Starting phenix.real_space_refine on Thu Mar 21 04:45:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zke_14762/03_2024/7zke_14762_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zke_14762/03_2024/7zke_14762.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zke_14762/03_2024/7zke_14762.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zke_14762/03_2024/7zke_14762.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zke_14762/03_2024/7zke_14762_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zke_14762/03_2024/7zke_14762_updated.pdb" } resolution = 3.6 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= 0.004 sd= 0.091 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: 9 Type Number sf(0) Gaussians P 22 5.49 5 Mg 1 5.21 5 S 73 5.16 5 Be 1 3.05 5 C 9225 2.51 5 N 2571 2.21 5 O 2728 1.98 5 F 3 1.80 5 H 14679 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D TYR 246": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 252": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 483": "OD1" <-> "OD2" Residue "E TYR 1429": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 29303 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 315 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} Chain: "B" Number of atoms: 315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 315 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} Chain: "D" Number of atoms: 2907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 2907 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 8, 'TRANS': 169} Chain: "E" Number of atoms: 25766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1626, 25766 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'peptide': 1623, 'undetermined': 3} Link IDs: {'PTRANS': 84, 'TRANS': 1538, None: 3} Not linked: pdbres="GLN E1886 " pdbres=" MG E1901 " Not linked: pdbres=" MG E1901 " pdbres="ADP E1902 " Not linked: pdbres="ADP E1902 " pdbres="BEF E1903 " Chain breaks: 7 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Time building chain proxies: 13.22, per 1000 atoms: 0.45 Number of scatterers: 29303 At special positions: 0 Unit cell: (100.416, 121.336, 149.578, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) S 73 16.00 P 22 15.00 Mg 1 11.99 F 3 9.00 O 2728 8.00 N 2571 7.00 C 9225 6.00 Be 1 4.00 H 14679 1.00 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: 23.46 Conformation dependent library (CDL) restraints added in 3.1 seconds 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3408 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 92 helices and 4 sheets defined 59.7% alpha, 4.6% beta 9 base pairs and 13 stacking pairs defined. Time for finding SS restraints: 17.01 Creating SS restraints... Processing helix chain 'D' and resid 97 through 103 removed outlier: 3.606A pdb=" N ALA D 101 " --> pdb=" O LEU D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 160 Processing helix chain 'D' and resid 187 through 192 Processing helix chain 'D' and resid 235 through 251 Proline residue: D 247 - end of helix removed outlier: 4.677A pdb=" N ASP D 251 " --> pdb=" O PRO D 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 12 removed outlier: 3.931A pdb=" N LEU E 12 " --> pdb=" O LEU E 8 " (cutoff:3.500A) Processing helix chain 'E' and resid 18 through 34 Processing helix chain 'E' and resid 36 through 51 removed outlier: 4.483A pdb=" N PHE E 40 " --> pdb=" O GLU E 37 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N SER E 44 " --> pdb=" O ASN E 41 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N VAL E 47 " --> pdb=" O SER E 44 " (cutoff:3.500A) Proline residue: E 48 - end of helix removed outlier: 3.562A pdb=" N ARG E 51 " --> pdb=" O PRO E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 71 removed outlier: 3.655A pdb=" N ASN E 71 " --> pdb=" O LYS E 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 114 No H-bonds generated for 'chain 'E' and resid 112 through 114' Processing helix chain 'E' and resid 117 through 122 Processing helix chain 'E' and resid 135 through 138 No H-bonds generated for 'chain 'E' and resid 135 through 138' Processing helix chain 'E' and resid 142 through 156 removed outlier: 4.041A pdb=" N ASN E 154 " --> pdb=" O LYS E 150 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N GLY E 155 " --> pdb=" O LYS E 151 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 168 No H-bonds generated for 'chain 'E' and resid 166 through 168' Processing helix chain 'E' and resid 312 through 325 removed outlier: 4.198A pdb=" N ARG E 315 " --> pdb=" O PRO E 312 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LYS E 321 " --> pdb=" O GLU E 318 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU E 324 " --> pdb=" O LYS E 321 " (cutoff:3.500A) Processing helix chain 'E' and resid 329 through 349 removed outlier: 6.755A pdb=" N ALA E 348 " --> pdb=" O ARG E 344 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N GLY E 349 " --> pdb=" O VAL E 345 " (cutoff:3.500A) Processing helix chain 'E' and resid 358 through 382 removed outlier: 3.538A pdb=" N ARG E 375 " --> pdb=" O ASP E 371 " (cutoff:3.500A) Processing helix chain 'E' and resid 396 through 410 Processing helix chain 'E' and resid 414 through 429 removed outlier: 3.807A pdb=" N HIS E 418 " --> pdb=" O VAL E 414 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA E 419 " --> pdb=" O GLU E 415 " (cutoff:3.500A) Processing helix chain 'E' and resid 437 through 456 removed outlier: 3.626A pdb=" N ALA E 441 " --> pdb=" O ASN E 438 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL E 442 " --> pdb=" O MET E 439 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL E 454 " --> pdb=" O ARG E 451 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N VAL E 456 " --> pdb=" O VAL E 453 " (cutoff:3.500A) Processing helix chain 'E' and resid 458 through 461 No H-bonds generated for 'chain 'E' and resid 458 through 461' Processing helix chain 'E' and resid 465 through 479 Processing helix chain 'E' and resid 484 through 501 removed outlier: 3.707A pdb=" N LEU E 494 " --> pdb=" O SER E 490 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ILE E 495 " --> pdb=" O ALA E 491 " (cutoff:3.500A) Proline residue: E 496 - end of helix removed outlier: 5.517A pdb=" N LYS E 499 " --> pdb=" O ILE E 495 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N GLU E 500 " --> pdb=" O PRO E 496 " (cutoff:3.500A) Processing helix chain 'E' and resid 506 through 518 Processing helix chain 'E' and resid 531 through 543 Processing helix chain 'E' and resid 545 through 555 Processing helix chain 'E' and resid 559 through 561 No H-bonds generated for 'chain 'E' and resid 559 through 561' Processing helix chain 'E' and resid 563 through 573 Proline residue: E 568 - end of helix removed outlier: 4.329A pdb=" N TYR E 571 " --> pdb=" O VAL E 567 " (cutoff:3.500A) Proline residue: E 572 - end of helix Processing helix chain 'E' and resid 579 through 593 Processing helix chain 'E' and resid 597 through 600 No H-bonds generated for 'chain 'E' and resid 597 through 600' Processing helix chain 'E' and resid 606 through 617 Processing helix chain 'E' and resid 622 through 642 removed outlier: 3.575A pdb=" N ARG E 642 " --> pdb=" O ARG E 638 " (cutoff:3.500A) Processing helix chain 'E' and resid 644 through 651 Processing helix chain 'E' and resid 655 through 662 Processing helix chain 'E' and resid 677 through 679 No H-bonds generated for 'chain 'E' and resid 677 through 679' Processing helix chain 'E' and resid 745 through 764 Processing helix chain 'E' and resid 768 through 770 No H-bonds generated for 'chain 'E' and resid 768 through 770' Processing helix chain 'E' and resid 772 through 782 removed outlier: 3.812A pdb=" N ALA E 781 " --> pdb=" O ALA E 777 " (cutoff:3.500A) Processing helix chain 'E' and resid 787 through 803 Processing helix chain 'E' and resid 811 through 822 removed outlier: 4.594A pdb=" N GLU E 815 " --> pdb=" O ARG E 812 " (cutoff:3.500A) Proline residue: E 816 - end of helix removed outlier: 3.805A pdb=" N LYS E 819 " --> pdb=" O PRO E 816 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASP E 822 " --> pdb=" O LYS E 819 " (cutoff:3.500A) Processing helix chain 'E' and resid 830 through 852 removed outlier: 4.726A pdb=" N THR E 834 " --> pdb=" O ASP E 831 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASP E 852 " --> pdb=" O LEU E 849 " (cutoff:3.500A) Processing helix chain 'E' and resid 881 through 889 Processing helix chain 'E' and resid 891 through 898 Processing helix chain 'E' and resid 904 through 946 Proline residue: E 909 - end of helix removed outlier: 4.858A pdb=" N GLU E 913 " --> pdb=" O PRO E 909 " (cutoff:3.500A) Processing helix chain 'E' and resid 955 through 965 Processing helix chain 'E' and resid 971 through 991 removed outlier: 3.580A pdb=" N GLN E 986 " --> pdb=" O ALA E 982 " (cutoff:3.500A) Processing helix chain 'E' and resid 994 through 1009 removed outlier: 3.719A pdb=" N CYS E1009 " --> pdb=" O VAL E1005 " (cutoff:3.500A) Processing helix chain 'E' and resid 1018 through 1021 No H-bonds generated for 'chain 'E' and resid 1018 through 1021' Processing helix chain 'E' and resid 1029 through 1032 No H-bonds generated for 'chain 'E' and resid 1029 through 1032' Processing helix chain 'E' and resid 1045 through 1078 removed outlier: 6.722A pdb=" N ALA E1073 " --> pdb=" O LYS E1069 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N GLU E1074 " --> pdb=" O ASN E1070 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N LEU E1075 " --> pdb=" O PHE E1071 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N LEU E1076 " --> pdb=" O GLY E1072 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N GLU E1077 " --> pdb=" O ALA E1073 " (cutoff:3.500A) Processing helix chain 'E' and resid 1080 through 1094 Proline residue: E1089 - end of helix Processing helix chain 'E' and resid 1100 through 1103 Processing helix chain 'E' and resid 1109 through 1124 Processing helix chain 'E' and resid 1129 through 1146 Proline residue: E1133 - end of helix Proline residue: E1140 - end of helix removed outlier: 3.823A pdb=" N ILE E1143 " --> pdb=" O PRO E1140 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU E1146 " --> pdb=" O ILE E1143 " (cutoff:3.500A) Processing helix chain 'E' and resid 1151 through 1167 Processing helix chain 'E' and resid 1169 through 1179 removed outlier: 4.132A pdb=" N THR E1174 " --> pdb=" O VAL E1170 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA E1175 " --> pdb=" O ASP E1171 " (cutoff:3.500A) Processing helix chain 'E' and resid 1181 through 1183 No H-bonds generated for 'chain 'E' and resid 1181 through 1183' Processing helix chain 'E' and resid 1190 through 1207 Processing helix chain 'E' and resid 1210 through 1225 Proline residue: E1213 - end of helix removed outlier: 4.736A pdb=" N ILE E1216 " --> pdb=" O PRO E1213 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE E1219 " --> pdb=" O ILE E1216 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N VAL E1220 " --> pdb=" O PHE E1217 " (cutoff:3.500A) Proline residue: E1221 - end of helix removed outlier: 4.164A pdb=" N GLY E1224 " --> pdb=" O PRO E1221 " (cutoff:3.500A) Processing helix chain 'E' and resid 1231 through 1250 removed outlier: 3.532A pdb=" N THR E1243 " --> pdb=" O THR E1239 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N LYS E1246 " --> pdb=" O ALA E1242 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N LEU E1247 " --> pdb=" O THR E1243 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL E1248 " --> pdb=" O LEU E1244 " (cutoff:3.500A) Proline residue: E1249 - end of helix Processing helix chain 'E' and resid 1262 through 1279 removed outlier: 3.645A pdb=" N GLU E1271 " --> pdb=" O GLY E1267 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N THR E1273 " --> pdb=" O ASP E1269 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N PHE E1274 " --> pdb=" O ARG E1270 " (cutoff:3.500A) Processing helix chain 'E' and resid 1281 through 1283 No H-bonds generated for 'chain 'E' and resid 1281 through 1283' Processing helix chain 'E' and resid 1299 through 1314 Processing helix chain 'E' and resid 1328 through 1350 Processing helix chain 'E' and resid 1353 through 1355 No H-bonds generated for 'chain 'E' and resid 1353 through 1355' Processing helix chain 'E' and resid 1366 through 1379 removed outlier: 4.442A pdb=" N GLY E1370 " --> pdb=" O THR E1367 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TRP E1372 " --> pdb=" O SER E1369 " (cutoff:3.500A) Processing helix chain 'E' and resid 1392 through 1397 Processing helix chain 'E' and resid 1401 through 1404 Processing helix chain 'E' and resid 1412 through 1417 Processing helix chain 'E' and resid 1419 through 1424 removed outlier: 4.770A pdb=" N LYS E1424 " --> pdb=" O ASP E1420 " (cutoff:3.500A) Processing helix chain 'E' and resid 1435 through 1438 Processing helix chain 'E' and resid 1444 through 1451 removed outlier: 4.045A pdb=" N ARG E1451 " --> pdb=" O LEU E1447 " (cutoff:3.500A) Processing helix chain 'E' and resid 1469 through 1479 removed outlier: 3.534A pdb=" N TRP E1473 " --> pdb=" O LEU E1470 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N SER E1474 " --> pdb=" O GLU E1471 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU E1479 " --> pdb=" O PHE E1476 " (cutoff:3.500A) Processing helix chain 'E' and resid 1487 through 1493 Processing helix chain 'E' and resid 1495 through 1502 Processing helix chain 'E' and resid 1508 through 1525 Processing helix chain 'E' and resid 1534 through 1536 No H-bonds generated for 'chain 'E' and resid 1534 through 1536' Processing helix chain 'E' and resid 1555 through 1567 Processing helix chain 'E' and resid 1569 through 1577 removed outlier: 4.019A pdb=" N GLY E1577 " --> pdb=" O THR E1573 " (cutoff:3.500A) Processing helix chain 'E' and resid 1581 through 1599 Processing helix chain 'E' and resid 1601 through 1603 No H-bonds generated for 'chain 'E' and resid 1601 through 1603' Processing helix chain 'E' and resid 1612 through 1622 Processing helix chain 'E' and resid 1629 through 1631 No H-bonds generated for 'chain 'E' and resid 1629 through 1631' Processing helix chain 'E' and resid 1633 through 1644 removed outlier: 3.602A pdb=" N ARG E1639 " --> pdb=" O LEU E1635 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ASP E1640 " --> pdb=" O GLY E1636 " (cutoff:3.500A) Processing helix chain 'E' and resid 1674 through 1686 removed outlier: 4.020A pdb=" N LEU E1685 " --> pdb=" O GLN E1681 " (cutoff:3.500A) Processing helix chain 'E' and resid 1703 through 1715 removed outlier: 4.226A pdb=" N GLN E1707 " --> pdb=" O ALA E1703 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ASP E1708 " --> pdb=" O ASN E1704 " (cutoff:3.500A) Processing helix chain 'E' and resid 1726 through 1729 No H-bonds generated for 'chain 'E' and resid 1726 through 1729' Processing helix chain 'E' and resid 1750 through 1758 Processing helix chain 'E' and resid 1779 through 1784 Processing helix chain 'E' and resid 1787 through 1790 No H-bonds generated for 'chain 'E' and resid 1787 through 1790' Processing helix chain 'E' and resid 1857 through 1859 No H-bonds generated for 'chain 'E' and resid 1857 through 1859' Processing helix chain 'E' and resid 1869 through 1875 removed outlier: 4.179A pdb=" N GLU E1874 " --> pdb=" O GLN E1871 " (cutoff:3.500A) Processing helix chain 'E' and resid 1878 through 1884 removed outlier: 3.585A pdb=" N THR E1884 " --> pdb=" O GLY E1880 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'D' and resid 87 through 90 Processing sheet with id= B, first strand: chain 'D' and resid 208 through 211 removed outlier: 3.677A pdb=" N ASN D 84 " --> pdb=" O VAL D 176 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N SER D 178 " --> pdb=" O LEU D 82 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N LEU D 82 " --> pdb=" O SER D 178 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'E' and resid 1318 through 1320 removed outlier: 4.026A pdb=" N GLY E1318 " --> pdb=" O ARG E1457 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE E1459 " --> pdb=" O GLY E1318 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LEU E1361 " --> pdb=" O VAL E1431 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'E' and resid 1544 through 1551 removed outlier: 6.500A pdb=" N VAL E1769 " --> pdb=" O ILE E1545 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N GLN E1547 " --> pdb=" O VAL E1769 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N VAL E1771 " --> pdb=" O GLN E1547 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N TYR E1549 " --> pdb=" O VAL E1771 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N ARG E1773 " --> pdb=" O TYR E1549 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N CYS E1551 " --> pdb=" O ARG E1773 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ILE E1775 " --> pdb=" O CYS E1551 " (cutoff:3.500A) 679 hydrogen bonds defined for protein. 1776 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 27 hydrogen bonds 54 hydrogen bond angles 0 basepair planarities 9 basepair parallelities 13 stacking parallelities Total time for adding SS restraints: 11.80 Time building geometry restraints manager: 24.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 14657 1.03 - 1.22: 22 1.22 - 1.42: 5999 1.42 - 1.62: 8805 1.62 - 1.81: 128 Bond restraints: 29611 Sorted by residual: bond pdb=" C1' ADP E1902 " pdb=" C2' ADP E1902 " ideal model delta sigma weight residual 1.524 1.302 0.222 2.00e-02 2.50e+03 1.23e+02 bond pdb=" C1' ADP E1902 " pdb=" O4' ADP E1902 " ideal model delta sigma weight residual 1.426 1.622 -0.196 2.00e-02 2.50e+03 9.58e+01 bond pdb=" C4 ADP E1902 " pdb=" C5 ADP E1902 " ideal model delta sigma weight residual 1.490 1.329 0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" C4' ADP E1902 " pdb=" O4' ADP E1902 " ideal model delta sigma weight residual 1.426 1.303 0.123 2.00e-02 2.50e+03 3.81e+01 bond pdb=" C5 ADP E1902 " pdb=" C6 ADP E1902 " ideal model delta sigma weight residual 1.490 1.370 0.120 2.00e-02 2.50e+03 3.57e+01 ... (remaining 29606 not shown) Histogram of bond angle deviations from ideal: 97.40 - 105.59: 436 105.59 - 113.77: 36169 113.77 - 121.95: 12470 121.95 - 130.14: 4584 130.14 - 138.32: 86 Bond angle restraints: 53745 Sorted by residual: angle pdb=" N1 ADP E1902 " pdb=" C6 ADP E1902 " pdb=" N6 ADP E1902 " ideal model delta sigma weight residual 120.00 101.52 18.48 3.00e+00 1.11e-01 3.79e+01 angle pdb=" C5 ADP E1902 " pdb=" C6 ADP E1902 " pdb=" N6 ADP E1902 " ideal model delta sigma weight residual 120.00 138.32 -18.32 3.00e+00 1.11e-01 3.73e+01 angle pdb=" F2 BEF E1903 " pdb=" BE BEF E1903 " pdb=" F3 BEF E1903 " ideal model delta sigma weight residual 119.96 107.32 12.64 3.00e+00 1.11e-01 1.78e+01 angle pdb=" O2B ADP E1902 " pdb=" PB ADP E1902 " pdb=" O3B ADP E1902 " ideal model delta sigma weight residual 119.90 109.05 10.85 3.00e+00 1.11e-01 1.31e+01 angle pdb=" O1A ADP E1902 " pdb=" PA ADP E1902 " pdb=" O2A ADP E1902 " ideal model delta sigma weight residual 119.90 109.81 10.09 3.00e+00 1.11e-01 1.13e+01 ... (remaining 53740 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.50: 12541 19.50 - 38.99: 861 38.99 - 58.49: 249 58.49 - 77.99: 36 77.99 - 97.48: 11 Dihedral angle restraints: 13698 sinusoidal: 7759 harmonic: 5939 Sorted by residual: dihedral pdb=" O1B ADP E1902 " pdb=" O3A ADP E1902 " pdb=" PB ADP E1902 " pdb=" PA ADP E1902 " ideal model delta sinusoidal sigma weight residual -60.00 -157.49 97.48 1 2.00e+01 2.50e-03 2.71e+01 dihedral pdb=" CA ALA E1667 " pdb=" C ALA E1667 " pdb=" N LEU E1668 " pdb=" CA LEU E1668 " ideal model delta harmonic sigma weight residual 180.00 157.59 22.41 0 5.00e+00 4.00e-02 2.01e+01 dihedral pdb=" CA ASP D 96 " pdb=" C ASP D 96 " pdb=" N LEU D 97 " pdb=" CA LEU D 97 " ideal model delta harmonic sigma weight residual -180.00 -158.20 -21.80 0 5.00e+00 4.00e-02 1.90e+01 ... (remaining 13695 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1519 0.035 - 0.070: 579 0.070 - 0.106: 154 0.106 - 0.141: 79 0.141 - 0.176: 6 Chirality restraints: 2337 Sorted by residual: chirality pdb=" CA THR E1124 " pdb=" N THR E1124 " pdb=" C THR E1124 " pdb=" CB THR E1124 " both_signs ideal model delta sigma weight residual False 2.53 2.35 0.18 2.00e-01 2.50e+01 7.74e-01 chirality pdb=" CA ILE E 766 " pdb=" N ILE E 766 " pdb=" C ILE E 766 " pdb=" CB ILE E 766 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.89e-01 chirality pdb=" CA THR E 768 " pdb=" N THR E 768 " pdb=" C THR E 768 " pdb=" CB THR E 768 " both_signs ideal model delta sigma weight residual False 2.53 2.36 0.16 2.00e-01 2.50e+01 6.55e-01 ... (remaining 2334 not shown) Planarity restraints: 4246 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL E 567 " -0.034 5.00e-02 4.00e+02 5.11e-02 4.18e+00 pdb=" N PRO E 568 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO E 568 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO E 568 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS E1132 " 0.030 5.00e-02 4.00e+02 4.49e-02 3.23e+00 pdb=" N PRO E1133 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO E1133 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO E1133 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU E 815 " -0.029 5.00e-02 4.00e+02 4.38e-02 3.07e+00 pdb=" N PRO E 816 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO E 816 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO E 816 " -0.025 5.00e-02 4.00e+02 ... (remaining 4243 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.24: 2667 2.24 - 2.83: 65302 2.83 - 3.42: 77810 3.42 - 4.01: 104133 4.01 - 4.60: 162645 Nonbonded interactions: 412557 Sorted by model distance: nonbonded pdb=" OE1 GLU E 619 " pdb=" H GLU E 619 " model vdw 1.644 1.850 nonbonded pdb="HH11 ARG D 105 " pdb=" OH TYR E1872 " model vdw 1.661 1.850 nonbonded pdb=" HE ARG E1395 " pdb=" OD2 ASP E1418 " model vdw 1.666 1.850 nonbonded pdb=" OE1 GLU E1017 " pdb=" H GLU E1017 " model vdw 1.671 1.850 nonbonded pdb=" O ASN D 90 " pdb=" HG1 THR D 168 " model vdw 1.682 1.850 ... (remaining 412552 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: 1.300 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: 0.430 Extract box with map and model: 6.320 Check model and map are aligned: 0.450 Set scattering table: 0.300 Process input model: 105.900 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 118.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6607 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 0.222 14932 Z= 0.409 Angle : 0.788 18.475 20293 Z= 0.413 Chirality : 0.043 0.176 2337 Planarity : 0.005 0.051 2535 Dihedral : 13.108 97.485 5692 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 1.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 0.26 % Allowed : 2.92 % Favored : 96.82 % 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: 0.40 (0.20), residues: 1783 helix: 0.52 (0.16), residues: 997 sheet: -0.89 (0.43), residues: 114 loop : 0.36 (0.26), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 55 HIS 0.007 0.001 HIS E 333 PHE 0.015 0.002 PHE E1192 TYR 0.016 0.002 TYR E1155 ARG 0.010 0.001 ARG E1595 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 507 is missing expected H atoms. Skipping. Evaluate side-chains 383 residues out of total 1544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 379 time to evaluate : 2.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 439 MET cc_start: 0.6073 (ttm) cc_final: 0.5531 (tpp) REVERT: E 493 THR cc_start: 0.5454 (m) cc_final: 0.5234 (m) REVERT: E 827 SER cc_start: 0.8011 (p) cc_final: 0.7756 (t) REVERT: E 1066 ILE cc_start: 0.8284 (mt) cc_final: 0.8032 (mt) REVERT: E 1491 LEU cc_start: 0.7548 (mt) cc_final: 0.6951 (tp) REVERT: E 1549 TYR cc_start: 0.6198 (t80) cc_final: 0.5755 (t80) REVERT: E 1707 GLN cc_start: 0.7951 (tp40) cc_final: 0.7707 (tp40) outliers start: 4 outliers final: 0 residues processed: 381 average time/residue: 0.6530 time to fit residues: 354.5551 Evaluate side-chains 215 residues out of total 1544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 215 time to evaluate : 2.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 152 optimal weight: 4.9990 chunk 137 optimal weight: 0.9990 chunk 76 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 141 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 chunk 86 optimal weight: 8.9990 chunk 105 optimal weight: 2.9990 chunk 164 optimal weight: 6.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 803 ASN E 910 GLN E1032 GLN E1589 GLN E1599 ASN ** E1734 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 moved from start: 0.3570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 14932 Z= 0.352 Angle : 0.676 7.824 20293 Z= 0.355 Chirality : 0.043 0.199 2337 Planarity : 0.006 0.047 2535 Dihedral : 9.878 68.191 2157 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.30 % Allowed : 9.92 % Favored : 88.79 % 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 (0.20), residues: 1783 helix: 0.66 (0.16), residues: 1003 sheet: -1.05 (0.41), residues: 121 loop : 0.30 (0.27), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E1859 HIS 0.006 0.001 HIS E1341 PHE 0.017 0.002 PHE E 850 TYR 0.018 0.002 TYR E1155 ARG 0.020 0.001 ARG E 894 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 507 is missing expected H atoms. Skipping. Evaluate side-chains 241 residues out of total 1544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 221 time to evaluate : 2.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 136 MET cc_start: 0.8699 (ttm) cc_final: 0.8365 (ttm) REVERT: E 439 MET cc_start: 0.6551 (ttm) cc_final: 0.6317 (mtp) REVERT: E 827 SER cc_start: 0.8166 (p) cc_final: 0.7966 (t) REVERT: E 1347 PHE cc_start: 0.7531 (t80) cc_final: 0.7294 (t80) REVERT: E 1665 HIS cc_start: 0.5462 (m90) cc_final: 0.5224 (m-70) outliers start: 20 outliers final: 13 residues processed: 231 average time/residue: 0.5830 time to fit residues: 200.3145 Evaluate side-chains 204 residues out of total 1544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 191 time to evaluate : 1.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 133 SER Chi-restraints excluded: chain D residue 139 THR Chi-restraints excluded: chain D residue 196 ASN Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain E residue 454 VAL Chi-restraints excluded: chain E residue 1148 SER Chi-restraints excluded: chain E residue 1334 CYS Chi-restraints excluded: chain E residue 1339 ASP Chi-restraints excluded: chain E residue 1423 GLU Chi-restraints excluded: chain E residue 1723 LEU Chi-restraints excluded: chain E residue 1769 VAL Chi-restraints excluded: chain E residue 1849 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 91 optimal weight: 5.9990 chunk 51 optimal weight: 0.5980 chunk 136 optimal weight: 8.9990 chunk 111 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 164 optimal weight: 10.0000 chunk 177 optimal weight: 7.9990 chunk 146 optimal weight: 2.9990 chunk 163 optimal weight: 10.0000 chunk 56 optimal weight: 1.9990 chunk 132 optimal weight: 8.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 522 ASN E 910 GLN E1317 HIS ** E1466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1734 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1749 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.4748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 14932 Z= 0.312 Angle : 0.598 6.128 20293 Z= 0.313 Chirality : 0.040 0.168 2337 Planarity : 0.005 0.037 2535 Dihedral : 9.746 69.739 2157 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.69 % Allowed : 10.50 % Favored : 87.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.20), residues: 1783 helix: 0.88 (0.16), residues: 1008 sheet: -0.94 (0.44), residues: 115 loop : 0.14 (0.26), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP E 55 HIS 0.009 0.001 HIS E 333 PHE 0.014 0.001 PHE D 242 TYR 0.018 0.002 TYR E1155 ARG 0.008 0.001 ARG E 410 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 507 is missing expected H atoms. Skipping. Evaluate side-chains 220 residues out of total 1544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 194 time to evaluate : 2.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 439 MET cc_start: 0.6550 (ttm) cc_final: 0.6289 (mtp) REVERT: E 627 MET cc_start: 0.7908 (tpp) cc_final: 0.7595 (tpp) REVERT: E 1156 MET cc_start: 0.7267 (mmm) cc_final: 0.7002 (mmm) REVERT: E 1347 PHE cc_start: 0.7803 (t80) cc_final: 0.7524 (t80) outliers start: 26 outliers final: 20 residues processed: 212 average time/residue: 0.6376 time to fit residues: 197.5981 Evaluate side-chains 195 residues out of total 1544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 175 time to evaluate : 2.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 133 SER Chi-restraints excluded: chain D residue 139 THR Chi-restraints excluded: chain D residue 178 SER Chi-restraints excluded: chain D residue 196 ASN Chi-restraints excluded: chain E residue 337 MET Chi-restraints excluded: chain E residue 371 ASP Chi-restraints excluded: chain E residue 454 VAL Chi-restraints excluded: chain E residue 504 MET Chi-restraints excluded: chain E residue 910 GLN Chi-restraints excluded: chain E residue 955 SER Chi-restraints excluded: chain E residue 1124 THR Chi-restraints excluded: chain E residue 1148 SER Chi-restraints excluded: chain E residue 1167 VAL Chi-restraints excluded: chain E residue 1334 CYS Chi-restraints excluded: chain E residue 1423 GLU Chi-restraints excluded: chain E residue 1429 TYR Chi-restraints excluded: chain E residue 1710 VAL Chi-restraints excluded: chain E residue 1723 LEU Chi-restraints excluded: chain E residue 1793 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 162 optimal weight: 9.9990 chunk 123 optimal weight: 0.4980 chunk 85 optimal weight: 8.9990 chunk 18 optimal weight: 4.9990 chunk 78 optimal weight: 0.9980 chunk 110 optimal weight: 2.9990 chunk 165 optimal weight: 0.9990 chunk 174 optimal weight: 7.9990 chunk 86 optimal weight: 5.9990 chunk 156 optimal weight: 9.9990 chunk 47 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E1466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1734 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1749 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1869 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.5305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 14932 Z= 0.252 Angle : 0.553 6.108 20293 Z= 0.286 Chirality : 0.039 0.145 2337 Planarity : 0.004 0.046 2535 Dihedral : 9.586 69.164 2157 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.69 % Allowed : 11.08 % Favored : 87.23 % 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: 0.75 (0.20), residues: 1783 helix: 1.08 (0.17), residues: 1006 sheet: -1.12 (0.42), residues: 122 loop : 0.09 (0.26), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E1859 HIS 0.006 0.001 HIS E 333 PHE 0.014 0.001 PHE D 242 TYR 0.014 0.001 TYR E1155 ARG 0.004 0.000 ARG D 113 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 507 is missing expected H atoms. Skipping. Evaluate side-chains 207 residues out of total 1544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 181 time to evaluate : 2.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 140 LEU cc_start: 0.7611 (OUTLIER) cc_final: 0.7071 (tt) REVERT: E 439 MET cc_start: 0.6558 (ttm) cc_final: 0.6196 (mtp) REVERT: E 521 SER cc_start: 0.7973 (t) cc_final: 0.7700 (p) REVERT: E 627 MET cc_start: 0.8016 (tpp) cc_final: 0.7685 (tpp) REVERT: E 735 MET cc_start: 0.9068 (tpt) cc_final: 0.8736 (tpt) outliers start: 26 outliers final: 18 residues processed: 197 average time/residue: 0.6326 time to fit residues: 189.7938 Evaluate side-chains 186 residues out of total 1544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 167 time to evaluate : 1.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 133 SER Chi-restraints excluded: chain D residue 139 THR Chi-restraints excluded: chain D residue 196 ASN Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 337 MET Chi-restraints excluded: chain E residue 454 VAL Chi-restraints excluded: chain E residue 1148 SER Chi-restraints excluded: chain E residue 1167 VAL Chi-restraints excluded: chain E residue 1334 CYS Chi-restraints excluded: chain E residue 1411 SER Chi-restraints excluded: chain E residue 1423 GLU Chi-restraints excluded: chain E residue 1429 TYR Chi-restraints excluded: chain E residue 1641 LEU Chi-restraints excluded: chain E residue 1723 LEU Chi-restraints excluded: chain E residue 1758 ASP Chi-restraints excluded: chain E residue 1793 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 145 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 130 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 149 optimal weight: 10.0000 chunk 120 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 89 optimal weight: 2.9990 chunk 157 optimal weight: 9.9990 chunk 44 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 615 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1734 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1749 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.5793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 14932 Z= 0.245 Angle : 0.537 5.648 20293 Z= 0.279 Chirality : 0.039 0.154 2337 Planarity : 0.004 0.035 2535 Dihedral : 9.490 67.960 2157 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.27 % Allowed : 11.41 % Favored : 86.33 % 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: 0.84 (0.21), residues: 1783 helix: 1.21 (0.17), residues: 1010 sheet: -1.00 (0.42), residues: 126 loop : 0.02 (0.26), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 31 HIS 0.007 0.001 HIS E 333 PHE 0.015 0.001 PHE D 242 TYR 0.033 0.002 TYR E1300 ARG 0.004 0.000 ARG E 145 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 507 is missing expected H atoms. Skipping. Evaluate side-chains 212 residues out of total 1544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 177 time to evaluate : 2.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 521 SER cc_start: 0.8041 (t) cc_final: 0.7725 (p) REVERT: E 627 MET cc_start: 0.8029 (tpp) cc_final: 0.7722 (tpp) REVERT: E 735 MET cc_start: 0.9131 (tpt) cc_final: 0.8887 (tpt) outliers start: 35 outliers final: 25 residues processed: 200 average time/residue: 0.5763 time to fit residues: 175.4533 Evaluate side-chains 191 residues out of total 1544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 166 time to evaluate : 2.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 133 SER Chi-restraints excluded: chain D residue 139 THR Chi-restraints excluded: chain D residue 196 ASN Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain E residue 145 ARG Chi-restraints excluded: chain E residue 337 MET Chi-restraints excluded: chain E residue 371 ASP Chi-restraints excluded: chain E residue 454 VAL Chi-restraints excluded: chain E residue 504 MET Chi-restraints excluded: chain E residue 535 MET Chi-restraints excluded: chain E residue 980 THR Chi-restraints excluded: chain E residue 1124 THR Chi-restraints excluded: chain E residue 1167 VAL Chi-restraints excluded: chain E residue 1334 CYS Chi-restraints excluded: chain E residue 1411 SER Chi-restraints excluded: chain E residue 1423 GLU Chi-restraints excluded: chain E residue 1429 TYR Chi-restraints excluded: chain E residue 1444 LYS Chi-restraints excluded: chain E residue 1491 LEU Chi-restraints excluded: chain E residue 1641 LEU Chi-restraints excluded: chain E residue 1723 LEU Chi-restraints excluded: chain E residue 1793 ASP Chi-restraints excluded: chain E residue 1863 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 58 optimal weight: 5.9990 chunk 157 optimal weight: 20.0000 chunk 34 optimal weight: 1.9990 chunk 102 optimal weight: 8.9990 chunk 43 optimal weight: 1.9990 chunk 175 optimal weight: 10.0000 chunk 145 optimal weight: 3.9990 chunk 81 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 91 optimal weight: 6.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 615 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 664 HIS ** E1466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1734 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1749 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.6218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 14932 Z= 0.304 Angle : 0.555 6.002 20293 Z= 0.291 Chirality : 0.040 0.151 2337 Planarity : 0.004 0.036 2535 Dihedral : 9.477 65.701 2157 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.01 % Allowed : 12.77 % Favored : 85.22 % 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: 0.74 (0.20), residues: 1783 helix: 1.15 (0.17), residues: 1008 sheet: -0.95 (0.43), residues: 126 loop : -0.11 (0.26), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP E 31 HIS 0.007 0.001 HIS E 333 PHE 0.015 0.001 PHE D 242 TYR 0.021 0.002 TYR E1300 ARG 0.005 0.000 ARG E 904 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 507 is missing expected H atoms. Skipping. Evaluate side-chains 203 residues out of total 1544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 172 time to evaluate : 2.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 490 SER cc_start: 0.9206 (m) cc_final: 0.8974 (p) REVERT: E 627 MET cc_start: 0.8001 (tpp) cc_final: 0.7711 (tpp) REVERT: E 735 MET cc_start: 0.9192 (tpt) cc_final: 0.8967 (tpt) REVERT: E 803 ASN cc_start: 0.8379 (OUTLIER) cc_final: 0.8178 (m-40) outliers start: 31 outliers final: 25 residues processed: 193 average time/residue: 0.6278 time to fit residues: 183.2883 Evaluate side-chains 187 residues out of total 1544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 161 time to evaluate : 2.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 133 SER Chi-restraints excluded: chain D residue 139 THR Chi-restraints excluded: chain D residue 178 SER Chi-restraints excluded: chain D residue 196 ASN Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain E residue 145 ARG Chi-restraints excluded: chain E residue 337 MET Chi-restraints excluded: chain E residue 438 ASN Chi-restraints excluded: chain E residue 454 VAL Chi-restraints excluded: chain E residue 504 MET Chi-restraints excluded: chain E residue 535 MET Chi-restraints excluded: chain E residue 803 ASN Chi-restraints excluded: chain E residue 955 SER Chi-restraints excluded: chain E residue 980 THR Chi-restraints excluded: chain E residue 1124 THR Chi-restraints excluded: chain E residue 1167 VAL Chi-restraints excluded: chain E residue 1334 CYS Chi-restraints excluded: chain E residue 1411 SER Chi-restraints excluded: chain E residue 1423 GLU Chi-restraints excluded: chain E residue 1429 TYR Chi-restraints excluded: chain E residue 1641 LEU Chi-restraints excluded: chain E residue 1723 LEU Chi-restraints excluded: chain E residue 1758 ASP Chi-restraints excluded: chain E residue 1793 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 168 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 chunk 147 optimal weight: 8.9990 chunk 97 optimal weight: 0.9980 chunk 174 optimal weight: 3.9990 chunk 109 optimal weight: 0.9980 chunk 106 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 chunk 107 optimal weight: 0.6980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 615 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1277 GLN ** E1466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1734 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1749 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.6416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14932 Z= 0.197 Angle : 0.515 5.778 20293 Z= 0.265 Chirality : 0.038 0.162 2337 Planarity : 0.004 0.037 2535 Dihedral : 9.392 65.520 2157 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.62 % Allowed : 13.35 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.21), residues: 1783 helix: 1.41 (0.17), residues: 1011 sheet: -0.84 (0.44), residues: 126 loop : 0.02 (0.26), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP E 31 HIS 0.006 0.001 HIS E 333 PHE 0.014 0.001 PHE D 242 TYR 0.031 0.001 TYR E1300 ARG 0.003 0.000 ARG E 904 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 507 is missing expected H atoms. Skipping. Evaluate side-chains 194 residues out of total 1544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 169 time to evaluate : 2.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 490 SER cc_start: 0.9226 (m) cc_final: 0.8980 (p) REVERT: E 627 MET cc_start: 0.7943 (tpp) cc_final: 0.7716 (tpp) REVERT: E 735 MET cc_start: 0.9172 (tpt) cc_final: 0.8796 (mmm) outliers start: 25 outliers final: 20 residues processed: 187 average time/residue: 0.6580 time to fit residues: 183.9138 Evaluate side-chains 181 residues out of total 1544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 161 time to evaluate : 2.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 133 SER Chi-restraints excluded: chain D residue 139 THR Chi-restraints excluded: chain D residue 196 ASN Chi-restraints excluded: chain E residue 145 ARG Chi-restraints excluded: chain E residue 337 MET Chi-restraints excluded: chain E residue 438 ASN Chi-restraints excluded: chain E residue 625 LEU Chi-restraints excluded: chain E residue 955 SER Chi-restraints excluded: chain E residue 980 THR Chi-restraints excluded: chain E residue 1167 VAL Chi-restraints excluded: chain E residue 1207 MET Chi-restraints excluded: chain E residue 1334 CYS Chi-restraints excluded: chain E residue 1411 SER Chi-restraints excluded: chain E residue 1423 GLU Chi-restraints excluded: chain E residue 1429 TYR Chi-restraints excluded: chain E residue 1641 LEU Chi-restraints excluded: chain E residue 1723 LEU Chi-restraints excluded: chain E residue 1793 ASP Chi-restraints excluded: chain E residue 1863 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 69 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 110 optimal weight: 0.6980 chunk 118 optimal weight: 0.9980 chunk 86 optimal weight: 8.9990 chunk 16 optimal weight: 3.9990 chunk 137 optimal weight: 7.9990 chunk 158 optimal weight: 9.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 615 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1522 HIS ** E1734 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1749 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.6668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14932 Z= 0.272 Angle : 0.537 5.768 20293 Z= 0.280 Chirality : 0.039 0.172 2337 Planarity : 0.004 0.037 2535 Dihedral : 9.393 63.285 2157 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.88 % Allowed : 13.80 % Favored : 84.32 % 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: 0.92 (0.21), residues: 1783 helix: 1.33 (0.17), residues: 1010 sheet: -0.85 (0.44), residues: 126 loop : -0.09 (0.26), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP E 31 HIS 0.007 0.001 HIS E 333 PHE 0.016 0.001 PHE D 242 TYR 0.026 0.001 TYR E1300 ARG 0.004 0.000 ARG D 113 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 507 is missing expected H atoms. Skipping. Evaluate side-chains 191 residues out of total 1544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 162 time to evaluate : 2.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 490 SER cc_start: 0.9244 (m) cc_final: 0.9028 (p) REVERT: E 627 MET cc_start: 0.7953 (tpp) cc_final: 0.7727 (tpp) REVERT: E 735 MET cc_start: 0.9182 (tpt) cc_final: 0.8816 (mmm) outliers start: 29 outliers final: 27 residues processed: 182 average time/residue: 0.5717 time to fit residues: 157.4767 Evaluate side-chains 177 residues out of total 1544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 150 time to evaluate : 2.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 133 SER Chi-restraints excluded: chain D residue 139 THR Chi-restraints excluded: chain D residue 178 SER Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 196 ASN Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain D residue 251 ASP Chi-restraints excluded: chain E residue 145 ARG Chi-restraints excluded: chain E residue 337 MET Chi-restraints excluded: chain E residue 438 ASN Chi-restraints excluded: chain E residue 625 LEU Chi-restraints excluded: chain E residue 955 SER Chi-restraints excluded: chain E residue 980 THR Chi-restraints excluded: chain E residue 1167 VAL Chi-restraints excluded: chain E residue 1207 MET Chi-restraints excluded: chain E residue 1334 CYS Chi-restraints excluded: chain E residue 1411 SER Chi-restraints excluded: chain E residue 1423 GLU Chi-restraints excluded: chain E residue 1429 TYR Chi-restraints excluded: chain E residue 1491 LEU Chi-restraints excluded: chain E residue 1525 VAL Chi-restraints excluded: chain E residue 1641 LEU Chi-restraints excluded: chain E residue 1723 LEU Chi-restraints excluded: chain E residue 1793 ASP Chi-restraints excluded: chain E residue 1863 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 167 optimal weight: 4.9990 chunk 152 optimal weight: 0.9980 chunk 162 optimal weight: 9.9990 chunk 97 optimal weight: 0.7980 chunk 70 optimal weight: 0.9990 chunk 127 optimal weight: 0.0040 chunk 49 optimal weight: 4.9990 chunk 146 optimal weight: 3.9990 chunk 153 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 171 optimal weight: 5.9990 overall best weight: 0.9596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 615 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1522 HIS ** E1734 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1749 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.6775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 14932 Z= 0.174 Angle : 0.504 5.662 20293 Z= 0.259 Chirality : 0.038 0.168 2337 Planarity : 0.004 0.054 2535 Dihedral : 9.353 62.984 2157 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.56 % Allowed : 13.74 % Favored : 84.71 % 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: 1.16 (0.21), residues: 1783 helix: 1.48 (0.17), residues: 1017 sheet: -0.59 (0.44), residues: 122 loop : 0.03 (0.26), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP E 31 HIS 0.005 0.001 HIS E 333 PHE 0.015 0.001 PHE D 242 TYR 0.030 0.001 TYR E1300 ARG 0.013 0.000 ARG D 113 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 507 is missing expected H atoms. Skipping. Evaluate side-chains 175 residues out of total 1544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 151 time to evaluate : 2.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 168 THR cc_start: 0.8155 (p) cc_final: 0.7906 (t) REVERT: E 490 SER cc_start: 0.9249 (m) cc_final: 0.8996 (p) REVERT: E 735 MET cc_start: 0.9165 (tpt) cc_final: 0.8811 (mmm) outliers start: 24 outliers final: 21 residues processed: 169 average time/residue: 0.5750 time to fit residues: 147.9188 Evaluate side-chains 169 residues out of total 1544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 148 time to evaluate : 2.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 139 THR Chi-restraints excluded: chain D residue 196 ASN Chi-restraints excluded: chain E residue 145 ARG Chi-restraints excluded: chain E residue 337 MET Chi-restraints excluded: chain E residue 438 ASN Chi-restraints excluded: chain E residue 955 SER Chi-restraints excluded: chain E residue 980 THR Chi-restraints excluded: chain E residue 1167 VAL Chi-restraints excluded: chain E residue 1207 MET Chi-restraints excluded: chain E residue 1269 ASP Chi-restraints excluded: chain E residue 1334 CYS Chi-restraints excluded: chain E residue 1411 SER Chi-restraints excluded: chain E residue 1423 GLU Chi-restraints excluded: chain E residue 1429 TYR Chi-restraints excluded: chain E residue 1491 LEU Chi-restraints excluded: chain E residue 1525 VAL Chi-restraints excluded: chain E residue 1641 LEU Chi-restraints excluded: chain E residue 1723 LEU Chi-restraints excluded: chain E residue 1793 ASP Chi-restraints excluded: chain E residue 1863 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 104 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 119 optimal weight: 0.7980 chunk 180 optimal weight: 2.9990 chunk 165 optimal weight: 10.0000 chunk 143 optimal weight: 0.3980 chunk 14 optimal weight: 0.8980 chunk 110 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 114 optimal weight: 0.9990 chunk 152 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 615 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1522 HIS ** E1734 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1749 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.6898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14932 Z= 0.168 Angle : 0.500 5.736 20293 Z= 0.255 Chirality : 0.038 0.168 2337 Planarity : 0.004 0.046 2535 Dihedral : 9.322 61.928 2157 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.43 % Allowed : 14.13 % Favored : 84.45 % 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 (0.21), residues: 1783 helix: 1.63 (0.17), residues: 1019 sheet: -0.55 (0.44), residues: 122 loop : 0.09 (0.26), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP E 31 HIS 0.006 0.001 HIS E 333 PHE 0.014 0.001 PHE D 242 TYR 0.030 0.001 TYR E1300 ARG 0.007 0.000 ARG D 113 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 507 is missing expected H atoms. Skipping. Evaluate side-chains 183 residues out of total 1544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 161 time to evaluate : 2.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 168 THR cc_start: 0.8115 (p) cc_final: 0.7863 (t) REVERT: E 490 SER cc_start: 0.9229 (m) cc_final: 0.8989 (p) REVERT: E 962 MET cc_start: 0.9178 (mmt) cc_final: 0.8240 (mmt) REVERT: E 1674 LYS cc_start: 0.7851 (mtmm) cc_final: 0.7503 (mtmm) outliers start: 22 outliers final: 21 residues processed: 175 average time/residue: 0.5872 time to fit residues: 155.2807 Evaluate side-chains 173 residues out of total 1544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 152 time to evaluate : 2.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 139 THR Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 251 ASP Chi-restraints excluded: chain E residue 145 ARG Chi-restraints excluded: chain E residue 337 MET Chi-restraints excluded: chain E residue 438 ASN Chi-restraints excluded: chain E residue 861 LEU Chi-restraints excluded: chain E residue 955 SER Chi-restraints excluded: chain E residue 980 THR Chi-restraints excluded: chain E residue 1167 VAL Chi-restraints excluded: chain E residue 1207 MET Chi-restraints excluded: chain E residue 1334 CYS Chi-restraints excluded: chain E residue 1411 SER Chi-restraints excluded: chain E residue 1423 GLU Chi-restraints excluded: chain E residue 1429 TYR Chi-restraints excluded: chain E residue 1491 LEU Chi-restraints excluded: chain E residue 1525 VAL Chi-restraints excluded: chain E residue 1641 LEU Chi-restraints excluded: chain E residue 1723 LEU Chi-restraints excluded: chain E residue 1793 ASP Chi-restraints excluded: chain E residue 1863 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 43 optimal weight: 1.9990 chunk 132 optimal weight: 7.9990 chunk 21 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 143 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 147 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 126 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 615 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1277 GLN ** E1466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1522 HIS ** E1734 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1749 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.148114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.105733 restraints weight = 60193.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.108821 restraints weight = 57470.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.110096 restraints weight = 36628.876| |-----------------------------------------------------------------------------| r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.7062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 14932 Z= 0.302 Angle : 0.545 5.720 20293 Z= 0.284 Chirality : 0.040 0.170 2337 Planarity : 0.004 0.051 2535 Dihedral : 9.416 60.147 2157 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.56 % Allowed : 14.13 % Favored : 84.32 % 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: 1.02 (0.21), residues: 1783 helix: 1.40 (0.17), residues: 1021 sheet: -0.89 (0.44), residues: 126 loop : -0.04 (0.26), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP E 31 HIS 0.007 0.001 HIS E 35 PHE 0.014 0.001 PHE D 242 TYR 0.028 0.002 TYR E1300 ARG 0.008 0.000 ARG D 113 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5572.32 seconds wall clock time: 99 minutes 10.21 seconds (5950.21 seconds total)