Starting phenix.real_space_refine on Fri Jul 3 01:00:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7s5v_24840/07_2026/7s5v_24840.cif Found real_map, /net/cci-nas-00/data/ceres_data/7s5v_24840/07_2026/7s5v_24840.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7s5v_24840/07_2026/7s5v_24840.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7s5v_24840/07_2026/7s5v_24840.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7s5v_24840/07_2026/7s5v_24840.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7s5v_24840/07_2026/7s5v_24840.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7s5v_24840/07_2026/7s5v_24840.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7s5v_24840/07_2026/7s5v_24840.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.005 sd= 0.083 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 P 5 5.49 5 Mg 2 5.21 5 S 56 5.16 5 C 7119 2.51 5 N 1852 2.21 5 O 1930 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 64 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10964 Number of models: 1 Model: "" Number of chains: 2 Chain: "E" Number of atoms: 10904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1397, 10904 Classifications: {'peptide': 1397} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 45, 'TRANS': 1351} Chain breaks: 8 Unresolved non-hydrogen bonds: 141 Unresolved non-hydrogen angles: 172 Unresolved non-hydrogen dihedrals: 114 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLU:plan': 8, 'ARG:plan': 5, 'PHE:plan': 2, 'ASP:plan': 4, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 84 Chain: "E" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 60 Unusual residues: {' MG': 2, 'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 2.63, per 1000 atoms: 0.24 Number of scatterers: 10964 At special positions: 0 Unit cell: (114.4, 97.5, 139.1, 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) S 56 16.00 P 5 15.00 Mg 2 11.99 O 1930 8.00 N 1852 7.00 C 7119 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.92 Conformation dependent library (CDL) restraints added in 550.0 milliseconds 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2644 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 5 sheets defined 63.9% alpha, 4.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'E' and resid 34 through 51 Proline residue: E 46 - end of helix Processing helix chain 'E' and resid 71 through 100 removed outlier: 3.533A pdb=" N ALA E 91 " --> pdb=" O VAL E 87 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N VAL E 99 " --> pdb=" O LEU E 95 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N THR E 100 " --> pdb=" O SER E 96 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 130 removed outlier: 3.662A pdb=" N ALA E 114 " --> pdb=" O PRO E 110 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL E 119 " --> pdb=" O PHE E 115 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N THR E 120 " --> pdb=" O MET E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 136 Processing helix chain 'E' and resid 137 through 157 removed outlier: 4.070A pdb=" N TRP E 144 " --> pdb=" O LEU E 140 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N THR E 145 " --> pdb=" O LEU E 141 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ALA E 147 " --> pdb=" O TYR E 143 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N PHE E 148 " --> pdb=" O TRP E 144 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LYS E 154 " --> pdb=" O THR E 150 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 192 removed outlier: 3.824A pdb=" N CYS E 171 " --> pdb=" O GLN E 167 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL E 190 " --> pdb=" O VAL E 186 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ILE E 191 " --> pdb=" O GLU E 187 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ARG E 192 " --> pdb=" O VAL E 188 " (cutoff:3.500A) Processing helix chain 'E' and resid 224 through 230 Processing helix chain 'E' and resid 231 through 233 No H-bonds generated for 'chain 'E' and resid 231 through 233' Processing helix chain 'E' and resid 234 through 240 removed outlier: 3.820A pdb=" N LYS E 239 " --> pdb=" O ASN E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 273 removed outlier: 3.752A pdb=" N ARG E 266 " --> pdb=" O THR E 262 " (cutoff:3.500A) Processing helix chain 'E' and resid 285 through 296 removed outlier: 4.077A pdb=" N TRP E 289 " --> pdb=" O ALA E 285 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N HIS E 294 " --> pdb=" O GLN E 290 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA E 295 " --> pdb=" O ALA E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 296 through 315 removed outlier: 3.975A pdb=" N LEU E 300 " --> pdb=" O PHE E 296 " (cutoff:3.500A) Processing helix chain 'E' and resid 316 through 329 removed outlier: 3.519A pdb=" N VAL E 325 " --> pdb=" O ILE E 321 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY E 329 " --> pdb=" O VAL E 325 " (cutoff:3.500A) Processing helix chain 'E' and resid 356 through 401 removed outlier: 3.655A pdb=" N LEU E 369 " --> pdb=" O LEU E 365 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N THR E 372 " --> pdb=" O LEU E 368 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLN E 375 " --> pdb=" O ARG E 371 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL E 380 " --> pdb=" O ALA E 376 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N THR E 394 " --> pdb=" O GLY E 390 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 424 Processing helix chain 'E' and resid 424 through 433 Processing helix chain 'E' and resid 435 through 457 Proline residue: E 443 - end of helix Processing helix chain 'E' and resid 459 through 464 removed outlier: 3.859A pdb=" N ILE E 463 " --> pdb=" O VAL E 459 " (cutoff:3.500A) Processing helix chain 'E' and resid 465 through 505 removed outlier: 3.596A pdb=" N ALA E 472 " --> pdb=" O ILE E 468 " (cutoff:3.500A) Proline residue: E 473 - end of helix removed outlier: 3.797A pdb=" N ALA E 479 " --> pdb=" O GLN E 475 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ARG E 487 " --> pdb=" O SER E 483 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N LEU E 490 " --> pdb=" O GLN E 486 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLU E 491 " --> pdb=" O ARG E 487 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ASN E 494 " --> pdb=" O LEU E 490 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASN E 501 " --> pdb=" O LEU E 497 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N MET E 503 " --> pdb=" O GLN E 499 " (cutoff:3.500A) Processing helix chain 'E' and resid 506 through 511 Processing helix chain 'E' and resid 515 through 565 removed outlier: 3.636A pdb=" N THR E 526 " --> pdb=" O ARG E 522 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SER E 533 " --> pdb=" O LYS E 529 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N TYR E 540 " --> pdb=" O ALA E 536 " (cutoff:3.500A) Proline residue: E 552 - end of helix removed outlier: 3.755A pdb=" N VAL E 564 " --> pdb=" O PHE E 560 " (cutoff:3.500A) Processing helix chain 'E' and resid 573 through 587 removed outlier: 3.731A pdb=" N SER E 582 " --> pdb=" O PHE E 578 " (cutoff:3.500A) Processing helix chain 'E' and resid 590 through 601 removed outlier: 4.505A pdb=" N SER E 595 " --> pdb=" O LEU E 591 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N SER E 596 " --> pdb=" O PHE E 592 " (cutoff:3.500A) Processing helix chain 'E' and resid 605 through 616 Processing helix chain 'E' and resid 719 through 728 removed outlier: 3.636A pdb=" N LEU E 728 " --> pdb=" O LEU E 724 " (cutoff:3.500A) Processing helix chain 'E' and resid 785 through 790 Processing helix chain 'E' and resid 795 through 806 Processing helix chain 'E' and resid 808 through 815 removed outlier: 3.579A pdb=" N ILE E 814 " --> pdb=" O PRO E 810 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU E 815 " --> pdb=" O ASP E 811 " (cutoff:3.500A) Processing helix chain 'E' and resid 817 through 821 removed outlier: 3.693A pdb=" N GLN E 820 " --> pdb=" O HIS E 817 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N THR E 821 " --> pdb=" O GLY E 818 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 817 through 821' Processing helix chain 'E' and resid 831 through 844 removed outlier: 3.963A pdb=" N ARG E 835 " --> pdb=" O SER E 831 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLN E 836 " --> pdb=" O GLY E 832 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA E 843 " --> pdb=" O SER E 839 " (cutoff:3.500A) Processing helix chain 'E' and resid 861 through 871 removed outlier: 3.869A pdb=" N HIS E 867 " --> pdb=" O HIS E 863 " (cutoff:3.500A) Processing helix chain 'E' and resid 890 through 897 removed outlier: 3.611A pdb=" N TYR E 893 " --> pdb=" O LYS E 890 " (cutoff:3.500A) Proline residue: E 895 - end of helix Processing helix chain 'E' and resid 913 through 920 Processing helix chain 'E' and resid 923 through 930 Processing helix chain 'E' and resid 998 through 1007 removed outlier: 4.055A pdb=" N ALA E1002 " --> pdb=" O TRP E 998 " (cutoff:3.500A) Processing helix chain 'E' and resid 1009 through 1018 Processing helix chain 'E' and resid 1020 through 1033 removed outlier: 3.785A pdb=" N ALA E1029 " --> pdb=" O MET E1025 " (cutoff:3.500A) Processing helix chain 'E' and resid 1037 through 1042 removed outlier: 3.920A pdb=" N LEU E1042 " --> pdb=" O ASP E1039 " (cutoff:3.500A) Processing helix chain 'E' and resid 1068 through 1073 Processing helix chain 'E' and resid 1076 through 1107 removed outlier: 4.047A pdb=" N VAL E1081 " --> pdb=" O VAL E1077 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N THR E1082 " --> pdb=" O LEU E1078 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLU E1087 " --> pdb=" O SER E1083 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA E1094 " --> pdb=" O GLY E1090 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N HIS E1098 " --> pdb=" O ALA E1094 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER E1100 " --> pdb=" O ARG E1096 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU E1101 " --> pdb=" O LEU E1097 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG E1104 " --> pdb=" O SER E1100 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE E1106 " --> pdb=" O LEU E1102 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LEU E1107 " --> pdb=" O ASN E1103 " (cutoff:3.500A) Processing helix chain 'E' and resid 1109 through 1116 removed outlier: 3.606A pdb=" N PHE E1113 " --> pdb=" O PRO E1109 " (cutoff:3.500A) Processing helix chain 'E' and resid 1117 through 1127 removed outlier: 3.812A pdb=" N ILE E1121 " --> pdb=" O PRO E1117 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE E1125 " --> pdb=" O ILE E1121 " (cutoff:3.500A) Processing helix chain 'E' and resid 1127 through 1135 removed outlier: 4.313A pdb=" N ASP E1133 " --> pdb=" O CYS E1129 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLN E1134 " --> pdb=" O ASN E1130 " (cutoff:3.500A) Processing helix chain 'E' and resid 1135 through 1155 removed outlier: 3.908A pdb=" N GLU E1141 " --> pdb=" O PRO E1137 " (cutoff:3.500A) Processing helix chain 'E' and resid 1162 through 1167 removed outlier: 4.001A pdb=" N VAL E1166 " --> pdb=" O PRO E1162 " (cutoff:3.500A) Processing helix chain 'E' and resid 1168 through 1191 removed outlier: 3.777A pdb=" N ILE E1173 " --> pdb=" O LEU E1169 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N VAL E1174 " --> pdb=" O PRO E1170 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N TYR E1181 " --> pdb=" O PHE E1177 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL E1184 " --> pdb=" O LYS E1180 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ALA E1185 " --> pdb=" O TYR E1181 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASP E1188 " --> pdb=" O VAL E1184 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLN E1191 " --> pdb=" O ARG E1187 " (cutoff:3.500A) Processing helix chain 'E' and resid 1196 through 1210 removed outlier: 3.894A pdb=" N LEU E1200 " --> pdb=" O THR E1196 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N VAL E1208 " --> pdb=" O PHE E1204 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU E1209 " --> pdb=" O ALA E1205 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLY E1210 " --> pdb=" O GLU E1206 " (cutoff:3.500A) Processing helix chain 'E' and resid 1210 through 1217 Processing helix chain 'E' and resid 1219 through 1273 removed outlier: 3.546A pdb=" N TYR E1230 " --> pdb=" O LYS E1226 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N SER E1233 " --> pdb=" O GLU E1229 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA E1237 " --> pdb=" O SER E1233 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU E1241 " --> pdb=" O ALA E1237 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N SER E1267 " --> pdb=" O ALA E1263 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ASN E1270 " --> pdb=" O THR E1266 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N HIS E1273 " --> pdb=" O SER E1269 " (cutoff:3.500A) Processing helix chain 'E' and resid 1278 through 1295 removed outlier: 3.928A pdb=" N GLY E1282 " --> pdb=" O ALA E1278 " (cutoff:3.500A) Processing helix chain 'E' and resid 1295 through 1320 removed outlier: 4.138A pdb=" N GLY E1310 " --> pdb=" O GLU E1306 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ALA E1311 " --> pdb=" O LEU E1307 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N VAL E1312 " --> pdb=" O GLN E1308 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS E1320 " --> pdb=" O HIS E1316 " (cutoff:3.500A) Processing helix chain 'E' and resid 1384 through 1391 Processing helix chain 'E' and resid 1414 through 1419 Processing helix chain 'E' and resid 1420 through 1422 No H-bonds generated for 'chain 'E' and resid 1420 through 1422' Processing helix chain 'E' and resid 1436 through 1441 Processing helix chain 'E' and resid 1449 through 1457 removed outlier: 3.772A pdb=" N LEU E1455 " --> pdb=" O LEU E1451 " (cutoff:3.500A) Processing helix chain 'E' and resid 1460 through 1465 Processing helix chain 'E' and resid 1476 through 1480 removed outlier: 3.920A pdb=" N GLU E1480 " --> pdb=" O GLU E1477 " (cutoff:3.500A) Processing helix chain 'E' and resid 1484 through 1497 removed outlier: 3.816A pdb=" N GLN E1488 " --> pdb=" O GLN E1484 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL E1497 " --> pdb=" O ALA E1493 " (cutoff:3.500A) Processing helix chain 'E' and resid 1508 through 1511 removed outlier: 4.559A pdb=" N SER E1511 " --> pdb=" O ALA E1508 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 1508 through 1511' Processing helix chain 'E' and resid 1513 through 1528 removed outlier: 3.672A pdb=" N LYS E1522 " --> pdb=" O ASN E1518 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N THR E1526 " --> pdb=" O LYS E1522 " (cutoff:3.500A) Processing helix chain 'E' and resid 1562 through 1568 Processing helix chain 'E' and resid 1572 through 1578 Processing sheet with id=AA1, first strand: chain 'E' and resid 697 through 700 removed outlier: 3.793A pdb=" N ASN E 699 " --> pdb=" O GLY E 685 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N GLY E 685 " --> pdb=" O ASN E 699 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 771 through 773 removed outlier: 7.271A pdb=" N LEU E 709 " --> pdb=" O TRP E 899 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N ILE E 901 " --> pdb=" O LEU E 709 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N MET E 711 " --> pdb=" O ILE E 901 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N MET E 903 " --> pdb=" O MET E 711 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N VAL E 713 " --> pdb=" O MET E 903 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ILE E 900 " --> pdb=" O GLU E 911 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N GLU E 911 " --> pdb=" O ILE E 900 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ALA E 902 " --> pdb=" O GLN E 909 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 1365 through 1368 removed outlier: 5.248A pdb=" N VAL E1365 " --> pdb=" O ASN E1349 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LEU E1350 " --> pdb=" O GLU E1400 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N GLU E1400 " --> pdb=" O LEU E1350 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 1423 through 1425 removed outlier: 6.270A pdb=" N GLY E1376 " --> pdb=" O ILE E1550 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N LEU E1552 " --> pdb=" O GLY E1376 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N CYS E1378 " --> pdb=" O LEU E1552 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N VAL E1549 " --> pdb=" O PHE E1560 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N PHE E1560 " --> pdb=" O VAL E1549 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N VAL E1551 " --> pdb=" O LEU E1558 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 1434 through 1435 568 hydrogen bonds defined for protein. 1665 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: 2.18 Time building geometry restraints manager: 1.25 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: 3436 1.34 - 1.46: 2590 1.46 - 1.58: 5073 1.58 - 1.70: 8 1.70 - 1.82: 88 Bond restraints: 11195 Sorted by residual: bond pdb=" C4 ATP E1604 " pdb=" C5 ATP E1604 " ideal model delta sigma weight residual 1.388 1.464 -0.076 1.00e-02 1.00e+04 5.82e+01 bond pdb=" C5 ATP E1604 " pdb=" C6 ATP E1604 " ideal model delta sigma weight residual 1.409 1.472 -0.063 1.00e-02 1.00e+04 4.02e+01 bond pdb=" C5 ATP E1604 " pdb=" N7 ATP E1604 " ideal model delta sigma weight residual 1.387 1.337 0.050 1.00e-02 1.00e+04 2.48e+01 bond pdb=" C4 ATP E1604 " pdb=" N9 ATP E1604 " ideal model delta sigma weight residual 1.374 1.326 0.048 1.00e-02 1.00e+04 2.26e+01 bond pdb=" C LEU E1169 " pdb=" N PRO E1170 " ideal model delta sigma weight residual 1.334 1.371 -0.037 8.40e-03 1.42e+04 1.93e+01 ... (remaining 11190 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.29: 15131 4.29 - 8.59: 80 8.59 - 12.88: 5 12.88 - 17.17: 1 17.17 - 21.47: 1 Bond angle restraints: 15218 Sorted by residual: angle pdb=" PB ATP E1604 " pdb=" O3B ATP E1604 " pdb=" PG ATP E1604 " ideal model delta sigma weight residual 139.87 118.40 21.47 1.00e+00 1.00e+00 4.61e+02 angle pdb=" PA ATP E1604 " pdb=" O3A ATP E1604 " pdb=" PB ATP E1604 " ideal model delta sigma weight residual 136.83 119.81 17.02 1.00e+00 1.00e+00 2.90e+02 angle pdb=" C5 ATP E1604 " pdb=" C4 ATP E1604 " pdb=" N3 ATP E1604 " ideal model delta sigma weight residual 126.80 118.81 7.99 1.00e+00 1.00e+00 6.38e+01 angle pdb=" N3 ATP E1604 " pdb=" C4 ATP E1604 " pdb=" N9 ATP E1604 " ideal model delta sigma weight residual 127.04 135.19 -8.15 1.15e+00 7.59e-01 5.04e+01 angle pdb=" N1 ATP E1604 " pdb=" C2 ATP E1604 " pdb=" N3 ATP E1604 " ideal model delta sigma weight residual 128.69 123.69 5.00 1.00e+00 1.00e+00 2.50e+01 ... (remaining 15213 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.19: 6156 24.19 - 48.38: 414 48.38 - 72.56: 42 72.56 - 96.75: 4 96.75 - 120.94: 1 Dihedral angle restraints: 6617 sinusoidal: 2547 harmonic: 4070 Sorted by residual: dihedral pdb=" O1B ADP E1601 " pdb=" O3A ADP E1601 " pdb=" PB ADP E1601 " pdb=" PA ADP E1601 " ideal model delta sinusoidal sigma weight residual -60.00 60.94 -120.94 1 2.00e+01 2.50e-03 3.63e+01 dihedral pdb=" CA GLY E 411 " pdb=" C GLY E 411 " pdb=" N GLU E 412 " pdb=" CA GLU E 412 " ideal model delta harmonic sigma weight residual -180.00 -150.01 -29.99 0 5.00e+00 4.00e-02 3.60e+01 dihedral pdb=" CA ASP E 854 " pdb=" C ASP E 854 " pdb=" N ASP E 855 " pdb=" CA ASP E 855 " ideal model delta harmonic sigma weight residual -180.00 -152.05 -27.95 0 5.00e+00 4.00e-02 3.12e+01 ... (remaining 6614 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1537 0.069 - 0.139: 251 0.139 - 0.208: 23 0.208 - 0.278: 1 0.278 - 0.347: 1 Chirality restraints: 1813 Sorted by residual: chirality pdb=" CG LEU E1227 " pdb=" CB LEU E1227 " pdb=" CD1 LEU E1227 " pdb=" CD2 LEU E1227 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.35 2.00e-01 2.50e+01 3.02e+00 chirality pdb=" CB ILE E 138 " pdb=" CA ILE E 138 " pdb=" CG1 ILE E 138 " pdb=" CG2 ILE E 138 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" CB VAL E 598 " pdb=" CA VAL E 598 " pdb=" CG1 VAL E 598 " pdb=" CG2 VAL E 598 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 1.01e+00 ... (remaining 1810 not shown) Planarity restraints: 1872 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU E 894 " 0.050 5.00e-02 4.00e+02 7.51e-02 9.02e+00 pdb=" N PRO E 895 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO E 895 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO E 895 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE E 45 " -0.046 5.00e-02 4.00e+02 6.88e-02 7.58e+00 pdb=" N PRO E 46 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO E 46 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO E 46 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA E1370 " -0.042 5.00e-02 4.00e+02 6.36e-02 6.47e+00 pdb=" N PRO E1371 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO E1371 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO E1371 " -0.035 5.00e-02 4.00e+02 ... (remaining 1869 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 161 2.65 - 3.22: 9753 3.22 - 3.78: 17288 3.78 - 4.34: 23714 4.34 - 4.90: 38902 Nonbonded interactions: 89818 Sorted by model distance: nonbonded pdb="MG MG E1602 " pdb=" O3B ATP E1604 " model vdw 2.093 2.170 nonbonded pdb=" OE1 GLN E 775 " pdb="MG MG E1602 " model vdw 2.096 2.170 nonbonded pdb=" OG SER E1386 " pdb="MG MG E1603 " model vdw 2.191 2.170 nonbonded pdb=" NE2 GLN E 775 " pdb="MG MG E1602 " model vdw 2.278 2.250 nonbonded pdb="MG MG E1602 " pdb=" O2G ATP E1604 " model vdw 2.284 2.170 ... (remaining 89813 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 individual isotropic 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: 4.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.380 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 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:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 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 0.076 11195 Z= 0.295 Angle : 0.876 21.467 15218 Z= 0.518 Chirality : 0.051 0.347 1813 Planarity : 0.007 0.075 1872 Dihedral : 15.450 120.941 3973 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 4.27 % Allowed : 15.13 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.70 (0.16), residues: 1379 helix: -3.19 (0.11), residues: 890 sheet: -2.40 (0.67), residues: 46 loop : -2.54 (0.26), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 798 TYR 0.014 0.002 TYR E1287 PHE 0.016 0.002 PHE E1399 TRP 0.014 0.002 TRP E1339 HIS 0.009 0.001 HIS E 847 Details of bonding type rmsd/Z covalent geometry : bond 0.00607 / 0.30 (11195) covalent geometry : angle 0.87580 / 0.52 (15218) hydrogen bonds : bond 0.16521 / 11.10 ( 568) hydrogen bonds : angle 7.57238 / 5.37 ( 1665) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 172 time to evaluate : 0.424 Fit side-chains REVERT: E 95 LEU cc_start: 0.8127 (OUTLIER) cc_final: 0.7868 (tt) REVERT: E 133 PHE cc_start: 0.7790 (m-10) cc_final: 0.7538 (m-80) REVERT: E 222 PHE cc_start: 0.8739 (OUTLIER) cc_final: 0.8008 (m-80) REVERT: E 531 MET cc_start: 0.8519 (tpp) cc_final: 0.8173 (mmm) REVERT: E 547 MET cc_start: 0.8896 (tpp) cc_final: 0.8600 (mmt) REVERT: E 560 PHE cc_start: 0.8895 (m-80) cc_final: 0.8612 (m-80) REVERT: E 1193 ASP cc_start: 0.7861 (t0) cc_final: 0.7537 (t0) REVERT: E 1261 LEU cc_start: 0.9275 (tp) cc_final: 0.9069 (tt) REVERT: E 1319 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8825 (tt) REVERT: E 1506 ASP cc_start: 0.8584 (t0) cc_final: 0.8365 (t0) REVERT: E 1514 MET cc_start: 0.8867 (mtp) cc_final: 0.8635 (mtp) outliers start: 50 outliers final: 31 residues processed: 220 average time/residue: 0.1022 time to fit residues: 32.2891 Evaluate side-chains 165 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 131 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 128 ILE Chi-restraints excluded: chain E residue 131 SER Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 191 ILE Chi-restraints excluded: chain E residue 222 PHE Chi-restraints excluded: chain E residue 235 ASN Chi-restraints excluded: chain E residue 347 VAL Chi-restraints excluded: chain E residue 348 SER Chi-restraints excluded: chain E residue 362 LEU Chi-restraints excluded: chain E residue 469 ILE Chi-restraints excluded: chain E residue 564 VAL Chi-restraints excluded: chain E residue 680 VAL Chi-restraints excluded: chain E residue 688 THR Chi-restraints excluded: chain E residue 690 THR Chi-restraints excluded: chain E residue 700 ILE Chi-restraints excluded: chain E residue 710 THR Chi-restraints excluded: chain E residue 812 ILE Chi-restraints excluded: chain E residue 828 ILE Chi-restraints excluded: chain E residue 850 VAL Chi-restraints excluded: chain E residue 913 THR Chi-restraints excluded: chain E residue 916 ASP Chi-restraints excluded: chain E residue 1063 VAL Chi-restraints excluded: chain E residue 1091 LEU Chi-restraints excluded: chain E residue 1147 THR Chi-restraints excluded: chain E residue 1171 LEU Chi-restraints excluded: chain E residue 1319 LEU Chi-restraints excluded: chain E residue 1386 SER Chi-restraints excluded: chain E residue 1511 SER Chi-restraints excluded: chain E residue 1536 ILE Chi-restraints excluded: chain E residue 1539 ARG Chi-restraints excluded: chain E residue 1543 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 98 optimal weight: 0.2980 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 73 ASN E 104 HIS E 212 GLN E 220 GLN E 327 HIS E 350 GLN E 375 GLN E 407 ASN E 475 GLN E 499 GLN E 708 GLN E 732 GLN E 781 ASN E 836 GLN E1061 GLN E1134 GLN E1518 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.103836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.087872 restraints weight = 18041.231| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 2.10 r_work: 0.2978 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.1450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11195 Z= 0.138 Angle : 0.567 8.256 15218 Z= 0.287 Chirality : 0.040 0.160 1813 Planarity : 0.004 0.049 1872 Dihedral : 7.889 99.709 1562 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.56 % Allowed : 18.38 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.60 (0.20), residues: 1379 helix: -1.41 (0.15), residues: 909 sheet: -1.73 (0.70), residues: 51 loop : -2.06 (0.28), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E1444 TYR 0.010 0.001 TYR E 125 PHE 0.011 0.001 PHE E1223 TRP 0.012 0.001 TRP E1339 HIS 0.009 0.001 HIS E 847 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 (11195) covalent geometry : angle 0.56708 / 0.29 (15218) hydrogen bonds : bond 0.03545 / 2.38 ( 568) hydrogen bonds : angle 4.43514 / 3.11 ( 1665) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 151 time to evaluate : 0.422 Fit side-chains REVERT: E 113 MET cc_start: 0.8345 (mmm) cc_final: 0.7701 (tpt) REVERT: E 222 PHE cc_start: 0.8975 (OUTLIER) cc_final: 0.8342 (m-80) REVERT: E 301 VAL cc_start: 0.9130 (OUTLIER) cc_final: 0.8832 (p) REVERT: E 560 PHE cc_start: 0.8842 (m-80) cc_final: 0.8633 (m-80) REVERT: E 878 ARG cc_start: 0.7852 (mmm-85) cc_final: 0.7346 (tpt-90) REVERT: E 1187 ARG cc_start: 0.8194 (ppt170) cc_final: 0.7425 (ptt180) REVERT: E 1193 ASP cc_start: 0.8562 (t0) cc_final: 0.8245 (t0) outliers start: 30 outliers final: 17 residues processed: 177 average time/residue: 0.0793 time to fit residues: 21.2470 Evaluate side-chains 148 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 129 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 81 MET Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 191 ILE Chi-restraints excluded: chain E residue 222 PHE Chi-restraints excluded: chain E residue 235 ASN Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 422 VAL Chi-restraints excluded: chain E residue 573 SER Chi-restraints excluded: chain E residue 608 VAL Chi-restraints excluded: chain E residue 690 THR Chi-restraints excluded: chain E residue 710 THR Chi-restraints excluded: chain E residue 821 THR Chi-restraints excluded: chain E residue 828 ILE Chi-restraints excluded: chain E residue 916 ASP Chi-restraints excluded: chain E residue 943 THR Chi-restraints excluded: chain E residue 1105 ILE Chi-restraints excluded: chain E residue 1410 ILE Chi-restraints excluded: chain E residue 1541 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 15 optimal weight: 4.9990 chunk 8 optimal weight: 7.9990 chunk 56 optimal weight: 3.9990 chunk 112 optimal weight: 0.7980 chunk 104 optimal weight: 0.8980 chunk 127 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 72 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.102848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.086758 restraints weight = 18292.883| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 2.12 r_work: 0.2954 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2828 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11195 Z= 0.156 Angle : 0.555 8.205 15218 Z= 0.278 Chirality : 0.041 0.150 1813 Planarity : 0.004 0.042 1872 Dihedral : 6.860 93.046 1521 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.25 % Allowed : 18.38 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.67 (0.22), residues: 1379 helix: -0.59 (0.17), residues: 915 sheet: -1.32 (0.74), residues: 51 loop : -2.00 (0.28), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 599 TYR 0.010 0.001 TYR E1181 PHE 0.008 0.001 PHE E 155 TRP 0.010 0.001 TRP E1247 HIS 0.009 0.001 HIS E 847 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.16 (11195) covalent geometry : angle 0.55539 / 0.28 (15218) hydrogen bonds : bond 0.03432 / 2.32 ( 568) hydrogen bonds : angle 4.12440 / 2.87 ( 1665) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 144 time to evaluate : 0.428 Fit side-chains REVERT: E 95 LEU cc_start: 0.7805 (OUTLIER) cc_final: 0.7464 (tt) REVERT: E 146 LEU cc_start: 0.7337 (OUTLIER) cc_final: 0.7043 (pt) REVERT: E 222 PHE cc_start: 0.9020 (OUTLIER) cc_final: 0.8403 (m-80) REVERT: E 237 PHE cc_start: 0.8844 (OUTLIER) cc_final: 0.8077 (t80) REVERT: E 301 VAL cc_start: 0.9136 (OUTLIER) cc_final: 0.8829 (p) REVERT: E 364 PHE cc_start: 0.9289 (t80) cc_final: 0.8803 (t80) REVERT: E 440 TRP cc_start: 0.7970 (m-10) cc_final: 0.7467 (m-10) REVERT: E 486 GLN cc_start: 0.8770 (mm-40) cc_final: 0.8484 (mm110) REVERT: E 509 LEU cc_start: 0.9244 (tt) cc_final: 0.9021 (tt) REVERT: E 531 MET cc_start: 0.8672 (tpp) cc_final: 0.8414 (tpt) REVERT: E 599 ARG cc_start: 0.7925 (ttm110) cc_final: 0.7404 (ttt180) REVERT: E 878 ARG cc_start: 0.7845 (mmm-85) cc_final: 0.7354 (tpt-90) REVERT: E 1187 ARG cc_start: 0.8156 (ppt170) cc_final: 0.7953 (ppt170) REVERT: E 1193 ASP cc_start: 0.8588 (t0) cc_final: 0.8270 (t0) REVERT: E 1413 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8374 (mp) outliers start: 38 outliers final: 23 residues processed: 173 average time/residue: 0.0838 time to fit residues: 22.3115 Evaluate side-chains 161 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 132 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 81 MET Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 191 ILE Chi-restraints excluded: chain E residue 222 PHE Chi-restraints excluded: chain E residue 235 ASN Chi-restraints excluded: chain E residue 237 PHE Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 377 SER Chi-restraints excluded: chain E residue 421 LEU Chi-restraints excluded: chain E residue 422 VAL Chi-restraints excluded: chain E residue 567 PHE Chi-restraints excluded: chain E residue 573 SER Chi-restraints excluded: chain E residue 608 VAL Chi-restraints excluded: chain E residue 690 THR Chi-restraints excluded: chain E residue 710 THR Chi-restraints excluded: chain E residue 821 THR Chi-restraints excluded: chain E residue 828 ILE Chi-restraints excluded: chain E residue 916 ASP Chi-restraints excluded: chain E residue 932 MET Chi-restraints excluded: chain E residue 943 THR Chi-restraints excluded: chain E residue 1005 LEU Chi-restraints excluded: chain E residue 1105 ILE Chi-restraints excluded: chain E residue 1410 ILE Chi-restraints excluded: chain E residue 1413 LEU Chi-restraints excluded: chain E residue 1541 HIS Chi-restraints excluded: chain E residue 1576 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 112 optimal weight: 1.9990 chunk 111 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 40 optimal weight: 0.2980 chunk 74 optimal weight: 0.6980 chunk 132 optimal weight: 0.8980 chunk 54 optimal weight: 0.6980 chunk 75 optimal weight: 0.6980 chunk 51 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 104 HIS E 836 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.103578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.087494 restraints weight = 18106.546| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 2.07 r_work: 0.2974 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11195 Z= 0.133 Angle : 0.533 8.758 15218 Z= 0.267 Chirality : 0.040 0.137 1813 Planarity : 0.003 0.040 1872 Dihedral : 6.689 95.910 1521 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.50 % Allowed : 18.29 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.23), residues: 1379 helix: -0.13 (0.18), residues: 905 sheet: -1.12 (0.76), residues: 51 loop : -1.76 (0.28), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 599 TYR 0.015 0.001 TYR E 125 PHE 0.013 0.001 PHE E 315 TRP 0.010 0.001 TRP E1247 HIS 0.008 0.001 HIS E 847 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (11195) covalent geometry : angle 0.53342 / 0.27 (15218) hydrogen bonds : bond 0.03212 / 2.17 ( 568) hydrogen bonds : angle 3.93028 / 2.73 ( 1665) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 145 time to evaluate : 0.402 Fit side-chains REVERT: E 95 LEU cc_start: 0.7739 (OUTLIER) cc_final: 0.7443 (tt) REVERT: E 146 LEU cc_start: 0.7273 (OUTLIER) cc_final: 0.6849 (pt) REVERT: E 222 PHE cc_start: 0.9040 (OUTLIER) cc_final: 0.8365 (m-80) REVERT: E 237 PHE cc_start: 0.8813 (OUTLIER) cc_final: 0.7997 (t80) REVERT: E 269 GLU cc_start: 0.8311 (mt-10) cc_final: 0.8040 (tp30) REVERT: E 301 VAL cc_start: 0.9119 (OUTLIER) cc_final: 0.8824 (p) REVERT: E 413 MET cc_start: 0.8686 (ptp) cc_final: 0.8453 (ptp) REVERT: E 440 TRP cc_start: 0.7898 (m-10) cc_final: 0.7386 (m-10) REVERT: E 531 MET cc_start: 0.8671 (tpp) cc_final: 0.8406 (tpp) REVERT: E 878 ARG cc_start: 0.7863 (mmm-85) cc_final: 0.7657 (tpt170) REVERT: E 916 ASP cc_start: 0.8823 (OUTLIER) cc_final: 0.8584 (t0) REVERT: E 1188 ASP cc_start: 0.9012 (t0) cc_final: 0.8599 (t0) REVERT: E 1193 ASP cc_start: 0.8589 (t0) cc_final: 0.8306 (t0) REVERT: E 1251 ARG cc_start: 0.8947 (OUTLIER) cc_final: 0.8320 (mpt180) outliers start: 41 outliers final: 27 residues processed: 176 average time/residue: 0.0913 time to fit residues: 24.2400 Evaluate side-chains 173 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 139 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 81 MET Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 191 ILE Chi-restraints excluded: chain E residue 222 PHE Chi-restraints excluded: chain E residue 235 ASN Chi-restraints excluded: chain E residue 237 PHE Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 421 LEU Chi-restraints excluded: chain E residue 422 VAL Chi-restraints excluded: chain E residue 567 PHE Chi-restraints excluded: chain E residue 573 SER Chi-restraints excluded: chain E residue 608 VAL Chi-restraints excluded: chain E residue 680 VAL Chi-restraints excluded: chain E residue 690 THR Chi-restraints excluded: chain E residue 710 THR Chi-restraints excluded: chain E residue 821 THR Chi-restraints excluded: chain E residue 828 ILE Chi-restraints excluded: chain E residue 916 ASP Chi-restraints excluded: chain E residue 932 MET Chi-restraints excluded: chain E residue 943 THR Chi-restraints excluded: chain E residue 998 TRP Chi-restraints excluded: chain E residue 1005 LEU Chi-restraints excluded: chain E residue 1026 VAL Chi-restraints excluded: chain E residue 1105 ILE Chi-restraints excluded: chain E residue 1148 LEU Chi-restraints excluded: chain E residue 1251 ARG Chi-restraints excluded: chain E residue 1255 ILE Chi-restraints excluded: chain E residue 1410 ILE Chi-restraints excluded: chain E residue 1541 HIS Chi-restraints excluded: chain E residue 1576 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 17 optimal weight: 0.0980 chunk 31 optimal weight: 1.9990 chunk 11 optimal weight: 0.1980 chunk 0 optimal weight: 8.9990 chunk 128 optimal weight: 0.0370 chunk 14 optimal weight: 0.9980 chunk 43 optimal weight: 0.0970 chunk 100 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 122 optimal weight: 0.9980 overall best weight: 0.2656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 104 HIS E 263 ASN E 486 GLN E 836 GLN E 933 ASN E1541 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.106218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.090243 restraints weight = 17709.676| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 2.06 r_work: 0.3016 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 11195 Z= 0.095 Angle : 0.517 9.030 15218 Z= 0.253 Chirality : 0.039 0.222 1813 Planarity : 0.003 0.038 1872 Dihedral : 6.398 98.929 1521 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.08 % Allowed : 18.80 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.23), residues: 1379 helix: 0.24 (0.18), residues: 905 sheet: -0.89 (0.77), residues: 51 loop : -1.61 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 599 TYR 0.017 0.001 TYR E1032 PHE 0.008 0.001 PHE E 315 TRP 0.011 0.001 TRP E1339 HIS 0.007 0.001 HIS E 847 Details of bonding type rmsd/Z covalent geometry : bond 0.00206 / 0.10 (11195) covalent geometry : angle 0.51673 / 0.25 (15218) hydrogen bonds : bond 0.02910 / 1.96 ( 568) hydrogen bonds : angle 3.69019 / 2.56 ( 1665) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 158 time to evaluate : 0.391 Fit side-chains revert: symmetry clash REVERT: E 95 LEU cc_start: 0.7495 (OUTLIER) cc_final: 0.7222 (tt) REVERT: E 146 LEU cc_start: 0.7333 (OUTLIER) cc_final: 0.6984 (pt) REVERT: E 152 THR cc_start: 0.7408 (m) cc_final: 0.7060 (m) REVERT: E 222 PHE cc_start: 0.9008 (OUTLIER) cc_final: 0.8430 (m-80) REVERT: E 237 PHE cc_start: 0.8806 (OUTLIER) cc_final: 0.7889 (t80) REVERT: E 269 GLU cc_start: 0.8317 (mt-10) cc_final: 0.8038 (tp30) REVERT: E 301 VAL cc_start: 0.9085 (OUTLIER) cc_final: 0.8810 (p) REVERT: E 440 TRP cc_start: 0.7855 (m-10) cc_final: 0.7370 (m-10) REVERT: E 491 GLU cc_start: 0.8559 (tt0) cc_final: 0.8290 (tp30) REVERT: E 531 MET cc_start: 0.8735 (tpp) cc_final: 0.8493 (tpt) REVERT: E 586 ILE cc_start: 0.9232 (OUTLIER) cc_final: 0.9016 (tt) REVERT: E 903 MET cc_start: 0.8969 (mtp) cc_final: 0.8651 (mtp) REVERT: E 916 ASP cc_start: 0.8668 (OUTLIER) cc_final: 0.8467 (t0) REVERT: E 1188 ASP cc_start: 0.9017 (t0) cc_final: 0.8538 (t0) REVERT: E 1193 ASP cc_start: 0.8637 (t0) cc_final: 0.8363 (t0) REVERT: E 1251 ARG cc_start: 0.8918 (OUTLIER) cc_final: 0.8148 (mpt90) REVERT: E 1322 GLU cc_start: 0.8611 (mp0) cc_final: 0.8271 (mp0) outliers start: 36 outliers final: 22 residues processed: 186 average time/residue: 0.0867 time to fit residues: 24.2599 Evaluate side-chains 177 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 147 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 191 ILE Chi-restraints excluded: chain E residue 222 PHE Chi-restraints excluded: chain E residue 235 ASN Chi-restraints excluded: chain E residue 237 PHE Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 421 LEU Chi-restraints excluded: chain E residue 567 PHE Chi-restraints excluded: chain E residue 573 SER Chi-restraints excluded: chain E residue 586 ILE Chi-restraints excluded: chain E residue 608 VAL Chi-restraints excluded: chain E residue 680 VAL Chi-restraints excluded: chain E residue 690 THR Chi-restraints excluded: chain E residue 710 THR Chi-restraints excluded: chain E residue 828 ILE Chi-restraints excluded: chain E residue 916 ASP Chi-restraints excluded: chain E residue 932 MET Chi-restraints excluded: chain E residue 943 THR Chi-restraints excluded: chain E residue 998 TRP Chi-restraints excluded: chain E residue 1105 ILE Chi-restraints excluded: chain E residue 1148 LEU Chi-restraints excluded: chain E residue 1251 ARG Chi-restraints excluded: chain E residue 1410 ILE Chi-restraints excluded: chain E residue 1539 ARG Chi-restraints excluded: chain E residue 1576 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 124 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 123 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 80 optimal weight: 0.9990 chunk 8 optimal weight: 5.9990 chunk 114 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 chunk 36 optimal weight: 0.0050 chunk 106 optimal weight: 0.5980 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 104 HIS E 836 GLN E1541 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.104167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.088016 restraints weight = 17969.365| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 2.08 r_work: 0.2986 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11195 Z= 0.134 Angle : 0.529 8.852 15218 Z= 0.262 Chirality : 0.041 0.259 1813 Planarity : 0.003 0.041 1872 Dihedral : 6.417 103.707 1521 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.68 % Allowed : 19.15 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.23), residues: 1379 helix: 0.36 (0.18), residues: 911 sheet: -0.85 (0.76), residues: 51 loop : -1.65 (0.28), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 599 TYR 0.017 0.001 TYR E 799 PHE 0.009 0.001 PHE E 155 TRP 0.010 0.001 TRP E1247 HIS 0.007 0.001 HIS E 847 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 (11195) covalent geometry : angle 0.52949 / 0.26 (15218) hydrogen bonds : bond 0.03069 / 2.07 ( 568) hydrogen bonds : angle 3.72671 / 2.59 ( 1665) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 149 time to evaluate : 0.360 Fit side-chains revert: symmetry clash REVERT: E 95 LEU cc_start: 0.7689 (OUTLIER) cc_final: 0.7434 (tt) REVERT: E 146 LEU cc_start: 0.7300 (OUTLIER) cc_final: 0.6864 (pt) REVERT: E 222 PHE cc_start: 0.9066 (OUTLIER) cc_final: 0.8353 (m-80) REVERT: E 237 PHE cc_start: 0.8779 (OUTLIER) cc_final: 0.7831 (t80) REVERT: E 269 GLU cc_start: 0.8286 (mt-10) cc_final: 0.8080 (tp30) REVERT: E 301 VAL cc_start: 0.9131 (OUTLIER) cc_final: 0.8842 (p) REVERT: E 440 TRP cc_start: 0.7859 (m-10) cc_final: 0.7366 (m-10) REVERT: E 491 GLU cc_start: 0.8694 (tt0) cc_final: 0.8422 (tp30) REVERT: E 531 MET cc_start: 0.8733 (tpp) cc_final: 0.8524 (tpp) REVERT: E 586 ILE cc_start: 0.9260 (OUTLIER) cc_final: 0.9042 (tt) REVERT: E 1188 ASP cc_start: 0.9019 (t0) cc_final: 0.8588 (t0) REVERT: E 1193 ASP cc_start: 0.8731 (t0) cc_final: 0.8404 (t0) REVERT: E 1251 ARG cc_start: 0.9027 (OUTLIER) cc_final: 0.8345 (mpt180) REVERT: E 1258 CYS cc_start: 0.9050 (t) cc_final: 0.8212 (m) REVERT: E 1322 GLU cc_start: 0.8624 (mp0) cc_final: 0.8168 (mp0) REVERT: E 1413 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8325 (mp) REVERT: E 1444 ARG cc_start: 0.8275 (ttm-80) cc_final: 0.7991 (ttm-80) outliers start: 43 outliers final: 29 residues processed: 184 average time/residue: 0.0833 time to fit residues: 23.4796 Evaluate side-chains 180 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 143 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 81 MET Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 191 ILE Chi-restraints excluded: chain E residue 222 PHE Chi-restraints excluded: chain E residue 235 ASN Chi-restraints excluded: chain E residue 237 PHE Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 347 VAL Chi-restraints excluded: chain E residue 377 SER Chi-restraints excluded: chain E residue 388 LEU Chi-restraints excluded: chain E residue 421 LEU Chi-restraints excluded: chain E residue 422 VAL Chi-restraints excluded: chain E residue 567 PHE Chi-restraints excluded: chain E residue 573 SER Chi-restraints excluded: chain E residue 586 ILE Chi-restraints excluded: chain E residue 591 LEU Chi-restraints excluded: chain E residue 608 VAL Chi-restraints excluded: chain E residue 680 VAL Chi-restraints excluded: chain E residue 690 THR Chi-restraints excluded: chain E residue 710 THR Chi-restraints excluded: chain E residue 821 THR Chi-restraints excluded: chain E residue 828 ILE Chi-restraints excluded: chain E residue 943 THR Chi-restraints excluded: chain E residue 998 TRP Chi-restraints excluded: chain E residue 1105 ILE Chi-restraints excluded: chain E residue 1148 LEU Chi-restraints excluded: chain E residue 1251 ARG Chi-restraints excluded: chain E residue 1318 LEU Chi-restraints excluded: chain E residue 1410 ILE Chi-restraints excluded: chain E residue 1413 LEU Chi-restraints excluded: chain E residue 1539 ARG Chi-restraints excluded: chain E residue 1576 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 109 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 18 optimal weight: 8.9990 chunk 129 optimal weight: 0.5980 chunk 90 optimal weight: 2.9990 chunk 112 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 43 optimal weight: 0.2980 chunk 88 optimal weight: 0.1980 chunk 59 optimal weight: 0.5980 chunk 54 optimal weight: 0.6980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 104 HIS E 836 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.105247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.089184 restraints weight = 17746.772| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 2.07 r_work: 0.3006 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11195 Z= 0.112 Angle : 0.521 8.946 15218 Z= 0.257 Chirality : 0.040 0.256 1813 Planarity : 0.003 0.040 1872 Dihedral : 6.170 108.214 1519 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 3.85 % Allowed : 20.09 % Favored : 76.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.23), residues: 1379 helix: 0.52 (0.18), residues: 907 sheet: -0.74 (0.77), residues: 51 loop : -1.64 (0.28), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 599 TYR 0.022 0.001 TYR E 125 PHE 0.013 0.001 PHE E1223 TRP 0.010 0.001 TRP E1247 HIS 0.007 0.001 HIS E 847 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (11195) covalent geometry : angle 0.52114 / 0.26 (15218) hydrogen bonds : bond 0.02958 / 1.99 ( 568) hydrogen bonds : angle 3.65917 / 2.54 ( 1665) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 152 time to evaluate : 0.415 Fit side-chains revert: symmetry clash REVERT: E 95 LEU cc_start: 0.7661 (OUTLIER) cc_final: 0.7417 (tt) REVERT: E 146 LEU cc_start: 0.7283 (OUTLIER) cc_final: 0.6869 (pt) REVERT: E 152 THR cc_start: 0.7485 (m) cc_final: 0.7128 (m) REVERT: E 222 PHE cc_start: 0.9050 (OUTLIER) cc_final: 0.8388 (m-80) REVERT: E 237 PHE cc_start: 0.8758 (OUTLIER) cc_final: 0.7794 (t80) REVERT: E 269 GLU cc_start: 0.8289 (mt-10) cc_final: 0.8076 (tp30) REVERT: E 301 VAL cc_start: 0.9116 (OUTLIER) cc_final: 0.8827 (p) REVERT: E 440 TRP cc_start: 0.7851 (m-10) cc_final: 0.7361 (m-10) REVERT: E 491 GLU cc_start: 0.8712 (tt0) cc_final: 0.8345 (tp30) REVERT: E 531 MET cc_start: 0.8726 (tpp) cc_final: 0.8522 (tpp) REVERT: E 586 ILE cc_start: 0.9241 (OUTLIER) cc_final: 0.9024 (tt) REVERT: E 903 MET cc_start: 0.8948 (mtp) cc_final: 0.8622 (mtp) REVERT: E 1165 LEU cc_start: 0.8824 (mt) cc_final: 0.8615 (mt) REVERT: E 1188 ASP cc_start: 0.9015 (t0) cc_final: 0.8575 (t0) REVERT: E 1193 ASP cc_start: 0.8736 (t0) cc_final: 0.8427 (t0) REVERT: E 1251 ARG cc_start: 0.8937 (OUTLIER) cc_final: 0.8242 (mpt90) REVERT: E 1258 CYS cc_start: 0.9016 (t) cc_final: 0.8183 (m) REVERT: E 1322 GLU cc_start: 0.8597 (mp0) cc_final: 0.8164 (mp0) REVERT: E 1444 ARG cc_start: 0.8307 (ttm-80) cc_final: 0.8027 (ttm-80) outliers start: 45 outliers final: 31 residues processed: 189 average time/residue: 0.0805 time to fit residues: 23.2789 Evaluate side-chains 184 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 146 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 75 ARG Chi-restraints excluded: chain E residue 81 MET Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 191 ILE Chi-restraints excluded: chain E residue 222 PHE Chi-restraints excluded: chain E residue 235 ASN Chi-restraints excluded: chain E residue 237 PHE Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 347 VAL Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 377 SER Chi-restraints excluded: chain E residue 388 LEU Chi-restraints excluded: chain E residue 421 LEU Chi-restraints excluded: chain E residue 567 PHE Chi-restraints excluded: chain E residue 573 SER Chi-restraints excluded: chain E residue 586 ILE Chi-restraints excluded: chain E residue 591 LEU Chi-restraints excluded: chain E residue 608 VAL Chi-restraints excluded: chain E residue 680 VAL Chi-restraints excluded: chain E residue 690 THR Chi-restraints excluded: chain E residue 710 THR Chi-restraints excluded: chain E residue 821 THR Chi-restraints excluded: chain E residue 828 ILE Chi-restraints excluded: chain E residue 943 THR Chi-restraints excluded: chain E residue 998 TRP Chi-restraints excluded: chain E residue 1105 ILE Chi-restraints excluded: chain E residue 1148 LEU Chi-restraints excluded: chain E residue 1251 ARG Chi-restraints excluded: chain E residue 1255 ILE Chi-restraints excluded: chain E residue 1318 LEU Chi-restraints excluded: chain E residue 1410 ILE Chi-restraints excluded: chain E residue 1539 ARG Chi-restraints excluded: chain E residue 1576 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 43 optimal weight: 2.9990 chunk 132 optimal weight: 0.6980 chunk 137 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 51 optimal weight: 0.6980 chunk 0 optimal weight: 8.9990 chunk 86 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 104 HIS E 836 GLN ** E1541 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.103497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.087264 restraints weight = 17855.729| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 2.07 r_work: 0.2973 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 11195 Z= 0.158 Angle : 0.545 8.728 15218 Z= 0.271 Chirality : 0.041 0.173 1813 Planarity : 0.004 0.066 1872 Dihedral : 6.223 115.342 1519 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 4.19 % Allowed : 19.66 % Favored : 76.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.23), residues: 1379 helix: 0.56 (0.18), residues: 901 sheet: -0.78 (0.77), residues: 51 loop : -1.56 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 599 TYR 0.018 0.001 TYR E 125 PHE 0.013 0.001 PHE E1223 TRP 0.008 0.001 TRP E1247 HIS 0.007 0.001 HIS E 847 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.16 (11195) covalent geometry : angle 0.54511 / 0.27 (15218) hydrogen bonds : bond 0.03172 / 2.14 ( 568) hydrogen bonds : angle 3.76639 / 2.61 ( 1665) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 144 time to evaluate : 0.372 Fit side-chains revert: symmetry clash REVERT: E 95 LEU cc_start: 0.7631 (OUTLIER) cc_final: 0.7386 (tt) REVERT: E 146 LEU cc_start: 0.7301 (OUTLIER) cc_final: 0.6838 (pt) REVERT: E 222 PHE cc_start: 0.9080 (OUTLIER) cc_final: 0.8301 (m-80) REVERT: E 237 PHE cc_start: 0.8781 (OUTLIER) cc_final: 0.7942 (t80) REVERT: E 269 GLU cc_start: 0.8366 (mt-10) cc_final: 0.8157 (tp30) REVERT: E 301 VAL cc_start: 0.9178 (OUTLIER) cc_final: 0.8894 (p) REVERT: E 440 TRP cc_start: 0.7772 (m-10) cc_final: 0.7270 (m-10) REVERT: E 491 GLU cc_start: 0.8742 (tt0) cc_final: 0.8397 (tp30) REVERT: E 531 MET cc_start: 0.8724 (tpp) cc_final: 0.8504 (tpt) REVERT: E 586 ILE cc_start: 0.9263 (OUTLIER) cc_final: 0.9049 (tt) REVERT: E 1165 LEU cc_start: 0.8837 (mt) cc_final: 0.8622 (mt) REVERT: E 1188 ASP cc_start: 0.9042 (t0) cc_final: 0.8596 (t0) REVERT: E 1193 ASP cc_start: 0.8789 (t0) cc_final: 0.8459 (t0) REVERT: E 1251 ARG cc_start: 0.9024 (OUTLIER) cc_final: 0.8375 (mpt180) REVERT: E 1258 CYS cc_start: 0.9036 (t) cc_final: 0.8231 (m) REVERT: E 1322 GLU cc_start: 0.8633 (mp0) cc_final: 0.8163 (mp0) REVERT: E 1443 GLU cc_start: 0.8458 (OUTLIER) cc_final: 0.8136 (pm20) REVERT: E 1444 ARG cc_start: 0.8303 (ttm-80) cc_final: 0.8046 (ttm-80) outliers start: 49 outliers final: 34 residues processed: 182 average time/residue: 0.0804 time to fit residues: 22.2951 Evaluate side-chains 181 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 139 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 81 MET Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 191 ILE Chi-restraints excluded: chain E residue 222 PHE Chi-restraints excluded: chain E residue 235 ASN Chi-restraints excluded: chain E residue 237 PHE Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 347 VAL Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 377 SER Chi-restraints excluded: chain E residue 388 LEU Chi-restraints excluded: chain E residue 421 LEU Chi-restraints excluded: chain E residue 422 VAL Chi-restraints excluded: chain E residue 463 ILE Chi-restraints excluded: chain E residue 567 PHE Chi-restraints excluded: chain E residue 573 SER Chi-restraints excluded: chain E residue 586 ILE Chi-restraints excluded: chain E residue 591 LEU Chi-restraints excluded: chain E residue 608 VAL Chi-restraints excluded: chain E residue 680 VAL Chi-restraints excluded: chain E residue 690 THR Chi-restraints excluded: chain E residue 710 THR Chi-restraints excluded: chain E residue 801 MET Chi-restraints excluded: chain E residue 821 THR Chi-restraints excluded: chain E residue 828 ILE Chi-restraints excluded: chain E residue 943 THR Chi-restraints excluded: chain E residue 1105 ILE Chi-restraints excluded: chain E residue 1148 LEU Chi-restraints excluded: chain E residue 1251 ARG Chi-restraints excluded: chain E residue 1255 ILE Chi-restraints excluded: chain E residue 1318 LEU Chi-restraints excluded: chain E residue 1347 ILE Chi-restraints excluded: chain E residue 1410 ILE Chi-restraints excluded: chain E residue 1443 GLU Chi-restraints excluded: chain E residue 1539 ARG Chi-restraints excluded: chain E residue 1576 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 67 optimal weight: 0.0570 chunk 65 optimal weight: 0.6980 chunk 13 optimal weight: 3.9990 chunk 1 optimal weight: 0.0970 chunk 116 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 103 optimal weight: 0.5980 chunk 125 optimal weight: 0.0370 overall best weight: 0.2974 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 104 HIS E 836 GLN ** E1541 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.106651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.090549 restraints weight = 17614.313| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 2.07 r_work: 0.3020 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 11195 Z= 0.099 Angle : 0.511 9.038 15218 Z= 0.252 Chirality : 0.040 0.268 1813 Planarity : 0.003 0.046 1872 Dihedral : 6.017 121.931 1519 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 3.59 % Allowed : 20.26 % Favored : 76.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.23), residues: 1379 helix: 0.78 (0.18), residues: 907 sheet: -0.65 (0.79), residues: 51 loop : -1.49 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 599 TYR 0.014 0.001 TYR E 799 PHE 0.010 0.001 PHE E1223 TRP 0.011 0.001 TRP E1247 HIS 0.006 0.001 HIS E 847 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.10 (11195) covalent geometry : angle 0.51122 / 0.25 (15218) hydrogen bonds : bond 0.02862 / 1.92 ( 568) hydrogen bonds : angle 3.56962 / 2.47 ( 1665) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 154 time to evaluate : 0.411 Fit side-chains revert: symmetry clash REVERT: E 95 LEU cc_start: 0.7562 (OUTLIER) cc_final: 0.7357 (tt) REVERT: E 146 LEU cc_start: 0.7226 (OUTLIER) cc_final: 0.6830 (pt) REVERT: E 152 THR cc_start: 0.7410 (m) cc_final: 0.7064 (m) REVERT: E 222 PHE cc_start: 0.9060 (OUTLIER) cc_final: 0.8428 (m-80) REVERT: E 237 PHE cc_start: 0.8750 (OUTLIER) cc_final: 0.7733 (t80) REVERT: E 272 ASP cc_start: 0.7959 (p0) cc_final: 0.7640 (p0) REVERT: E 301 VAL cc_start: 0.9083 (OUTLIER) cc_final: 0.8801 (p) REVERT: E 440 TRP cc_start: 0.7870 (m-10) cc_final: 0.7405 (m-10) REVERT: E 491 GLU cc_start: 0.8721 (tt0) cc_final: 0.8324 (tp30) REVERT: E 531 MET cc_start: 0.8696 (tpp) cc_final: 0.8474 (tpt) REVERT: E 586 ILE cc_start: 0.9184 (OUTLIER) cc_final: 0.8941 (tt) REVERT: E 599 ARG cc_start: 0.8058 (ttm110) cc_final: 0.7441 (ttt180) REVERT: E 1188 ASP cc_start: 0.9045 (t0) cc_final: 0.8580 (t0) REVERT: E 1193 ASP cc_start: 0.8960 (t0) cc_final: 0.8652 (t0) REVERT: E 1251 ARG cc_start: 0.8909 (OUTLIER) cc_final: 0.8093 (mpt90) REVERT: E 1258 CYS cc_start: 0.9037 (t) cc_final: 0.8169 (m) REVERT: E 1443 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.8142 (pm20) REVERT: E 1444 ARG cc_start: 0.8372 (ttm-80) cc_final: 0.8065 (ttm-80) outliers start: 42 outliers final: 29 residues processed: 186 average time/residue: 0.0885 time to fit residues: 25.0760 Evaluate side-chains 181 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 144 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 81 MET Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 191 ILE Chi-restraints excluded: chain E residue 222 PHE Chi-restraints excluded: chain E residue 235 ASN Chi-restraints excluded: chain E residue 237 PHE Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 347 VAL Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 388 LEU Chi-restraints excluded: chain E residue 421 LEU Chi-restraints excluded: chain E residue 482 LEU Chi-restraints excluded: chain E residue 539 ILE Chi-restraints excluded: chain E residue 567 PHE Chi-restraints excluded: chain E residue 573 SER Chi-restraints excluded: chain E residue 586 ILE Chi-restraints excluded: chain E residue 608 VAL Chi-restraints excluded: chain E residue 680 VAL Chi-restraints excluded: chain E residue 690 THR Chi-restraints excluded: chain E residue 710 THR Chi-restraints excluded: chain E residue 821 THR Chi-restraints excluded: chain E residue 828 ILE Chi-restraints excluded: chain E residue 943 THR Chi-restraints excluded: chain E residue 1105 ILE Chi-restraints excluded: chain E residue 1148 LEU Chi-restraints excluded: chain E residue 1251 ARG Chi-restraints excluded: chain E residue 1255 ILE Chi-restraints excluded: chain E residue 1318 LEU Chi-restraints excluded: chain E residue 1347 ILE Chi-restraints excluded: chain E residue 1410 ILE Chi-restraints excluded: chain E residue 1443 GLU Chi-restraints excluded: chain E residue 1539 ARG Chi-restraints excluded: chain E residue 1576 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 0 optimal weight: 8.9990 chunk 63 optimal weight: 0.6980 chunk 83 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 122 optimal weight: 0.0070 chunk 112 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 overall best weight: 0.9000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 104 HIS E 836 GLN ** E1541 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.103754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.087556 restraints weight = 17891.776| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 2.08 r_work: 0.2972 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 11195 Z= 0.167 Angle : 0.556 8.725 15218 Z= 0.277 Chirality : 0.042 0.281 1813 Planarity : 0.003 0.053 1872 Dihedral : 6.220 125.585 1519 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 3.25 % Allowed : 20.85 % Favored : 75.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.23), residues: 1379 helix: 0.73 (0.18), residues: 901 sheet: -0.69 (0.78), residues: 51 loop : -1.45 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 599 TYR 0.027 0.001 TYR E 125 PHE 0.013 0.001 PHE E1223 TRP 0.008 0.001 TRP E1247 HIS 0.007 0.001 HIS E 847 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.17 (11195) covalent geometry : angle 0.55595 / 0.28 (15218) hydrogen bonds : bond 0.03229 / 2.17 ( 568) hydrogen bonds : angle 3.75820 / 2.62 ( 1665) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 144 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 95 LEU cc_start: 0.7592 (OUTLIER) cc_final: 0.7376 (tt) REVERT: E 146 LEU cc_start: 0.7324 (OUTLIER) cc_final: 0.6856 (pt) REVERT: E 152 THR cc_start: 0.7482 (m) cc_final: 0.7092 (m) REVERT: E 222 PHE cc_start: 0.9096 (OUTLIER) cc_final: 0.8357 (m-80) REVERT: E 237 PHE cc_start: 0.8777 (OUTLIER) cc_final: 0.7802 (t80) REVERT: E 256 ILE cc_start: 0.9474 (tp) cc_final: 0.8907 (tp) REVERT: E 301 VAL cc_start: 0.9179 (OUTLIER) cc_final: 0.8898 (p) REVERT: E 440 TRP cc_start: 0.7715 (m-10) cc_final: 0.7200 (m-10) REVERT: E 491 GLU cc_start: 0.8752 (tt0) cc_final: 0.8410 (tp30) REVERT: E 586 ILE cc_start: 0.9191 (OUTLIER) cc_final: 0.8968 (tt) REVERT: E 1188 ASP cc_start: 0.9045 (t0) cc_final: 0.8590 (t0) REVERT: E 1193 ASP cc_start: 0.9000 (t0) cc_final: 0.8685 (t0) REVERT: E 1251 ARG cc_start: 0.9018 (OUTLIER) cc_final: 0.8442 (mpt180) REVERT: E 1258 CYS cc_start: 0.9078 (t) cc_final: 0.8244 (m) REVERT: E 1413 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8279 (mp) REVERT: E 1443 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.8168 (pm20) REVERT: E 1444 ARG cc_start: 0.8380 (ttm-80) cc_final: 0.8091 (ttm-80) outliers start: 38 outliers final: 28 residues processed: 176 average time/residue: 0.0868 time to fit residues: 23.3373 Evaluate side-chains 179 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 142 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 81 MET Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 191 ILE Chi-restraints excluded: chain E residue 222 PHE Chi-restraints excluded: chain E residue 235 ASN Chi-restraints excluded: chain E residue 237 PHE Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 347 VAL Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 388 LEU Chi-restraints excluded: chain E residue 421 LEU Chi-restraints excluded: chain E residue 482 LEU Chi-restraints excluded: chain E residue 567 PHE Chi-restraints excluded: chain E residue 573 SER Chi-restraints excluded: chain E residue 586 ILE Chi-restraints excluded: chain E residue 608 VAL Chi-restraints excluded: chain E residue 680 VAL Chi-restraints excluded: chain E residue 690 THR Chi-restraints excluded: chain E residue 710 THR Chi-restraints excluded: chain E residue 801 MET Chi-restraints excluded: chain E residue 821 THR Chi-restraints excluded: chain E residue 828 ILE Chi-restraints excluded: chain E residue 1105 ILE Chi-restraints excluded: chain E residue 1148 LEU Chi-restraints excluded: chain E residue 1251 ARG Chi-restraints excluded: chain E residue 1318 LEU Chi-restraints excluded: chain E residue 1347 ILE Chi-restraints excluded: chain E residue 1410 ILE Chi-restraints excluded: chain E residue 1413 LEU Chi-restraints excluded: chain E residue 1443 GLU Chi-restraints excluded: chain E residue 1539 ARG Chi-restraints excluded: chain E residue 1576 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 6 optimal weight: 0.9980 chunk 98 optimal weight: 0.3980 chunk 120 optimal weight: 0.6980 chunk 104 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 32 optimal weight: 0.5980 chunk 40 optimal weight: 0.7980 chunk 69 optimal weight: 0.0270 chunk 96 optimal weight: 1.9990 chunk 107 optimal weight: 0.6980 chunk 91 optimal weight: 0.0970 overall best weight: 0.3636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 104 HIS E 836 GLN ** E1541 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.107607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.091340 restraints weight = 17717.918| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 2.11 r_work: 0.3016 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11195 Z= 0.104 Angle : 0.526 8.987 15218 Z= 0.260 Chirality : 0.040 0.262 1813 Planarity : 0.003 0.041 1872 Dihedral : 6.088 126.840 1519 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.33 % Allowed : 21.11 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.23), residues: 1379 helix: 0.89 (0.18), residues: 901 sheet: -0.66 (0.78), residues: 51 loop : -1.36 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 599 TYR 0.018 0.001 TYR E 125 PHE 0.012 0.001 PHE E1223 TRP 0.010 0.001 TRP E1247 HIS 0.007 0.001 HIS E 402 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.10 (11195) covalent geometry : angle 0.52623 / 0.26 (15218) hydrogen bonds : bond 0.02944 / 1.97 ( 568) hydrogen bonds : angle 3.59789 / 2.49 ( 1665) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2502.69 seconds wall clock time: 43 minutes 42.88 seconds (2622.88 seconds total)