Starting phenix.real_space_refine on Wed Mar 4 05:45:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7s5v_24840/03_2026/7s5v_24840.cif Found real_map, /net/cci-nas-00/data/ceres_data/7s5v_24840/03_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_24840/03_2026/7s5v_24840.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7s5v_24840/03_2026/7s5v_24840.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7s5v_24840/03_2026/7s5v_24840.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7s5v_24840/03_2026/7s5v_24840.map" } 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-5986/lib/python3.9/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: 2.48, per 1000 atoms: 0.23 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: 0.98 Conformation dependent library (CDL) restraints added in 539.4 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: 0.44 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: 2.09 Time building geometry restraints manager: 1.30 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: 6171 24.19 - 48.38: 430 48.38 - 72.56: 42 72.56 - 96.75: 4 96.75 - 120.94: 1 Dihedral angle restraints: 6648 sinusoidal: 2578 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 6645 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: 3.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 11.840 Find NCS groups from input model: 0.050 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: 0.000 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 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 : 15.543 120.941 4004 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 covalent geometry : bond 0.00607 (11195) covalent geometry : angle 0.87580 (15218) hydrogen bonds : bond 0.16521 ( 568) hydrogen bonds : angle 7.57238 ( 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 : 0.394 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: 0.1036 time to fit residues: 32.5651 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 : 0.418 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3324 r_free = 0.3324 target = 0.103681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.087629 restraints weight = 18104.333| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 2.12 r_work: 0.2975 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.1421 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 : 0.570 8.311 15218 Z= 0.289 Chirality : 0.040 0.163 1813 Planarity : 0.004 0.049 1872 Dihedral : 8.786 101.287 1593 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.48 % Allowed : 18.72 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.64 (0.20), residues: 1379 helix: -1.44 (0.15), residues: 909 sheet: -1.74 (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 E 487 TYR 0.010 0.001 TYR E1181 PHE 0.011 0.001 PHE E1223 TRP 0.011 0.001 TRP E1339 HIS 0.009 0.001 HIS E 847 Details of bonding type rmsd covalent geometry : bond 0.00304 (11195) covalent geometry : angle 0.57044 (15218) hydrogen bonds : bond 0.03629 ( 568) hydrogen bonds : angle 4.47942 ( 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 178 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 149 time to evaluate : 0.378 Fit side-chains REVERT: E 113 MET cc_start: 0.8345 (mmm) cc_final: 0.7712 (tpt) REVERT: E 222 PHE cc_start: 0.8969 (OUTLIER) cc_final: 0.8335 (m-80) REVERT: E 301 VAL cc_start: 0.9142 (OUTLIER) cc_final: 0.8841 (p) REVERT: E 560 PHE cc_start: 0.8820 (m-80) cc_final: 0.8582 (m-10) REVERT: E 878 ARG cc_start: 0.7859 (mmm-85) cc_final: 0.7353 (tpt-90) REVERT: E 1187 ARG cc_start: 0.8204 (ppt170) cc_final: 0.7427 (ptt180) REVERT: E 1193 ASP cc_start: 0.8545 (t0) cc_final: 0.8224 (t0) outliers start: 29 outliers final: 17 residues processed: 174 average time/residue: 0.0886 time to fit residues: 22.9534 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 : 0.406 ------------------------------------------------------------------------------- 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: 3.9990 chunk 8 optimal weight: 7.9990 chunk 56 optimal weight: 0.3980 chunk 112 optimal weight: 0.6980 chunk 104 optimal weight: 0.9980 chunk 127 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 4 optimal weight: 0.0980 chunk 65 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.104099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.088086 restraints weight = 18143.005| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 2.10 r_work: 0.2978 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2853 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11195 Z= 0.126 Angle : 0.538 8.397 15218 Z= 0.269 Chirality : 0.040 0.138 1813 Planarity : 0.004 0.040 1872 Dihedral : 7.916 92.087 1552 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.74 % Allowed : 19.23 % Favored : 78.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.57 (0.22), residues: 1379 helix: -0.53 (0.17), residues: 909 sheet: -1.31 (0.74), residues: 51 loop : -1.90 (0.28), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 599 TYR 0.010 0.001 TYR E1181 PHE 0.009 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 covalent geometry : bond 0.00282 (11195) covalent geometry : angle 0.53842 (15218) hydrogen bonds : bond 0.03264 ( 568) hydrogen bonds : angle 4.04499 ( 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 177 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 145 time to evaluate : 0.394 Fit side-chains REVERT: E 95 LEU cc_start: 0.7702 (OUTLIER) cc_final: 0.7390 (tt) REVERT: E 182 MET cc_start: 0.8480 (mmm) cc_final: 0.8093 (mmp) REVERT: E 222 PHE cc_start: 0.9003 (OUTLIER) cc_final: 0.8378 (m-80) REVERT: E 237 PHE cc_start: 0.8858 (OUTLIER) cc_final: 0.8089 (t80) REVERT: E 301 VAL cc_start: 0.9116 (OUTLIER) cc_final: 0.8815 (p) REVERT: E 440 TRP cc_start: 0.7952 (m-10) cc_final: 0.7417 (m-10) REVERT: E 486 GLN cc_start: 0.8736 (mm-40) cc_final: 0.8528 (mm110) REVERT: E 509 LEU cc_start: 0.9202 (tt) cc_final: 0.8982 (tt) REVERT: E 531 MET cc_start: 0.8675 (tpp) cc_final: 0.8416 (tpt) REVERT: E 599 ARG cc_start: 0.7951 (ttm110) cc_final: 0.7444 (ttt180) REVERT: E 916 ASP cc_start: 0.8813 (OUTLIER) cc_final: 0.8528 (t0) REVERT: E 1187 ARG cc_start: 0.8154 (ppt170) cc_final: 0.7423 (ptt180) REVERT: E 1188 ASP cc_start: 0.9096 (t0) cc_final: 0.8709 (t0) REVERT: E 1193 ASP cc_start: 0.8594 (t0) cc_final: 0.8301 (t0) REVERT: E 1253 GLU cc_start: 0.8411 (mt-10) cc_final: 0.8103 (mt-10) outliers start: 32 outliers final: 19 residues processed: 169 average time/residue: 0.0852 time to fit residues: 22.1393 Evaluate side-chains 156 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 132 time to evaluate : 0.380 ------------------------------------------------------------------------------- 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 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 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 998 TRP Chi-restraints excluded: chain E residue 1105 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 112 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 70 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 74 optimal weight: 0.6980 chunk 132 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 75 optimal weight: 0.5980 chunk 51 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3322 r_free = 0.3322 target = 0.103209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.087125 restraints weight = 18087.320| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 2.07 r_work: 0.2969 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.1879 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= 0.145 Angle : 0.538 7.859 15218 Z= 0.270 Chirality : 0.041 0.138 1813 Planarity : 0.003 0.041 1872 Dihedral : 7.784 96.191 1552 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 6.65 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: -1.09 (0.22), residues: 1379 helix: -0.11 (0.18), residues: 910 sheet: -1.16 (0.75), residues: 51 loop : -1.86 (0.28), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 599 TYR 0.014 0.001 TYR E1032 PHE 0.012 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 covalent geometry : bond 0.00330 (11195) covalent geometry : angle 0.53844 (15218) hydrogen bonds : bond 0.03263 ( 568) hydrogen bonds : angle 3.93438 ( 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 189 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 148 time to evaluate : 0.387 Fit side-chains REVERT: E 95 LEU cc_start: 0.7771 (OUTLIER) cc_final: 0.7487 (tt) REVERT: E 146 LEU cc_start: 0.7355 (OUTLIER) cc_final: 0.6882 (pt) REVERT: E 222 PHE cc_start: 0.9045 (OUTLIER) cc_final: 0.8419 (m-80) REVERT: E 237 PHE cc_start: 0.8812 (OUTLIER) cc_final: 0.8002 (t80) REVERT: E 269 GLU cc_start: 0.8320 (mt-10) cc_final: 0.8061 (tp30) REVERT: E 301 VAL cc_start: 0.9131 (OUTLIER) cc_final: 0.8837 (p) REVERT: E 364 PHE cc_start: 0.9288 (t80) cc_final: 0.8796 (t80) REVERT: E 413 MET cc_start: 0.8706 (ptp) cc_final: 0.8463 (ptp) REVERT: E 531 MET cc_start: 0.8700 (tpp) cc_final: 0.8449 (tpp) REVERT: E 916 ASP cc_start: 0.8818 (OUTLIER) cc_final: 0.8577 (t0) REVERT: E 1188 ASP cc_start: 0.9007 (t0) cc_final: 0.8591 (t0) REVERT: E 1193 ASP cc_start: 0.8574 (t0) cc_final: 0.8282 (t0) REVERT: E 1251 ARG cc_start: 0.8968 (OUTLIER) cc_final: 0.8332 (mpt180) REVERT: E 1253 GLU cc_start: 0.8491 (mt-10) cc_final: 0.8246 (mt-10) REVERT: E 1413 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8302 (mp) outliers start: 41 outliers final: 26 residues processed: 179 average time/residue: 0.0869 time to fit residues: 23.5547 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 : 0.389 ------------------------------------------------------------------------------- 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 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 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 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 1413 LEU 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: 0.6980 chunk 31 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 0 optimal weight: 8.9990 chunk 128 optimal weight: 0.5980 chunk 14 optimal weight: 0.0670 chunk 43 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 13 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 104 HIS E 263 ASN E 486 GLN E 836 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.104054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.088001 restraints weight = 17891.006| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 2.07 r_work: 0.2984 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.2027 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= 0.125 Angle : 0.530 8.030 15218 Z= 0.262 Chirality : 0.040 0.229 1813 Planarity : 0.003 0.041 1872 Dihedral : 7.643 99.685 1552 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 3.68 % Allowed : 18.21 % 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: -0.77 (0.23), residues: 1379 helix: 0.17 (0.18), residues: 909 sheet: -1.07 (0.75), residues: 51 loop : -1.78 (0.28), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 599 TYR 0.009 0.001 TYR E1181 PHE 0.009 0.001 PHE E 315 TRP 0.010 0.001 TRP E1247 HIS 0.007 0.001 HIS E 847 Details of bonding type rmsd covalent geometry : bond 0.00281 (11195) covalent geometry : angle 0.53003 (15218) hydrogen bonds : bond 0.03110 ( 568) hydrogen bonds : angle 3.80858 ( 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 190 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 147 time to evaluate : 0.444 Fit side-chains revert: symmetry clash REVERT: E 95 LEU cc_start: 0.7707 (OUTLIER) cc_final: 0.7428 (tt) REVERT: E 146 LEU cc_start: 0.7359 (OUTLIER) cc_final: 0.6881 (pt) REVERT: E 222 PHE cc_start: 0.9045 (OUTLIER) cc_final: 0.8445 (m-80) REVERT: E 237 PHE cc_start: 0.8798 (OUTLIER) cc_final: 0.8005 (t80) REVERT: E 269 GLU cc_start: 0.8318 (mt-10) cc_final: 0.8074 (tp30) REVERT: E 301 VAL cc_start: 0.9125 (OUTLIER) cc_final: 0.8834 (p) REVERT: E 364 PHE cc_start: 0.9236 (t80) cc_final: 0.8708 (t80) REVERT: E 413 MET cc_start: 0.8701 (ptp) cc_final: 0.8488 (ptp) REVERT: E 440 TRP cc_start: 0.7889 (m-10) cc_final: 0.7387 (m-10) REVERT: E 531 MET cc_start: 0.8672 (tpp) cc_final: 0.8436 (tpp) REVERT: E 586 ILE cc_start: 0.9250 (OUTLIER) cc_final: 0.9025 (tt) REVERT: E 916 ASP cc_start: 0.8793 (OUTLIER) cc_final: 0.8580 (t0) REVERT: E 1188 ASP cc_start: 0.9018 (t0) cc_final: 0.8566 (t0) REVERT: E 1193 ASP cc_start: 0.8561 (t0) cc_final: 0.8262 (t0) REVERT: E 1251 ARG cc_start: 0.8968 (OUTLIER) cc_final: 0.8243 (mpt180) REVERT: E 1413 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8288 (mp) outliers start: 43 outliers final: 29 residues processed: 180 average time/residue: 0.0891 time to fit residues: 24.2917 Evaluate side-chains 176 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 138 time to evaluate : 0.425 ------------------------------------------------------------------------------- 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 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 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 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 1413 LEU Chi-restraints excluded: chain E residue 1539 ARG Chi-restraints excluded: chain E residue 1541 HIS 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: 0.3980 chunk 123 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 80 optimal weight: 0.9990 chunk 8 optimal weight: 5.9990 chunk 114 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 106 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3322 r_free = 0.3322 target = 0.103198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.087109 restraints weight = 17998.952| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 2.06 r_work: 0.2967 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2841 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 11195 Z= 0.155 Angle : 0.541 7.906 15218 Z= 0.269 Chirality : 0.041 0.271 1813 Planarity : 0.003 0.042 1872 Dihedral : 7.597 105.205 1552 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 4.10 % Allowed : 18.55 % Favored : 77.35 % 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: -0.59 (0.23), residues: 1379 helix: 0.29 (0.18), residues: 905 sheet: -0.99 (0.76), residues: 51 loop : -1.65 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 599 TYR 0.009 0.001 TYR E1181 PHE 0.009 0.001 PHE E 315 TRP 0.009 0.001 TRP E1247 HIS 0.007 0.001 HIS E 847 Details of bonding type rmsd covalent geometry : bond 0.00354 (11195) covalent geometry : angle 0.54123 (15218) hydrogen bonds : bond 0.03225 ( 568) hydrogen bonds : angle 3.84749 ( 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 191 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 143 time to evaluate : 0.519 Fit side-chains REVERT: E 95 LEU cc_start: 0.7714 (OUTLIER) cc_final: 0.7432 (tt) REVERT: E 146 LEU cc_start: 0.7258 (OUTLIER) cc_final: 0.6677 (pt) REVERT: E 222 PHE cc_start: 0.9075 (OUTLIER) cc_final: 0.8384 (m-80) REVERT: E 237 PHE cc_start: 0.8792 (OUTLIER) cc_final: 0.7846 (t80) REVERT: E 301 VAL cc_start: 0.9183 (OUTLIER) cc_final: 0.8896 (p) REVERT: E 364 PHE cc_start: 0.9269 (t80) cc_final: 0.8732 (t80) REVERT: E 413 MET cc_start: 0.8722 (ptp) cc_final: 0.8521 (ptp) REVERT: E 440 TRP cc_start: 0.7888 (m-10) cc_final: 0.7372 (m-10) REVERT: E 491 GLU cc_start: 0.8618 (tt0) cc_final: 0.8385 (tp30) REVERT: E 586 ILE cc_start: 0.9248 (OUTLIER) cc_final: 0.9026 (tt) REVERT: E 1188 ASP cc_start: 0.9051 (t0) cc_final: 0.8612 (t0) REVERT: E 1193 ASP cc_start: 0.8736 (t0) cc_final: 0.8394 (t0) REVERT: E 1251 ARG cc_start: 0.9042 (OUTLIER) cc_final: 0.8449 (mpt180) REVERT: E 1413 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8250 (mp) REVERT: E 1444 ARG cc_start: 0.8320 (ttm-80) cc_final: 0.8043 (ttm-80) outliers start: 48 outliers final: 32 residues processed: 180 average time/residue: 0.0902 time to fit residues: 25.1024 Evaluate side-chains 174 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 134 time to evaluate : 0.431 ------------------------------------------------------------------------------- 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 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 1148 LEU Chi-restraints excluded: chain E residue 1251 ARG 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 1539 ARG Chi-restraints excluded: chain E residue 1541 HIS 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: 0.6980 chunk 73 optimal weight: 0.5980 chunk 18 optimal weight: 8.9990 chunk 129 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 112 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 43 optimal weight: 0.6980 chunk 88 optimal weight: 0.0050 chunk 59 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3336 r_free = 0.3336 target = 0.104266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.088285 restraints weight = 17807.245| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 2.06 r_work: 0.2987 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.2195 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= 0.121 Angle : 0.526 8.059 15218 Z= 0.260 Chirality : 0.041 0.254 1813 Planarity : 0.003 0.044 1872 Dihedral : 7.461 109.118 1552 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.93 % Allowed : 18.97 % Favored : 77.09 % 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: -0.39 (0.23), residues: 1379 helix: 0.45 (0.18), residues: 903 sheet: -0.85 (0.77), residues: 51 loop : -1.60 (0.29), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 599 TYR 0.016 0.001 TYR E 125 PHE 0.014 0.001 PHE E1223 TRP 0.009 0.001 TRP E1247 HIS 0.007 0.001 HIS E 847 Details of bonding type rmsd covalent geometry : bond 0.00275 (11195) covalent geometry : angle 0.52618 (15218) hydrogen bonds : bond 0.03045 ( 568) hydrogen bonds : angle 3.73849 ( 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 192 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 146 time to evaluate : 0.411 Fit side-chains revert: symmetry clash REVERT: E 95 LEU cc_start: 0.7692 (OUTLIER) cc_final: 0.7420 (tt) REVERT: E 146 LEU cc_start: 0.7261 (OUTLIER) cc_final: 0.6696 (pt) REVERT: E 222 PHE cc_start: 0.9053 (OUTLIER) cc_final: 0.8480 (m-80) REVERT: E 237 PHE cc_start: 0.8757 (OUTLIER) cc_final: 0.7812 (t80) REVERT: E 301 VAL cc_start: 0.9140 (OUTLIER) cc_final: 0.8845 (p) REVERT: E 364 PHE cc_start: 0.9256 (t80) cc_final: 0.8742 (t80) REVERT: E 440 TRP cc_start: 0.7849 (m-10) cc_final: 0.7380 (m-10) REVERT: E 491 GLU cc_start: 0.8712 (tt0) cc_final: 0.8378 (tp30) REVERT: E 586 ILE cc_start: 0.9246 (OUTLIER) cc_final: 0.9030 (tt) REVERT: E 903 MET cc_start: 0.8890 (mtp) cc_final: 0.8569 (mtp) REVERT: E 1188 ASP cc_start: 0.9034 (t0) cc_final: 0.8576 (t0) REVERT: E 1193 ASP cc_start: 0.8734 (t0) cc_final: 0.8402 (t0) REVERT: E 1251 ARG cc_start: 0.9029 (OUTLIER) cc_final: 0.8348 (mpt180) REVERT: E 1322 GLU cc_start: 0.8634 (mp0) cc_final: 0.8165 (mp0) REVERT: E 1444 ARG cc_start: 0.8304 (ttm-80) cc_final: 0.8014 (ttm-80) outliers start: 46 outliers final: 34 residues processed: 182 average time/residue: 0.0904 time to fit residues: 25.1777 Evaluate side-chains 176 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 135 time to evaluate : 0.440 ------------------------------------------------------------------------------- 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 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 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 1539 ARG Chi-restraints excluded: chain E residue 1541 HIS 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: 3.9990 chunk 132 optimal weight: 1.9990 chunk 137 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 70 optimal weight: 0.8980 chunk 118 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 0 optimal weight: 8.9990 chunk 86 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3322 r_free = 0.3322 target = 0.103258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.087177 restraints weight = 17884.098| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 2.06 r_work: 0.2969 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 11195 Z= 0.156 Angle : 0.548 8.107 15218 Z= 0.272 Chirality : 0.041 0.177 1813 Planarity : 0.003 0.044 1872 Dihedral : 7.428 114.887 1552 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 4.27 % Allowed : 19.23 % Favored : 76.50 % 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: -0.34 (0.23), residues: 1379 helix: 0.49 (0.18), residues: 903 sheet: -0.83 (0.77), residues: 51 loop : -1.59 (0.29), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 599 TYR 0.013 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 covalent geometry : bond 0.00357 (11195) covalent geometry : angle 0.54831 (15218) hydrogen bonds : bond 0.03190 ( 568) hydrogen bonds : angle 3.80100 ( 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 190 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 140 time to evaluate : 0.440 Fit side-chains revert: symmetry clash REVERT: E 95 LEU cc_start: 0.7669 (OUTLIER) cc_final: 0.7386 (tt) REVERT: E 146 LEU cc_start: 0.7262 (OUTLIER) cc_final: 0.6680 (pt) REVERT: E 222 PHE cc_start: 0.9093 (OUTLIER) cc_final: 0.8411 (m-80) REVERT: E 237 PHE cc_start: 0.8774 (OUTLIER) cc_final: 0.7799 (t80) REVERT: E 256 ILE cc_start: 0.9474 (tp) cc_final: 0.8909 (tp) REVERT: E 301 VAL cc_start: 0.9191 (OUTLIER) cc_final: 0.8904 (p) REVERT: E 364 PHE cc_start: 0.9269 (t80) cc_final: 0.8753 (t80) REVERT: E 440 TRP cc_start: 0.7782 (m-10) cc_final: 0.7307 (m-10) REVERT: E 491 GLU cc_start: 0.8724 (tt0) cc_final: 0.8391 (tp30) REVERT: E 586 ILE cc_start: 0.9244 (OUTLIER) cc_final: 0.9023 (tt) REVERT: E 1165 LEU cc_start: 0.8864 (mt) cc_final: 0.8660 (mt) REVERT: E 1188 ASP cc_start: 0.9053 (t0) cc_final: 0.8596 (t0) REVERT: E 1193 ASP cc_start: 0.8790 (t0) cc_final: 0.8449 (t0) REVERT: E 1251 ARG cc_start: 0.9034 (OUTLIER) cc_final: 0.8455 (mpt180) REVERT: E 1322 GLU cc_start: 0.8639 (mp0) cc_final: 0.8161 (mp0) REVERT: E 1413 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8303 (mp) REVERT: E 1443 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.8117 (pm20) REVERT: E 1444 ARG cc_start: 0.8315 (ttm-80) cc_final: 0.8047 (ttm-80) outliers start: 50 outliers final: 35 residues processed: 176 average time/residue: 0.0894 time to fit residues: 24.0337 Evaluate side-chains 182 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 138 time to evaluate : 0.381 ------------------------------------------------------------------------------- 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 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 801 MET 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 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 1541 HIS 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: 0.0270 chunk 65 optimal weight: 0.4980 chunk 13 optimal weight: 3.9990 chunk 1 optimal weight: 0.0040 chunk 116 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 68 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 103 optimal weight: 0.5980 chunk 125 optimal weight: 0.0980 overall best weight: 0.2450 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 104 HIS E 836 GLN E 933 ASN E1541 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.106863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.090908 restraints weight = 17601.959| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 2.06 r_work: 0.3027 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.2474 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= 0.096 Angle : 0.514 8.256 15218 Z= 0.252 Chirality : 0.039 0.272 1813 Planarity : 0.003 0.039 1872 Dihedral : 7.244 122.463 1552 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.33 % Allowed : 20.51 % 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: 0.77 (0.18), residues: 902 sheet: -0.69 (0.79), residues: 51 loop : -1.46 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 599 TYR 0.018 0.001 TYR E 125 PHE 0.010 0.001 PHE E 315 TRP 0.014 0.001 TRP E1339 HIS 0.006 0.001 HIS E 847 Details of bonding type rmsd covalent geometry : bond 0.00208 (11195) covalent geometry : angle 0.51440 (15218) hydrogen bonds : bond 0.02841 ( 568) hydrogen bonds : angle 3.57635 ( 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 190 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 151 time to evaluate : 0.420 Fit side-chains revert: symmetry clash REVERT: E 95 LEU cc_start: 0.7589 (OUTLIER) cc_final: 0.7346 (tt) REVERT: E 146 LEU cc_start: 0.7257 (OUTLIER) cc_final: 0.6770 (pt) REVERT: E 152 THR cc_start: 0.7406 (m) cc_final: 0.7061 (m) REVERT: E 222 PHE cc_start: 0.9028 (OUTLIER) cc_final: 0.8513 (m-80) REVERT: E 237 PHE cc_start: 0.8736 (OUTLIER) cc_final: 0.7719 (t80) REVERT: E 301 VAL cc_start: 0.9077 (OUTLIER) cc_final: 0.8792 (p) REVERT: E 364 PHE cc_start: 0.9251 (t80) cc_final: 0.8721 (t80) REVERT: E 440 TRP cc_start: 0.7722 (m-10) cc_final: 0.7286 (m-10) REVERT: E 491 GLU cc_start: 0.8720 (tt0) cc_final: 0.8307 (tp30) REVERT: E 586 ILE cc_start: 0.9174 (OUTLIER) cc_final: 0.8928 (tt) REVERT: E 731 MET cc_start: 0.8706 (mtp) cc_final: 0.7915 (ttm) REVERT: E 1188 ASP cc_start: 0.8992 (t0) cc_final: 0.8525 (t0) REVERT: E 1193 ASP cc_start: 0.8959 (t0) cc_final: 0.8639 (t0) REVERT: E 1251 ARG cc_start: 0.8980 (OUTLIER) cc_final: 0.8219 (mpt90) REVERT: E 1253 GLU cc_start: 0.8314 (mt-10) cc_final: 0.8089 (mt-10) REVERT: E 1322 GLU cc_start: 0.8565 (mp0) cc_final: 0.8130 (mp0) REVERT: E 1413 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8341 (mp) REVERT: E 1443 GLU cc_start: 0.8457 (OUTLIER) cc_final: 0.8123 (pm20) REVERT: E 1444 ARG cc_start: 0.8379 (ttm-80) cc_final: 0.8072 (ttm-80) outliers start: 39 outliers final: 25 residues processed: 182 average time/residue: 0.0843 time to fit residues: 23.5136 Evaluate side-chains 176 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 142 time to evaluate : 0.411 ------------------------------------------------------------------------------- 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 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 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 1005 LEU 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 1413 LEU Chi-restraints excluded: chain E residue 1443 GLU Chi-restraints excluded: chain E residue 1539 ARG 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: 0.8980 chunk 83 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 30 optimal weight: 0.0570 chunk 81 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 chunk 112 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 overall best weight: 0.7300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3341 r_free = 0.3341 target = 0.104620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.088450 restraints weight = 17844.658| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 2.07 r_work: 0.2989 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.2392 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= 0.144 Angle : 0.542 8.027 15218 Z= 0.270 Chirality : 0.042 0.352 1813 Planarity : 0.003 0.042 1872 Dihedral : 7.246 125.230 1552 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.25 % Allowed : 21.20 % 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: 0.02 (0.23), residues: 1379 helix: 0.75 (0.18), residues: 904 sheet: -0.64 (0.79), residues: 51 loop : -1.43 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 599 TYR 0.017 0.001 TYR E 125 PHE 0.014 0.001 PHE E1223 TRP 0.008 0.001 TRP E1247 HIS 0.007 0.001 HIS E 847 Details of bonding type rmsd covalent geometry : bond 0.00328 (11195) covalent geometry : angle 0.54242 (15218) hydrogen bonds : bond 0.03112 ( 568) hydrogen bonds : angle 3.68536 ( 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 186 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 148 time to evaluate : 0.404 Fit side-chains revert: symmetry clash REVERT: E 95 LEU cc_start: 0.7618 (OUTLIER) cc_final: 0.7370 (tt) REVERT: E 146 LEU cc_start: 0.7264 (OUTLIER) cc_final: 0.6751 (pt) REVERT: E 152 THR cc_start: 0.7474 (m) cc_final: 0.7089 (m) REVERT: E 222 PHE cc_start: 0.9079 (OUTLIER) cc_final: 0.8390 (m-80) REVERT: E 237 PHE cc_start: 0.8753 (OUTLIER) cc_final: 0.7755 (t80) REVERT: E 256 ILE cc_start: 0.9457 (tp) cc_final: 0.8885 (tp) REVERT: E 301 VAL cc_start: 0.9183 (OUTLIER) cc_final: 0.8903 (p) REVERT: E 364 PHE cc_start: 0.9264 (t80) cc_final: 0.8757 (t80) REVERT: E 440 TRP cc_start: 0.7722 (m-10) cc_final: 0.7244 (m-10) REVERT: E 491 GLU cc_start: 0.8724 (tt0) cc_final: 0.8360 (tp30) REVERT: E 586 ILE cc_start: 0.9174 (OUTLIER) cc_final: 0.8953 (tt) REVERT: E 1188 ASP cc_start: 0.9031 (t0) cc_final: 0.8575 (t0) REVERT: E 1193 ASP cc_start: 0.8940 (t0) cc_final: 0.8648 (t0) REVERT: E 1251 ARG cc_start: 0.9012 (OUTLIER) cc_final: 0.8392 (mpt180) REVERT: E 1322 GLU cc_start: 0.8613 (mp0) cc_final: 0.8176 (mp0) REVERT: E 1413 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8314 (mp) REVERT: E 1443 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.8145 (pm20) REVERT: E 1444 ARG cc_start: 0.8411 (ttm-80) cc_final: 0.8123 (ttm-80) outliers start: 38 outliers final: 27 residues processed: 179 average time/residue: 0.0829 time to fit residues: 22.3974 Evaluate side-chains 180 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 144 time to evaluate : 0.380 ------------------------------------------------------------------------------- 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 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 916 ASP 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 1318 LEU 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: 1.9990 chunk 98 optimal weight: 0.8980 chunk 120 optimal weight: 0.6980 chunk 104 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 107 optimal weight: 0.5980 chunk 91 optimal weight: 0.2980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3348 r_free = 0.3348 target = 0.105050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.088905 restraints weight = 17853.969| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 2.07 r_work: 0.2991 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11195 Z= 0.132 Angle : 0.539 8.034 15218 Z= 0.268 Chirality : 0.042 0.380 1813 Planarity : 0.003 0.041 1872 Dihedral : 7.186 126.832 1552 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 3.33 % Allowed : 21.45 % Favored : 75.21 % 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: 0.10 (0.23), residues: 1379 helix: 0.83 (0.18), residues: 895 sheet: -0.67 (0.78), residues: 51 loop : -1.36 (0.29), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 599 TYR 0.027 0.001 TYR E 125 PHE 0.013 0.001 PHE E1223 TRP 0.009 0.001 TRP E1247 HIS 0.006 0.001 HIS E 847 Details of bonding type rmsd covalent geometry : bond 0.00301 (11195) covalent geometry : angle 0.53889 (15218) hydrogen bonds : bond 0.03076 ( 568) hydrogen bonds : angle 3.68253 ( 1665) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2533.23 seconds wall clock time: 44 minutes 10.87 seconds (2650.87 seconds total)