Starting phenix.real_space_refine (version: 1.21rc1) on Sun Apr 23 06:38:34 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ojj_12953/04_2023/7ojj_12953.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ojj_12953/04_2023/7ojj_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_12953/04_2023/7ojj_12953.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ojj_12953/04_2023/7ojj_12953.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ojj_12953/04_2023/7ojj_12953.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ojj_12953/04_2023/7ojj_12953.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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: 7.47, per 1000 atoms: 0.52 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: 5.11 Conformation dependent library (CDL) restraints added in 2.0 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: 1.13 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: 5.73 Time building geometry restraints manager: 5.62 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: 8.000 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: 0.020 Extract box with map and model: 21.150 Check model and map are aligned: 0.230 Set scattering table: 0.130 Process input model: 39.660 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.050 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.460 ------------------------------------------------------------------------------- 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 % 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 *********************** 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 : 1.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 100 average time/residue: 0.3265 time to fit residues: 47.0218 Evaluate side-chains 74 residues out of total 1627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 73 time to evaluate : 1.854 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1234 time to fit residues: 2.4377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 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: 0.8634 moved from start: 0.1217 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= 0.151 Angle : 0.521 8.521 19696 Z= 0.269 Chirality : 0.038 0.198 2227 Planarity : 0.003 0.032 2494 Dihedral : 4.229 21.979 1924 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.95 % Favored : 91.99 % Rotamer Outliers : 0.49 % 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: -2.16 (0.19), residues: 1761 helix: 0.23 (0.18), residues: 901 sheet: -1.93 (0.46), residues: 114 loop : -3.59 (0.19), residues: 746 *********************** 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: 8 poor density : 85 time to evaluate : 1.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 90 average time/residue: 0.2897 time to fit residues: 40.6616 Evaluate side-chains 76 residues out of total 1627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 72 time to evaluate : 1.934 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1452 time to fit residues: 3.8882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 89 optimal weight: 0.9980 chunk 50 optimal weight: 10.0000 chunk 134 optimal weight: 0.8980 chunk 110 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 161 optimal weight: 4.9990 chunk 174 optimal weight: 7.9990 chunk 144 optimal weight: 0.0980 chunk 160 optimal weight: 0.9980 chunk 55 optimal weight: 0.6980 chunk 129 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L1481 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: 0.8626 moved from start: 0.1617 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= 0.141 Angle : 0.506 13.203 19696 Z= 0.253 Chirality : 0.038 0.171 2227 Planarity : 0.003 0.035 2494 Dihedral : 3.963 20.554 1924 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.40 % Favored : 91.60 % Rotamer Outliers : 0.74 % 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: -1.37 (0.20), residues: 1761 helix: 0.95 (0.18), residues: 888 sheet: -1.83 (0.47), residues: 116 loop : -3.21 (0.20), residues: 757 *********************** 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 90 residues out of total 1627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 78 time to evaluate : 1.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 6 residues processed: 90 average time/residue: 0.2691 time to fit residues: 38.2500 Evaluate side-chains 77 residues out of total 1627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 71 time to evaluate : 1.585 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1372 time to fit residues: 4.0126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 84 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 77 optimal weight: 0.0980 chunk 108 optimal weight: 0.9980 chunk 162 optimal weight: 9.9990 chunk 172 optimal weight: 3.9990 chunk 154 optimal weight: 0.0570 chunk 46 optimal weight: 2.9990 chunk 143 optimal weight: 0.4980 overall best weight: 0.5098 ------------------------------------------------------------------------------- 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 877 GLN ** L1510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L1528 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 14602 Z= 0.127 Angle : 0.506 9.440 19696 Z= 0.251 Chirality : 0.038 0.186 2227 Planarity : 0.003 0.037 2494 Dihedral : 3.816 20.606 1924 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer Outliers : 0.62 % 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: -1.03 (0.21), residues: 1761 helix: 1.17 (0.18), residues: 889 sheet: -1.57 (0.46), residues: 118 loop : -2.99 (0.21), residues: 754 *********************** 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 90 residues out of total 1627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 80 time to evaluate : 1.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 2 residues processed: 89 average time/residue: 0.2598 time to fit residues: 36.5698 Evaluate side-chains 75 residues out of total 1627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 73 time to evaluate : 1.756 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1294 time to fit residues: 3.0155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 128 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 146 optimal weight: 0.8980 chunk 118 optimal weight: 0.6980 chunk 0 optimal weight: 7.9990 chunk 87 optimal weight: 0.8980 chunk 154 optimal weight: 0.9980 chunk 43 optimal weight: 6.9990 chunk 57 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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: 0.8630 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 14602 Z= 0.164 Angle : 0.515 9.920 19696 Z= 0.259 Chirality : 0.038 0.154 2227 Planarity : 0.003 0.039 2494 Dihedral : 3.841 19.010 1924 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.95 % Favored : 92.05 % Rotamer Outliers : 0.62 % 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: -0.86 (0.21), residues: 1761 helix: 1.27 (0.18), residues: 890 sheet: -1.43 (0.46), residues: 118 loop : -2.87 (0.21), residues: 753 *********************** 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 84 residues out of total 1627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 74 time to evaluate : 1.633 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 7 residues processed: 83 average time/residue: 0.2626 time to fit residues: 34.4410 Evaluate side-chains 77 residues out of total 1627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 70 time to evaluate : 1.658 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1351 time to fit residues: 4.0721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 101 optimal weight: 0.6980 chunk 42 optimal weight: 0.9980 chunk 172 optimal weight: 3.9990 chunk 142 optimal weight: 0.0980 chunk 79 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 90 optimal weight: 0.9990 chunk 166 optimal weight: 0.0870 overall best weight: 0.5158 ------------------------------------------------------------------------------- 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: 0.8605 moved from start: 0.2240 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= 0.127 Angle : 0.501 10.718 19696 Z= 0.251 Chirality : 0.037 0.147 2227 Planarity : 0.003 0.040 2494 Dihedral : 3.744 19.907 1924 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer Outliers : 0.43 % 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: -0.70 (0.21), residues: 1761 helix: 1.31 (0.19), residues: 900 sheet: -1.09 (0.48), residues: 112 loop : -2.74 (0.21), residues: 749 *********************** 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 85 residues out of total 1627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 78 time to evaluate : 1.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 1 residues processed: 85 average time/residue: 0.2802 time to fit residues: 37.5177 Evaluate side-chains 76 residues out of total 1627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 75 time to evaluate : 1.650 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1274 time to fit residues: 2.6058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 19 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 chunk 125 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 144 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 chunk 171 optimal weight: 0.0370 chunk 107 optimal weight: 2.9990 chunk 104 optimal weight: 0.0070 chunk 79 optimal weight: 5.9990 chunk 106 optimal weight: 1.9990 overall best weight: 0.8080 ------------------------------------------------------------------------------- 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: 0.8623 moved from start: 0.2296 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= 0.157 Angle : 0.520 13.445 19696 Z= 0.256 Chirality : 0.038 0.151 2227 Planarity : 0.003 0.041 2494 Dihedral : 3.757 17.986 1924 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer Outliers : 0.49 % 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: -0.69 (0.21), residues: 1761 helix: 1.32 (0.19), residues: 894 sheet: -1.08 (0.47), residues: 118 loop : -2.72 (0.21), residues: 749 *********************** 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 87 residues out of total 1627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 79 time to evaluate : 1.836 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 86 average time/residue: 0.2887 time to fit residues: 38.6423 Evaluate side-chains 76 residues out of total 1627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 73 time to evaluate : 1.775 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1309 time to fit residues: 3.1690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 68 optimal weight: 0.5980 chunk 102 optimal weight: 0.9980 chunk 51 optimal weight: 7.9990 chunk 33 optimal weight: 5.9990 chunk 109 optimal weight: 7.9990 chunk 116 optimal weight: 4.9990 chunk 84 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 134 optimal weight: 0.0270 chunk 156 optimal weight: 6.9990 chunk 164 optimal weight: 5.9990 overall best weight: 1.7242 ------------------------------------------------------------------------------- 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** 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: 0.8679 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 14602 Z= 0.285 Angle : 0.597 12.450 19696 Z= 0.296 Chirality : 0.040 0.180 2227 Planarity : 0.003 0.044 2494 Dihedral : 4.076 18.688 1924 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer Outliers : 0.43 % 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: -0.85 (0.21), residues: 1761 helix: 1.13 (0.18), residues: 898 sheet: -1.27 (0.47), residues: 118 loop : -2.71 (0.21), residues: 745 *********************** 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 78 residues out of total 1627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 71 time to evaluate : 1.887 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 75 average time/residue: 0.2880 time to fit residues: 33.8259 Evaluate side-chains 72 residues out of total 1627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 69 time to evaluate : 2.001 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1680 time to fit residues: 3.3385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 149 optimal weight: 2.9990 chunk 159 optimal weight: 3.9990 chunk 164 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 125 optimal weight: 0.5980 chunk 49 optimal weight: 0.6980 chunk 144 optimal weight: 0.6980 chunk 151 optimal weight: 0.5980 chunk 104 optimal weight: 0.0870 chunk 169 optimal weight: 0.6980 overall best weight: 0.5358 ------------------------------------------------------------------------------- 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: 0.8619 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 14602 Z= 0.133 Angle : 0.548 12.844 19696 Z= 0.265 Chirality : 0.038 0.151 2227 Planarity : 0.003 0.046 2494 Dihedral : 3.805 20.045 1924 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer Outliers : 0.06 % 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: -0.60 (0.21), residues: 1761 helix: 1.36 (0.19), residues: 890 sheet: -1.06 (0.48), residues: 118 loop : -2.59 (0.21), residues: 753 *********************** 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 75 residues out of total 1627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 74 time to evaluate : 1.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 75 average time/residue: 0.2930 time to fit residues: 34.9775 Evaluate side-chains 72 residues out of total 1627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 1.776 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 chunk 177 optimal weight: 0.0060 chunk 163 optimal weight: 0.1980 chunk 141 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 109 optimal weight: 3.9990 chunk 86 optimal weight: 9.9990 chunk 112 optimal weight: 0.6980 chunk 150 optimal weight: 0.5980 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L1075 ASN ** 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: 0.8607 moved from start: 0.2593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 14602 Z= 0.129 Angle : 0.537 12.544 19696 Z= 0.262 Chirality : 0.038 0.148 2227 Planarity : 0.003 0.045 2494 Dihedral : 3.690 20.484 1924 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer Outliers : 0.00 % 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: -0.48 (0.21), residues: 1761 helix: 1.40 (0.19), residues: 895 sheet: -0.90 (0.48), residues: 117 loop : -2.49 (0.22), residues: 749 ********************** 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 75 residues out of total 1627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 1.867 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.2796 time to fit residues: 32.9483 Evaluate side-chains 71 residues out of total 1627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 1.761 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 43 optimal weight: 6.9990 chunk 130 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 39 optimal weight: 9.9990 chunk 141 optimal weight: 0.9980 chunk 59 optimal weight: 0.6980 chunk 145 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 124 optimal weight: 0.3980 chunk 8 optimal weight: 4.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.060308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.041341 restraints weight = 70652.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.042728 restraints weight = 35878.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.043616 restraints weight = 24039.973| |-----------------------------------------------------------------------------| r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.2605 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= 0.156 Angle : 0.547 10.922 19696 Z= 0.268 Chirality : 0.038 0.147 2227 Planarity : 0.003 0.042 2494 Dihedral : 3.710 20.452 1924 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer Outliers : 0.06 % 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: -0.47 (0.21), residues: 1761 helix: 1.38 (0.19), residues: 896 sheet: -0.86 (0.48), residues: 117 loop : -2.47 (0.22), residues: 748 =============================================================================== Job complete usr+sys time: 2563.41 seconds wall clock time: 48 minutes 32.60 seconds (2912.60 seconds total)