 through 1093 No H-bonds generated for 'chain 'B' and resid 1091 through 1093' Processing helix chain 'B' and resid 1108 through 1113 Processing helix chain 'B' and resid 1114 through 1120 Processing helix chain 'B' and resid 1121 through 1123 No H-bonds generated for 'chain 'B' and resid 1121 through 1123' Processing helix chain 'B' and resid 1201 through 1206 removed outlier: 3.678A pdb=" N THR B1206 " --> pdb=" O THR B1202 " (cutoff:3.500A) Processing helix chain 'B' and resid 1222 through 1233 Processing helix chain 'B' and resid 1268 through 1271 Processing helix chain 'B' and resid 1272 through 1280 removed outlier: 3.676A pdb=" N TYR B1276 " --> pdb=" O SER B1272 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR B1280 " --> pdb=" O TYR B1276 " (cutoff:3.500A) Processing helix chain 'B' and resid 1283 through 1292 Processing helix chain 'B' and resid 1294 through 1325 removed outlier: 4.225A pdb=" N HIS B1298 " --> pdb=" O HIS B1294 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLN B1305 " --> pdb=" O ASN B1301 " (cutoff:3.500A) Processing helix chain 'B' and resid 1348 through 1378 removed outlier: 4.239A pdb=" N VAL B1355 " --> pdb=" O ALA B1351 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ARG B1356 " --> pdb=" O VAL B1352 " (cutoff:3.500A) Proline residue: B1372 - end of helix Processing helix chain 'B' and resid 1437 through 1446 removed outlier: 3.524A pdb=" N PHE B1445 " --> pdb=" O LEU B1441 " (cutoff:3.500A) Processing helix chain 'B' and resid 1450 through 1467 removed outlier: 3.542A pdb=" N MET B1459 " --> pdb=" O ARG B1455 " (cutoff:3.500A) Processing helix chain 'B' and resid 1471 through 1489 removed outlier: 3.894A pdb=" N PHE B1475 " --> pdb=" O PRO B1471 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ALA B1477 " --> pdb=" O LEU B1473 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER B1478 " --> pdb=" O TRP B1474 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER B1480 " --> pdb=" O TRP B1476 " (cutoff:3.500A) Proline residue: B1486 - end of helix removed outlier: 3.581A pdb=" N PHE B1489 " --> pdb=" O ALA B1485 " (cutoff:3.500A) Processing helix chain 'B' and resid 1495 through 1511 Processing helix chain 'B' and resid 1556 through 1562 removed outlier: 3.892A pdb=" N MET B1562 " --> pdb=" O THR B1558 " (cutoff:3.500A) Processing helix chain 'B' and resid 1565 through 1583 removed outlier: 3.730A pdb=" N TYR B1571 " --> pdb=" O PRO B1567 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA B1572 " --> pdb=" O CYS B1568 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA B1578 " --> pdb=" O GLY B1574 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASN B1583 " --> pdb=" O PHE B1579 " (cutoff:3.500A) Processing helix chain 'B' and resid 1598 through 1623 Proline residue: B1609 - end of helix Processing helix chain 'B' and resid 1627 through 1635 removed outlier: 3.897A pdb=" N PHE B1631 " --> pdb=" O SER B1627 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLY B1632 " --> pdb=" O GLY B1628 " (cutoff:3.500A) Processing helix chain 'B' and resid 1637 through 1663 removed outlier: 3.998A pdb=" N VAL B1641 " --> pdb=" O LYS B1637 " (cutoff:3.500A) Processing helix chain 'B' and resid 1672 through 1696 removed outlier: 3.618A pdb=" N THR B1696 " --> pdb=" O ALA B1692 " (cutoff:3.500A) Processing helix chain 'B' and resid 1723 through 1753 removed outlier: 3.590A pdb=" N ARG B1728 " --> pdb=" O THR B1724 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE B1735 " --> pdb=" O THR B1731 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N CYS B1753 " --> pdb=" O VAL B1749 " (cutoff:3.500A) Processing helix chain 'B' and resid 1754 through 1760 removed outlier: 4.009A pdb=" N ILE B1760 " --> pdb=" O PRO B1756 " (cutoff:3.500A) Processing helix chain 'B' and resid 1762 through 1774 removed outlier: 3.856A pdb=" N PHE B1766 " --> pdb=" O LYS B1762 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N MET B1770 " --> pdb=" O PHE B1766 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU B1771 " --> pdb=" O HIS B1767 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE B1772 " --> pdb=" O SER B1768 " (cutoff:3.500A) Processing helix chain 'B' and resid 1786 through 1825 removed outlier: 3.503A pdb=" N LEU B1792 " --> pdb=" O LYS B1788 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ILE B1815 " --> pdb=" O PHE B1811 " (cutoff:3.500A) Proline residue: B1818 - end of helix removed outlier: 3.932A pdb=" N ALA B1823 " --> pdb=" O ALA B1819 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 370 through 373 Processing sheet with id=AA2, first strand: chain 'H' and resid 1068 through 1072 removed outlier: 3.889A pdb=" N PHE H1068 " --> pdb=" O LEU H1051 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ILE H1047 " --> pdb=" O LEU H1072 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N PHE H1000 " --> pdb=" O GLN H1029 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N ALA H1031 " --> pdb=" O PHE H1000 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N VAL H1002 " --> pdb=" O ALA H1031 " (cutoff:3.500A) removed outlier: 8.866A pdb=" N LEU H1033 " --> pdb=" O VAL H1002 " (cutoff:3.500A) removed outlier: 9.184A pdb=" N MET H1004 " --> pdb=" O LEU H1033 " (cutoff:3.500A) removed outlier: 11.154A pdb=" N GLU H1035 " --> pdb=" O MET H1004 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N PHE H 842 " --> pdb=" O LYS H 999 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N LEU H1001 " --> pdb=" O PHE H 842 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N VAL H 844 " --> pdb=" O LEU H1001 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N SER H1003 " --> pdb=" O VAL H 844 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N THR H 846 " --> pdb=" O SER H1003 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL H1151 " --> pdb=" O PHE H1198 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASN H1200 " --> pdb=" O ALA H1149 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N ALA H1149 " --> pdb=" O ASN H1200 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N VAL H1148 " --> pdb=" O ARG H1235 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N LYS H1237 " --> pdb=" O VAL H1148 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ILE H1150 " --> pdb=" O LYS H1237 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N CYS H1239 " --> pdb=" O ILE H1150 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N GLY H1152 " --> pdb=" O CYS H1239 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 1327 through 1328 removed outlier: 3.888A pdb=" N CYS H1328 " --> pdb=" O TYR H1346 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 370 through 373 Processing sheet with id=AA5, first strand: chain 'B' and resid 1068 through 1071 removed outlier: 4.095A pdb=" N PHE B1068 " --> pdb=" O LEU B1051 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLN B1029 " --> pdb=" O PHE B1000 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N LEU B1033 " --> pdb=" O MET B1004 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N PHE B 842 " --> pdb=" O LYS B 999 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N LEU B1001 " --> pdb=" O PHE B 842 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N VAL B 844 " --> pdb=" O LEU B1001 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N SER B1003 " --> pdb=" O VAL B 844 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N THR B 846 " --> pdb=" O SER B1003 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ALA B1149 " --> pdb=" O ASN B1200 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N ARG B1235 " --> pdb=" O VAL B1148 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE B1150 " --> pdb=" O ARG B1235 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1105 through 1106 removed outlier: 3.718A pdb=" N ASP B1106 " --> pdb=" O GLY B1245 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N GLY B1245 " --> pdb=" O ASP B1106 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 1327 through 1328 removed outlier: 3.775A pdb=" N CYS B1328 " --> pdb=" O TYR B1346 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 1238 hydrogen bonds defined for protein. 3630 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 26 hydrogen bonds 44 hydrogen bond angles 0 basepair planarities 10 basepair parallelities 28 stacking parallelities Total time for adding SS restraints: 5.60 Time building geometry restraints manager: 3.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 3720 1.30 - 1.43: 7569 1.43 - 1.56: 14476 1.56 - 1.69: 152 1.69 - 1.82: 235 Bond restraints: 26152 Sorted by residual: bond pdb=" C2 I A 34 " pdb=" N3 I A 34 " ideal model delta sigma weight residual 1.293 1.452 -0.159 2.00e-02 2.50e+03 6.33e+01 bond pdb=" C4 I A 34 " pdb=" N3 I A 34 " ideal model delta sigma weight residual 1.350 1.491 -0.141 2.00e-02 2.50e+03 4.94e+01 bond pdb=" C10 PEF H1910 " pdb=" O2 PEF H1910 " ideal model delta sigma weight residual 1.330 1.447 -0.117 2.00e-02 2.50e+03 3.40e+01 bond pdb=" C10 PEF B1912 " pdb=" O2 PEF B1912 " ideal model delta sigma weight residual 1.330 1.441 -0.111 2.00e-02 2.50e+03 3.07e+01 bond pdb=" C30 PEF B1912 " pdb=" O3 PEF B1912 " ideal model delta sigma weight residual 1.333 1.440 -0.107 2.00e-02 2.50e+03 2.87e+01 ... (remaining 26147 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.00: 35142 4.00 - 8.00: 389 8.00 - 12.00: 30 12.00 - 15.99: 5 15.99 - 19.99: 2 Bond angle restraints: 35568 Sorted by residual: angle pdb=" CA PRO B1342 " pdb=" N PRO B1342 " pdb=" CD PRO B1342 " ideal model delta sigma weight residual 112.00 92.01 19.99 1.40e+00 5.10e-01 2.04e+02 angle pdb=" C3' U A 47 " pdb=" O3' U A 47 " pdb=" P C A 48 " ideal model delta sigma weight residual 119.70 109.29 10.41 1.20e+00 6.94e-01 7.52e+01 angle pdb=" O3P PEF H1910 " pdb=" P PEF H1910 " pdb=" O4P PEF H1910 " ideal model delta sigma weight residual 93.96 109.98 -16.02 3.00e+00 1.11e-01 2.85e+01 angle pdb=" O3P PEF B1912 " pdb=" P PEF B1912 " pdb=" O4P PEF B1912 " ideal model delta sigma weight residual 93.96 109.59 -15.63 3.00e+00 1.11e-01 2.71e+01 angle pdb=" C PHE H1092 " pdb=" N TYR H1093 " pdb=" CA TYR H1093 " ideal model delta sigma weight residual 122.07 112.62 9.45 2.01e+00 2.48e-01 2.21e+01 ... (remaining 35563 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.26: 15105 33.26 - 66.53: 603 66.53 - 99.79: 88 99.79 - 133.06: 1 133.06 - 166.32: 3 Dihedral angle restraints: 15800 sinusoidal: 7350 harmonic: 8450 Sorted by residual: dihedral pdb=" C6 XKP B1911 " pdb=" C7 XKP B1911 " pdb=" C8 XKP B1911 " pdb=" O2 XKP B1911 " ideal model delta sinusoidal sigma weight residual 292.10 125.78 166.32 1 3.00e+01 1.11e-03 2.10e+01 dihedral pdb=" CB CYS H1328 " pdb=" SG CYS H1328 " pdb=" SG CYS H1345 " pdb=" CB CYS H1345 " ideal model delta sinusoidal sigma weight residual -86.00 -124.57 38.57 1 1.00e+01 1.00e-02 2.09e+01 dihedral pdb=" C6 XKP H1909 " pdb=" C7 XKP H1909 " pdb=" C8 XKP H1909 " pdb=" O2 XKP H1909 " ideal model delta sinusoidal sigma weight residual 292.10 128.92 163.18 1 3.00e+01 1.11e-03 2.09e+01 ... (remaining 15797 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 3618 0.089 - 0.178: 309 0.178 - 0.266: 5 0.266 - 0.355: 0 0.355 - 0.444: 2 Chirality restraints: 3934 Sorted by residual: chirality pdb=" P U A 47 " pdb=" OP1 U A 47 " pdb=" OP2 U A 47 " pdb=" O5' U A 47 " both_signs ideal model delta sigma weight residual True 2.41 -2.85 -0.44 2.00e-01 2.50e+01 4.93e+00 chirality pdb=" P C A 48 " pdb=" OP1 C A 48 " pdb=" OP2 C A 48 " pdb=" O5' C A 48 " both_signs ideal model delta sigma weight residual True 2.41 -2.82 -0.41 2.00e-01 2.50e+01 4.16e+00 chirality pdb=" C1 BGC J 2 " pdb=" O3 BGC J 1 " pdb=" C2 BGC J 2 " pdb=" O5 BGC J 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.38 -0.02 2.00e-02 2.50e+03 1.51e+00 ... (remaining 3931 not shown) Planarity restraints: 4168 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B1566 " -0.069 5.00e-02 4.00e+02 1.02e-01 1.68e+01 pdb=" N PRO B1567 " 0.177 5.00e-02 4.00e+02 pdb=" CA PRO B1567 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO B1567 " -0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B1341 " 0.074 5.00e-02 4.00e+02 9.92e-02 1.57e+01 pdb=" N PRO B1342 " -0.171 5.00e-02 4.00e+02 pdb=" CA PRO B1342 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO B1342 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 942 " 0.024 2.00e-02 2.50e+03 2.22e-02 1.23e+01 pdb=" CG TRP B 942 " -0.058 2.00e-02 2.50e+03 pdb=" CD1 TRP B 942 " 0.030 2.00e-02 2.50e+03 pdb=" CD2 TRP B 942 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 942 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP B 942 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 942 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 942 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 942 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP B 942 " 0.006 2.00e-02 2.50e+03 ... (remaining 4165 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 161 2.59 - 3.17: 21022 3.17 - 3.75: 37757 3.75 - 4.32: 50186 4.32 - 4.90: 82616 Nonbonded interactions: 191742 Sorted by model distance: nonbonded pdb=" OE1 GLU H 514 " pdb=" NH2 ARG H 531 " model vdw 2.016 3.120 nonbonded pdb=" NZ LYS B1246 " pdb="MG MG B1901 " model vdw 2.107 2.250 nonbonded pdb=" O ALA H1201 " pdb=" OG1 THR H1205 " model vdw 2.111 3.040 nonbonded pdb=" OD1 ASP H 233 " pdb=" OG1 THR H 605 " model vdw 2.117 3.040 nonbonded pdb=" O2' C A 36 " pdb=" O4' A A 37 " model vdw 2.189 3.040 ... (remaining 191737 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 Found NCS groups: ncs_group { reference = (chain 'B' and (resid 144 through 1908 or resid 1913 through 1914 or resid 1916 \ or resid 1918)) selection = (chain 'H' and (resid 144 through 1908 or resid 1913 through 1914 or resid 1916 \ or resid 1918)) } ncs_group { reference = chain 'C' selection = chain 'G' } 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: 5.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.500 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 27.650 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6316 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 : 0.006 0.237 26161 Z= 0.279 Angle : 0.992 19.992 35581 Z= 0.495 Chirality : 0.049 0.444 3934 Planarity : 0.007 0.102 4168 Dihedral : 17.273 166.322 10326 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.15), residues: 2820 helix: 0.76 (0.13), residues: 1658 sheet: 1.80 (0.58), residues: 78 loop : -0.50 (0.18), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 995 TYR 0.055 0.003 TYR H1093 PHE 0.036 0.003 PHE B1000 TRP 0.058 0.003 TRP B 942 HIS 0.008 0.001 HIS B1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00604 / 0.28 (26152) covalent geometry : angle 0.98813 / 0.49 (35568) SS BOND : bond 0.01005 / 0.48 ( 2) SS BOND : angle 2.05840 / 1.04 ( 4) hydrogen bonds : bond 0.16817 / 10.81 ( 1264) hydrogen bonds : angle 5.64022 / 4.07 ( 3674) Misc. bond : bond 0.02207 / 1.10 ( 4) link_BETA1-3 : bond 0.00980 / 0.42 ( 3) link_BETA1-3 : angle 5.21047 / 3.21 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5640 Ramachandran restraints generated. 2820 Oldfield, 0 Emsley, 2820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5640 Ramachandran restraints generated. 2820 Oldfield, 0 Emsley, 2820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 279 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 182 MET cc_start: 0.3722 (ppp) cc_final: 0.3310 (pp-130) REVERT: H 185 MET cc_start: 0.2338 (mmm) cc_final: 0.2063 (mmm) REVERT: H 620 MET cc_start: 0.0771 (mtm) cc_final: -0.1347 (tpt) REVERT: H 656 MET cc_start: 0.1371 (ttt) cc_final: 0.0843 (ptm) REVERT: H 757 ILE cc_start: 0.3040 (mt) cc_final: 0.2707 (tt) REVERT: H 1204 MET cc_start: -0.0958 (tpt) cc_final: -0.1558 (tpt) REVERT: H 1312 MET cc_start: -0.1491 (tpp) cc_final: -0.3872 (ptt) REVERT: H 1562 MET cc_start: 0.2836 (ptp) cc_final: 0.2379 (mmt) REVERT: B 1794 LYS cc_start: 0.6960 (mmtt) cc_final: 0.6734 (mmpt) outliers start: 0 outliers final: 1 residues processed: 279 average time/residue: 0.5469 time to fit residues: 178.5790 Evaluate side-chains 215 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 214 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 702 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: [197, 215, 20, 132, 261, 248, 207, 155, 244, 183, 111] chunk 197 optimal weight: 0.0980 chunk 215 optimal weight: 0.3980 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 0.0670 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 0.9990 chunk 111 optimal weight: 0.0060 overall best weight: 0.2534 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 240 ASN H 316 ASN ** H 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 948 GLN ** H1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1085 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H1104 ASN B 316 ASN B 542 ASN B 824 GLN B1104 ASN B1243 GLN B1683 GLN B1748 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5012 r_free = 0.5012 target = 0.279788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4707 r_free = 0.4707 target = 0.242632 restraints weight = 38023.548| |-----------------------------------------------------------------------------| r_work (start): 0.4693 rms_B_bonded: 2.87 r_work: 0.4323 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work: 0.4259 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.4259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6562 moved from start: 0.1292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 26161 Z= 0.140 Angle : 0.598 9.150 35581 Z= 0.309 Chirality : 0.041 0.282 3934 Planarity : 0.005 0.052 4168 Dihedral : 16.463 170.362 4778 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 0.95 % Allowed : 7.54 % Favored : 91.51 % 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: 1.12 (0.16), residues: 2820 helix: 1.37 (0.13), residues: 1676 sheet: 1.97 (0.67), residues: 58 loop : -0.23 (0.19), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H1791 TYR 0.022 0.002 TYR H1330 PHE 0.023 0.002 PHE H 550 TRP 0.016 0.001 TRP B1662 HIS 0.004 0.001 HIS H 527 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.14 (26152) covalent geometry : angle 0.59509 / 0.31 (35568) SS BOND : bond 0.00275 / 0.13 ( 2) SS BOND : angle 0.92470 / 0.52 ( 4) hydrogen bonds : bond 0.05841 / 3.83 ( 1264) hydrogen bonds : angle 4.26896 / 3.06 ( 3674) Misc. bond : bond 0.00508 / 0.25 ( 4) link_BETA1-3 : bond 0.01347 / 0.66 ( 3) link_BETA1-3 : angle 3.81069 / 2.38 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5640 Ramachandran restraints generated. 2820 Oldfield, 0 Emsley, 2820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5640 Ramachandran restraints generated. 2820 Oldfield, 0 Emsley, 2820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 242 time to evaluate : 0.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 182 MET cc_start: 0.3227 (ppp) cc_final: 0.2904 (pp-130) REVERT: H 620 MET cc_start: 0.0790 (mtm) cc_final: -0.1437 (tpt) REVERT: H 656 MET cc_start: 0.1763 (ttt) cc_final: 0.0983 (ptm) REVERT: H 978 MET cc_start: 0.0629 (ppp) cc_final: -0.0981 (ppp) REVERT: H 1230 MET cc_start: -0.0384 (ttm) cc_final: -0.1584 (pmm) REVERT: H 1312 MET cc_start: -0.1861 (tpp) cc_final: -0.3554 (ptm) REVERT: H 1562 MET cc_start: 0.2875 (ptp) cc_final: 0.2283 (mmt) REVERT: B 1794 LYS cc_start: 0.6964 (mmtt) cc_final: 0.6655 (mmpt) outliers start: 24 outliers final: 8 residues processed: 251 average time/residue: 0.5877 time to fit residues: 172.3798 Evaluate side-chains 221 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 213 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 713 ILE Chi-restraints excluded: chain H residue 731 TYR Chi-restraints excluded: chain H residue 795 PHE Chi-restraints excluded: chain H residue 945 LEU Chi-restraints excluded: chain H residue 1098 ILE Chi-restraints excluded: chain H residue 1772 PHE Chi-restraints excluded: chain B residue 1057 GLU Chi-restraints excluded: chain B residue 1078 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: [1, 176, 69, 166, 170, 105, 135, 17, 161, 276, 269] chunk 1 optimal weight: 1.9990 chunk 176 optimal weight: 4.9990 chunk 69 optimal weight: 0.9990 chunk 166 optimal weight: 1.9990 chunk 170 optimal weight: 0.9990 chunk 105 optimal weight: 5.9990 chunk 135 optimal weight: 0.9990 chunk 17 optimal weight: 4.9990 chunk 161 optimal weight: 0.5980 chunk 276 optimal weight: 8.9990 chunk 269 optimal weight: 0.9980 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 563 HIS ** H1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H1688 HIS B 542 ASN B1748 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4999 r_free = 0.4999 target = 0.278465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4681 r_free = 0.4681 target = 0.239564 restraints weight = 37432.458| |-----------------------------------------------------------------------------| r_work (start): 0.4666 rms_B_bonded: 2.98 r_work: 0.4285 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.4285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6572 moved from start: 0.1564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 26161 Z= 0.142 Angle : 0.576 12.272 35581 Z= 0.294 Chirality : 0.041 0.304 3934 Planarity : 0.005 0.054 4168 Dihedral : 16.178 172.692 4776 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.31 % Allowed : 9.76 % Favored : 88.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.16), residues: 2820 helix: 1.49 (0.13), residues: 1674 sheet: 1.63 (0.63), residues: 70 loop : -0.25 (0.19), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H1508 TYR 0.020 0.001 TYR H 329 PHE 0.024 0.002 PHE B 795 TRP 0.019 0.001 TRP H 754 HIS 0.007 0.001 HIS B1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 (26152) covalent geometry : angle 0.57329 / 0.29 (35568) SS BOND : bond 0.00104 / 0.05 ( 2) SS BOND : angle 0.85691 / 0.48 ( 4) hydrogen bonds : bond 0.05535 / 3.64 ( 1264) hydrogen bonds : angle 4.09968 / 2.94 ( 3674) Misc. bond : bond 0.00284 / 0.12 ( 4) link_BETA1-3 : bond 0.01100 / 0.54 ( 3) link_BETA1-3 : angle 3.71575 / 2.29 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5640 Ramachandran restraints generated. 2820 Oldfield, 0 Emsley, 2820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5640 Ramachandran restraints generated. 2820 Oldfield, 0 Emsley, 2820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 229 time to evaluate : 0.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 182 MET cc_start: 0.2964 (ppp) cc_final: 0.2760 (pp-130) REVERT: H 241 MET cc_start: -0.0520 (mmt) cc_final: -0.1838 (ppp) REVERT: H 563 HIS cc_start: 0.3476 (OUTLIER) cc_final: 0.3212 (t70) REVERT: H 620 MET cc_start: 0.0532 (mtm) cc_final: -0.1509 (tpt) REVERT: H 656 MET cc_start: 0.1624 (ttt) cc_final: 0.0805 (ptm) REVERT: H 725 ARG cc_start: 0.2158 (OUTLIER) cc_final: -0.0622 (ptm-80) REVERT: H 1154 ARG cc_start: 0.3184 (OUTLIER) cc_final: 0.1229 (ttt180) REVERT: H 1212 LYS cc_start: 0.1317 (mptt) cc_final: 0.1086 (mptt) REVERT: H 1230 MET cc_start: -0.0337 (ttm) cc_final: -0.1601 (pmm) REVERT: H 1312 MET cc_start: -0.2123 (tpp) cc_final: -0.3498 (ptt) REVERT: H 1487 PHE cc_start: 0.3819 (OUTLIER) cc_final: 0.3047 (m-80) REVERT: H 1562 MET cc_start: 0.3191 (ptp) cc_final: 0.2397 (mmt) REVERT: H 1796 MET cc_start: 0.2673 (mmm) cc_final: 0.1305 (mmt) REVERT: B 761 MET cc_start: 0.8001 (OUTLIER) cc_final: 0.7572 (ttm) REVERT: B 1582 ILE cc_start: 0.8267 (OUTLIER) cc_final: 0.7868 (tt) REVERT: B 1642 MET cc_start: 0.5671 (ptm) cc_final: 0.5421 (ptp) REVERT: B 1794 LYS cc_start: 0.6984 (mmtt) cc_final: 0.6626 (mmpt) outliers start: 33 outliers final: 9 residues processed: 247 average time/residue: 0.5789 time to fit residues: 167.1509 Evaluate side-chains 225 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 210 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 563 HIS Chi-restraints excluded: chain H residue 565 VAL Chi-restraints excluded: chain H residue 713 ILE Chi-restraints excluded: chain H residue 725 ARG Chi-restraints excluded: chain H residue 795 PHE Chi-restraints excluded: chain H residue 945 LEU Chi-restraints excluded: chain H residue 1154 ARG Chi-restraints excluded: chain H residue 1270 MET Chi-restraints excluded: chain H residue 1487 PHE Chi-restraints excluded: chain H residue 1772 PHE Chi-restraints excluded: chain B residue 761 MET Chi-restraints excluded: chain B residue 978 MET Chi-restraints excluded: chain B residue 1057 GLU Chi-restraints excluded: chain B residue 1078 LEU Chi-restraints excluded: chain B residue 1582 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: [57, 81, 238, 148, 78, 94, 82, 4, 159, 195, 248] chunk 57 optimal weight: 0.6980 chunk 81 optimal weight: 4.9990 chunk 238 optimal weight: 0.4980 chunk 148 optimal weight: 0.6980 chunk 78 optimal weight: 5.9990 chunk 94 optimal weight: 10.0000 chunk 82 optimal weight: 10.0000 chunk 4 optimal weight: 0.8980 chunk 159 optimal weight: 1.9990 chunk 195 optimal weight: 1.9990 chunk 248 optimal weight: 0.4980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 563 HIS H1129 GLN B1061 ASN B1305 GLN B1748 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5003 r_free = 0.5003 target = 0.278897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4683 r_free = 0.4683 target = 0.239643 restraints weight = 37327.388| |-----------------------------------------------------------------------------| r_work (start): 0.4670 rms_B_bonded: 2.95 r_work: 0.3980 rms_B_bonded: 4.91 restraints_weight: 0.5000 r_work (final): 0.3980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7106 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 26161 Z= 0.121 Angle : 0.549 11.322 35581 Z= 0.279 Chirality : 0.040 0.301 3934 Planarity : 0.005 0.054 4168 Dihedral : 15.971 174.452 4776 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.67 % Allowed : 11.23 % Favored : 87.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.16), residues: 2820 helix: 1.62 (0.13), residues: 1670 sheet: 1.54 (0.62), residues: 70 loop : -0.25 (0.19), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 938 TYR 0.018 0.001 TYR H 329 PHE 0.028 0.001 PHE H1744 TRP 0.030 0.001 TRP H 754 HIS 0.007 0.001 HIS H 848 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 (26152) covalent geometry : angle 0.54615 / 0.28 (35568) SS BOND : bond 0.00072 / 0.04 ( 2) SS BOND : angle 0.72997 / 0.41 ( 4) hydrogen bonds : bond 0.04870 / 3.22 ( 1264) hydrogen bonds : angle 3.97953 / 2.86 ( 3674) Misc. bond : bond 0.00203 / 0.07 ( 4) link_BETA1-3 : bond 0.00997 / 0.48 ( 3) link_BETA1-3 : angle 3.62686 / 2.26 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5640 Ramachandran restraints generated. 2820 Oldfield, 0 Emsley, 2820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5640 Ramachandran restraints generated. 2820 Oldfield, 0 Emsley, 2820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 225 time to evaluate : 0.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 241 MET cc_start: -0.1381 (mmt) cc_final: -0.2033 (ppp) REVERT: H 620 MET cc_start: -0.0450 (mtm) cc_final: -0.1769 (tpt) REVERT: H 656 MET cc_start: 0.0439 (ttt) cc_final: -0.0196 (ptm) REVERT: H 978 MET cc_start: 0.1474 (ppp) cc_final: 0.0550 (ppp) REVERT: H 1004 MET cc_start: 0.2392 (OUTLIER) cc_final: 0.1774 (mmm) REVERT: H 1154 ARG cc_start: 0.2635 (OUTLIER) cc_final: 0.0854 (ttt180) REVERT: H 1212 LYS cc_start: 0.0568 (mptt) cc_final: 0.0089 (pmtt) REVERT: H 1230 MET cc_start: -0.2137 (ttm) cc_final: -0.2674 (pmm) REVERT: H 1487 PHE cc_start: 0.4914 (OUTLIER) cc_final: 0.4246 (m-80) REVERT: H 1503 TYR cc_start: 0.8174 (t80) cc_final: 0.7823 (t80) REVERT: H 1562 MET cc_start: 0.3250 (ptp) cc_final: 0.2231 (mmt) REVERT: H 1737 LEU cc_start: 0.6237 (mt) cc_final: 0.5220 (tt) REVERT: B 343 GLN cc_start: 0.7705 (OUTLIER) cc_final: 0.7393 (mp10) REVERT: B 761 MET cc_start: 0.8057 (OUTLIER) cc_final: 0.7676 (ttm) REVERT: B 938 ARG cc_start: 0.6750 (mtp-110) cc_final: 0.6135 (ttp-170) REVERT: B 1061 ASN cc_start: 0.8499 (OUTLIER) cc_final: 0.8267 (m-40) REVERT: B 1582 ILE cc_start: 0.7941 (OUTLIER) cc_final: 0.7664 (tt) REVERT: B 1642 MET cc_start: 0.6208 (ptm) cc_final: 0.5809 (ptp) outliers start: 42 outliers final: 14 residues processed: 247 average time/residue: 0.5551 time to fit residues: 161.2096 Evaluate side-chains 235 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 214 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 186 PHE Chi-restraints excluded: chain H residue 465 MET Chi-restraints excluded: chain H residue 713 ILE Chi-restraints excluded: chain H residue 753 VAL Chi-restraints excluded: chain H residue 795 PHE Chi-restraints excluded: chain H residue 945 LEU Chi-restraints excluded: chain H residue 993 MET Chi-restraints excluded: chain H residue 1004 MET Chi-restraints excluded: chain H residue 1154 ARG Chi-restraints excluded: chain H residue 1270 MET Chi-restraints excluded: chain H residue 1487 PHE Chi-restraints excluded: chain H residue 1772 PHE Chi-restraints excluded: chain B residue 343 GLN Chi-restraints excluded: chain B residue 761 MET Chi-restraints excluded: chain B residue 978 MET Chi-restraints excluded: chain B residue 1061 ASN Chi-restraints excluded: chain B residue 1078 LEU Chi-restraints excluded: chain B residue 1306 LEU Chi-restraints excluded: chain B residue 1368 ILE Chi-restraints excluded: chain B residue 1580 THR Chi-restraints excluded: chain B residue 1582 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: [135, 119, 56, 255, 87, 137, 203, 228, 170, 90, 112] chunk 135 optimal weight: 9.9990 chunk 119 optimal weight: 10.0000 chunk 56 optimal weight: 4.9990 chunk 255 optimal weight: 3.9990 chunk 87 optimal weight: 0.9990 chunk 137 optimal weight: 3.9990 chunk 203 optimal weight: 0.0670 chunk 228 optimal weight: 0.1980 chunk 170 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 chunk 112 optimal weight: 3.9990 overall best weight: 1.6524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 316 ASN ** H 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1085 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1556 HIS B1613 ASN B1748 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4977 r_free = 0.4977 target = 0.275777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4665 r_free = 0.4665 target = 0.237943 restraints weight = 37096.691| |-----------------------------------------------------------------------------| r_work (start): 0.4652 rms_B_bonded: 2.89 r_work: 0.4278 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work: 0.4228 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.4228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6632 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 26161 Z= 0.184 Angle : 0.625 10.190 35581 Z= 0.319 Chirality : 0.042 0.312 3934 Planarity : 0.006 0.055 4168 Dihedral : 15.984 176.632 4776 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.98 % Allowed : 12.26 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.16), residues: 2820 helix: 1.29 (0.13), residues: 1698 sheet: 1.49 (0.62), residues: 70 loop : -0.44 (0.19), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B1063 TYR 0.032 0.002 TYR B 762 PHE 0.024 0.002 PHE H1744 TRP 0.024 0.002 TRP H 754 HIS 0.011 0.001 HIS B1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.18 (26152) covalent geometry : angle 0.62229 / 0.32 (35568) SS BOND : bond 0.00104 / 0.05 ( 2) SS BOND : angle 1.01038 / 0.57 ( 4) hydrogen bonds : bond 0.06074 / 4.01 ( 1264) hydrogen bonds : angle 4.10060 / 2.94 ( 3674) Misc. bond : bond 0.00241 / 0.08 ( 4) link_BETA1-3 : bond 0.00932 / 0.46 ( 3) link_BETA1-3 : angle 3.65065 / 2.30 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5640 Ramachandran restraints generated. 2820 Oldfield, 0 Emsley, 2820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5640 Ramachandran restraints generated. 2820 Oldfield, 0 Emsley, 2820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 223 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 241 MET cc_start: -0.0475 (mmt) cc_final: -0.1714 (ppp) REVERT: H 620 MET cc_start: 0.0768 (mtm) cc_final: -0.1419 (tpt) REVERT: H 757 ILE cc_start: 0.3545 (mt) cc_final: 0.2945 (tt) REVERT: H 885 GLU cc_start: 0.5462 (mm-30) cc_final: 0.5248 (pp20) REVERT: H 1004 MET cc_start: 0.2800 (OUTLIER) cc_final: 0.2184 (mmm) REVERT: H 1154 ARG cc_start: 0.3021 (OUTLIER) cc_final: 0.1273 (ttt180) REVERT: H 1230 MET cc_start: -0.0278 (ttm) cc_final: -0.1593 (pmm) REVERT: H 1487 PHE cc_start: 0.3802 (OUTLIER) cc_final: 0.3114 (m-80) REVERT: H 1562 MET cc_start: 0.3456 (ptp) cc_final: 0.2592 (mmt) REVERT: H 1796 MET cc_start: 0.2428 (mmm) cc_final: 0.1100 (mmt) REVERT: B 343 GLN cc_start: 0.7808 (OUTLIER) cc_final: 0.7466 (mp10) REVERT: B 773 GLN cc_start: 0.7368 (tm-30) cc_final: 0.7130 (tp-100) REVERT: B 1088 HIS cc_start: 0.8853 (OUTLIER) cc_final: 0.8507 (p90) REVERT: B 1642 MET cc_start: 0.5705 (ptm) cc_final: 0.5371 (ptp) REVERT: B 1794 LYS cc_start: 0.7166 (mmtt) cc_final: 0.6788 (mmpt) outliers start: 50 outliers final: 18 residues processed: 248 average time/residue: 0.5372 time to fit residues: 157.3197 Evaluate side-chains 231 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 208 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 186 PHE Chi-restraints excluded: chain H residue 713 ILE Chi-restraints excluded: chain H residue 753 VAL Chi-restraints excluded: chain H residue 795 PHE Chi-restraints excluded: chain H residue 945 LEU Chi-restraints excluded: chain H residue 993 MET Chi-restraints excluded: chain H residue 1004 MET Chi-restraints excluded: chain H residue 1010 PHE Chi-restraints excluded: chain H residue 1061 ASN Chi-restraints excluded: chain H residue 1154 ARG Chi-restraints excluded: chain H residue 1270 MET Chi-restraints excluded: chain H residue 1487 PHE Chi-restraints excluded: chain H residue 1588 VAL Chi-restraints excluded: chain H residue 1674 ILE Chi-restraints excluded: chain H residue 1772 PHE Chi-restraints excluded: chain B residue 343 GLN Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 702 ILE Chi-restraints excluded: chain B residue 978 MET Chi-restraints excluded: chain B residue 1078 LEU Chi-restraints excluded: chain B residue 1088 HIS Chi-restraints excluded: chain B residue 1306 LEU Chi-restraints excluded: chain B residue 1580 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: [120, 63, 228, 157, 79, 238, 128, 86, 248, 101, 122] chunk 120 optimal weight: 5.9990 chunk 63 optimal weight: 0.8980 chunk 228 optimal weight: 4.9990 chunk 157 optimal weight: 0.6980 chunk 79 optimal weight: 2.9990 chunk 238 optimal weight: 0.9980 chunk 128 optimal weight: 9.9990 chunk 86 optimal weight: 8.9990 chunk 248 optimal weight: 0.0170 chunk 101 optimal weight: 0.0870 chunk 122 optimal weight: 6.9990 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 563 HIS ** H1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1085 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1104 ASN B1748 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4996 r_free = 0.4996 target = 0.278002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4684 r_free = 0.4684 target = 0.239847 restraints weight = 37479.049| |-----------------------------------------------------------------------------| r_work (start): 0.4671 rms_B_bonded: 2.86 r_work: 0.4032 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.4032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7051 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 26161 Z= 0.116 Angle : 0.543 10.611 35581 Z= 0.276 Chirality : 0.039 0.299 3934 Planarity : 0.004 0.058 4168 Dihedral : 15.727 178.682 4776 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.31 % Allowed : 13.93 % 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: 1.25 (0.16), residues: 2820 helix: 1.57 (0.13), residues: 1682 sheet: 1.55 (0.62), residues: 70 loop : -0.36 (0.19), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 852 TYR 0.020 0.001 TYR H 951 PHE 0.018 0.001 PHE H1744 TRP 0.015 0.001 TRP B 456 HIS 0.005 0.001 HIS H1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.12 (26152) covalent geometry : angle 0.54016 / 0.28 (35568) SS BOND : bond 0.00066 / 0.03 ( 2) SS BOND : angle 0.61168 / 0.35 ( 4) hydrogen bonds : bond 0.04576 / 3.03 ( 1264) hydrogen bonds : angle 3.93635 / 2.82 ( 3674) Misc. bond : bond 0.00198 / 0.07 ( 4) link_BETA1-3 : bond 0.01015 / 0.49 ( 3) link_BETA1-3 : angle 3.61750 / 2.29 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5640 Ramachandran restraints generated. 2820 Oldfield, 0 Emsley, 2820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5640 Ramachandran restraints generated. 2820 Oldfield, 0 Emsley, 2820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 225 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 241 MET cc_start: -0.1117 (mmt) cc_final: -0.1833 (ppp) REVERT: H 377 PHE cc_start: 0.4515 (OUTLIER) cc_final: 0.3480 (t80) REVERT: H 396 LEU cc_start: 0.1266 (OUTLIER) cc_final: 0.1013 (mm) REVERT: H 620 MET cc_start: -0.0306 (mtm) cc_final: -0.1863 (tpt) REVERT: H 656 MET cc_start: 0.1326 (ttt) cc_final: 0.0504 (ptm) REVERT: H 885 GLU cc_start: 0.6613 (mm-30) cc_final: 0.6015 (pp20) REVERT: H 993 MET cc_start: -0.2363 (pp-130) cc_final: -0.2948 (mpt) REVERT: H 1004 MET cc_start: 0.2488 (OUTLIER) cc_final: 0.1815 (mmm) REVERT: H 1154 ARG cc_start: 0.2710 (OUTLIER) cc_final: 0.1079 (ttt180) REVERT: H 1204 MET cc_start: -0.0943 (tpt) cc_final: -0.1192 (tpt) REVERT: H 1230 MET cc_start: -0.2465 (ttm) cc_final: -0.2781 (pmm) REVERT: H 1312 MET cc_start: -0.1547 (tpp) cc_final: -0.1833 (tpp) REVERT: H 1459 MET cc_start: -0.0751 (pmm) cc_final: -0.2783 (mmm) REVERT: H 1487 PHE cc_start: 0.4796 (OUTLIER) cc_final: 0.4040 (m-80) REVERT: H 1562 MET cc_start: 0.3371 (ptp) cc_final: 0.2334 (mmt) REVERT: H 1737 LEU cc_start: 0.6159 (mt) cc_final: 0.5171 (tt) REVERT: B 293 MET cc_start: 0.8419 (mmt) cc_final: 0.8138 (mmp) REVERT: B 343 GLN cc_start: 0.7761 (OUTLIER) cc_final: 0.7481 (mp10) REVERT: B 938 ARG cc_start: 0.6818 (mtm110) cc_final: 0.6507 (ttp80) REVERT: B 1582 ILE cc_start: 0.7919 (tt) cc_final: 0.7685 (tt) REVERT: B 1642 MET cc_start: 0.6198 (ptm) cc_final: 0.5700 (ptt) outliers start: 33 outliers final: 16 residues processed: 248 average time/residue: 0.5468 time to fit residues: 159.8754 Evaluate side-chains 236 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 214 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 186 PHE Chi-restraints excluded: chain H residue 377 PHE Chi-restraints excluded: chain H residue 396 LEU Chi-restraints excluded: chain H residue 563 HIS Chi-restraints excluded: chain H residue 565 VAL Chi-restraints excluded: chain H residue 713 ILE Chi-restraints excluded: chain H residue 753 VAL Chi-restraints excluded: chain H residue 945 LEU Chi-restraints excluded: chain H residue 1004 MET Chi-restraints excluded: chain H residue 1010 PHE Chi-restraints excluded: chain H residue 1061 ASN Chi-restraints excluded: chain H residue 1154 ARG Chi-restraints excluded: chain H residue 1270 MET Chi-restraints excluded: chain H residue 1487 PHE Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 343 GLN Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 702 ILE Chi-restraints excluded: chain B residue 978 MET Chi-restraints excluded: chain B residue 1078 LEU Chi-restraints excluded: chain B residue 1306 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: [202, 18, 172, 266, 158, 196, 16, 255, 63, 186, 125] chunk 202 optimal weight: 0.9980 chunk 18 optimal weight: 6.9990 chunk 172 optimal weight: 0.5980 chunk 266 optimal weight: 4.9990 chunk 158 optimal weight: 1.9990 chunk 196 optimal weight: 0.5980 chunk 16 optimal weight: 6.9990 chunk 255 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 186 optimal weight: 3.9990 chunk 125 optimal weight: 10.0000 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 563 HIS ** H1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1085 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1088 HIS B1104 ASN B1748 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4986 r_free = 0.4986 target = 0.276847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4658 r_free = 0.4658 target = 0.236772 restraints weight = 37135.167| |-----------------------------------------------------------------------------| r_work (start): 0.4647 rms_B_bonded: 3.03 r_work: 0.4195 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.4195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6801 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 26161 Z= 0.134 Angle : 0.563 9.649 35581 Z= 0.286 Chirality : 0.040 0.294 3934 Planarity : 0.005 0.058 4168 Dihedral : 15.648 179.369 4776 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.67 % Allowed : 14.44 % Favored : 83.89 % 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: 1.19 (0.16), residues: 2820 helix: 1.51 (0.13), residues: 1686 sheet: 1.53 (0.61), residues: 70 loop : -0.38 (0.19), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 852 TYR 0.021 0.001 TYR H 329 PHE 0.031 0.002 PHE H1740 TRP 0.018 0.001 TRP B1476 HIS 0.007 0.001 HIS H 563 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (26152) covalent geometry : angle 0.55985 / 0.28 (35568) SS BOND : bond 0.00073 / 0.04 ( 2) SS BOND : angle 0.71758 / 0.42 ( 4) hydrogen bonds : bond 0.04937 / 3.25 ( 1264) hydrogen bonds : angle 3.94431 / 2.83 ( 3674) Misc. bond : bond 0.00249 / 0.08 ( 4) link_BETA1-3 : bond 0.00934 / 0.45 ( 3) link_BETA1-3 : angle 3.55079 / 2.25 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5640 Ramachandran restraints generated. 2820 Oldfield, 0 Emsley, 2820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5640 Ramachandran restraints generated. 2820 Oldfield, 0 Emsley, 2820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 222 time to evaluate : 0.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 241 MET cc_start: -0.0485 (mmt) cc_final: -0.1683 (ppp) REVERT: H 396 LEU cc_start: 0.1521 (OUTLIER) cc_final: 0.1284 (mm) REVERT: H 620 MET cc_start: 0.0245 (mtm) cc_final: -0.1695 (tpt) REVERT: H 656 MET cc_start: 0.1996 (ttt) cc_final: 0.1269 (ptm) REVERT: H 757 ILE cc_start: 0.3324 (mt) cc_final: 0.2918 (tt) REVERT: H 839 MET cc_start: -0.3170 (OUTLIER) cc_final: -0.3696 (tpt) REVERT: H 885 GLU cc_start: 0.6071 (mm-30) cc_final: 0.5818 (pp20) REVERT: H 1004 MET cc_start: 0.2755 (OUTLIER) cc_final: 0.2080 (mmm) REVERT: H 1154 ARG cc_start: 0.2989 (OUTLIER) cc_final: 0.1253 (ttt180) REVERT: H 1204 MET cc_start: -0.0464 (tpt) cc_final: -0.0914 (tpt) REVERT: H 1487 PHE cc_start: 0.4087 (OUTLIER) cc_final: 0.3362 (m-80) REVERT: H 1562 MET cc_start: 0.3142 (ptp) cc_final: 0.2329 (mmt) REVERT: H 1796 MET cc_start: 0.1937 (mmm) cc_final: 0.0971 (mmt) REVERT: B 293 MET cc_start: 0.8355 (mmt) cc_final: 0.8106 (mmp) REVERT: B 343 GLN cc_start: 0.7825 (OUTLIER) cc_final: 0.7536 (mp10) REVERT: B 773 GLN cc_start: 0.7300 (tm-30) cc_final: 0.7054 (tp-100) REVERT: B 1582 ILE cc_start: 0.7915 (tt) cc_final: 0.7695 (tt) REVERT: B 1642 MET cc_start: 0.5988 (ptm) cc_final: 0.5506 (ptt) outliers start: 42 outliers final: 21 residues processed: 249 average time/residue: 0.5448 time to fit residues: 160.0402 Evaluate side-chains 239 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 212 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 186 PHE Chi-restraints excluded: chain H residue 388 VAL Chi-restraints excluded: chain H residue 396 LEU Chi-restraints excluded: chain H residue 563 HIS Chi-restraints excluded: chain H residue 565 VAL Chi-restraints excluded: chain H residue 711 LEU Chi-restraints excluded: chain H residue 731 TYR Chi-restraints excluded: chain H residue 753 VAL Chi-restraints excluded: chain H residue 795 PHE Chi-restraints excluded: chain H residue 839 MET Chi-restraints excluded: chain H residue 945 LEU Chi-restraints excluded: chain H residue 993 MET Chi-restraints excluded: chain H residue 1004 MET Chi-restraints excluded: chain H residue 1061 ASN Chi-restraints excluded: chain H residue 1154 ARG Chi-restraints excluded: chain H residue 1270 MET Chi-restraints excluded: chain H residue 1487 PHE Chi-restraints excluded: chain H residue 1772 PHE Chi-restraints excluded: chain B residue 343 GLN Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 702 ILE Chi-restraints excluded: chain B residue 978 MET Chi-restraints excluded: chain B residue 1078 LEU Chi-restraints excluded: chain B residue 1306 LEU Chi-restraints excluded: chain B residue 1368 ILE Chi-restraints excluded: chain B residue 1670 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: [184, 271, 151, 261, 30, 205, 177, 198, 262, 247, 133] chunk 184 optimal weight: 0.0970 chunk 271 optimal weight: 3.9990 chunk 151 optimal weight: 1.9990 chunk 261 optimal weight: 3.9990 chunk 30 optimal weight: 0.0470 chunk 205 optimal weight: 0.4980 chunk 177 optimal weight: 1.9990 chunk 198 optimal weight: 0.7980 chunk 262 optimal weight: 0.9990 chunk 247 optimal weight: 0.5980 chunk 133 optimal weight: 20.0000 overall best weight: 0.4076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 563 HIS ** H1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1085 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1088 HIS B1104 ASN B1748 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4995 r_free = 0.4995 target = 0.277838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4687 r_free = 0.4687 target = 0.240100 restraints weight = 37335.949| |-----------------------------------------------------------------------------| r_work (start): 0.4679 rms_B_bonded: 2.89 r_work: 0.4294 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.4294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6594 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 26161 Z= 0.112 Angle : 0.545 10.590 35581 Z= 0.277 Chirality : 0.039 0.291 3934 Planarity : 0.004 0.061 4168 Dihedral : 15.499 179.281 4776 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.63 % Allowed : 14.92 % Favored : 83.45 % 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: 1.33 (0.16), residues: 2820 helix: 1.61 (0.13), residues: 1680 sheet: 1.58 (0.61), residues: 70 loop : -0.27 (0.19), residues: 1070 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 791 TYR 0.020 0.001 TYR H 951 PHE 0.031 0.001 PHE H1740 TRP 0.014 0.001 TRP H 942 HIS 0.006 0.001 HIS H 563 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 (26152) covalent geometry : angle 0.54231 / 0.28 (35568) SS BOND : bond 0.00058 / 0.03 ( 2) SS BOND : angle 0.57224 / 0.33 ( 4) hydrogen bonds : bond 0.04332 / 2.85 ( 1264) hydrogen bonds : angle 3.89325 / 2.79 ( 3674) Misc. bond : bond 0.00201 / 0.07 ( 4) link_BETA1-3 : bond 0.00989 / 0.47 ( 3) link_BETA1-3 : angle 3.52706 / 2.24 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5640 Ramachandran restraints generated. 2820 Oldfield, 0 Emsley, 2820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5640 Ramachandran restraints generated. 2820 Oldfield, 0 Emsley, 2820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 221 time to evaluate : 0.809 Fit side-chains revert: symmetry clash REVERT: H 241 MET cc_start: -0.0271 (mmt) cc_final: -0.1631 (ppp) REVERT: H 620 MET cc_start: 0.0171 (mtm) cc_final: -0.1602 (tpt) REVERT: H 656 MET cc_start: 0.2175 (ttt) cc_final: 0.1503 (ptm) REVERT: H 757 ILE cc_start: 0.3737 (mt) cc_final: 0.3190 (tt) REVERT: H 1004 MET cc_start: 0.2373 (OUTLIER) cc_final: 0.1993 (tpt) REVERT: H 1010 PHE cc_start: 0.0222 (OUTLIER) cc_final: -0.0250 (t80) REVERT: H 1154 ARG cc_start: 0.2960 (OUTLIER) cc_final: 0.1242 (ttt180) REVERT: H 1204 MET cc_start: -0.0487 (tpt) cc_final: -0.1707 (ttt) REVERT: H 1230 MET cc_start: -0.0934 (ttm) cc_final: -0.1774 (pmm) REVERT: H 1459 MET cc_start: -0.0852 (pmm) cc_final: -0.3161 (mmm) REVERT: H 1487 PHE cc_start: 0.3806 (OUTLIER) cc_final: 0.3101 (m-80) REVERT: H 1562 MET cc_start: 0.3043 (ptp) cc_final: 0.2349 (mmt) REVERT: H 1737 LEU cc_start: 0.5022 (mt) cc_final: 0.4360 (tt) REVERT: H 1766 PHE cc_start: 0.2536 (OUTLIER) cc_final: 0.2325 (t80) REVERT: H 1796 MET cc_start: 0.2264 (mmm) cc_final: 0.1262 (mmt) REVERT: B 293 MET cc_start: 0.8273 (mmt) cc_final: 0.7876 (mmp) REVERT: B 343 GLN cc_start: 0.7671 (OUTLIER) cc_final: 0.7364 (mp10) REVERT: B 993 MET cc_start: 0.8795 (tpp) cc_final: 0.8306 (tpt) REVERT: B 1633 MET cc_start: 0.0606 (mtp) cc_final: 0.0353 (mtm) REVERT: B 1642 MET cc_start: 0.5601 (ptm) cc_final: 0.5280 (ptp) outliers start: 41 outliers final: 19 residues processed: 249 average time/residue: 0.5475 time to fit residues: 164.3243 Evaluate side-chains 232 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 207 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 186 PHE Chi-restraints excluded: chain H residue 388 VAL Chi-restraints excluded: chain H residue 563 HIS Chi-restraints excluded: chain H residue 565 VAL Chi-restraints excluded: chain H residue 753 VAL Chi-restraints excluded: chain H residue 775 LEU Chi-restraints excluded: chain H residue 795 PHE Chi-restraints excluded: chain H residue 945 LEU Chi-restraints excluded: chain H residue 1004 MET Chi-restraints excluded: chain H residue 1010 PHE Chi-restraints excluded: chain H residue 1061 ASN Chi-restraints excluded: chain H residue 1154 ARG Chi-restraints excluded: chain H residue 1270 MET Chi-restraints excluded: chain H residue 1487 PHE Chi-restraints excluded: chain H residue 1766 PHE Chi-restraints excluded: chain H residue 1825 ILE Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 343 GLN Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1078 LEU Chi-restraints excluded: chain B residue 1306 LEU Chi-restraints excluded: chain B residue 1580 THR Chi-restraints excluded: chain B residue 1670 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: [204, 238, 201, 45, 259, 232, 87, 195, 80, 75, 268] chunk 204 optimal weight: 0.3980 chunk 238 optimal weight: 1.9990 chunk 201 optimal weight: 0.0370 chunk 45 optimal weight: 5.9990 chunk 259 optimal weight: 0.9980 chunk 232 optimal weight: 0.6980 chunk 87 optimal weight: 4.9990 chunk 195 optimal weight: 0.7980 chunk 80 optimal weight: 5.9990 chunk 75 optimal weight: 7.9990 chunk 268 optimal weight: 10.0000 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 563 HIS ** H1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1085 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 778 HIS B1088 HIS B1104 ASN B1748 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4993 r_free = 0.4993 target = 0.277678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4679 r_free = 0.4679 target = 0.239194 restraints weight = 37381.368| |-----------------------------------------------------------------------------| r_work (start): 0.4672 rms_B_bonded: 2.89 r_work: 0.3985 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.3985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7090 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 26161 Z= 0.117 Angle : 0.570 11.374 35581 Z= 0.287 Chirality : 0.040 0.288 3934 Planarity : 0.005 0.062 4168 Dihedral : 15.401 178.445 4776 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.43 % Allowed : 15.60 % Favored : 82.98 % 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: 1.30 (0.16), residues: 2820 helix: 1.56 (0.13), residues: 1692 sheet: 1.55 (0.61), residues: 70 loop : -0.26 (0.19), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 852 TYR 0.022 0.001 TYR H 951 PHE 0.035 0.001 PHE H1740 TRP 0.036 0.001 TRP H 942 HIS 0.005 0.001 HIS H1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.12 (26152) covalent geometry : angle 0.56730 / 0.29 (35568) SS BOND : bond 0.00053 / 0.03 ( 2) SS BOND : angle 0.64422 / 0.38 ( 4) hydrogen bonds : bond 0.04362 / 2.88 ( 1264) hydrogen bonds : angle 3.94835 / 2.83 ( 3674) Misc. bond : bond 0.00203 / 0.07 ( 4) link_BETA1-3 : bond 0.00951 / 0.46 ( 3) link_BETA1-3 : angle 3.49883 / 2.22 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5640 Ramachandran restraints generated. 2820 Oldfield, 0 Emsley, 2820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5640 Ramachandran restraints generated. 2820 Oldfield, 0 Emsley, 2820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 214 time to evaluate : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 182 MET cc_start: 0.1671 (pp-130) cc_final: 0.0854 (pp-130) REVERT: H 241 MET cc_start: -0.1137 (mmt) cc_final: -0.1847 (ppp) REVERT: H 620 MET cc_start: -0.0429 (mtm) cc_final: -0.1705 (tpt) REVERT: H 656 MET cc_start: 0.0844 (ttt) cc_final: -0.0093 (ptp) REVERT: H 757 ILE cc_start: 0.3676 (mt) cc_final: 0.3320 (tt) REVERT: H 1004 MET cc_start: 0.2202 (tpt) cc_final: 0.1854 (tpt) REVERT: H 1154 ARG cc_start: 0.2408 (OUTLIER) cc_final: 0.0929 (ttt180) REVERT: H 1204 MET cc_start: -0.1574 (tpt) cc_final: -0.2657 (ttt) REVERT: H 1444 ARG cc_start: 0.4580 (mmm160) cc_final: 0.4350 (mmm160) REVERT: H 1459 MET cc_start: -0.0507 (pmm) cc_final: -0.2304 (mmm) REVERT: H 1487 PHE cc_start: 0.4998 (OUTLIER) cc_final: 0.4235 (m-80) REVERT: H 1562 MET cc_start: 0.3104 (ptp) cc_final: 0.2224 (mmt) REVERT: H 1737 LEU cc_start: 0.5973 (mt) cc_final: 0.4932 (tt) REVERT: H 1796 MET cc_start: 0.1923 (mmm) cc_final: 0.0869 (mmt) REVERT: B 293 MET cc_start: 0.8375 (mmt) cc_final: 0.8012 (mmp) REVERT: B 343 GLN cc_start: 0.7754 (OUTLIER) cc_final: 0.7483 (mp10) REVERT: B 1642 MET cc_start: 0.6229 (ptm) cc_final: 0.5764 (ptp) outliers start: 36 outliers final: 20 residues processed: 240 average time/residue: 0.5422 time to fit residues: 154.3165 Evaluate side-chains 229 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 206 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 186 PHE Chi-restraints excluded: chain H residue 388 VAL Chi-restraints excluded: chain H residue 565 VAL Chi-restraints excluded: chain H residue 731 TYR Chi-restraints excluded: chain H residue 753 VAL Chi-restraints excluded: chain H residue 775 LEU Chi-restraints excluded: chain H residue 795 PHE Chi-restraints excluded: chain H residue 945 LEU Chi-restraints excluded: chain H residue 993 MET Chi-restraints excluded: chain H residue 1061 ASN Chi-restraints excluded: chain H residue 1154 ARG Chi-restraints excluded: chain H residue 1270 MET Chi-restraints excluded: chain H residue 1487 PHE Chi-restraints excluded: chain H residue 1825 ILE Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 343 GLN Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 747 LYS Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1078 LEU Chi-restraints excluded: chain B residue 1580 THR Chi-restraints excluded: chain B residue 1670 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: [190, 196, 149, 176, 215, 44, 171, 178, 107, 193, 88] chunk 190 optimal weight: 0.1980 chunk 196 optimal weight: 1.9990 chunk 149 optimal weight: 0.9990 chunk 176 optimal weight: 4.9990 chunk 215 optimal weight: 0.9980 chunk 44 optimal weight: 0.0970 chunk 171 optimal weight: 1.9990 chunk 178 optimal weight: 0.9980 chunk 107 optimal weight: 0.0170 chunk 193 optimal weight: 0.9980 chunk 88 optimal weight: 0.7980 overall best weight: 0.4216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 316 ASN ** H 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1085 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1683 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1104 ASN B1748 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4998 r_free = 0.4998 target = 0.278317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4686 r_free = 0.4686 target = 0.239848 restraints weight = 37412.971| |-----------------------------------------------------------------------------| r_work (start): 0.4675 rms_B_bonded: 2.96 r_work: 0.4026 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.4026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7031 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 26161 Z= 0.113 Angle : 0.563 11.633 35581 Z= 0.285 Chirality : 0.039 0.342 3934 Planarity : 0.005 0.061 4168 Dihedral : 15.223 176.982 4776 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.23 % Allowed : 15.75 % Favored : 83.02 % 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: 1.37 (0.16), residues: 2820 helix: 1.61 (0.13), residues: 1696 sheet: 1.53 (0.61), residues: 70 loop : -0.23 (0.20), residues: 1054 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 852 TYR 0.026 0.001 TYR H 696 PHE 0.039 0.001 PHE H1740 TRP 0.033 0.001 TRP H 942 HIS 0.005 0.001 HIS H 563 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 (26152) covalent geometry : angle 0.55998 / 0.28 (35568) SS BOND : bond 0.00046 / 0.02 ( 2) SS BOND : angle 0.69642 / 0.41 ( 4) hydrogen bonds : bond 0.04088 / 2.70 ( 1264) hydrogen bonds : angle 3.93324 / 2.81 ( 3674) Misc. bond : bond 0.00190 / 0.07 ( 4) link_BETA1-3 : bond 0.00948 / 0.45 ( 3) link_BETA1-3 : angle 3.41323 / 2.17 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5640 Ramachandran restraints generated. 2820 Oldfield, 0 Emsley, 2820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5640 Ramachandran restraints generated. 2820 Oldfield, 0 Emsley, 2820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 214 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 182 MET cc_start: 0.1783 (pp-130) cc_final: 0.1021 (pp-130) REVERT: H 241 MET cc_start: -0.0964 (mmt) cc_final: -0.1798 (ppp) REVERT: H 620 MET cc_start: -0.0374 (mtm) cc_final: -0.1691 (tpt) REVERT: H 656 MET cc_start: 0.1102 (ttt) cc_final: 0.0137 (ptp) REVERT: H 757 ILE cc_start: 0.3839 (mt) cc_final: 0.3405 (tt) REVERT: H 1004 MET cc_start: 0.2242 (OUTLIER) cc_final: 0.1882 (tpt) REVERT: H 1154 ARG cc_start: 0.2428 (OUTLIER) cc_final: 0.0937 (ttt180) REVERT: H 1204 MET cc_start: -0.1371 (tpt) cc_final: -0.1901 (tpt) REVERT: H 1230 MET cc_start: -0.2451 (ttm) cc_final: -0.2656 (pmm) REVERT: H 1312 MET cc_start: -0.0244 (tpp) cc_final: -0.2772 (ptt) REVERT: H 1459 MET cc_start: -0.0768 (pmm) cc_final: -0.2256 (mmm) REVERT: H 1487 PHE cc_start: 0.4859 (OUTLIER) cc_final: 0.4102 (m-80) REVERT: H 1561 ILE cc_start: 0.1637 (OUTLIER) cc_final: 0.1339 (tp) REVERT: H 1737 LEU cc_start: 0.5812 (mt) cc_final: 0.4789 (tt) REVERT: H 1796 MET cc_start: 0.2071 (mmm) cc_final: 0.1052 (mmt) REVERT: B 293 MET cc_start: 0.8356 (mmt) cc_final: 0.8025 (mmp) REVERT: B 343 GLN cc_start: 0.7715 (OUTLIER) cc_final: 0.7463 (mp10) REVERT: B 997 LYS cc_start: 0.8989 (OUTLIER) cc_final: 0.8612 (mmpt) REVERT: B 1621 MET cc_start: 0.5580 (ptt) cc_final: 0.5378 (mmm) REVERT: B 1642 MET cc_start: 0.6262 (ptm) cc_final: 0.5790 (ptp) outliers start: 31 outliers final: 16 residues processed: 233 average time/residue: 0.5587 time to fit residues: 153.6693 Evaluate side-chains 231 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 209 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 186 PHE Chi-restraints excluded: chain H residue 388 VAL Chi-restraints excluded: chain H residue 731 TYR Chi-restraints excluded: chain H residue 753 VAL Chi-restraints excluded: chain H residue 775 LEU Chi-restraints excluded: chain H residue 795 PHE Chi-restraints excluded: chain H residue 945 LEU Chi-restraints excluded: chain H residue 1004 MET Chi-restraints excluded: chain H residue 1061 ASN Chi-restraints excluded: chain H residue 1154 ARG Chi-restraints excluded: chain H residue 1270 MET Chi-restraints excluded: chain H residue 1487 PHE Chi-restraints excluded: chain H residue 1561 ILE Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 343 GLN Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 747 LYS Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 997 LYS Chi-restraints excluded: chain B residue 1078 LEU Chi-restraints excluded: chain B residue 1670 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: [49, 85, 163, 201, 175, 78, 197, 165, 35, 273, 90] chunk 49 optimal weight: 0.9990 chunk 85 optimal weight: 4.9990 chunk 163 optimal weight: 1.9990 chunk 201 optimal weight: 0.0570 chunk 175 optimal weight: 0.5980 chunk 78 optimal weight: 0.8980 chunk 197 optimal weight: 0.0000 chunk 165 optimal weight: 1.9990 chunk 35 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 50.7445 > 50:) chunk 273 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 overall best weight: 0.5104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 563 HIS ** H1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1085 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1683 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1088 HIS B1104 ASN B1748 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4997 r_free = 0.4997 target = 0.278165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4684 r_free = 0.4684 target = 0.239705 restraints weight = 37247.040| |-----------------------------------------------------------------------------| r_work (start): 0.4674 rms_B_bonded: 2.98 r_work: 0.4200 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.4200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6795 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.067 26161 Z= 0.114 Angle : 0.566 11.854 35581 Z= 0.285 Chirality : 0.039 0.289 3934 Planarity : 0.005 0.064 4168 Dihedral : 15.097 175.848 4776 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.11 % Allowed : 16.07 % Favored : 82.82 % 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: 1.37 (0.16), residues: 2820 helix: 1.61 (0.13), residues: 1696 sheet: 1.62 (0.61), residues: 70 loop : -0.23 (0.20), residues: 1054 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG H1444 TYR 0.027 0.001 TYR H 951 PHE 0.035 0.001 PHE H1740 TRP 0.029 0.001 TRP H 942 HIS 0.005 0.000 HIS H1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 (26152) covalent geometry : angle 0.56339 / 0.28 (35568) SS BOND : bond 0.00048 / 0.02 ( 2) SS BOND : angle 0.71004 / 0.42 ( 4) hydrogen bonds : bond 0.04107 / 2.70 ( 1264) hydrogen bonds : angle 3.93522 / 2.82 ( 3674) Misc. bond : bond 0.00185 / 0.07 ( 4) link_BETA1-3 : bond 0.00932 / 0.44 ( 3) link_BETA1-3 : angle 3.37723 / 2.15 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7629.56 seconds wall clock time: 130 minutes 42.02 seconds (7842.02 seconds total)