Starting phenix.real_space_refine on Sat Mar 16 09:54:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ojj_12953/03_2024/7ojj_12953.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ojj_12953/03_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ojj_12953/03_2024/7ojj_12953.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ojj_12953/03_2024/7ojj_12953.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ojj_12953/03_2024/7ojj_12953.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ojj_12953/03_2024/7ojj_12953.pdb" } 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 Residue "L GLU 2": "OE1" <-> "OE2" Residue "L GLU 41": "OE1" <-> "OE2" Residue "L TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 475": "OE1" <-> "OE2" Residue "L GLU 900": "OE1" <-> "OE2" Residue "L GLU 1270": "OE1" <-> "OE2" Residue "L GLU 1814": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 14330 Number of models: 1 Model: "" Number of chains: 1 Chain: "L" Number of atoms: 14330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1787, 14330 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'peptide': 1785, 'undetermined': 2} Link IDs: {'PTRANS': 57, 'TRANS': 1727, None: 2} Not linked: pdbres="LYS L2208 " pdbres=" ZN L2301 " Not linked: pdbres=" ZN L2301 " pdbres=" MG L2302 " 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 Time building chain proxies: 7.94, per 1000 atoms: 0.55 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 - 3.50 Amino acid : False - 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: 5.65 Conformation dependent library (CDL) restraints added in 3.1 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: 2.31 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: 6.57 Time building geometry restraints manager: 6.10 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: 98.06 - 105.94: 238 105.94 - 113.81: 8571 113.81 - 121.69: 7864 121.69 - 129.56: 2937 129.56 - 137.44: 86 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 2.440 nonbonded pdb=" OG SER L1524 " pdb=" OG SER L1527 " model vdw 2.174 2.440 ... (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: 5.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 21.530 Check model and map are aligned: 0.240 Set scattering table: 0.130 Process input model: 46.280 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.620 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 2 poor density : 98 time to evaluate : 1.709 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: 0.3415 time to fit residues: 49.5776 Evaluate side-chains 76 residues out of total 1627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 75 time to evaluate : 1.781 ------------------------------------------------------------------------------- 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: 0.9990 chunk 134 optimal weight: 5.9990 chunk 74 optimal weight: 0.0000 chunk 46 optimal weight: 0.7980 chunk 91 optimal weight: 8.9990 chunk 72 optimal weight: 1.9990 chunk 139 optimal weight: 0.6980 chunk 53 optimal weight: 5.9990 chunk 84 optimal weight: 4.9990 chunk 103 optimal weight: 0.6980 chunk 161 optimal weight: 6.9990 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 32 GLN L 56 ASN L 414 ASN L 415 GLN L 441 HIS L 610 GLN L 736 HIS L 869 GLN L1095 ASN ** L1510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L1745 HIS L1894 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.1262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 14602 Z= 0.145 Angle : 0.512 8.579 19696 Z= 0.264 Chirality : 0.038 0.192 2227 Planarity : 0.003 0.033 2494 Dihedral : 4.205 22.105 1926 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.78 % Favored : 92.16 % Rotamer: Outliers : 0.43 % Allowed : 11.32 % Favored : 88.25 % 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: -2.07 (0.20), residues: 1761 helix: 0.29 (0.18), residues: 899 sheet: -1.90 (0.46), residues: 114 loop : -3.54 (0.19), residues: 748 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 0.013 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 93 residues out of total 1627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 86 time to evaluate : 1.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 446 MET cc_start: 0.8351 (tpt) cc_final: 0.8146 (tpt) REVERT: L 1250 MET cc_start: 0.8385 (tpp) cc_final: 0.7915 (tpp) REVERT: L 1869 HIS cc_start: 0.7975 (m-70) cc_final: 0.7707 (m90) REVERT: L 2107 GLU cc_start: 0.8866 (mt-10) cc_final: 0.8652 (mm-30) outliers start: 7 outliers final: 3 residues processed: 91 average time/residue: 0.2676 time to fit residues: 37.7562 Evaluate side-chains 76 residues out of total 1627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 73 time to evaluate : 1.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 50 optimal weight: 10.0000 chunk 134 optimal weight: 0.7980 chunk 110 optimal weight: 0.9990 chunk 44 optimal weight: 9.9990 chunk 161 optimal weight: 3.9990 chunk 174 optimal weight: 6.9990 chunk 144 optimal weight: 0.0970 chunk 160 optimal weight: 3.9990 chunk 55 optimal weight: 0.0470 chunk 129 optimal weight: 0.9980 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 694 ASN L1481 GLN ** L1510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L1528 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 14602 Z= 0.132 Angle : 0.492 13.242 19696 Z= 0.248 Chirality : 0.038 0.171 2227 Planarity : 0.003 0.038 2494 Dihedral : 3.912 20.432 1924 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 1.23 % Allowed : 13.28 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.33 (0.20), residues: 1761 helix: 0.99 (0.18), residues: 888 sheet: -1.84 (0.46), residues: 118 loop : -3.19 (0.20), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 155 HIS 0.003 0.000 HIS L 359 PHE 0.010 0.001 PHE L 349 TYR 0.010 0.001 TYR L1187 ARG 0.002 0.000 ARG L1881 *********************** 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 100 residues out of total 1627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 80 time to evaluate : 1.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 879 MET cc_start: 0.8983 (ppp) cc_final: 0.8673 (ppp) REVERT: L 1077 GLU cc_start: 0.8432 (mt-10) cc_final: 0.8228 (mt-10) REVERT: L 1869 HIS cc_start: 0.8021 (m-70) cc_final: 0.7741 (m90) REVERT: L 2107 GLU cc_start: 0.8895 (mt-10) cc_final: 0.8625 (mm-30) REVERT: L 2108 MET cc_start: 0.8906 (ppp) cc_final: 0.8702 (ppp) outliers start: 20 outliers final: 9 residues processed: 98 average time/residue: 0.2565 time to fit residues: 39.6147 Evaluate side-chains 83 residues out of total 1627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 74 time to evaluate : 1.738 ------------------------------------------------------------------------------- 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 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: 0.8980 chunk 84 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 chunk 162 optimal weight: 10.0000 chunk 172 optimal weight: 4.9990 chunk 154 optimal weight: 4.9990 chunk 46 optimal weight: 0.9980 chunk 143 optimal weight: 0.4980 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 547 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 694 ASN L 877 GLN ** L1510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 14602 Z= 0.337 Angle : 0.581 9.129 19696 Z= 0.297 Chirality : 0.040 0.176 2227 Planarity : 0.003 0.039 2494 Dihedral : 4.242 19.352 1924 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.80 % Favored : 91.20 % Rotamer: Outliers : 1.29 % Allowed : 15.50 % Favored : 83.21 % 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: -1.39 (0.20), residues: 1761 helix: 0.88 (0.18), residues: 895 sheet: -1.90 (0.44), residues: 130 loop : -3.18 (0.20), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 155 HIS 0.003 0.001 HIS L1236 PHE 0.015 0.001 PHE L2109 TYR 0.009 0.001 TYR L1361 ARG 0.005 0.000 ARG L 363 *********************** 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 93 residues out of total 1627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 72 time to evaluate : 1.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 879 MET cc_start: 0.8942 (ppp) cc_final: 0.8714 (ppp) REVERT: L 1719 ASN cc_start: 0.8866 (OUTLIER) cc_final: 0.8448 (p0) REVERT: L 1842 MET cc_start: 0.8543 (tpp) cc_final: 0.8325 (tpp) REVERT: L 1869 HIS cc_start: 0.8064 (m-70) cc_final: 0.7794 (m90) outliers start: 21 outliers final: 15 residues processed: 89 average time/residue: 0.2353 time to fit residues: 33.4040 Evaluate side-chains 85 residues out of total 1627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 69 time to evaluate : 1.792 ------------------------------------------------------------------------------- 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 1121 LEU Chi-restraints excluded: chain L residue 1298 HIS Chi-restraints excluded: chain L residue 1300 THR Chi-restraints excluded: chain L residue 1328 THR Chi-restraints excluded: chain L residue 1362 MET Chi-restraints excluded: chain L residue 1466 VAL Chi-restraints excluded: chain L residue 1496 MET Chi-restraints excluded: chain L residue 1672 ASP Chi-restraints excluded: chain L residue 1719 ASN 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 2115 ASP 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: 0.6980 chunk 2 optimal weight: 0.8980 chunk 128 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 146 optimal weight: 0.6980 chunk 118 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 87 optimal weight: 1.9990 chunk 154 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 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 547 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 694 ASN ** L1510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.1939 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= 0.153 Angle : 0.499 8.966 19696 Z= 0.254 Chirality : 0.038 0.158 2227 Planarity : 0.003 0.042 2494 Dihedral : 3.965 20.924 1924 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 1.17 % Allowed : 16.36 % Favored : 82.47 % 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: -0.96 (0.21), residues: 1761 helix: 1.23 (0.18), residues: 889 sheet: -1.50 (0.47), residues: 118 loop : -2.95 (0.21), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 155 HIS 0.002 0.000 HIS L1510 PHE 0.009 0.001 PHE L2109 TYR 0.007 0.001 TYR L1663 ARG 0.003 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 95 residues out of total 1627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 76 time to evaluate : 1.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 395 TRP cc_start: 0.8765 (t-100) cc_final: 0.8158 (t60) REVERT: L 879 MET cc_start: 0.8973 (ppp) cc_final: 0.8749 (ppp) REVERT: L 1719 ASN cc_start: 0.8818 (OUTLIER) cc_final: 0.8343 (p0) REVERT: L 1771 MET cc_start: 0.8803 (pmm) cc_final: 0.8266 (ppp) REVERT: L 1869 HIS cc_start: 0.8027 (m-70) cc_final: 0.7712 (m90) outliers start: 19 outliers final: 11 residues processed: 94 average time/residue: 0.2416 time to fit residues: 35.3488 Evaluate side-chains 84 residues out of total 1627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 72 time to evaluate : 1.961 ------------------------------------------------------------------------------- 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 882 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 1362 MET Chi-restraints excluded: chain L residue 1719 ASN 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: 4.9990 chunk 34 optimal weight: 8.9990 chunk 101 optimal weight: 0.6980 chunk 42 optimal weight: 0.9980 chunk 172 optimal weight: 6.9990 chunk 142 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 14 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 166 optimal weight: 4.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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** L 694 ASN ** L1510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 14602 Z= 0.192 Angle : 0.519 9.409 19696 Z= 0.262 Chirality : 0.038 0.148 2227 Planarity : 0.003 0.043 2494 Dihedral : 3.969 19.377 1924 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % Rotamer: Outliers : 1.48 % Allowed : 16.54 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.88 (0.21), residues: 1761 helix: 1.22 (0.18), residues: 889 sheet: -1.39 (0.47), residues: 118 loop : -2.83 (0.21), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 155 HIS 0.002 0.000 HIS L1236 PHE 0.010 0.001 PHE L 349 TYR 0.007 0.001 TYR L1450 ARG 0.003 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 101 residues out of total 1627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 77 time to evaluate : 1.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 1719 ASN cc_start: 0.8797 (OUTLIER) cc_final: 0.8346 (p0) REVERT: L 1771 MET cc_start: 0.8834 (pmm) cc_final: 0.8314 (ppp) REVERT: L 1869 HIS cc_start: 0.8022 (m-70) cc_final: 0.7719 (m90) REVERT: L 2136 ARG cc_start: 0.8879 (mmm160) cc_final: 0.8609 (mmm160) REVERT: L 2137 MET cc_start: 0.6547 (mpp) cc_final: 0.5194 (mpp) outliers start: 24 outliers final: 20 residues processed: 99 average time/residue: 0.2613 time to fit residues: 40.3262 Evaluate side-chains 95 residues out of total 1627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 74 time to evaluate : 1.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 154 ASP Chi-restraints excluded: chain L residue 255 THR Chi-restraints excluded: chain L residue 348 ILE Chi-restraints excluded: chain L residue 378 VAL Chi-restraints excluded: chain L residue 380 ASP Chi-restraints excluded: chain L residue 486 VAL Chi-restraints excluded: chain L residue 601 VAL 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 1362 MET Chi-restraints excluded: chain L residue 1408 ILE Chi-restraints excluded: chain L residue 1466 VAL Chi-restraints excluded: chain L residue 1672 ASP Chi-restraints excluded: chain L residue 1719 ASN 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 19 optimal weight: 6.9990 chunk 98 optimal weight: 0.7980 chunk 125 optimal weight: 0.8980 chunk 97 optimal weight: 0.9990 chunk 144 optimal weight: 0.5980 chunk 96 optimal weight: 0.6980 chunk 171 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 104 optimal weight: 0.6980 chunk 79 optimal weight: 3.9990 chunk 106 optimal weight: 0.3980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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** L 694 ASN L1426 GLN ** L1510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 14602 Z= 0.135 Angle : 0.489 10.176 19696 Z= 0.246 Chirality : 0.038 0.147 2227 Planarity : 0.003 0.043 2494 Dihedral : 3.796 20.378 1924 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 1.72 % Allowed : 16.48 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.72 (0.21), residues: 1761 helix: 1.32 (0.18), residues: 893 sheet: -1.24 (0.47), residues: 118 loop : -2.73 (0.21), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 395 HIS 0.002 0.000 HIS L1510 PHE 0.010 0.001 PHE L 349 TYR 0.007 0.001 TYR L1663 ARG 0.004 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 108 residues out of total 1627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 80 time to evaluate : 1.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 1719 ASN cc_start: 0.8801 (OUTLIER) cc_final: 0.8323 (p0) REVERT: L 1771 MET cc_start: 0.8817 (pmm) cc_final: 0.8326 (ppp) REVERT: L 1869 HIS cc_start: 0.8043 (m-70) cc_final: 0.7748 (m90) REVERT: L 2136 ARG cc_start: 0.8866 (mmm160) cc_final: 0.8592 (mmm160) REVERT: L 2137 MET cc_start: 0.6422 (mpp) cc_final: 0.4976 (mpp) outliers start: 28 outliers final: 18 residues processed: 107 average time/residue: 0.2686 time to fit residues: 44.0484 Evaluate side-chains 93 residues out of total 1627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 74 time to evaluate : 1.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 154 ASP 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 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 1408 ILE Chi-restraints excluded: chain L residue 1466 VAL Chi-restraints excluded: chain L residue 1672 ASP Chi-restraints excluded: chain L residue 1719 ASN Chi-restraints excluded: chain L residue 1786 LEU Chi-restraints excluded: chain L residue 1871 THR Chi-restraints excluded: chain L residue 2115 ASP 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: 0.8980 chunk 102 optimal weight: 0.9990 chunk 51 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 109 optimal weight: 5.9990 chunk 116 optimal weight: 4.9990 chunk 84 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 134 optimal weight: 0.1980 chunk 156 optimal weight: 0.9980 chunk 164 optimal weight: 5.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 694 ASN ** L1510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 14602 Z= 0.151 Angle : 0.520 12.411 19696 Z= 0.257 Chirality : 0.038 0.217 2227 Planarity : 0.003 0.044 2494 Dihedral : 3.797 18.752 1924 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 1.41 % Allowed : 16.97 % Favored : 81.61 % 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: -0.68 (0.21), residues: 1761 helix: 1.30 (0.18), residues: 892 sheet: -1.16 (0.48), residues: 118 loop : -2.64 (0.21), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP L 395 HIS 0.002 0.000 HIS L1406 PHE 0.016 0.001 PHE L1358 TYR 0.007 0.001 TYR L1361 ARG 0.009 0.000 ARG L 169 *********************** 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 100 residues out of total 1627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 77 time to evaluate : 1.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 1719 ASN cc_start: 0.8806 (OUTLIER) cc_final: 0.8328 (p0) REVERT: L 1771 MET cc_start: 0.8848 (pmm) cc_final: 0.8358 (ppp) REVERT: L 1869 HIS cc_start: 0.8093 (m-70) cc_final: 0.7798 (m90) REVERT: L 2108 MET cc_start: 0.8942 (ppp) cc_final: 0.8561 (ppp) REVERT: L 2136 ARG cc_start: 0.8871 (mmm160) cc_final: 0.8626 (mmm160) REVERT: L 2137 MET cc_start: 0.6318 (mpp) cc_final: 0.5078 (mpp) outliers start: 23 outliers final: 19 residues processed: 100 average time/residue: 0.2683 time to fit residues: 41.3361 Evaluate side-chains 95 residues out of total 1627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 75 time to evaluate : 1.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 154 ASP 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 380 ASP Chi-restraints excluded: chain L residue 486 VAL Chi-restraints excluded: chain L residue 601 VAL 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 1408 ILE Chi-restraints excluded: chain L residue 1466 VAL Chi-restraints excluded: chain L residue 1672 ASP Chi-restraints excluded: chain L residue 1719 ASN Chi-restraints excluded: chain L residue 1786 LEU Chi-restraints excluded: chain L residue 1871 THR Chi-restraints excluded: chain L residue 2115 ASP 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: 3.9990 chunk 164 optimal weight: 5.9990 chunk 96 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 125 optimal weight: 0.4980 chunk 49 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 chunk 151 optimal weight: 0.5980 chunk 104 optimal weight: 0.0970 chunk 169 optimal weight: 3.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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** L 694 ASN L1426 GLN ** L1510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14602 Z= 0.188 Angle : 0.549 12.593 19696 Z= 0.269 Chirality : 0.039 0.202 2227 Planarity : 0.003 0.043 2494 Dihedral : 3.854 18.895 1924 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 1.48 % Allowed : 16.91 % Favored : 81.61 % 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: -0.73 (0.21), residues: 1761 helix: 1.24 (0.18), residues: 894 sheet: -1.17 (0.48), residues: 118 loop : -2.65 (0.21), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP L 395 HIS 0.002 0.000 HIS L1236 PHE 0.024 0.001 PHE L1358 TYR 0.007 0.001 TYR L 871 ARG 0.008 0.000 ARG L 169 *********************** 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 97 residues out of total 1627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 73 time to evaluate : 1.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 1719 ASN cc_start: 0.8788 (OUTLIER) cc_final: 0.8345 (p0) REVERT: L 1771 MET cc_start: 0.8837 (pmm) cc_final: 0.8346 (ppp) REVERT: L 1869 HIS cc_start: 0.8117 (m-70) cc_final: 0.7833 (m90) REVERT: L 2108 MET cc_start: 0.8954 (ppp) cc_final: 0.8590 (ppp) REVERT: L 2136 ARG cc_start: 0.8898 (mmm160) cc_final: 0.8643 (mmm160) REVERT: L 2137 MET cc_start: 0.6506 (mpp) cc_final: 0.5066 (mpp) outliers start: 24 outliers final: 20 residues processed: 96 average time/residue: 0.2499 time to fit residues: 37.8610 Evaluate side-chains 94 residues out of total 1627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 73 time to evaluate : 1.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 154 ASP 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 380 ASP Chi-restraints excluded: chain L residue 486 VAL Chi-restraints excluded: chain L residue 601 VAL 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 1408 ILE Chi-restraints excluded: chain L residue 1466 VAL Chi-restraints excluded: chain L residue 1496 MET Chi-restraints excluded: chain L residue 1672 ASP Chi-restraints excluded: chain L residue 1719 ASN Chi-restraints excluded: chain L residue 1786 LEU Chi-restraints excluded: chain L residue 1871 THR Chi-restraints excluded: chain L residue 2115 ASP 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: 2.9990 chunk 80 optimal weight: 1.9990 chunk 117 optimal weight: 0.0270 chunk 177 optimal weight: 4.9990 chunk 163 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 chunk 14 optimal weight: 0.3980 chunk 109 optimal weight: 5.9990 chunk 86 optimal weight: 8.9990 chunk 112 optimal weight: 0.9990 chunk 150 optimal weight: 4.9990 overall best weight: 1.0844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 694 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14602 Z= 0.195 Angle : 0.558 12.791 19696 Z= 0.273 Chirality : 0.039 0.225 2227 Planarity : 0.003 0.045 2494 Dihedral : 3.889 18.684 1924 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 1.41 % Allowed : 17.16 % Favored : 81.43 % 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: -0.76 (0.21), residues: 1761 helix: 1.15 (0.18), residues: 904 sheet: -1.10 (0.48), residues: 118 loop : -2.64 (0.21), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP L 395 HIS 0.005 0.001 HIS L1510 PHE 0.022 0.001 PHE L1358 TYR 0.008 0.001 TYR L1361 ARG 0.008 0.000 ARG L 169 ********************** 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 97 residues out of total 1627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 74 time to evaluate : 1.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 1719 ASN cc_start: 0.8779 (OUTLIER) cc_final: 0.8343 (p0) REVERT: L 1771 MET cc_start: 0.8845 (pmm) cc_final: 0.8390 (ppp) REVERT: L 2108 MET cc_start: 0.8972 (ppp) cc_final: 0.8613 (ppp) REVERT: L 2136 ARG cc_start: 0.8914 (mmm160) cc_final: 0.8655 (mmm160) REVERT: L 2137 MET cc_start: 0.6587 (mpp) cc_final: 0.5101 (mpp) outliers start: 23 outliers final: 20 residues processed: 95 average time/residue: 0.2447 time to fit residues: 36.9810 Evaluate side-chains 92 residues out of total 1627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 71 time to evaluate : 1.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 154 ASP 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 380 ASP Chi-restraints excluded: chain L residue 486 VAL Chi-restraints excluded: chain L residue 601 VAL 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 1408 ILE Chi-restraints excluded: chain L residue 1466 VAL Chi-restraints excluded: chain L residue 1496 MET Chi-restraints excluded: chain L residue 1672 ASP Chi-restraints excluded: chain L residue 1719 ASN Chi-restraints excluded: chain L residue 1786 LEU Chi-restraints excluded: chain L residue 1871 THR Chi-restraints excluded: chain L residue 2115 ASP 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: 2.9990 chunk 130 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 chunk 141 optimal weight: 0.7980 chunk 59 optimal weight: 0.5980 chunk 145 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 124 optimal weight: 0.5980 chunk 8 optimal weight: 0.2980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L1510 HIS ** 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 = 0.3412 r_free = 0.3412 target = 0.060007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.040422 restraints weight = 70653.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.041833 restraints weight = 36119.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.042732 restraints weight = 24428.919| |-----------------------------------------------------------------------------| r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 14602 Z= 0.140 Angle : 0.541 12.645 19696 Z= 0.261 Chirality : 0.038 0.226 2227 Planarity : 0.003 0.045 2494 Dihedral : 3.736 19.514 1924 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 1.23 % Allowed : 17.40 % Favored : 81.37 % 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: -0.59 (0.21), residues: 1761 helix: 1.32 (0.18), residues: 895 sheet: -1.06 (0.48), residues: 120 loop : -2.55 (0.22), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP L 395 HIS 0.006 0.000 HIS L1510 PHE 0.023 0.001 PHE L1358 TYR 0.008 0.001 TYR L 471 ARG 0.007 0.000 ARG L 169 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2673.61 seconds wall clock time: 49 minutes 50.58 seconds (2990.58 seconds total)