Starting phenix.real_space_refine on Tue Dec 31 02:09:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ojj_12953/12_2024/7ojj_12953.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ojj_12953/12_2024/7ojj_12953.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ojj_12953/12_2024/7ojj_12953.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ojj_12953/12_2024/7ojj_12953.map" model { file = "/net/cci-nas-00/data/ceres_data/7ojj_12953/12_2024/7ojj_12953.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ojj_12953/12_2024/7ojj_12953.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 Mg 1 5.21 5 S 89 5.16 5 C 9131 2.51 5 N 2416 2.21 5 O 2692 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 14330 Number of models: 1 Model: "" Number of chains: 2 Chain: "L" Number of atoms: 14328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1785, 14328 Classifications: {'peptide': 1785} Link IDs: {'PTRANS': 57, 'TRANS': 1727} Unresolved chain links: 1 Chain breaks: 10 Unresolved chain link angles: 3 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 9.61, per 1000 atoms: 0.67 Number of scatterers: 14330 At special positions: 0 Unit cell: (114.84, 133.11, 160.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 89 16.00 Mg 1 11.99 O 2692 8.00 N 2416 7.00 C 9131 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.26 Conformation dependent library (CDL) restraints added in 2.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN L2301 " pdb="ZN ZN L2301 " - pdb=" NE2 HIS L 316 " 3522 Ramachandran restraints generated. 1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3408 Finding SS restraints... Secondary structure from input PDB file: 83 helices and 12 sheets defined 54.6% alpha, 5.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.30 Creating SS restraints... Processing helix chain 'L' and resid 1 through 16 removed outlier: 3.833A pdb=" N LEU L 16 " --> pdb=" O VAL L 12 " (cutoff:3.500A) Processing helix chain 'L' and resid 22 through 30 Processing helix chain 'L' and resid 34 through 59 Processing helix chain 'L' and resid 68 through 75 Processing helix chain 'L' and resid 112 through 131 removed outlier: 3.722A pdb=" N TYR L 116 " --> pdb=" O PHE L 112 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LEU L 126 " --> pdb=" O LYS L 122 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ASP L 129 " --> pdb=" O GLN L 125 " (cutoff:3.500A) Processing helix chain 'L' and resid 132 through 134 No H-bonds generated for 'chain 'L' and resid 132 through 134' Processing helix chain 'L' and resid 153 through 168 removed outlier: 3.720A pdb=" N THR L 163 " --> pdb=" O LYS L 159 " (cutoff:3.500A) Processing helix chain 'L' and resid 170 through 176 Processing helix chain 'L' and resid 179 through 188 removed outlier: 3.606A pdb=" N TYR L 183 " --> pdb=" O GLU L 179 " (cutoff:3.500A) Processing helix chain 'L' and resid 200 through 206 Processing helix chain 'L' and resid 211 through 222 Processing helix chain 'L' and resid 232 through 251 removed outlier: 4.040A pdb=" N LEU L 236 " --> pdb=" O HIS L 232 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS L 251 " --> pdb=" O ASN L 247 " (cutoff:3.500A) Processing helix chain 'L' and resid 262 through 272 Processing helix chain 'L' and resid 284 through 293 removed outlier: 3.602A pdb=" N LYS L 293 " --> pdb=" O ILE L 289 " (cutoff:3.500A) Processing helix chain 'L' and resid 296 through 304 removed outlier: 3.627A pdb=" N TYR L 303 " --> pdb=" O LEU L 299 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA L 304 " --> pdb=" O ARG L 300 " (cutoff:3.500A) Processing helix chain 'L' and resid 311 through 315 removed outlier: 3.627A pdb=" N ARG L 314 " --> pdb=" O GLY L 311 " (cutoff:3.500A) Processing helix chain 'L' and resid 321 through 335 removed outlier: 3.952A pdb=" N TYR L 325 " --> pdb=" O CYS L 321 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N SER L 335 " --> pdb=" O ASN L 331 " (cutoff:3.500A) Processing helix chain 'L' and resid 345 through 365 Processing helix chain 'L' and resid 385 through 405 Processing helix chain 'L' and resid 412 through 420 Processing helix chain 'L' and resid 421 through 432 Processing helix chain 'L' and resid 445 through 449 removed outlier: 3.902A pdb=" N VAL L 448 " --> pdb=" O ASN L 445 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ILE L 449 " --> pdb=" O MET L 446 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 445 through 449' Processing helix chain 'L' and resid 452 through 459 Processing helix chain 'L' and resid 492 through 507 removed outlier: 3.627A pdb=" N ARG L 496 " --> pdb=" O THR L 492 " (cutoff:3.500A) Processing helix chain 'L' and resid 580 through 584 removed outlier: 4.204A pdb=" N ALA L 583 " --> pdb=" O TYR L 580 " (cutoff:3.500A) Processing helix chain 'L' and resid 587 through 599 removed outlier: 3.791A pdb=" N GLN L 591 " --> pdb=" O ALA L 587 " (cutoff:3.500A) Processing helix chain 'L' and resid 604 through 609 removed outlier: 5.367A pdb=" N GLU L 609 " --> pdb=" O GLU L 606 " (cutoff:3.500A) Processing helix chain 'L' and resid 610 through 628 removed outlier: 4.237A pdb=" N LYS L 619 " --> pdb=" O ASN L 615 " (cutoff:3.500A) Processing helix chain 'L' and resid 630 through 639 Processing helix chain 'L' and resid 639 through 649 removed outlier: 3.979A pdb=" N PHE L 643 " --> pdb=" O ASN L 639 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL L 648 " --> pdb=" O ILE L 644 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N SER L 649 " --> pdb=" O MET L 645 " (cutoff:3.500A) Processing helix chain 'L' and resid 656 through 661 removed outlier: 3.942A pdb=" N ARG L 661 " --> pdb=" O ASP L 658 " (cutoff:3.500A) Processing helix chain 'L' and resid 668 through 684 Processing helix chain 'L' and resid 691 through 704 removed outlier: 3.875A pdb=" N ARG L 695 " --> pdb=" O MET L 691 " (cutoff:3.500A) Processing helix chain 'L' and resid 705 through 709 removed outlier: 3.622A pdb=" N ILE L 709 " --> pdb=" O CYS L 706 " (cutoff:3.500A) Processing helix chain 'L' and resid 718 through 729 removed outlier: 4.176A pdb=" N LYS L 722 " --> pdb=" O THR L 718 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N CYS L 723 " --> pdb=" O ASP L 719 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N PHE L 724 " --> pdb=" O GLN L 720 " (cutoff:3.500A) Processing helix chain 'L' and resid 729 through 734 removed outlier: 3.635A pdb=" N GLU L 733 " --> pdb=" O GLU L 729 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N PHE L 734 " --> pdb=" O PRO L 730 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 729 through 734' Processing helix chain 'L' and resid 746 through 761 removed outlier: 4.024A pdb=" N LEU L 750 " --> pdb=" O THR L 746 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU L 761 " --> pdb=" O ALA L 757 " (cutoff:3.500A) Processing helix chain 'L' and resid 780 through 792 Processing helix chain 'L' and resid 798 through 803 Processing helix chain 'L' and resid 818 through 823 removed outlier: 3.818A pdb=" N SER L 823 " --> pdb=" O ASP L 820 " (cutoff:3.500A) Processing helix chain 'L' and resid 842 through 859 removed outlier: 3.700A pdb=" N THR L 847 " --> pdb=" O PHE L 843 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ALA L 848 " --> pdb=" O ASN L 844 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU L 849 " --> pdb=" O LYS L 845 " (cutoff:3.500A) Processing helix chain 'L' and resid 872 through 884 removed outlier: 3.734A pdb=" N VAL L 883 " --> pdb=" O MET L 879 " (cutoff:3.500A) Processing helix chain 'L' and resid 897 through 904 Processing helix chain 'L' and resid 908 through 923 removed outlier: 3.819A pdb=" N ASP L 923 " --> pdb=" O GLU L 919 " (cutoff:3.500A) Processing helix chain 'L' and resid 1062 through 1067 removed outlier: 3.876A pdb=" N VAL L1067 " --> pdb=" O LEU L1063 " (cutoff:3.500A) Processing helix chain 'L' and resid 1074 through 1084 removed outlier: 4.072A pdb=" N ALA L1078 " --> pdb=" O SER L1074 " (cutoff:3.500A) Processing helix chain 'L' and resid 1093 through 1098 removed outlier: 3.738A pdb=" N PHE L1098 " --> pdb=" O LYS L1094 " (cutoff:3.500A) Processing helix chain 'L' and resid 1137 through 1156 removed outlier: 3.711A pdb=" N LEU L1146 " --> pdb=" O MET L1142 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ILE L1147 " --> pdb=" O PHE L1143 " (cutoff:3.500A) Processing helix chain 'L' and resid 1166 through 1181 Processing helix chain 'L' and resid 1199 through 1208 removed outlier: 3.756A pdb=" N PHE L1203 " --> pdb=" O CYS L1199 " (cutoff:3.500A) Processing helix chain 'L' and resid 1219 through 1236 removed outlier: 3.688A pdb=" N ASP L1225 " --> pdb=" O ILE L1221 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N TYR L1226 " --> pdb=" O LYS L1222 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU L1227 " --> pdb=" O GLY L1223 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N HIS L1236 " --> pdb=" O THR L1232 " (cutoff:3.500A) Processing helix chain 'L' and resid 1242 through 1259 removed outlier: 3.756A pdb=" N VAL L1246 " --> pdb=" O PRO L1242 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LEU L1258 " --> pdb=" O ILE L1254 " (cutoff:3.500A) Processing helix chain 'L' and resid 1267 through 1278 removed outlier: 3.863A pdb=" N ASP L1271 " --> pdb=" O SER L1267 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N PHE L1272 " --> pdb=" O ILE L1268 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N PHE L1273 " --> pdb=" O THR L1269 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ASN L1276 " --> pdb=" O PHE L1272 " (cutoff:3.500A) Processing helix chain 'L' and resid 1297 through 1320 Processing helix chain 'L' and resid 1338 through 1348 removed outlier: 3.975A pdb=" N GLN L1346 " --> pdb=" O THR L1342 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ARG L1347 " --> pdb=" O GLU L1343 " (cutoff:3.500A) Processing helix chain 'L' and resid 1348 through 1365 Processing helix chain 'L' and resid 1396 through 1406 removed outlier: 3.574A pdb=" N PHE L1400 " --> pdb=" O LEU L1396 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL L1401 " --> pdb=" O LEU L1397 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N HIS L1406 " --> pdb=" O ALA L1402 " (cutoff:3.500A) Processing helix chain 'L' and resid 1412 through 1429 removed outlier: 3.635A pdb=" N LEU L1416 " --> pdb=" O GLU L1412 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ALA L1417 " --> pdb=" O PRO L1413 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N GLU L1418 " --> pdb=" O HIS L1414 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA L1429 " --> pdb=" O ASP L1425 " (cutoff:3.500A) Processing helix chain 'L' and resid 1433 through 1451 removed outlier: 3.782A pdb=" N CYS L1437 " --> pdb=" O PRO L1433 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALA L1451 " --> pdb=" O LEU L1447 " (cutoff:3.500A) Processing helix chain 'L' and resid 1465 through 1471 removed outlier: 3.649A pdb=" N TRP L1469 " --> pdb=" O ASP L1465 " (cutoff:3.500A) Processing helix chain 'L' and resid 1473 through 1486 Processing helix chain 'L' and resid 1489 through 1505 removed outlier: 3.767A pdb=" N ILE L1493 " --> pdb=" O ALA L1489 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS L1499 " --> pdb=" O SER L1495 " (cutoff:3.500A) Processing helix chain 'L' and resid 1524 through 1534 Processing helix chain 'L' and resid 1539 through 1543 removed outlier: 3.532A pdb=" N LEU L1543 " --> pdb=" O GLU L1540 " (cutoff:3.500A) Processing helix chain 'L' and resid 1613 through 1624 Processing helix chain 'L' and resid 1639 through 1649 removed outlier: 3.925A pdb=" N ILE L1649 " --> pdb=" O LEU L1645 " (cutoff:3.500A) Processing helix chain 'L' and resid 1676 through 1680 removed outlier: 3.641A pdb=" N TYR L1680 " --> pdb=" O VAL L1677 " (cutoff:3.500A) Processing helix chain 'L' and resid 1684 through 1699 Processing helix chain 'L' and resid 1701 through 1705 removed outlier: 3.566A pdb=" N LEU L1704 " --> pdb=" O ALA L1701 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY L1705 " --> pdb=" O TRP L1702 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 1701 through 1705' Processing helix chain 'L' and resid 1740 through 1751 Processing helix chain 'L' and resid 1751 through 1757 removed outlier: 3.730A pdb=" N LYS L1757 " --> pdb=" O SER L1753 " (cutoff:3.500A) Processing helix chain 'L' and resid 1759 through 1764 Processing helix chain 'L' and resid 1777 through 1790 Processing helix chain 'L' and resid 1812 through 1816 removed outlier: 3.614A pdb=" N ARG L1816 " --> pdb=" O SER L1812 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 1812 through 1816' Processing helix chain 'L' and resid 1834 through 1852 removed outlier: 3.815A pdb=" N TYR L1850 " --> pdb=" O TYR L1846 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL L1851 " --> pdb=" O PHE L1847 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ARG L1852 " --> pdb=" O GLU L1848 " (cutoff:3.500A) Processing helix chain 'L' and resid 1860 through 1864 Processing helix chain 'L' and resid 1882 through 1884 No H-bonds generated for 'chain 'L' and resid 1882 through 1884' Processing helix chain 'L' and resid 1885 through 1892 removed outlier: 3.995A pdb=" N VAL L1889 " --> pdb=" O PHE L1885 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLU L1890 " --> pdb=" O SER L1886 " (cutoff:3.500A) Processing helix chain 'L' and resid 1902 through 1906 Processing helix chain 'L' and resid 2102 through 2114 Processing helix chain 'L' and resid 2118 through 2134 Processing helix chain 'L' and resid 2144 through 2152 Processing helix chain 'L' and resid 2155 through 2168 removed outlier: 3.841A pdb=" N VAL L2159 " --> pdb=" O ASN L2155 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ASP L2168 " --> pdb=" O LEU L2164 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 91 through 94 removed outlier: 3.533A pdb=" N LEU L 100 " --> pdb=" O ILE L 138 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 207 through 208 removed outlier: 6.242A pdb=" N LEU L 207 " --> pdb=" O TYR L1107 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLY L1111 " --> pdb=" O SER L1108 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 259 through 260 removed outlier: 3.803A pdb=" N HIS L 652 " --> pdb=" O LEU L 259 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TYR L 651 " --> pdb=" O ILE L1376 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE L1376 " --> pdb=" O TYR L 651 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 370 through 371 Processing sheet with id=AA5, first strand: chain 'L' and resid 535 through 541 removed outlier: 3.590A pdb=" N PHE L 573 " --> pdb=" O TYR L 560 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N CYS L 571 " --> pdb=" O ILE L 562 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 738 through 739 removed outlier: 3.588A pdb=" N SER L1287 " --> pdb=" O SER L 738 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LEU L1121 " --> pdb=" O GLU L1240 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 827 through 829 removed outlier: 3.736A pdb=" N GLU L1071 " --> pdb=" O VAL L 829 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 1653 through 1656 removed outlier: 3.599A pdb=" N GLU L1653 " --> pdb=" O ARG L1665 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG L1665 " --> pdb=" O GLU L1653 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N TRP L1664 " --> pdb=" O SER L1546 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ARG L1682 " --> pdb=" O TRP L1547 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 1707 through 1709 Processing sheet with id=AB1, first strand: chain 'L' and resid 1723 through 1726 removed outlier: 3.534A pdb=" N VAL L1810 " --> pdb=" O PHE L1724 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 1854 through 1855 removed outlier: 6.844A pdb=" N LEU L2087 " --> pdb=" O LEU L2094 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS L2092 " --> pdb=" O GLU L2089 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 2171 through 2172 removed outlier: 4.175A pdb=" N VAL L2171 " --> pdb=" O LEU L2178 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LEU L2178 " --> pdb=" O VAL L2171 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N ALA L2177 " --> pdb=" O HIS L2190 " (cutoff:3.500A) 649 hydrogen bonds defined for protein. 1839 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: 7.26 Time building geometry restraints manager: 4.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4646 1.34 - 1.46: 2565 1.46 - 1.57: 7255 1.57 - 1.69: 0 1.69 - 1.81: 136 Bond restraints: 14602 Sorted by residual: bond pdb=" N VAL L1851 " pdb=" CA VAL L1851 " ideal model delta sigma weight residual 1.460 1.495 -0.036 1.21e-02 6.83e+03 8.69e+00 bond pdb=" N VAL L1855 " pdb=" CA VAL L1855 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.32e-02 5.74e+03 8.12e+00 bond pdb=" N PHE L1854 " pdb=" CA PHE L1854 " ideal model delta sigma weight residual 1.455 1.487 -0.032 1.25e-02 6.40e+03 6.68e+00 bond pdb=" N SER L1853 " pdb=" CA SER L1853 " ideal model delta sigma weight residual 1.455 1.486 -0.031 1.21e-02 6.83e+03 6.46e+00 bond pdb=" N ARG L1852 " pdb=" CA ARG L1852 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.42e-02 4.96e+03 4.49e+00 ... (remaining 14597 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.62: 19692 5.62 - 11.24: 2 11.24 - 16.86: 1 16.86 - 22.48: 0 22.48 - 28.10: 1 Bond angle restraints: 19696 Sorted by residual: angle pdb=" N VAL L2167 " pdb=" CA VAL L2167 " pdb=" C VAL L2167 " ideal model delta sigma weight residual 109.34 137.44 -28.10 2.08e+00 2.31e-01 1.82e+02 angle pdb=" N ASP L2168 " pdb=" CA ASP L2168 " pdb=" C ASP L2168 " ideal model delta sigma weight residual 111.28 126.70 -15.42 1.35e+00 5.49e-01 1.30e+02 angle pdb=" N LYS L2195 " pdb=" CA LYS L2195 " pdb=" C LYS L2195 " ideal model delta sigma weight residual 114.56 110.08 4.48 1.27e+00 6.20e-01 1.24e+01 angle pdb=" CA VAL L1855 " pdb=" C VAL L1855 " pdb=" O VAL L1855 " ideal model delta sigma weight residual 121.59 118.40 3.19 1.03e+00 9.43e-01 9.62e+00 angle pdb=" CA LYS L1772 " pdb=" C LYS L1772 " pdb=" N TRP L1773 " ideal model delta sigma weight residual 118.59 123.50 -4.91 1.63e+00 3.76e-01 9.06e+00 ... (remaining 19691 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.93: 7925 16.93 - 33.87: 805 33.87 - 50.80: 131 50.80 - 67.74: 20 67.74 - 84.67: 9 Dihedral angle restraints: 8890 sinusoidal: 3646 harmonic: 5244 Sorted by residual: dihedral pdb=" C VAL L2167 " pdb=" N VAL L2167 " pdb=" CA VAL L2167 " pdb=" CB VAL L2167 " ideal model delta harmonic sigma weight residual -122.00 -159.50 37.50 0 2.50e+00 1.60e-01 2.25e+02 dihedral pdb=" N VAL L2167 " pdb=" C VAL L2167 " pdb=" CA VAL L2167 " pdb=" CB VAL L2167 " ideal model delta harmonic sigma weight residual 123.40 159.60 -36.20 0 2.50e+00 1.60e-01 2.10e+02 dihedral pdb=" N ASP L2168 " pdb=" C ASP L2168 " pdb=" CA ASP L2168 " pdb=" CB ASP L2168 " ideal model delta harmonic sigma weight residual 122.80 148.81 -26.01 0 2.50e+00 1.60e-01 1.08e+02 ... (remaining 8887 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.336: 2225 0.336 - 0.673: 0 0.673 - 1.009: 0 1.009 - 1.346: 1 1.346 - 1.682: 1 Chirality restraints: 2227 Sorted by residual: chirality pdb=" CA VAL L2167 " pdb=" N VAL L2167 " pdb=" C VAL L2167 " pdb=" CB VAL L2167 " both_signs ideal model delta sigma weight residual False 2.44 0.76 1.68 2.00e-01 2.50e+01 7.08e+01 chirality pdb=" CA ASP L2168 " pdb=" N ASP L2168 " pdb=" C ASP L2168 " pdb=" CB ASP L2168 " both_signs ideal model delta sigma weight residual False 2.51 1.30 1.21 2.00e-01 2.50e+01 3.64e+01 chirality pdb=" CA VAL L1855 " pdb=" N VAL L1855 " pdb=" C VAL L1855 " pdb=" CB VAL L1855 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.12e-01 ... (remaining 2224 not shown) Planarity restraints: 2494 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY L1195 " 0.024 5.00e-02 4.00e+02 3.60e-02 2.08e+00 pdb=" N PRO L1196 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO L1196 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO L1196 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE L 621 " 0.007 2.00e-02 2.50e+03 1.35e-02 1.83e+00 pdb=" C ILE L 621 " -0.023 2.00e-02 2.50e+03 pdb=" O ILE L 621 " 0.009 2.00e-02 2.50e+03 pdb=" N LEU L 622 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU L 624 " 0.006 2.00e-02 2.50e+03 1.25e-02 1.57e+00 pdb=" C LEU L 624 " -0.022 2.00e-02 2.50e+03 pdb=" O LEU L 624 " 0.008 2.00e-02 2.50e+03 pdb=" N ILE L 625 " 0.007 2.00e-02 2.50e+03 ... (remaining 2491 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 176 2.59 - 3.17: 12631 3.17 - 3.74: 20592 3.74 - 4.32: 27223 4.32 - 4.90: 45386 Nonbonded interactions: 106008 Sorted by model distance: nonbonded pdb=" OD1 ASP L1332 " pdb="MG MG L2302 " model vdw 2.009 2.170 nonbonded pdb=" OD1 ASP L1190 " pdb="MG MG L2302 " model vdw 2.021 2.170 nonbonded pdb=" OD2 ASP L1332 " pdb="MG MG L2302 " model vdw 2.075 2.170 nonbonded pdb=" O ILE L 709 " pdb=" OG1 THR L 710 " model vdw 2.160 3.040 nonbonded pdb=" OG SER L1524 " pdb=" OG SER L1527 " model vdw 2.174 3.040 ... (remaining 106003 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 11.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 41.370 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 14602 Z= 0.374 Angle : 0.663 28.097 19696 Z= 0.373 Chirality : 0.060 1.682 2227 Planarity : 0.003 0.036 2494 Dihedral : 13.626 84.671 5482 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.36 % Favored : 88.64 % Rotamer: Outliers : 0.12 % Allowed : 6.40 % Favored : 93.48 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.69 (0.17), residues: 1761 helix: -1.21 (0.15), residues: 894 sheet: -2.58 (0.45), residues: 108 loop : -4.07 (0.17), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 155 HIS 0.005 0.001 HIS L1435 PHE 0.017 0.001 PHE L2109 TYR 0.015 0.001 TYR L1187 ARG 0.003 0.000 ARG L 250 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3522 Ramachandran restraints generated. 1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3522 Ramachandran restraints generated. 1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 98 time to evaluate : 1.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 446 MET cc_start: 0.8392 (tpt) cc_final: 0.8027 (tpt) REVERT: L 1062 ARG cc_start: 0.8756 (mtt180) cc_final: 0.8522 (ttm110) REVERT: L 1842 MET cc_start: 0.8823 (mmt) cc_final: 0.8587 (tpp) REVERT: L 1869 HIS cc_start: 0.7946 (m-70) cc_final: 0.7706 (m90) REVERT: L 2107 GLU cc_start: 0.8887 (mt-10) cc_final: 0.8503 (mm-30) REVERT: L 2147 MET cc_start: 0.9194 (tmm) cc_final: 0.8689 (tmm) outliers start: 2 outliers final: 1 residues processed: 100 average time/residue: 0.3615 time to fit residues: 52.1894 Evaluate side-chains 76 residues out of total 1627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 75 time to evaluate : 1.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 2168 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 150 optimal weight: 0.6980 chunk 134 optimal weight: 0.3980 chunk 74 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 91 optimal weight: 10.0000 chunk 72 optimal weight: 0.8980 chunk 139 optimal weight: 0.9980 chunk 53 optimal weight: 8.9990 chunk 84 optimal weight: 8.9990 chunk 103 optimal weight: 0.9990 chunk 161 optimal weight: 7.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 32 GLN L 414 ASN L 415 GLN L 441 HIS L 610 GLN L 736 HIS L 869 GLN L1095 ASN L1481 GLN ** L1510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L1528 ASN L1745 HIS L1894 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.1332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14602 Z= 0.163 Angle : 0.538 8.603 19696 Z= 0.279 Chirality : 0.039 0.201 2227 Planarity : 0.003 0.033 2494 Dihedral : 4.296 22.783 1926 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 0.68 % Allowed : 9.96 % Favored : 89.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.19), residues: 1761 helix: 0.23 (0.18), residues: 897 sheet: -1.88 (0.48), residues: 104 loop : -3.44 (0.19), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP L 155 HIS 0.003 0.001 HIS L 359 PHE 0.010 0.001 PHE L1303 TYR 0.014 0.001 TYR L1187 ARG 0.005 0.000 ARG L 716 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3522 Ramachandran restraints generated. 1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3522 Ramachandran restraints generated. 1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 86 time to evaluate : 1.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 36 ARG cc_start: 0.7697 (mtt180) cc_final: 0.7377 (mtt180) REVERT: L 446 MET cc_start: 0.8362 (tpt) cc_final: 0.8153 (tpt) REVERT: L 854 LEU cc_start: 0.9357 (OUTLIER) cc_final: 0.9109 (pp) REVERT: L 1869 HIS cc_start: 0.7905 (m-70) cc_final: 0.7663 (m90) REVERT: L 2107 GLU cc_start: 0.8877 (mt-10) cc_final: 0.8569 (mm-30) REVERT: L 2147 MET cc_start: 0.8968 (tmm) cc_final: 0.8209 (tmm) outliers start: 11 outliers final: 4 residues processed: 94 average time/residue: 0.2843 time to fit residues: 41.3104 Evaluate side-chains 79 residues out of total 1627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 74 time to evaluate : 1.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 471 TYR Chi-restraints excluded: chain L residue 854 LEU Chi-restraints excluded: chain L residue 1298 HIS Chi-restraints excluded: chain L residue 1300 THR Chi-restraints excluded: chain L residue 2157 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 89 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 134 optimal weight: 0.2980 chunk 110 optimal weight: 2.9990 chunk 44 optimal weight: 0.0770 chunk 161 optimal weight: 1.9990 chunk 174 optimal weight: 10.0000 chunk 144 optimal weight: 0.8980 chunk 160 optimal weight: 4.9990 chunk 55 optimal weight: 0.6980 chunk 129 optimal weight: 0.3980 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 877 GLN ** L1510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 14602 Z= 0.125 Angle : 0.504 13.372 19696 Z= 0.256 Chirality : 0.038 0.169 2227 Planarity : 0.003 0.036 2494 Dihedral : 3.965 21.232 1924 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 1.05 % Allowed : 11.81 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.20), residues: 1761 helix: 0.94 (0.18), residues: 882 sheet: -1.90 (0.45), residues: 120 loop : -3.10 (0.20), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP L 395 HIS 0.003 0.000 HIS L 359 PHE 0.009 0.001 PHE L 349 TYR 0.010 0.001 TYR L1187 ARG 0.005 0.000 ARG L 716 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3522 Ramachandran restraints generated. 1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3522 Ramachandran restraints generated. 1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 80 time to evaluate : 1.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 821 LEU cc_start: 0.8643 (mm) cc_final: 0.7971 (tp) REVERT: L 854 LEU cc_start: 0.9321 (OUTLIER) cc_final: 0.9098 (pp) REVERT: L 1250 MET cc_start: 0.8388 (tpp) cc_final: 0.7976 (tpp) REVERT: L 1869 HIS cc_start: 0.7934 (m-70) cc_final: 0.7698 (m90) REVERT: L 2107 GLU cc_start: 0.8907 (mt-10) cc_final: 0.8521 (mm-30) outliers start: 17 outliers final: 9 residues processed: 95 average time/residue: 0.2661 time to fit residues: 39.4388 Evaluate side-chains 84 residues out of total 1627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 74 time to evaluate : 1.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 255 THR Chi-restraints excluded: chain L residue 486 VAL Chi-restraints excluded: chain L residue 704 TYR Chi-restraints excluded: chain L residue 854 LEU Chi-restraints excluded: chain L residue 1121 LEU Chi-restraints excluded: chain L residue 1300 THR Chi-restraints excluded: chain L residue 1780 LEU Chi-restraints excluded: chain L residue 1786 LEU Chi-restraints excluded: chain L residue 1871 THR Chi-restraints excluded: chain L residue 2157 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 159 optimal weight: 5.9990 chunk 121 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 chunk 17 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 108 optimal weight: 0.9980 chunk 162 optimal weight: 0.5980 chunk 172 optimal weight: 0.8980 chunk 154 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 143 optimal weight: 0.0040 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 547 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 14602 Z= 0.144 Angle : 0.496 9.610 19696 Z= 0.253 Chirality : 0.038 0.197 2227 Planarity : 0.003 0.038 2494 Dihedral : 3.870 20.461 1924 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 1.05 % Allowed : 13.71 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.21), residues: 1761 helix: 1.10 (0.18), residues: 883 sheet: -1.62 (0.45), residues: 122 loop : -2.93 (0.21), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 395 HIS 0.003 0.000 HIS L 359 PHE 0.010 0.001 PHE L 349 TYR 0.009 0.001 TYR L 871 ARG 0.004 0.000 ARG L 716 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3522 Ramachandran restraints generated. 1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3522 Ramachandran restraints generated. 1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 80 time to evaluate : 1.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 395 TRP cc_start: 0.8721 (t-100) cc_final: 0.8129 (t60) REVERT: L 821 LEU cc_start: 0.8618 (mm) cc_final: 0.7945 (tp) REVERT: L 854 LEU cc_start: 0.9346 (OUTLIER) cc_final: 0.9130 (pp) REVERT: L 1869 HIS cc_start: 0.7904 (m-70) cc_final: 0.7629 (m90) REVERT: L 2107 GLU cc_start: 0.8892 (mt-10) cc_final: 0.8458 (mm-30) REVERT: L 2137 MET cc_start: 0.7374 (mmm) cc_final: 0.6715 (mpp) outliers start: 17 outliers final: 10 residues processed: 96 average time/residue: 0.2638 time to fit residues: 39.7168 Evaluate side-chains 82 residues out of total 1627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 71 time to evaluate : 1.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 255 THR Chi-restraints excluded: chain L residue 378 VAL Chi-restraints excluded: chain L residue 486 VAL Chi-restraints excluded: chain L residue 601 VAL Chi-restraints excluded: chain L residue 854 LEU Chi-restraints excluded: chain L residue 1121 LEU Chi-restraints excluded: chain L residue 1300 THR Chi-restraints excluded: chain L residue 1328 THR Chi-restraints excluded: chain L residue 1786 LEU Chi-restraints excluded: chain L residue 1871 THR Chi-restraints excluded: chain L residue 2157 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 97 optimal weight: 0.9980 chunk 2 optimal weight: 0.5980 chunk 128 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 146 optimal weight: 0.9990 chunk 118 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 87 optimal weight: 0.5980 chunk 154 optimal weight: 4.9990 chunk 43 optimal weight: 8.9990 chunk 57 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 547 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14602 Z= 0.185 Angle : 0.511 9.093 19696 Z= 0.261 Chirality : 0.038 0.166 2227 Planarity : 0.003 0.039 2494 Dihedral : 3.898 19.412 1924 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 1.17 % Allowed : 14.39 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.21), residues: 1761 helix: 1.13 (0.18), residues: 885 sheet: -1.49 (0.46), residues: 122 loop : -2.83 (0.21), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 155 HIS 0.003 0.001 HIS L 359 PHE 0.012 0.001 PHE L2109 TYR 0.009 0.001 TYR L 871 ARG 0.004 0.000 ARG L 363 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3522 Ramachandran restraints generated. 1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3522 Ramachandran restraints generated. 1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 75 time to evaluate : 1.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 420 MET cc_start: 0.8667 (mpp) cc_final: 0.8449 (mpp) REVERT: L 854 LEU cc_start: 0.9350 (OUTLIER) cc_final: 0.9142 (pp) REVERT: L 1771 MET cc_start: 0.8813 (pmm) cc_final: 0.8401 (ppp) REVERT: L 1842 MET cc_start: 0.8492 (tpp) cc_final: 0.8284 (tpp) REVERT: L 1869 HIS cc_start: 0.7950 (m-70) cc_final: 0.7682 (m90) REVERT: L 2137 MET cc_start: 0.7445 (mmm) cc_final: 0.7236 (mmm) outliers start: 19 outliers final: 13 residues processed: 93 average time/residue: 0.2570 time to fit residues: 38.3818 Evaluate side-chains 87 residues out of total 1627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 73 time to evaluate : 1.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 255 THR Chi-restraints excluded: chain L residue 378 VAL Chi-restraints excluded: chain L residue 486 VAL Chi-restraints excluded: chain L residue 601 VAL Chi-restraints excluded: chain L residue 710 THR Chi-restraints excluded: chain L residue 854 LEU Chi-restraints excluded: chain L residue 1121 LEU Chi-restraints excluded: chain L residue 1234 HIS Chi-restraints excluded: chain L residue 1300 THR Chi-restraints excluded: chain L residue 1328 THR Chi-restraints excluded: chain L residue 1466 VAL Chi-restraints excluded: chain L residue 1786 LEU Chi-restraints excluded: chain L residue 1871 THR Chi-restraints excluded: chain L residue 2157 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 154 optimal weight: 5.9990 chunk 34 optimal weight: 7.9990 chunk 101 optimal weight: 0.6980 chunk 42 optimal weight: 5.9990 chunk 172 optimal weight: 0.9990 chunk 142 optimal weight: 0.9980 chunk 79 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 90 optimal weight: 0.0030 chunk 166 optimal weight: 0.8980 overall best weight: 0.7192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 547 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L1426 GLN ** L1510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 14602 Z= 0.143 Angle : 0.487 9.391 19696 Z= 0.248 Chirality : 0.038 0.148 2227 Planarity : 0.003 0.041 2494 Dihedral : 3.791 20.157 1924 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 1.35 % Allowed : 14.64 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.21), residues: 1761 helix: 1.20 (0.18), residues: 884 sheet: -1.28 (0.46), residues: 122 loop : -2.68 (0.21), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 155 HIS 0.002 0.000 HIS L1191 PHE 0.010 0.001 PHE L 349 TYR 0.008 0.001 TYR L 871 ARG 0.005 0.000 ARG L 363 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3522 Ramachandran restraints generated. 1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3522 Ramachandran restraints generated. 1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 77 time to evaluate : 1.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 879 MET cc_start: 0.8901 (ppp) cc_final: 0.8567 (ppp) REVERT: L 1771 MET cc_start: 0.8798 (pmm) cc_final: 0.8429 (ppp) REVERT: L 1869 HIS cc_start: 0.7963 (m-70) cc_final: 0.7716 (m90) REVERT: L 2137 MET cc_start: 0.7382 (mmm) cc_final: 0.7139 (mmm) outliers start: 22 outliers final: 15 residues processed: 95 average time/residue: 0.2580 time to fit residues: 39.1534 Evaluate side-chains 91 residues out of total 1627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 76 time to evaluate : 1.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 255 THR Chi-restraints excluded: chain L residue 378 VAL Chi-restraints excluded: chain L residue 486 VAL Chi-restraints excluded: chain L residue 601 VAL Chi-restraints excluded: chain L residue 871 TYR Chi-restraints excluded: chain L residue 882 LEU Chi-restraints excluded: chain L residue 1121 LEU Chi-restraints excluded: chain L residue 1234 HIS Chi-restraints excluded: chain L residue 1300 THR Chi-restraints excluded: chain L residue 1328 THR Chi-restraints excluded: chain L residue 1466 VAL Chi-restraints excluded: chain L residue 1786 LEU Chi-restraints excluded: chain L residue 1871 THR Chi-restraints excluded: chain L residue 2122 ILE Chi-restraints excluded: chain L residue 2157 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 19 optimal weight: 0.7980 chunk 98 optimal weight: 0.7980 chunk 125 optimal weight: 0.7980 chunk 97 optimal weight: 0.8980 chunk 144 optimal weight: 0.8980 chunk 96 optimal weight: 0.9980 chunk 171 optimal weight: 0.6980 chunk 107 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 79 optimal weight: 0.6980 chunk 106 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 547 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L1426 GLN ** L1510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 14602 Z= 0.149 Angle : 0.514 9.721 19696 Z= 0.258 Chirality : 0.038 0.157 2227 Planarity : 0.003 0.041 2494 Dihedral : 3.750 19.008 1924 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 1.29 % Allowed : 15.31 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.21), residues: 1761 helix: 1.20 (0.18), residues: 892 sheet: -1.17 (0.47), residues: 122 loop : -2.65 (0.21), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 395 HIS 0.002 0.000 HIS L1191 PHE 0.009 0.001 PHE L 349 TYR 0.008 0.001 TYR L 871 ARG 0.005 0.000 ARG L 363 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3522 Ramachandran restraints generated. 1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3522 Ramachandran restraints generated. 1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 78 time to evaluate : 1.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 879 MET cc_start: 0.8902 (ppp) cc_final: 0.8591 (ppp) REVERT: L 1771 MET cc_start: 0.8773 (pmm) cc_final: 0.8407 (ppp) REVERT: L 1869 HIS cc_start: 0.7977 (m-70) cc_final: 0.7739 (m90) REVERT: L 2137 MET cc_start: 0.7412 (mmm) cc_final: 0.7147 (mmm) outliers start: 21 outliers final: 15 residues processed: 98 average time/residue: 0.2526 time to fit residues: 39.4778 Evaluate side-chains 90 residues out of total 1627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 75 time to evaluate : 1.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 205 VAL Chi-restraints excluded: chain L residue 255 THR Chi-restraints excluded: chain L residue 378 VAL Chi-restraints excluded: chain L residue 486 VAL Chi-restraints excluded: chain L residue 601 VAL Chi-restraints excluded: chain L residue 871 TYR Chi-restraints excluded: chain L residue 882 LEU Chi-restraints excluded: chain L residue 1121 LEU Chi-restraints excluded: chain L residue 1234 HIS Chi-restraints excluded: chain L residue 1300 THR Chi-restraints excluded: chain L residue 1328 THR Chi-restraints excluded: chain L residue 1466 VAL Chi-restraints excluded: chain L residue 1786 LEU Chi-restraints excluded: chain L residue 1871 THR Chi-restraints excluded: chain L residue 2157 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 68 optimal weight: 1.9990 chunk 102 optimal weight: 0.5980 chunk 51 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 109 optimal weight: 1.9990 chunk 116 optimal weight: 0.6980 chunk 84 optimal weight: 0.9990 chunk 15 optimal weight: 0.4980 chunk 134 optimal weight: 0.4980 chunk 156 optimal weight: 6.9990 chunk 164 optimal weight: 3.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 547 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L1426 GLN ** L1510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 14602 Z= 0.138 Angle : 0.504 9.943 19696 Z= 0.252 Chirality : 0.038 0.156 2227 Planarity : 0.003 0.042 2494 Dihedral : 3.706 19.251 1924 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 1.29 % Allowed : 15.44 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.21), residues: 1761 helix: 1.19 (0.18), residues: 894 sheet: -1.03 (0.47), residues: 122 loop : -2.54 (0.22), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP L 395 HIS 0.002 0.000 HIS L1191 PHE 0.009 0.001 PHE L 349 TYR 0.008 0.001 TYR L 871 ARG 0.004 0.000 ARG L 363 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3522 Ramachandran restraints generated. 1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3522 Ramachandran restraints generated. 1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 76 time to evaluate : 1.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 879 MET cc_start: 0.8933 (ppp) cc_final: 0.8636 (ppp) REVERT: L 1771 MET cc_start: 0.8784 (pmm) cc_final: 0.8435 (ppp) REVERT: L 2137 MET cc_start: 0.7358 (mmm) cc_final: 0.7121 (mmm) outliers start: 21 outliers final: 16 residues processed: 94 average time/residue: 0.2595 time to fit residues: 38.4563 Evaluate side-chains 91 residues out of total 1627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 75 time to evaluate : 1.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 205 VAL Chi-restraints excluded: chain L residue 255 THR Chi-restraints excluded: chain L residue 378 VAL Chi-restraints excluded: chain L residue 446 MET Chi-restraints excluded: chain L residue 486 VAL Chi-restraints excluded: chain L residue 601 VAL Chi-restraints excluded: chain L residue 871 TYR Chi-restraints excluded: chain L residue 882 LEU Chi-restraints excluded: chain L residue 1121 LEU Chi-restraints excluded: chain L residue 1234 HIS Chi-restraints excluded: chain L residue 1300 THR Chi-restraints excluded: chain L residue 1328 THR Chi-restraints excluded: chain L residue 1466 VAL Chi-restraints excluded: chain L residue 1786 LEU Chi-restraints excluded: chain L residue 1871 THR Chi-restraints excluded: chain L residue 2157 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 149 optimal weight: 4.9990 chunk 159 optimal weight: 4.9990 chunk 164 optimal weight: 0.0010 chunk 96 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 125 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 144 optimal weight: 2.9990 chunk 151 optimal weight: 0.7980 chunk 104 optimal weight: 0.8980 chunk 169 optimal weight: 4.9990 overall best weight: 0.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 547 GLN L1426 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 14602 Z= 0.138 Angle : 0.526 13.030 19696 Z= 0.257 Chirality : 0.038 0.151 2227 Planarity : 0.003 0.044 2494 Dihedral : 3.654 18.341 1924 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 1.17 % Allowed : 15.81 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.21), residues: 1761 helix: 1.21 (0.18), residues: 900 sheet: -1.03 (0.46), residues: 127 loop : -2.49 (0.22), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP L 395 HIS 0.009 0.000 HIS L1510 PHE 0.009 0.001 PHE L 349 TYR 0.008 0.001 TYR L 871 ARG 0.004 0.000 ARG L 363 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3522 Ramachandran restraints generated. 1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3522 Ramachandran restraints generated. 1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 76 time to evaluate : 1.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 879 MET cc_start: 0.8915 (ppp) cc_final: 0.8614 (ppp) REVERT: L 1771 MET cc_start: 0.8777 (pmm) cc_final: 0.8442 (ppp) REVERT: L 2137 MET cc_start: 0.7330 (mmm) cc_final: 0.7069 (mmm) outliers start: 19 outliers final: 15 residues processed: 93 average time/residue: 0.2547 time to fit residues: 37.5720 Evaluate side-chains 89 residues out of total 1627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 74 time to evaluate : 1.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 205 VAL Chi-restraints excluded: chain L residue 255 THR Chi-restraints excluded: chain L residue 378 VAL Chi-restraints excluded: chain L residue 486 VAL Chi-restraints excluded: chain L residue 601 VAL Chi-restraints excluded: chain L residue 871 TYR Chi-restraints excluded: chain L residue 882 LEU Chi-restraints excluded: chain L residue 1121 LEU Chi-restraints excluded: chain L residue 1234 HIS Chi-restraints excluded: chain L residue 1300 THR Chi-restraints excluded: chain L residue 1328 THR Chi-restraints excluded: chain L residue 1466 VAL Chi-restraints excluded: chain L residue 1786 LEU Chi-restraints excluded: chain L residue 1871 THR Chi-restraints excluded: chain L residue 2157 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 103 optimal weight: 0.6980 chunk 80 optimal weight: 3.9990 chunk 117 optimal weight: 0.7980 chunk 177 optimal weight: 7.9990 chunk 163 optimal weight: 0.7980 chunk 141 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 109 optimal weight: 0.6980 chunk 86 optimal weight: 8.9990 chunk 112 optimal weight: 0.7980 chunk 150 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L1426 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 14602 Z= 0.152 Angle : 0.538 13.251 19696 Z= 0.262 Chirality : 0.038 0.167 2227 Planarity : 0.003 0.044 2494 Dihedral : 3.664 18.137 1924 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 0.92 % Allowed : 16.11 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.21), residues: 1761 helix: 1.23 (0.18), residues: 892 sheet: -1.03 (0.46), residues: 127 loop : -2.46 (0.22), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP L 395 HIS 0.014 0.001 HIS L1510 PHE 0.009 0.001 PHE L 349 TYR 0.008 0.001 TYR L 471 ARG 0.004 0.000 ARG L 363 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3522 Ramachandran restraints generated. 1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3522 Ramachandran restraints generated. 1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 76 time to evaluate : 1.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 574 TYR cc_start: 0.7623 (t80) cc_final: 0.7325 (t80) REVERT: L 879 MET cc_start: 0.8923 (ppp) cc_final: 0.8627 (ppp) REVERT: L 1771 MET cc_start: 0.8776 (pmm) cc_final: 0.8449 (ppp) REVERT: L 2137 MET cc_start: 0.7362 (mmm) cc_final: 0.7099 (mmm) outliers start: 15 outliers final: 15 residues processed: 90 average time/residue: 0.2751 time to fit residues: 39.0604 Evaluate side-chains 89 residues out of total 1627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 74 time to evaluate : 1.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 205 VAL Chi-restraints excluded: chain L residue 255 THR Chi-restraints excluded: chain L residue 378 VAL Chi-restraints excluded: chain L residue 486 VAL Chi-restraints excluded: chain L residue 601 VAL Chi-restraints excluded: chain L residue 871 TYR Chi-restraints excluded: chain L residue 882 LEU Chi-restraints excluded: chain L residue 1121 LEU Chi-restraints excluded: chain L residue 1234 HIS Chi-restraints excluded: chain L residue 1300 THR Chi-restraints excluded: chain L residue 1328 THR Chi-restraints excluded: chain L residue 1466 VAL Chi-restraints excluded: chain L residue 1786 LEU Chi-restraints excluded: chain L residue 1871 THR Chi-restraints excluded: chain L residue 2157 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 43 optimal weight: 5.9990 chunk 130 optimal weight: 0.5980 chunk 20 optimal weight: 0.0770 chunk 39 optimal weight: 3.9990 chunk 141 optimal weight: 0.8980 chunk 59 optimal weight: 0.7980 chunk 145 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 124 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 overall best weight: 0.6740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.060061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.040249 restraints weight = 70505.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.041664 restraints weight = 36262.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.042546 restraints weight = 24607.936| |-----------------------------------------------------------------------------| r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 14602 Z= 0.142 Angle : 0.532 12.921 19696 Z= 0.259 Chirality : 0.038 0.151 2227 Planarity : 0.003 0.045 2494 Dihedral : 3.622 18.196 1924 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 1.05 % Allowed : 16.11 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.21), residues: 1761 helix: 1.26 (0.18), residues: 899 sheet: -0.91 (0.47), residues: 121 loop : -2.39 (0.22), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP L 395 HIS 0.010 0.000 HIS L1510 PHE 0.009 0.001 PHE L 349 TYR 0.009 0.001 TYR L 471 ARG 0.004 0.000 ARG L 716 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2791.00 seconds wall clock time: 53 minutes 19.13 seconds (3199.13 seconds total)