Starting phenix.real_space_refine on Sun May 3 09:03:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lu8_63391/05_2026/9lu8_63391.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lu8_63391/05_2026/9lu8_63391.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9lu8_63391/05_2026/9lu8_63391.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lu8_63391/05_2026/9lu8_63391.map" model { file = "/net/cci-nas-00/data/ceres_data/9lu8_63391/05_2026/9lu8_63391.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lu8_63391/05_2026/9lu8_63391.cif" } resolution = 2.99 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= 0.060 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: 5 Type Number sf(0) Gaussians Mg 1 5.21 5 S 61 5.16 5 C 7591 2.51 5 N 1941 2.21 5 O 2037 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11631 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 11569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1524, 11569 Classifications: {'peptide': 1524} Incomplete info: {'truncation_to_alanine': 229} Link IDs: {'PTRANS': 68, 'TRANS': 1455} Chain breaks: 7 Unresolved non-hydrogen bonds: 895 Unresolved non-hydrogen angles: 1115 Unresolved non-hydrogen dihedrals: 745 Unresolved non-hydrogen chiralities: 58 Planarities with less than four sites: {'ASP:plan': 23, 'GLU:plan': 22, 'ARG:plan': 32, 'HIS:plan': 7, 'GLN:plan1': 11, 'PHE:plan': 9, 'TYR:plan': 8, 'TRP:plan': 2, 'ASN:plan1': 8} Unresolved non-hydrogen planarities: 548 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {'MAN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.61, per 1000 atoms: 0.22 Number of scatterers: 11631 At special positions: 0 Unit cell: (114.4, 129.8, 115.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 61 16.00 Mg 1 11.99 O 2037 8.00 N 1941 7.00 C 7591 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 677 " - pdb=" SG CYS A 688 " distance=2.03 Simple disulfide: pdb=" SG CYS A1347 " - pdb=" SG CYS A1364 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN B 1 " - " MAN B 2 " " MAN B 2 " - " MAN B 3 " BETA1-3 " NAG C 1 " - " NAG C 2 " Time building additional restraints: 0.96 Conformation dependent library (CDL) restraints added in 522.3 milliseconds 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2882 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 3 sheets defined 68.2% alpha, 3.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 167 through 173 removed outlier: 3.892A pdb=" N ASP A 173 " --> pdb=" O ALA A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 195 removed outlier: 3.592A pdb=" N ILE A 183 " --> pdb=" O PRO A 179 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE A 187 " --> pdb=" O ILE A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 217 removed outlier: 3.524A pdb=" N ASP A 206 " --> pdb=" O ARG A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 233 Processing helix chain 'A' and resid 238 through 248 removed outlier: 3.659A pdb=" N LYS A 242 " --> pdb=" O ALA A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 262 Processing helix chain 'A' and resid 300 through 313 Processing helix chain 'A' and resid 316 through 334 removed outlier: 3.586A pdb=" N PHE A 327 " --> pdb=" O GLN A 323 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA A 334 " --> pdb=" O CYS A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 339 Processing helix chain 'A' and resid 340 through 357 removed outlier: 3.529A pdb=" N LEU A 344 " --> pdb=" O THR A 340 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER A 357 " --> pdb=" O ASP A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 363 Processing helix chain 'A' and resid 370 through 376 Processing helix chain 'A' and resid 376 through 388 removed outlier: 4.297A pdb=" N LEU A 380 " --> pdb=" O VAL A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 414 Processing helix chain 'A' and resid 415 through 418 removed outlier: 4.070A pdb=" N TYR A 418 " --> pdb=" O LEU A 415 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 415 through 418' Processing helix chain 'A' and resid 421 through 425 removed outlier: 3.502A pdb=" N ILE A 425 " --> pdb=" O ILE A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 445 Processing helix chain 'A' and resid 449 through 453 removed outlier: 3.635A pdb=" N ASP A 452 " --> pdb=" O PRO A 449 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL A 453 " --> pdb=" O TRP A 450 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 449 through 453' Processing helix chain 'A' and resid 462 through 471 removed outlier: 3.758A pdb=" N HIS A 466 " --> pdb=" O ARG A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 489 removed outlier: 3.565A pdb=" N TRP A 475 " --> pdb=" O PHE A 471 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N HIS A 478 " --> pdb=" O ILE A 474 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N VAL A 481 " --> pdb=" O MET A 477 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASN A 489 " --> pdb=" O TYR A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 494 removed outlier: 3.520A pdb=" N TYR A 494 " --> pdb=" O PRO A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 516 removed outlier: 3.596A pdb=" N LYS A 511 " --> pdb=" O LEU A 507 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ALA A 515 " --> pdb=" O LYS A 511 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA A 516 " --> pdb=" O TRP A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 537 removed outlier: 3.822A pdb=" N VAL A 521 " --> pdb=" O LEU A 517 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ALA A 522 " --> pdb=" O GLY A 518 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N SER A 523 " --> pdb=" O GLY A 519 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N SER A 535 " --> pdb=" O LEU A 531 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N PHE A 536 " --> pdb=" O CYS A 532 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL A 537 " --> pdb=" O GLU A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 572 removed outlier: 3.732A pdb=" N ARG A 550 " --> pdb=" O HIS A 546 " (cutoff:3.500A) Proline residue: A 564 - end of helix Processing helix chain 'A' and resid 578 through 602 removed outlier: 3.767A pdb=" N HIS A 582 " --> pdb=" O SER A 578 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE A 589 " --> pdb=" O GLY A 585 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N PHE A 590 " --> pdb=" O ALA A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 622 through 627 removed outlier: 3.716A pdb=" N ALA A 627 " --> pdb=" O GLN A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 671 removed outlier: 4.383A pdb=" N TRP A 638 " --> pdb=" O GLY A 634 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N TRP A 644 " --> pdb=" O SER A 640 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE A 660 " --> pdb=" O TYR A 656 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N LEU A 661 " --> pdb=" O PHE A 657 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N SER A 662 " --> pdb=" O PHE A 658 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N ASP A 665 " --> pdb=" O LEU A 661 " (cutoff:3.500A) Proline residue: A 666 - end of helix Processing helix chain 'A' and resid 687 through 689 No H-bonds generated for 'chain 'A' and resid 687 through 689' Processing helix chain 'A' and resid 690 through 707 removed outlier: 3.509A pdb=" N ILE A 705 " --> pdb=" O ALA A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 730 removed outlier: 4.173A pdb=" N LEU A 713 " --> pdb=" O LEU A 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 753 removed outlier: 3.502A pdb=" N ILE A 741 " --> pdb=" O PRO A 737 " (cutoff:3.500A) Proline residue: A 746 - end of helix removed outlier: 3.545A pdb=" N TYR A 750 " --> pdb=" O PRO A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 764 through 783 removed outlier: 4.033A pdb=" N LEU A 768 " --> pdb=" O LYS A 764 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ALA A 775 " --> pdb=" O GLN A 771 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE A 776 " --> pdb=" O ILE A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 787 through 795 removed outlier: 3.644A pdb=" N LYS A 793 " --> pdb=" O ASP A 789 " (cutoff:3.500A) Processing helix chain 'A' and resid 812 through 817 removed outlier: 3.927A pdb=" N VAL A 816 " --> pdb=" O PRO A 812 " (cutoff:3.500A) Processing helix chain 'A' and resid 818 through 820 No H-bonds generated for 'chain 'A' and resid 818 through 820' Processing helix chain 'A' and resid 833 through 845 Processing helix chain 'A' and resid 854 through 858 Processing helix chain 'A' and resid 875 through 880 Processing helix chain 'A' and resid 890 through 899 Processing helix chain 'A' and resid 899 through 911 Processing helix chain 'A' and resid 956 through 966 Processing helix chain 'A' and resid 968 through 976 removed outlier: 3.747A pdb=" N THR A 972 " --> pdb=" O THR A 968 " (cutoff:3.500A) Processing helix chain 'A' and resid 977 through 991 removed outlier: 4.368A pdb=" N ARG A 981 " --> pdb=" O MET A 977 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASN A 991 " --> pdb=" O TYR A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 991 through 999 removed outlier: 4.393A pdb=" N VAL A 995 " --> pdb=" O ASN A 991 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLY A 999 " --> pdb=" O VAL A 995 " (cutoff:3.500A) Processing helix chain 'A' and resid 1001 through 1016 removed outlier: 3.682A pdb=" N LEU A1005 " --> pdb=" O ASN A1001 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N MET A1012 " --> pdb=" O GLU A1008 " (cutoff:3.500A) Processing helix chain 'A' and resid 1025 through 1029 removed outlier: 3.753A pdb=" N PHE A1029 " --> pdb=" O LEU A1026 " (cutoff:3.500A) Processing helix chain 'A' and resid 1030 through 1044 Processing helix chain 'A' and resid 1100 through 1108 removed outlier: 3.629A pdb=" N ALA A1108 " --> pdb=" O ASN A1104 " (cutoff:3.500A) Processing helix chain 'A' and resid 1109 through 1112 removed outlier: 3.734A pdb=" N TYR A1112 " --> pdb=" O LEU A1109 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1109 through 1112' Processing helix chain 'A' and resid 1127 through 1132 Processing helix chain 'A' and resid 1133 through 1138 Processing helix chain 'A' and resid 1139 through 1142 Processing helix chain 'A' and resid 1189 through 1206 removed outlier: 3.582A pdb=" N ALA A1200 " --> pdb=" O GLY A1196 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ILE A1206 " --> pdb=" O THR A1202 " (cutoff:3.500A) Processing helix chain 'A' and resid 1220 through 1225 removed outlier: 3.800A pdb=" N THR A1225 " --> pdb=" O THR A1221 " (cutoff:3.500A) Processing helix chain 'A' and resid 1239 through 1252 Processing helix chain 'A' and resid 1270 through 1289 removed outlier: 3.612A pdb=" N ILE A1281 " --> pdb=" O PHE A1277 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLY A1282 " --> pdb=" O THR A1278 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ALA A1283 " --> pdb=" O THR A1279 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLY A1284 " --> pdb=" O LYS A1280 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLU A1287 " --> pdb=" O ALA A1283 " (cutoff:3.500A) Processing helix chain 'A' and resid 1291 through 1299 removed outlier: 3.788A pdb=" N TYR A1295 " --> pdb=" O SER A1291 " (cutoff:3.500A) Processing helix chain 'A' and resid 1302 through 1313 Processing helix chain 'A' and resid 1313 through 1343 removed outlier: 4.677A pdb=" N HIS A1317 " --> pdb=" O HIS A1313 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU A1321 " --> pdb=" O HIS A1317 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU A1332 " --> pdb=" O GLN A1328 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASN A1336 " --> pdb=" O LEU A1332 " (cutoff:3.500A) Processing helix chain 'A' and resid 1367 through 1372 Processing helix chain 'A' and resid 1372 through 1390 removed outlier: 4.051A pdb=" N ARG A1376 " --> pdb=" O ASP A1372 " (cutoff:3.500A) Processing helix chain 'A' and resid 1390 through 1398 removed outlier: 4.204A pdb=" N GLU A1396 " --> pdb=" O ILE A1392 " (cutoff:3.500A) Processing helix chain 'A' and resid 1401 through 1411 Processing helix chain 'A' and resid 1456 through 1465 Processing helix chain 'A' and resid 1468 through 1486 removed outlier: 3.512A pdb=" N HIS A1486 " --> pdb=" O GLY A1482 " (cutoff:3.500A) Processing helix chain 'A' and resid 1488 through 1490 No H-bonds generated for 'chain 'A' and resid 1488 through 1490' Processing helix chain 'A' and resid 1491 through 1504 removed outlier: 3.734A pdb=" N TRP A1495 " --> pdb=" O LEU A1491 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ALA A1496 " --> pdb=" O LEU A1492 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N SER A1497 " --> pdb=" O TRP A1493 " (cutoff:3.500A) Processing helix chain 'A' and resid 1514 through 1531 Processing helix chain 'A' and resid 1540 through 1553 Processing helix chain 'A' and resid 1571 through 1582 Processing helix chain 'A' and resid 1584 through 1601 removed outlier: 3.768A pdb=" N ALA A1588 " --> pdb=" O ILE A1584 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA A1597 " --> pdb=" O GLY A1593 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE A1601 " --> pdb=" O ALA A1597 " (cutoff:3.500A) Processing helix chain 'A' and resid 1610 through 1614 removed outlier: 3.538A pdb=" N ASP A1613 " --> pdb=" O THR A1610 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ARG A1614 " --> pdb=" O ASP A1611 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1610 through 1614' Processing helix chain 'A' and resid 1617 through 1642 removed outlier: 3.926A pdb=" N ILE A1621 " --> pdb=" O SER A1617 " (cutoff:3.500A) Proline residue: A1628 - end of helix Processing helix chain 'A' and resid 1659 through 1684 removed outlier: 4.057A pdb=" N VAL A1670 " --> pdb=" O HIS A1666 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL A1671 " --> pdb=" O GLY A1667 " (cutoff:3.500A) Processing helix chain 'A' and resid 1687 through 1714 removed outlier: 3.504A pdb=" N MET A1691 " --> pdb=" O SER A1687 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE A1693 " --> pdb=" O VAL A1689 " (cutoff:3.500A) Processing helix chain 'A' and resid 1747 through 1772 removed outlier: 3.920A pdb=" N SER A1757 " --> pdb=" O VAL A1753 " (cutoff:3.500A) Processing helix chain 'A' and resid 1773 through 1778 Processing helix chain 'A' and resid 1782 through 1794 removed outlier: 3.672A pdb=" N HIS A1786 " --> pdb=" O ILE A1782 " (cutoff:3.500A) Processing helix chain 'A' and resid 1805 through 1841 removed outlier: 4.493A pdb=" N LEU A1811 " --> pdb=" O LYS A1807 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ARG A1817 " --> pdb=" O LYS A1813 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N LEU A1822 " --> pdb=" O ARG A1818 " (cutoff:3.500A) Proline residue: A1837 - end of helix Processing helix chain 'A' and resid 1853 through 1857 removed outlier: 3.885A pdb=" N PHE A1856 " --> pdb=" O THR A1853 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 389 through 392 Processing sheet with id=AA2, first strand: chain 'A' and resid 797 through 800 Processing sheet with id=AA3, first strand: chain 'A' and resid 1087 through 1090 removed outlier: 4.016A pdb=" N PHE A1087 " --> pdb=" O LEU A1070 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N LEU A1052 " --> pdb=" O MET A1023 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N PHE A 861 " --> pdb=" O LYS A1018 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N LEU A1020 " --> pdb=" O PHE A 861 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N VAL A 863 " --> pdb=" O LEU A1020 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N SER A1022 " --> pdb=" O VAL A 863 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N THR A 865 " --> pdb=" O SER A1022 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N THR A 862 " --> pdb=" O GLN A1118 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N ALA A1168 " --> pdb=" O ASN A1219 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N LYS A1256 " --> pdb=" O ALA A1168 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N VAL A1170 " --> pdb=" O LYS A1256 " (cutoff:3.500A) 654 hydrogen bonds defined for protein. 1917 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.78 Time building geometry restraints manager: 1.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3670 1.34 - 1.46: 2677 1.46 - 1.58: 5502 1.58 - 1.70: 0 1.70 - 1.81: 97 Bond restraints: 11946 Sorted by residual: bond pdb=" C1 NAG C 1 " pdb=" O5 NAG C 1 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.71e+00 bond pdb=" C1 MAN B 2 " pdb=" C2 MAN B 2 " ideal model delta sigma weight residual 1.526 1.560 -0.034 2.00e-02 2.50e+03 2.89e+00 bond pdb=" C5 MAN B 2 " pdb=" O5 MAN B 2 " ideal model delta sigma weight residual 1.418 1.451 -0.033 2.00e-02 2.50e+03 2.68e+00 bond pdb=" C1 MAN B 2 " pdb=" O5 MAN B 2 " ideal model delta sigma weight residual 1.399 1.430 -0.031 2.00e-02 2.50e+03 2.34e+00 bond pdb=" C5 MAN B 1 " pdb=" O5 MAN B 1 " ideal model delta sigma weight residual 1.418 1.448 -0.030 2.00e-02 2.50e+03 2.24e+00 ... (remaining 11941 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 16105 2.05 - 4.10: 170 4.10 - 6.15: 22 6.15 - 8.20: 6 8.20 - 10.25: 1 Bond angle restraints: 16304 Sorted by residual: angle pdb=" C LEU A1359 " pdb=" N TYR A1360 " pdb=" CA TYR A1360 " ideal model delta sigma weight residual 121.80 114.45 7.35 2.44e+00 1.68e-01 9.06e+00 angle pdb=" N ILE A1585 " pdb=" CA ILE A1585 " pdb=" C ILE A1585 " ideal model delta sigma weight residual 108.88 115.38 -6.50 2.16e+00 2.14e-01 9.06e+00 angle pdb=" N TYR A1360 " pdb=" CA TYR A1360 " pdb=" C TYR A1360 " ideal model delta sigma weight residual 109.81 116.29 -6.48 2.21e+00 2.05e-01 8.59e+00 angle pdb=" N HIS A1313 " pdb=" CA HIS A1313 " pdb=" C HIS A1313 " ideal model delta sigma weight residual 109.81 116.01 -6.20 2.21e+00 2.05e-01 7.87e+00 angle pdb=" C ARG A 664 " pdb=" N ASP A 665 " pdb=" CA ASP A 665 " ideal model delta sigma weight residual 119.78 123.07 -3.29 1.24e+00 6.50e-01 7.05e+00 ... (remaining 16299 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.47: 6420 17.47 - 34.93: 444 34.93 - 52.40: 110 52.40 - 69.86: 24 69.86 - 87.33: 3 Dihedral angle restraints: 7001 sinusoidal: 2538 harmonic: 4463 Sorted by residual: dihedral pdb=" CA TYR A1360 " pdb=" C TYR A1360 " pdb=" N PRO A1361 " pdb=" CA PRO A1361 " ideal model delta harmonic sigma weight residual 180.00 131.77 48.23 0 5.00e+00 4.00e-02 9.30e+01 dihedral pdb=" CB CYS A 677 " pdb=" SG CYS A 677 " pdb=" SG CYS A 688 " pdb=" CB CYS A 688 " ideal model delta sinusoidal sigma weight residual -86.00 -120.02 34.02 1 1.00e+01 1.00e-02 1.64e+01 dihedral pdb=" CA ILE A 233 " pdb=" C ILE A 233 " pdb=" N GLY A 234 " pdb=" CA GLY A 234 " ideal model delta harmonic sigma weight residual 180.00 -161.37 -18.63 0 5.00e+00 4.00e-02 1.39e+01 ... (remaining 6998 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1277 0.036 - 0.072: 431 0.072 - 0.108: 109 0.108 - 0.144: 37 0.144 - 0.180: 2 Chirality restraints: 1856 Sorted by residual: chirality pdb=" C1 MAN B 3 " pdb=" O2 MAN B 2 " pdb=" C2 MAN B 3 " pdb=" O5 MAN B 3 " both_signs ideal model delta sigma weight residual False 2.40 2.37 0.03 2.00e-02 2.50e+03 2.07e+00 chirality pdb=" C1 NAG C 2 " pdb=" O3 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.37 -0.03 2.00e-02 2.50e+03 1.81e+00 chirality pdb=" C2 MAN B 1 " pdb=" C1 MAN B 1 " pdb=" C3 MAN B 1 " pdb=" O2 MAN B 1 " both_signs ideal model delta sigma weight residual False 2.52 2.70 -0.18 2.00e-01 2.50e+01 8.14e-01 ... (remaining 1853 not shown) Planarity restraints: 2062 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A1360 " 0.046 5.00e-02 4.00e+02 7.01e-02 7.85e+00 pdb=" N PRO A1361 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO A1361 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO A1361 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A1836 " 0.025 5.00e-02 4.00e+02 3.72e-02 2.21e+00 pdb=" N PRO A1837 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO A1837 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A1837 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 853 " -0.023 5.00e-02 4.00e+02 3.45e-02 1.91e+00 pdb=" N PRO A 854 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO A 854 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 854 " -0.019 5.00e-02 4.00e+02 ... (remaining 2059 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 34 2.61 - 3.19: 9738 3.19 - 3.76: 16532 3.76 - 4.33: 21344 4.33 - 4.90: 37724 Nonbonded interactions: 85372 Sorted by model distance: nonbonded pdb=" OD1 ASP A1216 " pdb="MG MG A2001 " model vdw 2.044 2.170 nonbonded pdb=" NE2 HIS A1214 " pdb="MG MG A2001 " model vdw 2.107 2.250 nonbonded pdb=" OD1 ASN A 335 " pdb=" N GLN A 336 " model vdw 2.109 3.120 nonbonded pdb=" O SER A 622 " pdb=" OG1 THR A 626 " model vdw 2.278 3.040 nonbonded pdb=" OD2 ASP A1216 " pdb="MG MG A2001 " model vdw 2.316 2.170 ... (remaining 85367 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.610 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: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.210 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 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 : 0.003 0.043 11951 Z= 0.156 Angle : 0.560 10.246 16317 Z= 0.296 Chirality : 0.040 0.180 1856 Planarity : 0.005 0.070 2062 Dihedral : 13.114 87.329 4113 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 1.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 0.45 % Allowed : 8.21 % Favored : 91.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.47 % 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: 1.36 (0.21), residues: 1508 helix: 1.84 (0.17), residues: 897 sheet: 0.42 (0.63), residues: 53 loop : -0.59 (0.25), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A1088 TYR 0.014 0.001 TYR A1311 PHE 0.016 0.001 PHE A1316 TRP 0.012 0.001 TRP A 243 HIS 0.005 0.001 HIS A1767 Details of bonding type rmsd covalent geometry : bond 0.00292 (11946) covalent geometry : angle 0.55460 (16304) SS BOND : bond 0.00198 ( 2) SS BOND : angle 0.95176 ( 4) hydrogen bonds : bond 0.15454 ( 654) hydrogen bonds : angle 4.73434 ( 1917) link_ALPHA1-2 : bond 0.00376 ( 2) link_ALPHA1-2 : angle 2.09584 ( 6) link_BETA1-3 : bond 0.00013 ( 1) link_BETA1-3 : angle 5.11614 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 150 time to evaluate : 0.423 Fit side-chains REVERT: A 1608 LYS cc_start: 0.7910 (mptp) cc_final: 0.7680 (mptp) outliers start: 5 outliers final: 1 residues processed: 154 average time/residue: 0.5689 time to fit residues: 94.8980 Evaluate side-chains 124 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 123 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1359 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 5.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 561 ASN A1126 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.181079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.117328 restraints weight = 12795.263| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 2.69 r_work: 0.3167 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.0870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11951 Z= 0.152 Angle : 0.558 11.253 16317 Z= 0.293 Chirality : 0.040 0.230 1856 Planarity : 0.005 0.087 2062 Dihedral : 4.329 47.329 1744 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 1.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.26 % Allowed : 11.91 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.47 % 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: 1.45 (0.22), residues: 1508 helix: 1.91 (0.17), residues: 903 sheet: 0.83 (0.73), residues: 45 loop : -0.61 (0.25), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1007 TYR 0.014 0.001 TYR A 715 PHE 0.016 0.002 PHE A1677 TRP 0.013 0.001 TRP A 512 HIS 0.006 0.001 HIS A1107 Details of bonding type rmsd covalent geometry : bond 0.00332 (11946) covalent geometry : angle 0.55095 (16304) SS BOND : bond 0.00463 ( 2) SS BOND : angle 4.49190 ( 4) hydrogen bonds : bond 0.07091 ( 654) hydrogen bonds : angle 3.91010 ( 1917) link_ALPHA1-2 : bond 0.00684 ( 2) link_ALPHA1-2 : angle 1.91072 ( 6) link_BETA1-3 : bond 0.00069 ( 1) link_BETA1-3 : angle 2.97660 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 132 time to evaluate : 0.410 Fit side-chains REVERT: A 369 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7586 (tp30) REVERT: A 560 ILE cc_start: 0.7360 (OUTLIER) cc_final: 0.7084 (tt) REVERT: A 1126 ASN cc_start: 0.8906 (OUTLIER) cc_final: 0.8630 (t0) REVERT: A 1608 LYS cc_start: 0.7794 (mptp) cc_final: 0.7546 (mptp) outliers start: 25 outliers final: 12 residues processed: 149 average time/residue: 0.5739 time to fit residues: 92.8790 Evaluate side-chains 144 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 129 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 ASP Chi-restraints excluded: chain A residue 359 GLN Chi-restraints excluded: chain A residue 369 GLU Chi-restraints excluded: chain A residue 534 TRP Chi-restraints excluded: chain A residue 560 ILE Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain A residue 688 CYS Chi-restraints excluded: chain A residue 703 ASP Chi-restraints excluded: chain A residue 839 SER Chi-restraints excluded: chain A residue 1126 ASN Chi-restraints excluded: chain A residue 1359 LEU Chi-restraints excluded: chain A residue 1610 THR Chi-restraints excluded: chain A residue 1675 VAL Chi-restraints excluded: chain A residue 1771 ILE Chi-restraints excluded: chain A residue 1870 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 131 optimal weight: 1.9990 chunk 150 optimal weight: 7.9990 chunk 103 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 117 optimal weight: 0.9980 chunk 112 optimal weight: 5.9990 chunk 104 optimal weight: 0.9980 chunk 105 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1767 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.182253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.117971 restraints weight = 12921.598| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 2.75 r_work: 0.3160 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.1076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11951 Z= 0.151 Angle : 0.547 12.350 16317 Z= 0.285 Chirality : 0.040 0.212 1856 Planarity : 0.005 0.083 2062 Dihedral : 4.284 47.159 1744 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 1.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.17 % Allowed : 13.54 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.47 % 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: 1.47 (0.22), residues: 1508 helix: 1.95 (0.17), residues: 903 sheet: 0.62 (0.71), residues: 45 loop : -0.62 (0.25), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 981 TYR 0.013 0.001 TYR A 715 PHE 0.016 0.001 PHE A1676 TRP 0.013 0.001 TRP A 512 HIS 0.011 0.001 HIS A1707 Details of bonding type rmsd covalent geometry : bond 0.00339 (11946) covalent geometry : angle 0.54161 (16304) SS BOND : bond 0.00407 ( 2) SS BOND : angle 3.78565 ( 4) hydrogen bonds : bond 0.06753 ( 654) hydrogen bonds : angle 3.80484 ( 1917) link_ALPHA1-2 : bond 0.00823 ( 2) link_ALPHA1-2 : angle 1.72695 ( 6) link_BETA1-3 : bond 0.00030 ( 1) link_BETA1-3 : angle 2.82560 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 131 time to evaluate : 0.402 Fit side-chains REVERT: A 359 GLN cc_start: 0.6118 (OUTLIER) cc_final: 0.5844 (pm20) REVERT: A 369 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7559 (tp30) REVERT: A 560 ILE cc_start: 0.7372 (OUTLIER) cc_final: 0.7098 (tt) REVERT: A 793 LYS cc_start: 0.7317 (OUTLIER) cc_final: 0.7034 (mtpt) REVERT: A 1608 LYS cc_start: 0.7768 (mptp) cc_final: 0.7495 (mptp) outliers start: 24 outliers final: 11 residues processed: 147 average time/residue: 0.5234 time to fit residues: 83.8417 Evaluate side-chains 143 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 128 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 359 GLN Chi-restraints excluded: chain A residue 369 GLU Chi-restraints excluded: chain A residue 534 TRP Chi-restraints excluded: chain A residue 560 ILE Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain A residue 688 CYS Chi-restraints excluded: chain A residue 793 LYS Chi-restraints excluded: chain A residue 839 SER Chi-restraints excluded: chain A residue 843 GLN Chi-restraints excluded: chain A residue 1241 ASP Chi-restraints excluded: chain A residue 1359 LEU Chi-restraints excluded: chain A residue 1610 THR Chi-restraints excluded: chain A residue 1675 VAL Chi-restraints excluded: chain A residue 1771 ILE Chi-restraints excluded: chain A residue 1870 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 149 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 140 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 117 optimal weight: 3.9990 chunk 94 optimal weight: 0.0970 chunk 3 optimal weight: 4.9990 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.181900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.117606 restraints weight = 12901.086| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.75 r_work: 0.3154 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.1288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11951 Z= 0.149 Angle : 0.545 12.620 16317 Z= 0.283 Chirality : 0.040 0.216 1856 Planarity : 0.005 0.079 2062 Dihedral : 4.242 47.411 1744 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 1.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.07 % Allowed : 13.54 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.47 % 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: 1.44 (0.22), residues: 1508 helix: 1.94 (0.17), residues: 903 sheet: 0.51 (0.70), residues: 45 loop : -0.64 (0.25), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1007 TYR 0.014 0.001 TYR A1365 PHE 0.016 0.001 PHE A1676 TRP 0.013 0.001 TRP A 512 HIS 0.010 0.001 HIS A1707 Details of bonding type rmsd covalent geometry : bond 0.00338 (11946) covalent geometry : angle 0.53975 (16304) SS BOND : bond 0.00393 ( 2) SS BOND : angle 3.86651 ( 4) hydrogen bonds : bond 0.06542 ( 654) hydrogen bonds : angle 3.74078 ( 1917) link_ALPHA1-2 : bond 0.00942 ( 2) link_ALPHA1-2 : angle 1.76538 ( 6) link_BETA1-3 : bond 0.00151 ( 1) link_BETA1-3 : angle 2.59911 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 131 time to evaluate : 0.411 Fit side-chains REVERT: A 369 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7551 (tp30) REVERT: A 558 MET cc_start: 0.8290 (OUTLIER) cc_final: 0.7888 (ttp) REVERT: A 560 ILE cc_start: 0.7339 (OUTLIER) cc_final: 0.7074 (tt) REVERT: A 665 ASP cc_start: 0.7458 (OUTLIER) cc_final: 0.7209 (m-30) REVERT: A 1082 ARG cc_start: 0.6636 (mmm160) cc_final: 0.6301 (mtp85) REVERT: A 1608 LYS cc_start: 0.7809 (mptp) cc_final: 0.7517 (mptp) REVERT: A 1661 MET cc_start: 0.5678 (ppp) cc_final: 0.4599 (tpp) outliers start: 34 outliers final: 13 residues processed: 156 average time/residue: 0.5455 time to fit residues: 92.8738 Evaluate side-chains 145 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 128 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 369 GLU Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 534 TRP Chi-restraints excluded: chain A residue 558 MET Chi-restraints excluded: chain A residue 560 ILE Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain A residue 665 ASP Chi-restraints excluded: chain A residue 688 CYS Chi-restraints excluded: chain A residue 839 SER Chi-restraints excluded: chain A residue 865 THR Chi-restraints excluded: chain A residue 1241 ASP Chi-restraints excluded: chain A residue 1359 LEU Chi-restraints excluded: chain A residue 1610 THR Chi-restraints excluded: chain A residue 1675 VAL Chi-restraints excluded: chain A residue 1750 THR Chi-restraints excluded: chain A residue 1771 ILE Chi-restraints excluded: chain A residue 1870 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 126 optimal weight: 7.9990 chunk 100 optimal weight: 0.0980 chunk 143 optimal weight: 0.0570 chunk 39 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 80 optimal weight: 0.9990 chunk 111 optimal weight: 0.7980 chunk 127 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 142 optimal weight: 8.9990 overall best weight: 0.5902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.185737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.121805 restraints weight = 12940.175| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 2.77 r_work: 0.3210 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 11951 Z= 0.106 Angle : 0.485 10.362 16317 Z= 0.250 Chirality : 0.038 0.176 1856 Planarity : 0.004 0.073 2062 Dihedral : 3.948 46.167 1744 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 1.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.08 % Allowed : 15.16 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.47 % 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: 1.75 (0.22), residues: 1508 helix: 2.15 (0.17), residues: 904 sheet: 0.72 (0.69), residues: 45 loop : -0.46 (0.26), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 981 TYR 0.011 0.001 TYR A1311 PHE 0.013 0.001 PHE A 704 TRP 0.011 0.001 TRP A1373 HIS 0.008 0.001 HIS A1707 Details of bonding type rmsd covalent geometry : bond 0.00212 (11946) covalent geometry : angle 0.48054 (16304) SS BOND : bond 0.00262 ( 2) SS BOND : angle 3.41377 ( 4) hydrogen bonds : bond 0.04855 ( 654) hydrogen bonds : angle 3.54126 ( 1917) link_ALPHA1-2 : bond 0.00804 ( 2) link_ALPHA1-2 : angle 1.64768 ( 6) link_BETA1-3 : bond 0.00339 ( 1) link_BETA1-3 : angle 2.32211 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 127 time to evaluate : 0.407 Fit side-chains revert: symmetry clash REVERT: A 499 GLN cc_start: 0.6125 (OUTLIER) cc_final: 0.5232 (mp10) REVERT: A 558 MET cc_start: 0.8259 (OUTLIER) cc_final: 0.7853 (ttp) REVERT: A 560 ILE cc_start: 0.7098 (OUTLIER) cc_final: 0.6819 (tt) REVERT: A 981 ARG cc_start: 0.7199 (mtm-85) cc_final: 0.6966 (mtm180) REVERT: A 1082 ARG cc_start: 0.6655 (mmm160) cc_final: 0.6364 (mtp85) REVERT: A 1321 LEU cc_start: 0.7853 (OUTLIER) cc_final: 0.7369 (mp) REVERT: A 1661 MET cc_start: 0.5697 (ppp) cc_final: 0.4514 (tpp) outliers start: 23 outliers final: 12 residues processed: 145 average time/residue: 0.5276 time to fit residues: 83.7985 Evaluate side-chains 142 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 126 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 371 ASP Chi-restraints excluded: chain A residue 499 GLN Chi-restraints excluded: chain A residue 534 TRP Chi-restraints excluded: chain A residue 558 MET Chi-restraints excluded: chain A residue 560 ILE Chi-restraints excluded: chain A residue 688 CYS Chi-restraints excluded: chain A residue 839 SER Chi-restraints excluded: chain A residue 865 THR Chi-restraints excluded: chain A residue 1211 HIS Chi-restraints excluded: chain A residue 1229 VAL Chi-restraints excluded: chain A residue 1241 ASP Chi-restraints excluded: chain A residue 1321 LEU Chi-restraints excluded: chain A residue 1359 LEU Chi-restraints excluded: chain A residue 1612 GLU Chi-restraints excluded: chain A residue 1771 ILE Chi-restraints excluded: chain A residue 1870 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 19 optimal weight: 6.9990 chunk 4 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 130 optimal weight: 4.9990 chunk 112 optimal weight: 3.9990 chunk 125 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 111 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.183465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.119609 restraints weight = 12884.720| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 2.73 r_work: 0.3189 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11951 Z= 0.129 Angle : 0.513 10.729 16317 Z= 0.264 Chirality : 0.039 0.197 1856 Planarity : 0.005 0.076 2062 Dihedral : 3.973 46.077 1744 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 1.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.80 % Allowed : 15.16 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.47 % 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: 1.61 (0.22), residues: 1508 helix: 2.07 (0.17), residues: 907 sheet: 0.72 (0.69), residues: 45 loop : -0.59 (0.26), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1007 TYR 0.013 0.001 TYR A1311 PHE 0.015 0.001 PHE A 648 TRP 0.011 0.001 TRP A 512 HIS 0.011 0.001 HIS A1707 Details of bonding type rmsd covalent geometry : bond 0.00284 (11946) covalent geometry : angle 0.50901 (16304) SS BOND : bond 0.00238 ( 2) SS BOND : angle 2.80217 ( 4) hydrogen bonds : bond 0.05765 ( 654) hydrogen bonds : angle 3.56313 ( 1917) link_ALPHA1-2 : bond 0.00828 ( 2) link_ALPHA1-2 : angle 1.69841 ( 6) link_BETA1-3 : bond 0.00240 ( 1) link_BETA1-3 : angle 2.29317 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 129 time to evaluate : 0.423 Fit side-chains revert: symmetry clash REVERT: A 361 GLN cc_start: 0.7529 (OUTLIER) cc_final: 0.5986 (mt0) REVERT: A 499 GLN cc_start: 0.6147 (OUTLIER) cc_final: 0.5223 (mp10) REVERT: A 558 MET cc_start: 0.8252 (OUTLIER) cc_final: 0.7832 (ttp) REVERT: A 560 ILE cc_start: 0.7204 (OUTLIER) cc_final: 0.6943 (tt) REVERT: A 1082 ARG cc_start: 0.6692 (mmm160) cc_final: 0.6384 (mtp85) REVERT: A 1321 LEU cc_start: 0.7929 (OUTLIER) cc_final: 0.7374 (mp) REVERT: A 1343 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7811 (mm-30) REVERT: A 1608 LYS cc_start: 0.7739 (mptp) cc_final: 0.7427 (mptp) REVERT: A 1661 MET cc_start: 0.5677 (ppp) cc_final: 0.4494 (tpp) REVERT: A 1884 HIS cc_start: 0.4399 (OUTLIER) cc_final: 0.3396 (t70) outliers start: 31 outliers final: 13 residues processed: 152 average time/residue: 0.5367 time to fit residues: 89.0560 Evaluate side-chains 146 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 126 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 GLN Chi-restraints excluded: chain A residue 371 ASP Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 499 GLN Chi-restraints excluded: chain A residue 534 TRP Chi-restraints excluded: chain A residue 558 MET Chi-restraints excluded: chain A residue 560 ILE Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 688 CYS Chi-restraints excluded: chain A residue 839 SER Chi-restraints excluded: chain A residue 865 THR Chi-restraints excluded: chain A residue 1229 VAL Chi-restraints excluded: chain A residue 1321 LEU Chi-restraints excluded: chain A residue 1343 GLU Chi-restraints excluded: chain A residue 1359 LEU Chi-restraints excluded: chain A residue 1610 THR Chi-restraints excluded: chain A residue 1612 GLU Chi-restraints excluded: chain A residue 1771 ILE Chi-restraints excluded: chain A residue 1870 THR Chi-restraints excluded: chain A residue 1884 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 31 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 chunk 19 optimal weight: 10.0000 chunk 135 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 chunk 1 optimal weight: 0.7980 chunk 118 optimal weight: 0.9980 chunk 3 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1767 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.179964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.115748 restraints weight = 12972.063| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.73 r_work: 0.3128 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11951 Z= 0.184 Angle : 0.589 12.601 16317 Z= 0.304 Chirality : 0.042 0.230 1856 Planarity : 0.005 0.080 2062 Dihedral : 4.299 47.429 1744 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.71 % Allowed : 15.07 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.47 % 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: 1.27 (0.21), residues: 1508 helix: 1.81 (0.17), residues: 901 sheet: 0.53 (0.68), residues: 45 loop : -0.74 (0.25), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 981 TYR 0.017 0.002 TYR A1365 PHE 0.021 0.002 PHE A 648 TRP 0.015 0.002 TRP A 512 HIS 0.012 0.001 HIS A1707 Details of bonding type rmsd covalent geometry : bond 0.00437 (11946) covalent geometry : angle 0.58466 (16304) SS BOND : bond 0.00423 ( 2) SS BOND : angle 3.41739 ( 4) hydrogen bonds : bond 0.07380 ( 654) hydrogen bonds : angle 3.76383 ( 1917) link_ALPHA1-2 : bond 0.00971 ( 2) link_ALPHA1-2 : angle 1.86907 ( 6) link_BETA1-3 : bond 0.00104 ( 1) link_BETA1-3 : angle 2.53325 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 132 time to evaluate : 0.467 Fit side-chains revert: symmetry clash REVERT: A 361 GLN cc_start: 0.7634 (OUTLIER) cc_final: 0.7418 (mm-40) REVERT: A 499 GLN cc_start: 0.6212 (OUTLIER) cc_final: 0.5275 (mp10) REVERT: A 560 ILE cc_start: 0.7383 (OUTLIER) cc_final: 0.7113 (tt) REVERT: A 1343 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7961 (mm-30) REVERT: A 1375 ARG cc_start: 0.7471 (OUTLIER) cc_final: 0.6860 (ttm110) REVERT: A 1608 LYS cc_start: 0.7813 (mptp) cc_final: 0.7532 (mptp) REVERT: A 1884 HIS cc_start: 0.4452 (OUTLIER) cc_final: 0.3450 (t70) outliers start: 30 outliers final: 19 residues processed: 154 average time/residue: 0.5081 time to fit residues: 85.6791 Evaluate side-chains 155 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 130 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 GLN Chi-restraints excluded: chain A residue 371 ASP Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 499 GLN Chi-restraints excluded: chain A residue 534 TRP Chi-restraints excluded: chain A residue 560 ILE Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain A residue 688 CYS Chi-restraints excluded: chain A residue 839 SER Chi-restraints excluded: chain A residue 856 ASP Chi-restraints excluded: chain A residue 865 THR Chi-restraints excluded: chain A residue 1229 VAL Chi-restraints excluded: chain A residue 1241 ASP Chi-restraints excluded: chain A residue 1343 GLU Chi-restraints excluded: chain A residue 1359 LEU Chi-restraints excluded: chain A residue 1375 ARG Chi-restraints excluded: chain A residue 1492 LEU Chi-restraints excluded: chain A residue 1610 THR Chi-restraints excluded: chain A residue 1612 GLU Chi-restraints excluded: chain A residue 1675 VAL Chi-restraints excluded: chain A residue 1771 ILE Chi-restraints excluded: chain A residue 1870 THR Chi-restraints excluded: chain A residue 1884 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 73 optimal weight: 0.9990 chunk 117 optimal weight: 0.9990 chunk 119 optimal weight: 1.9990 chunk 142 optimal weight: 10.0000 chunk 93 optimal weight: 6.9990 chunk 50 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 92 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.182453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.123292 restraints weight = 12796.420| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 2.42 r_work: 0.3080 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11951 Z= 0.143 Angle : 0.544 11.885 16317 Z= 0.279 Chirality : 0.040 0.206 1856 Planarity : 0.005 0.077 2062 Dihedral : 4.164 47.523 1744 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.44 % Allowed : 16.06 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.47 % 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 (0.22), residues: 1508 helix: 1.88 (0.17), residues: 902 sheet: 0.59 (0.69), residues: 45 loop : -0.75 (0.25), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1007 TYR 0.014 0.001 TYR A1365 PHE 0.015 0.001 PHE A1676 TRP 0.012 0.001 TRP A 512 HIS 0.011 0.001 HIS A1707 Details of bonding type rmsd covalent geometry : bond 0.00323 (11946) covalent geometry : angle 0.53983 (16304) SS BOND : bond 0.00258 ( 2) SS BOND : angle 3.21174 ( 4) hydrogen bonds : bond 0.06268 ( 654) hydrogen bonds : angle 3.67287 ( 1917) link_ALPHA1-2 : bond 0.00918 ( 2) link_ALPHA1-2 : angle 1.78120 ( 6) link_BETA1-3 : bond 0.00185 ( 1) link_BETA1-3 : angle 2.45231 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 129 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 361 GLN cc_start: 0.7730 (OUTLIER) cc_final: 0.7482 (mm-40) REVERT: A 369 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.7632 (tp30) REVERT: A 497 ASN cc_start: 0.7127 (t0) cc_final: 0.6838 (t0) REVERT: A 499 GLN cc_start: 0.6253 (OUTLIER) cc_final: 0.5319 (mp10) REVERT: A 560 ILE cc_start: 0.7565 (OUTLIER) cc_final: 0.7283 (tt) REVERT: A 1082 ARG cc_start: 0.6744 (mmm160) cc_final: 0.6415 (mtp85) REVERT: A 1375 ARG cc_start: 0.7626 (OUTLIER) cc_final: 0.7099 (ttm110) REVERT: A 1608 LYS cc_start: 0.7911 (mptp) cc_final: 0.7639 (mptp) REVERT: A 1884 HIS cc_start: 0.4592 (OUTLIER) cc_final: 0.3531 (t70) outliers start: 27 outliers final: 19 residues processed: 152 average time/residue: 0.5512 time to fit residues: 91.2593 Evaluate side-chains 154 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 129 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 GLN Chi-restraints excluded: chain A residue 369 GLU Chi-restraints excluded: chain A residue 371 ASP Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 499 GLN Chi-restraints excluded: chain A residue 534 TRP Chi-restraints excluded: chain A residue 560 ILE Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain A residue 688 CYS Chi-restraints excluded: chain A residue 839 SER Chi-restraints excluded: chain A residue 865 THR Chi-restraints excluded: chain A residue 1229 VAL Chi-restraints excluded: chain A residue 1241 ASP Chi-restraints excluded: chain A residue 1359 LEU Chi-restraints excluded: chain A residue 1375 ARG Chi-restraints excluded: chain A residue 1492 LEU Chi-restraints excluded: chain A residue 1610 THR Chi-restraints excluded: chain A residue 1612 GLU Chi-restraints excluded: chain A residue 1750 THR Chi-restraints excluded: chain A residue 1771 ILE Chi-restraints excluded: chain A residue 1829 ILE Chi-restraints excluded: chain A residue 1870 THR Chi-restraints excluded: chain A residue 1884 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 10 optimal weight: 0.8980 chunk 96 optimal weight: 0.5980 chunk 75 optimal weight: 8.9990 chunk 17 optimal weight: 0.6980 chunk 121 optimal weight: 9.9990 chunk 140 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 131 optimal weight: 0.1980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1767 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.186078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.129053 restraints weight = 12612.931| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 2.20 r_work: 0.3190 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11951 Z= 0.110 Angle : 0.501 10.839 16317 Z= 0.255 Chirality : 0.038 0.179 1856 Planarity : 0.004 0.074 2062 Dihedral : 3.895 46.256 1744 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 1.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.99 % Allowed : 16.88 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.47 % 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: 1.63 (0.22), residues: 1508 helix: 2.12 (0.17), residues: 899 sheet: 0.75 (0.70), residues: 45 loop : -0.62 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 981 TYR 0.013 0.001 TYR A1311 PHE 0.012 0.001 PHE A1676 TRP 0.012 0.001 TRP A 464 HIS 0.010 0.001 HIS A1707 Details of bonding type rmsd covalent geometry : bond 0.00226 (11946) covalent geometry : angle 0.49677 (16304) SS BOND : bond 0.00201 ( 2) SS BOND : angle 2.85508 ( 4) hydrogen bonds : bond 0.04852 ( 654) hydrogen bonds : angle 3.50549 ( 1917) link_ALPHA1-2 : bond 0.00816 ( 2) link_ALPHA1-2 : angle 1.66754 ( 6) link_BETA1-3 : bond 0.00227 ( 1) link_BETA1-3 : angle 2.24449 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 131 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 361 GLN cc_start: 0.7697 (mp10) cc_final: 0.7444 (mm-40) REVERT: A 369 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7607 (tp30) REVERT: A 497 ASN cc_start: 0.7391 (t0) cc_final: 0.7050 (t0) REVERT: A 499 GLN cc_start: 0.6272 (OUTLIER) cc_final: 0.5333 (mp10) REVERT: A 560 ILE cc_start: 0.7450 (OUTLIER) cc_final: 0.7158 (tt) REVERT: A 1082 ARG cc_start: 0.6832 (mmm160) cc_final: 0.6543 (mtp85) REVERT: A 1608 LYS cc_start: 0.7889 (mptp) cc_final: 0.7595 (mptp) REVERT: A 1884 HIS cc_start: 0.4562 (OUTLIER) cc_final: 0.3524 (t70) outliers start: 22 outliers final: 14 residues processed: 151 average time/residue: 0.5415 time to fit residues: 89.3818 Evaluate side-chains 146 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 128 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 369 GLU Chi-restraints excluded: chain A residue 371 ASP Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 499 GLN Chi-restraints excluded: chain A residue 534 TRP Chi-restraints excluded: chain A residue 560 ILE Chi-restraints excluded: chain A residue 688 CYS Chi-restraints excluded: chain A residue 839 SER Chi-restraints excluded: chain A residue 856 ASP Chi-restraints excluded: chain A residue 865 THR Chi-restraints excluded: chain A residue 1229 VAL Chi-restraints excluded: chain A residue 1241 ASP Chi-restraints excluded: chain A residue 1359 LEU Chi-restraints excluded: chain A residue 1492 LEU Chi-restraints excluded: chain A residue 1750 THR Chi-restraints excluded: chain A residue 1870 THR Chi-restraints excluded: chain A residue 1884 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 107 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 136 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 101 optimal weight: 50.0000 chunk 81 optimal weight: 0.0370 chunk 65 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 overall best weight: 1.2064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1767 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.183661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.125948 restraints weight = 12818.260| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 2.36 r_work: 0.3172 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11951 Z= 0.135 Angle : 0.536 11.301 16317 Z= 0.274 Chirality : 0.039 0.201 1856 Planarity : 0.005 0.077 2062 Dihedral : 3.966 46.110 1744 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 2.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.90 % Allowed : 17.24 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.47 % 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: 1.48 (0.22), residues: 1508 helix: 1.99 (0.17), residues: 905 sheet: 0.71 (0.69), residues: 45 loop : -0.71 (0.25), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1007 TYR 0.013 0.001 TYR A1365 PHE 0.016 0.001 PHE A 648 TRP 0.010 0.001 TRP A 243 HIS 0.011 0.001 HIS A1707 Details of bonding type rmsd covalent geometry : bond 0.00305 (11946) covalent geometry : angle 0.53154 (16304) SS BOND : bond 0.00229 ( 2) SS BOND : angle 3.32348 ( 4) hydrogen bonds : bond 0.05818 ( 654) hydrogen bonds : angle 3.55329 ( 1917) link_ALPHA1-2 : bond 0.00840 ( 2) link_ALPHA1-2 : angle 1.73030 ( 6) link_BETA1-3 : bond 0.00256 ( 1) link_BETA1-3 : angle 2.25893 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 129 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 361 GLN cc_start: 0.7742 (mp10) cc_final: 0.7479 (mm-40) REVERT: A 369 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7622 (tp30) REVERT: A 497 ASN cc_start: 0.7480 (t0) cc_final: 0.7125 (t0) REVERT: A 499 GLN cc_start: 0.6386 (OUTLIER) cc_final: 0.5415 (mp10) REVERT: A 560 ILE cc_start: 0.7541 (OUTLIER) cc_final: 0.7258 (tt) REVERT: A 1608 LYS cc_start: 0.7930 (mptp) cc_final: 0.7665 (mptp) REVERT: A 1709 MET cc_start: 0.5513 (tmm) cc_final: 0.4871 (ttm) REVERT: A 1884 HIS cc_start: 0.4606 (OUTLIER) cc_final: 0.3546 (t70) outliers start: 21 outliers final: 14 residues processed: 148 average time/residue: 0.4949 time to fit residues: 80.5593 Evaluate side-chains 145 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 127 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 369 GLU Chi-restraints excluded: chain A residue 371 ASP Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 499 GLN Chi-restraints excluded: chain A residue 534 TRP Chi-restraints excluded: chain A residue 560 ILE Chi-restraints excluded: chain A residue 688 CYS Chi-restraints excluded: chain A residue 839 SER Chi-restraints excluded: chain A residue 856 ASP Chi-restraints excluded: chain A residue 865 THR Chi-restraints excluded: chain A residue 1229 VAL Chi-restraints excluded: chain A residue 1241 ASP Chi-restraints excluded: chain A residue 1359 LEU Chi-restraints excluded: chain A residue 1492 LEU Chi-restraints excluded: chain A residue 1750 THR Chi-restraints excluded: chain A residue 1870 THR Chi-restraints excluded: chain A residue 1884 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 130 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 chunk 31 optimal weight: 0.0770 chunk 3 optimal weight: 4.9990 chunk 66 optimal weight: 0.2980 chunk 71 optimal weight: 0.9990 chunk 144 optimal weight: 0.9990 chunk 113 optimal weight: 7.9990 chunk 121 optimal weight: 10.0000 chunk 126 optimal weight: 8.9990 overall best weight: 0.6342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.186296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.133224 restraints weight = 12772.460| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 2.50 r_work: 0.3176 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11951 Z= 0.107 Angle : 0.497 10.945 16317 Z= 0.254 Chirality : 0.038 0.180 1856 Planarity : 0.004 0.073 2062 Dihedral : 3.819 45.779 1744 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 1.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.90 % Allowed : 17.42 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.47 % 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: 1.65 (0.22), residues: 1508 helix: 2.12 (0.17), residues: 905 sheet: 0.87 (0.70), residues: 45 loop : -0.63 (0.25), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 981 TYR 0.015 0.001 TYR A 781 PHE 0.011 0.001 PHE A1382 TRP 0.011 0.001 TRP A 464 HIS 0.011 0.001 HIS A1707 Details of bonding type rmsd covalent geometry : bond 0.00219 (11946) covalent geometry : angle 0.49285 (16304) SS BOND : bond 0.00161 ( 2) SS BOND : angle 2.97629 ( 4) hydrogen bonds : bond 0.04829 ( 654) hydrogen bonds : angle 3.45912 ( 1917) link_ALPHA1-2 : bond 0.00881 ( 2) link_ALPHA1-2 : angle 1.67827 ( 6) link_BETA1-3 : bond 0.00319 ( 1) link_BETA1-3 : angle 2.17797 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3965.18 seconds wall clock time: 68 minutes 6.45 seconds (4086.45 seconds total)