Starting phenix.real_space_refine on Wed Mar 4 22:40:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pw7_13677/03_2026/7pw7_13677.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pw7_13677/03_2026/7pw7_13677.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7pw7_13677/03_2026/7pw7_13677.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pw7_13677/03_2026/7pw7_13677.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7pw7_13677/03_2026/7pw7_13677.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pw7_13677/03_2026/7pw7_13677.map" } resolution = 3.59 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= 0.003 sd= 0.065 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: 7 Type Number sf(0) Gaussians P 9 5.49 5 Mg 1 5.21 5 S 81 5.16 5 Cl 1 4.86 5 C 10404 2.51 5 N 2870 2.21 5 O 2861 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16227 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 9176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1295, 9176 Classifications: {'peptide': 1295} Incomplete info: {'truncation_to_alanine': 337} Link IDs: {'PTRANS': 35, 'TRANS': 1259} Chain breaks: 25 Unresolved non-hydrogen bonds: 926 Unresolved non-hydrogen angles: 1214 Unresolved non-hydrogen dihedrals: 672 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'UNK:plan-1': 121, 'PHE:plan': 5, 'ASN:plan1': 13, 'ARG:plan': 4, 'ASP:plan': 32, 'GLN:plan1': 9, 'TRP:plan': 2, 'GLU:plan': 44, 'TYR:plan': 2, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 560 Chain: "A" Number of atoms: 1423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1423 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 100} Link IDs: {'PTRANS': 7, 'TRANS': 208} Chain breaks: 6 Unresolved non-hydrogen bonds: 284 Unresolved non-hydrogen angles: 378 Unresolved non-hydrogen dihedrals: 202 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'UNK:plan-1': 42, 'GLU:plan': 7, 'ARG:plan': 3, 'ASP:plan': 6, 'GLN:plan1': 8, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 159 Chain: "A" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 196 Classifications: {'peptide': 38} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain breaks: 1 Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'UNK:plan-1': 16, 'GLU:plan': 3, 'TRP:plan': 1, 'PHE:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 2, 'ASN:plan1': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 66 Chain: "A" Number of atoms: 2929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 2929 Classifications: {'peptide': 395} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 72} Link IDs: {'PTRANS': 18, 'TRANS': 376} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 214 Unresolved non-hydrogen angles: 275 Unresolved non-hydrogen dihedrals: 154 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'UNK:plan-1': 16, 'ARG:plan': 3, 'GLU:plan': 16, 'ASN:plan1': 1, 'ASP:plan': 7, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 127 Chain: "C" Number of atoms: 2396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2396 Classifications: {'peptide': 307} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 16, 'TRANS': 290} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 118 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 8, 'ARG:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 70 Chain: "A" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 75 Unusual residues: {'88C': 1, 'IHP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb="MG MG C 602 " occ=0.00 Time building chain proxies: 3.66, per 1000 atoms: 0.23 Number of scatterers: 16227 At special positions: 0 Unit cell: (121.722, 108.102, 183.008, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Cl 1 17.00 S 81 16.00 P 9 15.00 Mg 1 11.99 O 2861 8.00 N 2870 7.00 C 10404 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.42 Conformation dependent library (CDL) restraints added in 731.1 milliseconds 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4342 Finding SS restraints... Secondary structure from input PDB file: 123 helices and 4 sheets defined 78.0% alpha, 3.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 147 through 156 removed outlier: 3.853A pdb=" N UNK A 154 " --> pdb=" O UNK A 150 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N UNK A 155 " --> pdb=" O UNK A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 170 Processing helix chain 'A' and resid 171 through 174 Processing helix chain 'A' and resid 192 through 198 Processing helix chain 'A' and resid 208 through 219 Processing helix chain 'A' and resid 230 through 244 removed outlier: 3.594A pdb=" N UNK A 234 " --> pdb=" O UNK A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 265 removed outlier: 3.948A pdb=" N UNK A 265 " --> pdb=" O UNK A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 285 removed outlier: 3.930A pdb=" N UNK A 284 " --> pdb=" O UNK A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 303 removed outlier: 3.989A pdb=" N UNK A 303 " --> pdb=" O UNK A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 323 removed outlier: 3.996A pdb=" N ASP A 317 " --> pdb=" O THR A 313 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N THR A 318 " --> pdb=" O ASN A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 347 removed outlier: 3.742A pdb=" N GLU A 347 " --> pdb=" O LEU A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 376 removed outlier: 3.988A pdb=" N GLY A 362 " --> pdb=" O THR A 358 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLN A 363 " --> pdb=" O THR A 359 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER A 376 " --> pdb=" O ALA A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 411 Processing helix chain 'A' and resid 428 through 444 removed outlier: 4.450A pdb=" N VAL A 432 " --> pdb=" O TYR A 428 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASN A 444 " --> pdb=" O VAL A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 467 removed outlier: 3.806A pdb=" N LEU A 467 " --> pdb=" O LEU A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 487 Processing helix chain 'A' and resid 493 through 511 removed outlier: 3.744A pdb=" N SER A 499 " --> pdb=" O ASP A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 522 removed outlier: 3.680A pdb=" N VAL A 520 " --> pdb=" O PRO A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 533 Processing helix chain 'A' and resid 538 through 554 removed outlier: 4.114A pdb=" N VAL A 542 " --> pdb=" O GLU A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 583 removed outlier: 3.974A pdb=" N THR A 563 " --> pdb=" O PRO A 559 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ALA A 564 " --> pdb=" O VAL A 560 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU A 583 " --> pdb=" O LEU A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 593 removed outlier: 4.150A pdb=" N ILE A 592 " --> pdb=" O CYS A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 598 Processing helix chain 'A' and resid 603 through 618 Processing helix chain 'A' and resid 618 through 623 Processing helix chain 'A' and resid 637 through 644 Processing helix chain 'A' and resid 647 through 651 removed outlier: 3.649A pdb=" N HIS A 650 " --> pdb=" O MET A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 657 removed outlier: 3.903A pdb=" N HIS A 656 " --> pdb=" O ASP A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 657 through 674 removed outlier: 4.088A pdb=" N GLN A 661 " --> pdb=" O PHE A 657 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARG A 674 " --> pdb=" O SER A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 675 through 679 Processing helix chain 'A' and resid 699 through 703 Processing helix chain 'A' and resid 706 through 720 removed outlier: 3.532A pdb=" N LYS A 720 " --> pdb=" O ILE A 716 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 743 removed outlier: 3.538A pdb=" N ARG A 743 " --> pdb=" O ALA A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 744 through 753 removed outlier: 7.055A pdb=" N THR A 747 " --> pdb=" O LYS A 744 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N TYR A 748 " --> pdb=" O SER A 745 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA A 749 " --> pdb=" O GLU A 746 " (cutoff:3.500A) Proline residue: A 750 - end of helix Processing helix chain 'A' and resid 754 through 768 removed outlier: 3.509A pdb=" N HIS A 758 " --> pdb=" O LEU A 754 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR A 768 " --> pdb=" O LEU A 764 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 786 removed outlier: 3.878A pdb=" N CYS A 776 " --> pdb=" O ASP A 772 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU A 786 " --> pdb=" O SER A 782 " (cutoff:3.500A) Processing helix chain 'A' and resid 791 through 806 removed outlier: 3.611A pdb=" N ARG A 797 " --> pdb=" O ASP A 793 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 823 Processing helix chain 'A' and resid 825 through 830 Processing helix chain 'A' and resid 835 through 851 Processing helix chain 'A' and resid 858 through 871 Processing helix chain 'A' and resid 882 through 890 Processing helix chain 'A' and resid 902 through 906 Processing helix chain 'A' and resid 908 through 927 Processing helix chain 'A' and resid 935 through 956 removed outlier: 3.662A pdb=" N THR A 939 " --> pdb=" O ARG A 935 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N PHE A 940 " --> pdb=" O ALA A 936 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU A 955 " --> pdb=" O ALA A 951 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASN A 956 " --> pdb=" O ALA A 952 " (cutoff:3.500A) Processing helix chain 'A' and resid 969 through 999 removed outlier: 3.824A pdb=" N HIS A 973 " --> pdb=" O ASN A 969 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLY A 974 " --> pdb=" O ASP A 970 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN A 977 " --> pdb=" O HIS A 973 " (cutoff:3.500A) Processing helix chain 'A' and resid 1009 through 1019 removed outlier: 3.859A pdb=" N THR A1018 " --> pdb=" O THR A1014 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASN A1019 " --> pdb=" O PHE A1015 " (cutoff:3.500A) Processing helix chain 'A' and resid 1019 through 1041 removed outlier: 4.534A pdb=" N LEU A1032 " --> pdb=" O THR A1028 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N SER A1033 " --> pdb=" O ARG A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1043 through 1058 removed outlier: 3.761A pdb=" N THR A1047 " --> pdb=" O GLN A1043 " (cutoff:3.500A) Processing helix chain 'A' and resid 1069 through 1083 Processing helix chain 'A' and resid 1085 through 1097 Processing helix chain 'A' and resid 1106 through 1116 removed outlier: 3.742A pdb=" N VAL A1110 " --> pdb=" O TRP A1106 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU A1115 " --> pdb=" O ALA A1111 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLY A1116 " --> pdb=" O GLN A1112 " (cutoff:3.500A) Processing helix chain 'A' and resid 1117 through 1134 Processing helix chain 'A' and resid 1143 through 1151 Processing helix chain 'A' and resid 1179 through 1197 removed outlier: 3.572A pdb=" N ILE A1197 " --> pdb=" O CYS A1193 " (cutoff:3.500A) Processing helix chain 'A' and resid 1199 through 1218 Processing helix chain 'A' and resid 1227 through 1240 removed outlier: 3.657A pdb=" N ILE A1231 " --> pdb=" O ASP A1227 " (cutoff:3.500A) Processing helix chain 'A' and resid 1241 through 1251 removed outlier: 3.636A pdb=" N GLU A1247 " --> pdb=" O VAL A1243 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU A1251 " --> pdb=" O GLU A1247 " (cutoff:3.500A) Processing helix chain 'A' and resid 1281 through 1305 removed outlier: 3.523A pdb=" N LEU A1285 " --> pdb=" O ASP A1281 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASN A1305 " --> pdb=" O ALA A1301 " (cutoff:3.500A) Processing helix chain 'A' and resid 1317 through 1331 removed outlier: 4.020A pdb=" N LYS A1322 " --> pdb=" O GLU A1318 " (cutoff:3.500A) Processing helix chain 'A' and resid 1332 through 1341 removed outlier: 3.790A pdb=" N THR A1341 " --> pdb=" O LEU A1337 " (cutoff:3.500A) Processing helix chain 'A' and resid 1347 through 1367 Processing helix chain 'A' and resid 1370 through 1374 Processing helix chain 'A' and resid 1378 through 1383 removed outlier: 3.564A pdb=" N ALA A1381 " --> pdb=" O PHE A1378 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG A1383 " --> pdb=" O GLU A1380 " (cutoff:3.500A) Processing helix chain 'A' and resid 1390 through 1407 removed outlier: 3.863A pdb=" N GLN A1395 " --> pdb=" O ARG A1391 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA A1396 " --> pdb=" O PRO A1392 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TYR A1402 " --> pdb=" O ARG A1398 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLN A1403 " --> pdb=" O TYR A1399 " (cutoff:3.500A) Processing helix chain 'A' and resid 1408 through 1410 No H-bonds generated for 'chain 'A' and resid 1408 through 1410' Processing helix chain 'A' and resid 1417 through 1434 Processing helix chain 'A' and resid 1437 through 1450 Processing helix chain 'A' and resid 1458 through 1467 removed outlier: 3.725A pdb=" N LEU A1462 " --> pdb=" O THR A1458 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL A1463 " --> pdb=" O ALA A1459 " (cutoff:3.500A) Processing helix chain 'A' and resid 1479 through 1494 Processing helix chain 'A' and resid 1496 through 1513 removed outlier: 3.943A pdb=" N LYS A1513 " --> pdb=" O ILE A1509 " (cutoff:3.500A) Processing helix chain 'A' and resid 1520 through 1535 Processing helix chain 'A' and resid 1535 through 1551 removed outlier: 5.509A pdb=" N GLY A1541 " --> pdb=" O LYS A1537 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N GLN A1542 " --> pdb=" O GLU A1538 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU A1543 " --> pdb=" O ILE A1539 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS A1544 " --> pdb=" O SER A1540 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N HIS A1551 " --> pdb=" O TYR A1547 " (cutoff:3.500A) Processing helix chain 'A' and resid 1559 through 1570 Processing helix chain 'A' and resid 1588 through 1592 removed outlier: 3.898A pdb=" N ILE A1592 " --> pdb=" O THR A1589 " (cutoff:3.500A) Processing helix chain 'A' and resid 1597 through 1612 removed outlier: 4.264A pdb=" N LEU A1601 " --> pdb=" O PRO A1597 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLY A1602 " --> pdb=" O ASP A1598 " (cutoff:3.500A) Processing helix chain 'A' and resid 1615 through 1637 removed outlier: 4.180A pdb=" N TRP A1619 " --> pdb=" O VAL A1615 " (cutoff:3.500A) Processing helix chain 'A' and resid 1647 through 1656 Processing helix chain 'A' and resid 1664 through 1674 removed outlier: 3.755A pdb=" N UNK A1674 " --> pdb=" O UNK A1670 " (cutoff:3.500A) Processing helix chain 'A' and resid 1704 through 1717 Processing helix chain 'A' and resid 1728 through 1740 Processing helix chain 'A' and resid 1742 through 1757 Processing helix chain 'A' and resid 1781 through 1799 removed outlier: 3.531A pdb=" N ILE A1785 " --> pdb=" O THR A1781 " (cutoff:3.500A) Processing helix chain 'A' and resid 1803 through 1811 removed outlier: 3.720A pdb=" N LEU A1807 " --> pdb=" O LEU A1803 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N HIS A1809 " --> pdb=" O GLN A1805 " (cutoff:3.500A) Processing helix chain 'A' and resid 1822 through 1829 Processing helix chain 'A' and resid 1835 through 1850 Processing helix chain 'A' and resid 1856 through 1865 removed outlier: 3.654A pdb=" N ALA A1860 " --> pdb=" O ILE A1856 " (cutoff:3.500A) Processing helix chain 'A' and resid 1924 through 1938 removed outlier: 3.969A pdb=" N CYS A1929 " --> pdb=" O MET A1925 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N TYR A1930 " --> pdb=" O MET A1926 " (cutoff:3.500A) Processing helix chain 'A' and resid 1941 through 1958 Processing helix chain 'A' and resid 1963 through 1978 removed outlier: 4.494A pdb=" N LEU A1978 " --> pdb=" O HIS A1974 " (cutoff:3.500A) Processing helix chain 'A' and resid 2007 through 2020 Processing helix chain 'A' and resid 2036 through 2044 Processing helix chain 'A' and resid 2046 through 2056 removed outlier: 4.059A pdb=" N LYS A2056 " --> pdb=" O LEU A2052 " (cutoff:3.500A) Processing helix chain 'A' and resid 2069 through 2083 removed outlier: 3.965A pdb=" N UNK A2083 " --> pdb=" O UNK A2079 " (cutoff:3.500A) Processing helix chain 'A' and resid 2160 through 2176 removed outlier: 3.509A pdb=" N ARG A2165 " --> pdb=" O HIS A2161 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N MET A2176 " --> pdb=" O ILE A2172 " (cutoff:3.500A) Processing helix chain 'A' and resid 2177 through 2178 No H-bonds generated for 'chain 'A' and resid 2177 through 2178' Processing helix chain 'A' and resid 2179 through 2183 removed outlier: 3.710A pdb=" N GLN A2183 " --> pdb=" O ILE A2180 " (cutoff:3.500A) Processing helix chain 'A' and resid 2214 through 2232 removed outlier: 3.775A pdb=" N TYR A2218 " --> pdb=" O LEU A2214 " (cutoff:3.500A) Processing helix chain 'A' and resid 2248 through 2265 removed outlier: 3.557A pdb=" N LYS A2256 " --> pdb=" O LEU A2252 " (cutoff:3.500A) Proline residue: A2259 - end of helix Processing helix chain 'A' and resid 2276 through 2289 removed outlier: 3.629A pdb=" N MET A2280 " --> pdb=" O PRO A2276 " (cutoff:3.500A) Processing helix chain 'A' and resid 2293 through 2304 removed outlier: 4.418A pdb=" N ALA A2297 " --> pdb=" O PRO A2293 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLU A2299 " --> pdb=" O LEU A2295 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU A2300 " --> pdb=" O LEU A2296 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N TRP A2301 " --> pdb=" O ALA A2297 " (cutoff:3.500A) Processing helix chain 'A' and resid 2306 through 2332 Processing helix chain 'A' and resid 2361 through 2365 removed outlier: 3.780A pdb=" N SER A2364 " --> pdb=" O LYS A2361 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU A2365 " --> pdb=" O GLY A2362 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2361 through 2365' Processing helix chain 'A' and resid 2376 through 2382 Processing helix chain 'A' and resid 2390 through 2406 removed outlier: 3.854A pdb=" N LEU A2394 " --> pdb=" O GLY A2390 " (cutoff:3.500A) Processing helix chain 'A' and resid 2406 through 2419 removed outlier: 4.023A pdb=" N LEU A2410 " --> pdb=" O GLY A2406 " (cutoff:3.500A) Processing helix chain 'A' and resid 3608 through 3622 Processing helix chain 'A' and resid 3632 through 3646 Processing helix chain 'A' and resid 3646 through 3651 removed outlier: 3.539A pdb=" N LEU A3650 " --> pdb=" O ASN A3646 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA A3651 " --> pdb=" O LEU A3647 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3646 through 3651' Processing helix chain 'A' and resid 3654 through 3658 Processing helix chain 'C' and resid 194 through 198 Processing helix chain 'C' and resid 216 through 226 Processing helix chain 'C' and resid 242 through 249 removed outlier: 4.016A pdb=" N GLU C 247 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ARG C 248 " --> pdb=" O GLU C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 284 removed outlier: 3.628A pdb=" N LEU C 279 " --> pdb=" O SER C 275 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ASN C 284 " --> pdb=" O ASP C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 314 removed outlier: 3.553A pdb=" N TYR C 299 " --> pdb=" O LEU C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 339 removed outlier: 3.552A pdb=" N MET C 339 " --> pdb=" O GLN C 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 375 through 379 Processing helix chain 'C' and resid 380 through 395 removed outlier: 3.524A pdb=" N GLN C 386 " --> pdb=" O ARG C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 412 removed outlier: 3.931A pdb=" N ASN C 412 " --> pdb=" O LEU C 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 418 through 422 Processing helix chain 'C' and resid 465 through 479 Processing helix chain 'C' and resid 491 through 508 removed outlier: 3.544A pdb=" N LYS C 508 " --> pdb=" O ASP C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 510 through 518 removed outlier: 3.608A pdb=" N LEU C 518 " --> pdb=" O GLU C 514 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2090 through 2091 removed outlier: 7.149A pdb=" N THR A2127 " --> pdb=" O LEU A2141 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N LEU A2141 " --> pdb=" O THR A2127 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N LEU A2141 " --> pdb=" O VAL A2124 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N VAL A2124 " --> pdb=" O LEU A2141 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N LEU A2143 " --> pdb=" O HIS A2122 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 2090 through 2091 removed outlier: 7.149A pdb=" N THR A2127 " --> pdb=" O LEU A2141 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N LEU A2141 " --> pdb=" O THR A2127 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TYR A2152 " --> pdb=" O LEU A2140 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 2212 through 2213 Processing sheet with id=AA4, first strand: chain 'C' and resid 181 through 184 removed outlier: 6.620A pdb=" N ILE C 256 " --> pdb=" O LEU C 183 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N LEU C 205 " --> pdb=" O VAL C 266 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N LEU C 268 " --> pdb=" O LEU C 205 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N VAL C 207 " --> pdb=" O LEU C 268 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N VAL C 206 " --> pdb=" O VAL C 317 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N ILE C 319 " --> pdb=" O VAL C 206 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N GLY C 208 " --> pdb=" O ILE C 319 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N VAL C 321 " --> pdb=" O GLY C 208 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N LEU C 210 " --> pdb=" O VAL C 321 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N PHE C 429 " --> pdb=" O LEU C 370 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N ASN C 372 " --> pdb=" O PHE C 429 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N VAL C 431 " --> pdb=" O ASN C 372 " (cutoff:3.500A) 1049 hydrogen bonds defined for protein. 3048 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.19 Time building geometry restraints manager: 1.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2544 1.31 - 1.44: 4312 1.44 - 1.57: 9517 1.57 - 1.69: 12 1.69 - 1.82: 128 Bond restraints: 16513 Sorted by residual: bond pdb=" C28 88C A3702 " pdb=" N30 88C A3702 " ideal model delta sigma weight residual 1.352 1.453 -0.101 2.00e-02 2.50e+03 2.57e+01 bond pdb=" C13 88C A3702 " pdb=" N12 88C A3702 " ideal model delta sigma weight residual 1.364 1.455 -0.091 2.00e-02 2.50e+03 2.09e+01 bond pdb=" C22 88C A3702 " pdb=" C23 88C A3702 " ideal model delta sigma weight residual 1.476 1.387 0.089 2.00e-02 2.50e+03 1.99e+01 bond pdb=" C17 88C A3702 " pdb=" C18 88C A3702 " ideal model delta sigma weight residual 1.480 1.391 0.089 2.00e-02 2.50e+03 1.97e+01 bond pdb=" C28 88C A3702 " pdb=" N27 88C A3702 " ideal model delta sigma weight residual 1.376 1.457 -0.081 2.00e-02 2.50e+03 1.63e+01 ... (remaining 16508 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.36: 22454 3.36 - 6.72: 89 6.72 - 10.08: 16 10.08 - 13.44: 0 13.44 - 16.80: 1 Bond angle restraints: 22560 Sorted by residual: angle pdb=" N VAL A 393 " pdb=" CA VAL A 393 " pdb=" C VAL A 393 " ideal model delta sigma weight residual 113.20 107.58 5.62 9.60e-01 1.09e+00 3.42e+01 angle pdb=" O07 88C A3702 " pdb=" S06 88C A3702 " pdb=" O08 88C A3702 " ideal model delta sigma weight residual 117.67 100.87 16.80 3.00e+00 1.11e-01 3.14e+01 angle pdb=" CA PRO C 272 " pdb=" N PRO C 272 " pdb=" CD PRO C 272 " ideal model delta sigma weight residual 112.00 105.58 6.42 1.40e+00 5.10e-01 2.10e+01 angle pdb=" N PRO C 272 " pdb=" CD PRO C 272 " pdb=" CG PRO C 272 " ideal model delta sigma weight residual 103.20 96.78 6.42 1.50e+00 4.44e-01 1.83e+01 angle pdb=" C ALA A 997 " pdb=" N TYR A 998 " pdb=" CA TYR A 998 " ideal model delta sigma weight residual 121.66 116.36 5.30 1.76e+00 3.23e-01 9.06e+00 ... (remaining 22555 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.89: 9626 33.89 - 67.78: 195 67.78 - 101.67: 25 101.67 - 135.55: 5 135.55 - 169.44: 2 Dihedral angle restraints: 9853 sinusoidal: 3244 harmonic: 6609 Sorted by residual: dihedral pdb=" C6 IHP A3701 " pdb=" C1 IHP A3701 " pdb=" C2 IHP A3701 " pdb=" O12 IHP A3701 " ideal model delta sinusoidal sigma weight residual 61.05 -108.39 169.44 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" C4 IHP A3701 " pdb=" C2 IHP A3701 " pdb=" C3 IHP A3701 " pdb=" O12 IHP A3701 " ideal model delta sinusoidal sigma weight residual 60.90 -162.83 -136.27 1 3.00e+01 1.11e-03 1.84e+01 dihedral pdb=" O12 IHP A3701 " pdb=" C2 IHP A3701 " pdb=" C3 IHP A3701 " pdb=" O13 IHP A3701 " ideal model delta sinusoidal sigma weight residual 64.08 -68.34 132.42 1 3.00e+01 1.11e-03 1.79e+01 ... (remaining 9850 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.008: 2780 1.008 - 2.016: 0 2.016 - 3.024: 0 3.024 - 4.031: 0 4.031 - 5.039: 3 Chirality restraints: 2783 Sorted by residual: chirality pdb=" C2 IHP A3701 " pdb=" C1 IHP A3701 " pdb=" C3 IHP A3701 " pdb=" O12 IHP A3701 " both_signs ideal model delta sigma weight residual False -2.52 2.52 -5.04 2.00e-01 2.50e+01 6.35e+02 chirality pdb=" C4 IHP A3701 " pdb=" C3 IHP A3701 " pdb=" C5 IHP A3701 " pdb=" O14 IHP A3701 " both_signs ideal model delta sigma weight residual False 2.48 -2.54 5.02 2.00e-01 2.50e+01 6.29e+02 chirality pdb=" C1 IHP A3701 " pdb=" C2 IHP A3701 " pdb=" C6 IHP A3701 " pdb=" O11 IHP A3701 " both_signs ideal model delta sigma weight residual False 2.32 -2.48 4.79 2.00e-01 2.50e+01 5.74e+02 ... (remaining 2780 not shown) Planarity restraints: 2806 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN C 271 " 0.056 5.00e-02 4.00e+02 8.22e-02 1.08e+01 pdb=" N PRO C 272 " -0.142 5.00e-02 4.00e+02 pdb=" CA PRO C 272 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO C 272 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A2417 " -0.021 2.00e-02 2.50e+03 1.89e-02 6.24e+00 pdb=" CG PHE A2417 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 PHE A2417 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE A2417 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A2417 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A2417 " -0.011 2.00e-02 2.50e+03 pdb=" CZ PHE A2417 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 421 " -0.013 2.00e-02 2.50e+03 1.39e-02 3.40e+00 pdb=" CG PHE C 421 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 PHE C 421 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE C 421 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE C 421 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE C 421 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE C 421 " -0.000 2.00e-02 2.50e+03 ... (remaining 2803 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 69 2.60 - 3.17: 13626 3.17 - 3.75: 24660 3.75 - 4.32: 30695 4.32 - 4.90: 53269 Nonbonded interactions: 122319 Sorted by model distance: nonbonded pdb=" O3B ATP C 601 " pdb="MG MG C 602 " model vdw 2.020 2.170 nonbonded pdb=" O2B ATP C 601 " pdb="MG MG C 602 " model vdw 2.172 2.170 nonbonded pdb=" O LEU C 367 " pdb=" ND2 ASN C 427 " model vdw 2.201 3.120 nonbonded pdb=" OG SER A1328 " pdb=" OG SER A1357 " model vdw 2.203 3.040 nonbonded pdb=" OH TYR A 669 " pdb=" OE1 GLU A 737 " model vdw 2.254 3.040 ... (remaining 122314 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 15.930 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 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 0.101 16514 Z= 0.163 Angle : 0.626 16.805 22560 Z= 0.327 Chirality : 0.167 5.039 2783 Planarity : 0.003 0.082 2806 Dihedral : 14.716 169.444 5511 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.00 % Allowed : 0.07 % Favored : 99.93 % 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: 1.95 (0.20), residues: 1994 helix: 2.57 (0.15), residues: 1258 sheet: 0.33 (0.60), residues: 75 loop : -1.22 (0.25), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A2405 TYR 0.029 0.001 TYR C 364 PHE 0.043 0.001 PHE A2417 TRP 0.024 0.001 TRP A1629 HIS 0.006 0.001 HIS A 536 Details of bonding type rmsd covalent geometry : bond 0.00322 (16513) covalent geometry : angle 0.62568 (22560) hydrogen bonds : bond 0.13925 ( 1045) hydrogen bonds : angle 4.23783 ( 3048) Misc. bond : bond 0.00008 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 0.628 Fit side-chains revert: symmetry clash REVERT: A 398 LEU cc_start: 0.9028 (mt) cc_final: 0.8776 (mt) REVERT: A 1950 MET cc_start: 0.6677 (tmm) cc_final: 0.6341 (ttt) outliers start: 0 outliers final: 0 residues processed: 144 average time/residue: 0.0949 time to fit residues: 23.2217 Evaluate side-chains 115 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 216 optimal weight: 0.0020 chunk 98 optimal weight: 0.6980 chunk 194 optimal weight: 0.7980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 30.0000 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 30.0000 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 chunk 200 optimal weight: 0.0970 chunk 212 optimal weight: 6.9990 overall best weight: 0.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.135448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.108039 restraints weight = 33860.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.110581 restraints weight = 19216.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.111947 restraints weight = 13052.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.113259 restraints weight = 10260.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.113842 restraints weight = 8520.311| |-----------------------------------------------------------------------------| r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.0867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 16514 Z= 0.100 Angle : 0.493 12.162 22560 Z= 0.235 Chirality : 0.036 0.178 2783 Planarity : 0.003 0.038 2806 Dihedral : 7.722 92.918 2457 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.34 % Allowed : 6.39 % Favored : 93.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.22 (0.20), residues: 1994 helix: 2.70 (0.15), residues: 1281 sheet: 0.67 (0.57), residues: 80 loop : -1.15 (0.26), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1838 TYR 0.023 0.001 TYR A 998 PHE 0.029 0.001 PHE A2417 TRP 0.040 0.001 TRP A1629 HIS 0.004 0.001 HIS A2337 Details of bonding type rmsd covalent geometry : bond 0.00209 (16513) covalent geometry : angle 0.49321 (22560) hydrogen bonds : bond 0.03524 ( 1045) hydrogen bonds : angle 3.33121 ( 3048) Misc. bond : bond 0.00063 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 115 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 398 LEU cc_start: 0.9101 (mt) cc_final: 0.8792 (mt) REVERT: A 1950 MET cc_start: 0.6628 (tmm) cc_final: 0.6373 (ttt) outliers start: 5 outliers final: 2 residues processed: 117 average time/residue: 0.0954 time to fit residues: 19.3944 Evaluate side-chains 109 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 107 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 3661 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 166 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 21 optimal weight: 6.9990 chunk 37 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 23 optimal weight: 0.0370 chunk 70 optimal weight: 1.9990 chunk 202 optimal weight: 3.9990 chunk 137 optimal weight: 1.9990 chunk 10 optimal weight: 30.0000 chunk 3 optimal weight: 50.0000 overall best weight: 2.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 706 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 881 ASN C 213 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.127563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.099420 restraints weight = 34297.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.101800 restraints weight = 19735.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.103396 restraints weight = 13632.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.104243 restraints weight = 10651.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.105028 restraints weight = 9152.891| |-----------------------------------------------------------------------------| r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16514 Z= 0.184 Angle : 0.590 10.853 22560 Z= 0.288 Chirality : 0.040 0.186 2783 Planarity : 0.004 0.041 2806 Dihedral : 7.745 95.063 2457 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 0.76 % Allowed : 9.83 % Favored : 89.42 % 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: 1.70 (0.20), residues: 1994 helix: 2.23 (0.15), residues: 1291 sheet: 0.63 (0.57), residues: 80 loop : -1.27 (0.26), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A2393 TYR 0.020 0.002 TYR A 998 PHE 0.022 0.002 PHE A2417 TRP 0.021 0.002 TRP A1629 HIS 0.010 0.001 HIS A2352 Details of bonding type rmsd covalent geometry : bond 0.00446 (16513) covalent geometry : angle 0.58969 (22560) hydrogen bonds : bond 0.04501 ( 1045) hydrogen bonds : angle 3.52973 ( 3048) Misc. bond : bond 0.00127 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 113 time to evaluate : 0.592 Fit side-chains revert: symmetry clash REVERT: A 398 LEU cc_start: 0.8999 (mt) cc_final: 0.8706 (mt) REVERT: A 405 PHE cc_start: 0.9052 (t80) cc_final: 0.8603 (t80) REVERT: A 1183 ILE cc_start: 0.8076 (mm) cc_final: 0.7867 (mm) REVERT: A 1950 MET cc_start: 0.6832 (tmm) cc_final: 0.6582 (ttt) REVERT: C 457 LEU cc_start: 0.7207 (OUTLIER) cc_final: 0.6931 (pp) outliers start: 11 outliers final: 8 residues processed: 120 average time/residue: 0.0964 time to fit residues: 19.8860 Evaluate side-chains 110 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 101 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 1259 LEU Chi-restraints excluded: chain A residue 1565 ILE Chi-restraints excluded: chain A residue 1835 VAL Chi-restraints excluded: chain A residue 2131 LEU Chi-restraints excluded: chain A residue 3661 VAL Chi-restraints excluded: chain C residue 395 MET Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 490 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 107 optimal weight: 0.4980 chunk 42 optimal weight: 0.9990 chunk 202 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 140 optimal weight: 4.9990 chunk 28 optimal weight: 0.0010 chunk 136 optimal weight: 0.8980 chunk 127 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 chunk 177 optimal weight: 0.3980 chunk 118 optimal weight: 0.7980 overall best weight: 0.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 578 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.130926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.103017 restraints weight = 33677.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.105639 restraints weight = 18399.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.107376 restraints weight = 12371.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.108324 restraints weight = 9461.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.109172 restraints weight = 8010.747| |-----------------------------------------------------------------------------| r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 16514 Z= 0.093 Angle : 0.473 11.019 22560 Z= 0.227 Chirality : 0.036 0.174 2783 Planarity : 0.003 0.038 2806 Dihedral : 7.356 91.685 2457 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.17 % Allowed : 10.03 % Favored : 88.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.07 (0.20), residues: 1994 helix: 2.53 (0.15), residues: 1290 sheet: 0.84 (0.57), residues: 80 loop : -1.15 (0.26), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1838 TYR 0.018 0.001 TYR A 998 PHE 0.020 0.001 PHE A2417 TRP 0.017 0.001 TRP A1629 HIS 0.004 0.001 HIS A2352 Details of bonding type rmsd covalent geometry : bond 0.00200 (16513) covalent geometry : angle 0.47274 (22560) hydrogen bonds : bond 0.03110 ( 1045) hydrogen bonds : angle 3.17505 ( 3048) Misc. bond : bond 0.00042 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 112 time to evaluate : 0.588 Fit side-chains revert: symmetry clash REVERT: A 405 PHE cc_start: 0.9092 (t80) cc_final: 0.8655 (t80) REVERT: A 849 MET cc_start: 0.8558 (ptp) cc_final: 0.8345 (ptp) REVERT: A 1183 ILE cc_start: 0.8034 (mm) cc_final: 0.7815 (mm) REVERT: A 1950 MET cc_start: 0.6698 (tmm) cc_final: 0.6448 (ttt) outliers start: 17 outliers final: 10 residues processed: 123 average time/residue: 0.0918 time to fit residues: 19.6020 Evaluate side-chains 115 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 105 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 1056 THR Chi-restraints excluded: chain A residue 1291 VAL Chi-restraints excluded: chain A residue 1565 ILE Chi-restraints excluded: chain A residue 2131 LEU Chi-restraints excluded: chain A residue 3661 VAL Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 314 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 127 optimal weight: 1.9990 chunk 133 optimal weight: 6.9990 chunk 144 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 139 optimal weight: 0.0770 chunk 153 optimal weight: 8.9990 chunk 205 optimal weight: 8.9990 chunk 19 optimal weight: 0.9980 chunk 118 optimal weight: 0.0770 chunk 170 optimal weight: 0.7980 chunk 210 optimal weight: 0.5980 overall best weight: 0.5096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 303 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.131193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.103369 restraints weight = 33816.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.105993 restraints weight = 18614.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.107740 restraints weight = 12484.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.108642 restraints weight = 9537.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.109507 restraints weight = 8100.591| |-----------------------------------------------------------------------------| r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 16514 Z= 0.089 Angle : 0.466 10.884 22560 Z= 0.222 Chirality : 0.036 0.168 2783 Planarity : 0.003 0.038 2806 Dihedral : 7.159 89.838 2457 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.44 % Allowed : 10.17 % Favored : 88.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.18 (0.20), residues: 1994 helix: 2.60 (0.15), residues: 1293 sheet: 0.97 (0.57), residues: 80 loop : -1.10 (0.26), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1391 TYR 0.019 0.001 TYR A 998 PHE 0.017 0.001 PHE A2417 TRP 0.024 0.001 TRP A1393 HIS 0.005 0.001 HIS A2352 Details of bonding type rmsd covalent geometry : bond 0.00196 (16513) covalent geometry : angle 0.46573 (22560) hydrogen bonds : bond 0.02915 ( 1045) hydrogen bonds : angle 3.08138 ( 3048) Misc. bond : bond 0.00049 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 113 time to evaluate : 0.533 Fit side-chains revert: symmetry clash REVERT: A 405 PHE cc_start: 0.9093 (t80) cc_final: 0.8653 (t80) REVERT: A 1183 ILE cc_start: 0.8078 (mm) cc_final: 0.7853 (mm) REVERT: A 1950 MET cc_start: 0.6690 (tmm) cc_final: 0.6459 (ttt) REVERT: C 457 LEU cc_start: 0.7256 (OUTLIER) cc_final: 0.6962 (pp) outliers start: 21 outliers final: 15 residues processed: 128 average time/residue: 0.0901 time to fit residues: 20.0725 Evaluate side-chains 123 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 107 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 563 THR Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 1291 VAL Chi-restraints excluded: chain A residue 1565 ILE Chi-restraints excluded: chain A residue 1790 LEU Chi-restraints excluded: chain A residue 1803 LEU Chi-restraints excluded: chain A residue 2131 LEU Chi-restraints excluded: chain A residue 3661 VAL Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 395 MET Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 490 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 207 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 15 optimal weight: 20.0000 chunk 176 optimal weight: 4.9990 chunk 154 optimal weight: 9.9990 chunk 120 optimal weight: 1.9990 chunk 164 optimal weight: 0.8980 chunk 63 optimal weight: 0.6980 chunk 35 optimal weight: 7.9990 chunk 175 optimal weight: 1.9990 chunk 202 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 303 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.128581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.100669 restraints weight = 33900.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.103209 restraints weight = 18731.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.104894 restraints weight = 12624.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.105834 restraints weight = 9713.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.106672 restraints weight = 8244.984| |-----------------------------------------------------------------------------| r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 16514 Z= 0.131 Angle : 0.506 10.837 22560 Z= 0.243 Chirality : 0.037 0.168 2783 Planarity : 0.003 0.038 2806 Dihedral : 7.114 88.245 2457 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.79 % Allowed : 10.72 % Favored : 87.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.02 (0.20), residues: 1994 helix: 2.49 (0.15), residues: 1287 sheet: 0.85 (0.58), residues: 80 loop : -1.14 (0.26), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A2393 TYR 0.019 0.001 TYR A 998 PHE 0.016 0.001 PHE A 940 TRP 0.023 0.001 TRP A1393 HIS 0.007 0.001 HIS A2352 Details of bonding type rmsd covalent geometry : bond 0.00317 (16513) covalent geometry : angle 0.50591 (22560) hydrogen bonds : bond 0.03475 ( 1045) hydrogen bonds : angle 3.20120 ( 3048) Misc. bond : bond 0.00073 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 109 time to evaluate : 0.519 Fit side-chains revert: symmetry clash REVERT: A 405 PHE cc_start: 0.9084 (t80) cc_final: 0.8613 (t80) REVERT: A 849 MET cc_start: 0.8419 (ptp) cc_final: 0.8116 (ptp) REVERT: A 1183 ILE cc_start: 0.8081 (mm) cc_final: 0.7875 (mm) REVERT: C 457 LEU cc_start: 0.7315 (OUTLIER) cc_final: 0.7001 (pp) outliers start: 26 outliers final: 21 residues processed: 127 average time/residue: 0.0915 time to fit residues: 20.0235 Evaluate side-chains 126 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 104 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 563 THR Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 1001 CYS Chi-restraints excluded: chain A residue 1040 LEU Chi-restraints excluded: chain A residue 1056 THR Chi-restraints excluded: chain A residue 1099 ILE Chi-restraints excluded: chain A residue 1259 LEU Chi-restraints excluded: chain A residue 1291 VAL Chi-restraints excluded: chain A residue 1565 ILE Chi-restraints excluded: chain A residue 1790 LEU Chi-restraints excluded: chain A residue 2131 LEU Chi-restraints excluded: chain A residue 2196 THR Chi-restraints excluded: chain A residue 3661 VAL Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 395 MET Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 490 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 65 optimal weight: 0.0980 chunk 169 optimal weight: 1.9990 chunk 6 optimal weight: 50.0000 chunk 70 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 31 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 18 optimal weight: 8.9990 chunk 89 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 123 optimal weight: 0.7980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1447 GLN C 303 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.129074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.101277 restraints weight = 33497.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.103822 restraints weight = 18477.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.105531 restraints weight = 12443.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.106638 restraints weight = 9546.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.107151 restraints weight = 7989.998| |-----------------------------------------------------------------------------| r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16514 Z= 0.108 Angle : 0.492 10.785 22560 Z= 0.236 Chirality : 0.037 0.185 2783 Planarity : 0.003 0.038 2806 Dihedral : 7.008 86.867 2457 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.92 % Allowed : 11.13 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.11 (0.20), residues: 1994 helix: 2.57 (0.15), residues: 1286 sheet: 0.93 (0.58), residues: 80 loop : -1.15 (0.26), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 885 TYR 0.018 0.001 TYR A 998 PHE 0.015 0.001 PHE A2417 TRP 0.016 0.001 TRP A1393 HIS 0.005 0.001 HIS A2352 Details of bonding type rmsd covalent geometry : bond 0.00254 (16513) covalent geometry : angle 0.49238 (22560) hydrogen bonds : bond 0.03197 ( 1045) hydrogen bonds : angle 3.14910 ( 3048) Misc. bond : bond 0.00043 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 112 time to evaluate : 0.605 Fit side-chains revert: symmetry clash REVERT: A 405 PHE cc_start: 0.9080 (t80) cc_final: 0.8574 (t80) REVERT: A 849 MET cc_start: 0.8419 (ptp) cc_final: 0.8155 (ptp) REVERT: A 1183 ILE cc_start: 0.8072 (mm) cc_final: 0.7871 (mm) REVERT: C 457 LEU cc_start: 0.7265 (OUTLIER) cc_final: 0.6934 (pp) outliers start: 28 outliers final: 21 residues processed: 133 average time/residue: 0.0909 time to fit residues: 20.9728 Evaluate side-chains 130 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 108 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 563 THR Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 1001 CYS Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1056 THR Chi-restraints excluded: chain A residue 1099 ILE Chi-restraints excluded: chain A residue 1259 LEU Chi-restraints excluded: chain A residue 1291 VAL Chi-restraints excluded: chain A residue 1354 LEU Chi-restraints excluded: chain A residue 1565 ILE Chi-restraints excluded: chain A residue 1790 LEU Chi-restraints excluded: chain A residue 1803 LEU Chi-restraints excluded: chain A residue 2131 LEU Chi-restraints excluded: chain A residue 2196 THR Chi-restraints excluded: chain A residue 3661 VAL Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 395 MET Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 490 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 30 optimal weight: 1.9990 chunk 172 optimal weight: 0.9990 chunk 10 optimal weight: 30.0000 chunk 59 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 63 optimal weight: 4.9990 chunk 104 optimal weight: 0.7980 chunk 46 optimal weight: 4.9990 chunk 67 optimal weight: 0.9990 chunk 109 optimal weight: 1.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 767 ASN C 303 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.128581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.100588 restraints weight = 33924.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.103208 restraints weight = 18722.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.104900 restraints weight = 12589.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.105995 restraints weight = 9682.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.106609 restraints weight = 8122.127| |-----------------------------------------------------------------------------| r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 16514 Z= 0.119 Angle : 0.508 10.069 22560 Z= 0.246 Chirality : 0.037 0.217 2783 Planarity : 0.003 0.038 2806 Dihedral : 6.983 85.698 2457 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.92 % Allowed : 11.62 % Favored : 86.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.07 (0.20), residues: 1994 helix: 2.55 (0.15), residues: 1283 sheet: 1.03 (0.57), residues: 80 loop : -1.17 (0.26), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 885 TYR 0.019 0.001 TYR A 998 PHE 0.014 0.001 PHE A2417 TRP 0.030 0.001 TRP A1393 HIS 0.005 0.001 HIS A2352 Details of bonding type rmsd covalent geometry : bond 0.00286 (16513) covalent geometry : angle 0.50780 (22560) hydrogen bonds : bond 0.03340 ( 1045) hydrogen bonds : angle 3.20083 ( 3048) Misc. bond : bond 0.00050 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 112 time to evaluate : 0.628 Fit side-chains revert: symmetry clash REVERT: A 405 PHE cc_start: 0.9096 (t80) cc_final: 0.8632 (t80) REVERT: A 963 GLN cc_start: 0.7967 (OUTLIER) cc_final: 0.7723 (pm20) REVERT: A 1407 LEU cc_start: 0.7469 (mt) cc_final: 0.7254 (mt) REVERT: C 457 LEU cc_start: 0.7287 (OUTLIER) cc_final: 0.6960 (pp) outliers start: 28 outliers final: 23 residues processed: 132 average time/residue: 0.0911 time to fit residues: 20.9712 Evaluate side-chains 130 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 105 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 563 THR Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 963 GLN Chi-restraints excluded: chain A residue 1001 CYS Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1056 THR Chi-restraints excluded: chain A residue 1099 ILE Chi-restraints excluded: chain A residue 1259 LEU Chi-restraints excluded: chain A residue 1291 VAL Chi-restraints excluded: chain A residue 1565 ILE Chi-restraints excluded: chain A residue 1790 LEU Chi-restraints excluded: chain A residue 1803 LEU Chi-restraints excluded: chain A residue 2131 LEU Chi-restraints excluded: chain A residue 2196 THR Chi-restraints excluded: chain A residue 2209 ASP Chi-restraints excluded: chain A residue 3661 VAL Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 395 MET Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 490 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 75 optimal weight: 0.9990 chunk 112 optimal weight: 2.9990 chunk 27 optimal weight: 7.9990 chunk 104 optimal weight: 0.9980 chunk 18 optimal weight: 8.9990 chunk 203 optimal weight: 0.5980 chunk 179 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 105 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 217 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1460 GLN C 303 GLN ** C 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.128234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.100290 restraints weight = 33792.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.102815 restraints weight = 18986.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.104500 restraints weight = 12927.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.105419 restraints weight = 9993.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.106246 restraints weight = 8524.888| |-----------------------------------------------------------------------------| r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 16514 Z= 0.107 Angle : 0.492 9.830 22560 Z= 0.240 Chirality : 0.037 0.240 2783 Planarity : 0.003 0.040 2806 Dihedral : 6.936 89.701 2457 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.72 % Allowed : 12.30 % Favored : 85.98 % 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: 2.17 (0.20), residues: 1994 helix: 2.63 (0.15), residues: 1283 sheet: 1.12 (0.57), residues: 80 loop : -1.15 (0.26), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 885 TYR 0.018 0.001 TYR A 998 PHE 0.015 0.001 PHE A2417 TRP 0.024 0.001 TRP A1393 HIS 0.005 0.001 HIS A2352 Details of bonding type rmsd covalent geometry : bond 0.00255 (16513) covalent geometry : angle 0.49152 (22560) hydrogen bonds : bond 0.03174 ( 1045) hydrogen bonds : angle 3.14979 ( 3048) Misc. bond : bond 0.00042 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 114 time to evaluate : 0.569 Fit side-chains revert: symmetry clash REVERT: A 405 PHE cc_start: 0.9107 (t80) cc_final: 0.8670 (t80) REVERT: A 963 GLN cc_start: 0.7946 (OUTLIER) cc_final: 0.7710 (pm20) REVERT: A 1407 LEU cc_start: 0.7464 (mt) cc_final: 0.7244 (mt) REVERT: C 457 LEU cc_start: 0.7315 (OUTLIER) cc_final: 0.6989 (pp) outliers start: 25 outliers final: 19 residues processed: 132 average time/residue: 0.0917 time to fit residues: 21.1503 Evaluate side-chains 129 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 108 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 563 THR Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 963 GLN Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1056 THR Chi-restraints excluded: chain A residue 1259 LEU Chi-restraints excluded: chain A residue 1291 VAL Chi-restraints excluded: chain A residue 1565 ILE Chi-restraints excluded: chain A residue 1790 LEU Chi-restraints excluded: chain A residue 1803 LEU Chi-restraints excluded: chain A residue 2131 LEU Chi-restraints excluded: chain A residue 2196 THR Chi-restraints excluded: chain A residue 2209 ASP Chi-restraints excluded: chain A residue 3661 VAL Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 490 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 12 optimal weight: 10.0000 chunk 57 optimal weight: 0.9990 chunk 170 optimal weight: 3.9990 chunk 216 optimal weight: 0.0060 chunk 86 optimal weight: 0.6980 chunk 70 optimal weight: 3.9990 chunk 115 optimal weight: 0.9980 chunk 167 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 191 optimal weight: 0.9990 chunk 202 optimal weight: 4.9990 overall best weight: 0.7400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1460 GLN ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.128471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.100389 restraints weight = 34089.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.102928 restraints weight = 19367.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.104652 restraints weight = 13251.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.105784 restraints weight = 10239.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.106372 restraints weight = 8613.298| |-----------------------------------------------------------------------------| r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.076 16514 Z= 0.101 Angle : 0.489 10.992 22560 Z= 0.240 Chirality : 0.037 0.220 2783 Planarity : 0.003 0.040 2806 Dihedral : 6.789 87.272 2457 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.72 % Allowed : 12.23 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.21 (0.20), residues: 1994 helix: 2.64 (0.15), residues: 1283 sheet: 1.16 (0.58), residues: 80 loop : -1.09 (0.26), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 885 TYR 0.019 0.001 TYR A 998 PHE 0.016 0.001 PHE A2417 TRP 0.023 0.001 TRP A1393 HIS 0.005 0.001 HIS A2352 Details of bonding type rmsd covalent geometry : bond 0.00235 (16513) covalent geometry : angle 0.48922 (22560) hydrogen bonds : bond 0.03033 ( 1045) hydrogen bonds : angle 3.13368 ( 3048) Misc. bond : bond 0.00041 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 108 time to evaluate : 0.600 Fit side-chains revert: symmetry clash REVERT: A 405 PHE cc_start: 0.9110 (t80) cc_final: 0.8688 (t80) REVERT: A 963 GLN cc_start: 0.7962 (OUTLIER) cc_final: 0.7728 (pm20) REVERT: A 1407 LEU cc_start: 0.7421 (mt) cc_final: 0.7204 (mt) REVERT: C 457 LEU cc_start: 0.7339 (OUTLIER) cc_final: 0.7007 (pp) outliers start: 25 outliers final: 21 residues processed: 126 average time/residue: 0.0925 time to fit residues: 20.4435 Evaluate side-chains 130 residues out of total 1833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 107 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 563 THR Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 963 GLN Chi-restraints excluded: chain A residue 1001 CYS Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1056 THR Chi-restraints excluded: chain A residue 1099 ILE Chi-restraints excluded: chain A residue 1259 LEU Chi-restraints excluded: chain A residue 1291 VAL Chi-restraints excluded: chain A residue 1565 ILE Chi-restraints excluded: chain A residue 1790 LEU Chi-restraints excluded: chain A residue 1803 LEU Chi-restraints excluded: chain A residue 2131 LEU Chi-restraints excluded: chain A residue 2196 THR Chi-restraints excluded: chain A residue 2209 ASP Chi-restraints excluded: chain A residue 3661 VAL Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 490 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 105 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 96 optimal weight: 0.2980 chunk 23 optimal weight: 0.0370 chunk 9 optimal weight: 50.0000 chunk 110 optimal weight: 0.7980 chunk 175 optimal weight: 4.9990 chunk 181 optimal weight: 0.9980 chunk 63 optimal weight: 0.9980 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 427 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.128986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.100982 restraints weight = 34041.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.103539 restraints weight = 19334.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.105248 restraints weight = 13239.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.106391 restraints weight = 10226.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.107136 restraints weight = 8549.233| |-----------------------------------------------------------------------------| r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.069 16514 Z= 0.094 Angle : 0.482 9.784 22560 Z= 0.234 Chirality : 0.037 0.188 2783 Planarity : 0.003 0.040 2806 Dihedral : 6.590 85.254 2457 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.65 % Allowed : 12.51 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.30 (0.20), residues: 1994 helix: 2.71 (0.15), residues: 1283 sheet: 1.19 (0.58), residues: 80 loop : -1.04 (0.26), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 885 TYR 0.019 0.001 TYR A 998 PHE 0.016 0.001 PHE A2417 TRP 0.027 0.001 TRP A2425 HIS 0.004 0.000 HIS A2352 Details of bonding type rmsd covalent geometry : bond 0.00214 (16513) covalent geometry : angle 0.48164 (22560) hydrogen bonds : bond 0.02869 ( 1045) hydrogen bonds : angle 3.08931 ( 3048) Misc. bond : bond 0.00024 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2708.30 seconds wall clock time: 47 minutes 23.35 seconds (2843.35 seconds total)