Starting phenix.real_space_refine on Tue Jul 29 10:53:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7s5v_24840/07_2025/7s5v_24840.cif Found real_map, /net/cci-nas-00/data/ceres_data/7s5v_24840/07_2025/7s5v_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7s5v_24840/07_2025/7s5v_24840.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7s5v_24840/07_2025/7s5v_24840.map" model { file = "/net/cci-nas-00/data/ceres_data/7s5v_24840/07_2025/7s5v_24840.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7s5v_24840/07_2025/7s5v_24840.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.005 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'PHE:plan': 2, 'GLU:plan': 8, 'ARG:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 4} 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: 7.44, per 1000 atoms: 0.68 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: 3.03 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 1.81 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: 4.27 Time building geometry restraints manager: 3.61 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: 3.710 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: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 31.660 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.400 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.014 0.002 TRP E1339 HIS 0.009 0.001 HIS E 847 PHE 0.016 0.002 PHE E1399 TYR 0.014 0.002 TYR E1287 ARG 0.003 0.000 ARG E 798 Details of bonding type rmsd hydrogen bonds : bond 0.16521 ( 568) hydrogen bonds : angle 7.57238 ( 1665) covalent geometry : bond 0.00607 (11195) covalent geometry : angle 0.87580 (15218) *********************** 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 : 1.306 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: 0.8009 (m-80) REVERT: E 531 MET cc_start: 0.8519 (tpp) cc_final: 0.8174 (mmm) REVERT: E 547 MET cc_start: 0.8896 (tpp) cc_final: 0.8602 (mmt) REVERT: E 560 PHE cc_start: 0.8894 (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: 0.2528 time to fit residues: 79.3927 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 : 1.379 ------------------------------------------------------------------------------- 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 117 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 chunk 58 optimal weight: 0.0370 chunk 35 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 108 optimal weight: 0.6980 chunk 42 optimal weight: 4.9990 chunk 66 optimal weight: 0.6980 chunk 81 optimal weight: 2.9990 chunk 126 optimal weight: 0.0980 overall best weight: 0.4658 ------------------------------------------------------------------------------- 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 327 HIS E 350 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 E1541 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.104774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.088672 restraints weight = 18046.824| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 2.12 r_work: 0.2992 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.1491 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= 0.119 Angle : 0.558 8.219 15218 Z= 0.281 Chirality : 0.040 0.161 1813 Planarity : 0.004 0.048 1872 Dihedral : 8.686 100.414 1593 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.74 % Allowed : 18.21 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.55 (0.20), residues: 1379 helix: -1.37 (0.15), residues: 909 sheet: -1.69 (0.71), residues: 51 loop : -2.05 (0.28), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E1339 HIS 0.009 0.001 HIS E 847 PHE 0.011 0.001 PHE E 115 TYR 0.010 0.001 TYR E 125 ARG 0.003 0.000 ARG E 487 Details of bonding type rmsd hydrogen bonds : bond 0.03461 ( 568) hydrogen bonds : angle 4.39656 ( 1665) covalent geometry : bond 0.00260 (11195) covalent geometry : angle 0.55804 (15218) *********************** 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 187 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 155 time to evaluate : 1.459 Fit side-chains REVERT: E 95 LEU cc_start: 0.7691 (OUTLIER) cc_final: 0.7249 (tt) REVERT: E 113 MET cc_start: 0.8341 (mmm) cc_final: 0.7689 (tpt) REVERT: E 222 PHE cc_start: 0.8938 (OUTLIER) cc_final: 0.8382 (m-80) REVERT: E 301 VAL cc_start: 0.9115 (OUTLIER) cc_final: 0.8817 (p) REVERT: E 878 ARG cc_start: 0.7844 (mmm-85) cc_final: 0.7349 (tpt-90) REVERT: E 1187 ARG cc_start: 0.8190 (ppt170) cc_final: 0.7409 (ptt180) REVERT: E 1193 ASP cc_start: 0.8551 (t0) cc_final: 0.8237 (t0) outliers start: 32 outliers final: 17 residues processed: 183 average time/residue: 0.2804 time to fit residues: 78.2955 Evaluate side-chains 149 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 129 time to evaluate : 4.132 ------------------------------------------------------------------------------- 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 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 1132 ILE Chi-restraints excluded: chain E residue 1410 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 101 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 220 GLN E 375 GLN E1541 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.101641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.085558 restraints weight = 18311.647| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 2.12 r_work: 0.2933 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11195 Z= 0.197 Angle : 0.586 8.327 15218 Z= 0.295 Chirality : 0.042 0.147 1813 Planarity : 0.004 0.047 1872 Dihedral : 8.110 95.371 1554 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 3.08 % Allowed : 19.06 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.22), residues: 1379 helix: -0.62 (0.17), residues: 909 sheet: -1.23 (0.81), residues: 46 loop : -2.06 (0.27), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E1247 HIS 0.009 0.001 HIS E 847 PHE 0.009 0.001 PHE E1223 TYR 0.014 0.001 TYR E1032 ARG 0.002 0.000 ARG E 599 Details of bonding type rmsd hydrogen bonds : bond 0.03620 ( 568) hydrogen bonds : angle 4.22531 ( 1665) covalent geometry : bond 0.00450 (11195) covalent geometry : angle 0.58620 (15218) *********************** 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 173 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 137 time to evaluate : 1.208 Fit side-chains REVERT: E 146 LEU cc_start: 0.7272 (OUTLIER) cc_final: 0.6922 (pt) REVERT: E 222 PHE cc_start: 0.9039 (OUTLIER) cc_final: 0.8342 (m-80) REVERT: E 237 PHE cc_start: 0.8857 (OUTLIER) cc_final: 0.8083 (t80) REVERT: E 301 VAL cc_start: 0.9149 (OUTLIER) cc_final: 0.8839 (p) REVERT: E 364 PHE cc_start: 0.9299 (t80) cc_final: 0.8807 (t80) REVERT: E 440 TRP cc_start: 0.7978 (m-10) cc_final: 0.7478 (m-10) REVERT: E 509 LEU cc_start: 0.9253 (tt) cc_final: 0.9032 (tt) REVERT: E 531 MET cc_start: 0.8713 (tpp) cc_final: 0.8455 (tpt) REVERT: E 599 ARG cc_start: 0.7811 (ttm110) cc_final: 0.7304 (ttt180) REVERT: E 878 ARG cc_start: 0.7905 (mmm-85) cc_final: 0.7388 (tpt-90) REVERT: E 1187 ARG cc_start: 0.8175 (ppt170) cc_final: 0.7424 (ptt180) REVERT: E 1193 ASP cc_start: 0.8596 (t0) cc_final: 0.8269 (t0) REVERT: E 1253 GLU cc_start: 0.8378 (mt-10) cc_final: 0.8151 (mt-10) REVERT: E 1413 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8294 (mp) outliers start: 36 outliers final: 24 residues processed: 163 average time/residue: 0.1933 time to fit residues: 47.8215 Evaluate side-chains 160 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 131 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 81 MET Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 191 ILE Chi-restraints excluded: chain E residue 222 PHE Chi-restraints excluded: chain E residue 235 ASN Chi-restraints excluded: chain E residue 237 PHE Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 377 SER Chi-restraints excluded: chain E residue 421 LEU Chi-restraints excluded: chain E residue 422 VAL Chi-restraints excluded: chain E residue 442 MET Chi-restraints excluded: chain E residue 567 PHE Chi-restraints excluded: chain E residue 573 SER Chi-restraints excluded: chain E residue 608 VAL Chi-restraints excluded: chain E residue 690 THR Chi-restraints excluded: chain E residue 710 THR Chi-restraints excluded: chain E residue 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 1105 ILE Chi-restraints excluded: chain E residue 1410 ILE Chi-restraints excluded: chain E residue 1413 LEU 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 120 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 115 optimal weight: 0.9990 chunk 123 optimal weight: 0.8980 chunk 56 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 116 optimal weight: 0.9990 chunk 0 optimal weight: 8.9990 chunk 125 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3312 r_free = 0.3312 target = 0.102532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.086514 restraints weight = 17914.592| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 2.05 r_work: 0.2959 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 11195 Z= 0.158 Angle : 0.550 8.577 15218 Z= 0.276 Chirality : 0.041 0.137 1813 Planarity : 0.004 0.041 1872 Dihedral : 7.921 95.331 1552 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 3.76 % Allowed : 18.46 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.22), residues: 1379 helix: -0.21 (0.17), residues: 905 sheet: -1.26 (0.73), residues: 51 loop : -1.78 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E1247 HIS 0.008 0.001 HIS E 847 PHE 0.009 0.001 PHE E1164 TYR 0.014 0.001 TYR E 125 ARG 0.002 0.000 ARG E 75 Details of bonding type rmsd hydrogen bonds : bond 0.03336 ( 568) hydrogen bonds : angle 4.01392 ( 1665) covalent geometry : bond 0.00360 (11195) covalent geometry : angle 0.54976 (15218) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 142 time to evaluate : 1.168 Fit side-chains REVERT: E 95 LEU cc_start: 0.7757 (OUTLIER) cc_final: 0.7408 (tt) REVERT: E 146 LEU cc_start: 0.7192 (OUTLIER) cc_final: 0.6670 (pt) REVERT: E 222 PHE cc_start: 0.9051 (OUTLIER) cc_final: 0.8293 (m-80) REVERT: E 237 PHE cc_start: 0.8827 (OUTLIER) cc_final: 0.8029 (t80) REVERT: E 301 VAL cc_start: 0.9148 (OUTLIER) cc_final: 0.8850 (p) REVERT: E 364 PHE cc_start: 0.9273 (t80) cc_final: 0.8765 (t80) REVERT: E 440 TRP cc_start: 0.7930 (m-10) cc_final: 0.7443 (m-10) REVERT: E 531 MET cc_start: 0.8644 (tpp) cc_final: 0.8389 (tpp) REVERT: E 586 ILE cc_start: 0.9319 (OUTLIER) cc_final: 0.9087 (tt) REVERT: E 878 ARG cc_start: 0.7876 (mmm-85) cc_final: 0.7656 (tpt170) REVERT: E 1188 ASP cc_start: 0.9033 (t0) cc_final: 0.8712 (t0) REVERT: E 1193 ASP cc_start: 0.8603 (t0) cc_final: 0.8292 (t0) REVERT: E 1251 ARG cc_start: 0.8950 (OUTLIER) cc_final: 0.8332 (mpt180) REVERT: E 1253 GLU cc_start: 0.8439 (mt-10) cc_final: 0.8208 (mt-10) outliers start: 44 outliers final: 29 residues processed: 176 average time/residue: 0.2002 time to fit residues: 53.0032 Evaluate side-chains 172 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 136 time to evaluate : 1.196 ------------------------------------------------------------------------------- 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 152 THR 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 442 MET 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 1026 VAL Chi-restraints excluded: chain E residue 1105 ILE Chi-restraints excluded: chain E residue 1148 LEU Chi-restraints excluded: chain E residue 1251 ARG Chi-restraints excluded: chain E residue 1410 ILE 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 73 optimal weight: 0.8980 chunk 121 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 116 optimal weight: 0.5980 chunk 138 optimal weight: 0.7980 chunk 91 optimal weight: 0.9980 chunk 59 optimal weight: 0.9980 chunk 68 optimal weight: 0.5980 chunk 40 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 836 GLN E1541 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.102978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.086990 restraints weight = 17910.906| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 2.05 r_work: 0.2968 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.1974 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= 0.143 Angle : 0.544 8.609 15218 Z= 0.270 Chirality : 0.041 0.236 1813 Planarity : 0.003 0.044 1872 Dihedral : 7.776 98.201 1552 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 3.93 % Allowed : 18.63 % Favored : 77.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.23), residues: 1379 helix: 0.04 (0.18), residues: 910 sheet: -1.13 (0.74), residues: 51 loop : -1.81 (0.28), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E1247 HIS 0.007 0.001 HIS E 847 PHE 0.013 0.001 PHE E 315 TYR 0.010 0.001 TYR E 125 ARG 0.004 0.000 ARG E 599 Details of bonding type rmsd hydrogen bonds : bond 0.03226 ( 568) hydrogen bonds : angle 3.91119 ( 1665) covalent geometry : bond 0.00325 (11195) covalent geometry : angle 0.54425 (15218) *********************** 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 193 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 147 time to evaluate : 1.600 Fit side-chains revert: symmetry clash REVERT: E 95 LEU cc_start: 0.7711 (OUTLIER) cc_final: 0.7405 (tt) REVERT: E 146 LEU cc_start: 0.7214 (OUTLIER) cc_final: 0.6701 (pt) REVERT: E 222 PHE cc_start: 0.9054 (OUTLIER) cc_final: 0.8304 (m-80) REVERT: E 237 PHE cc_start: 0.8815 (OUTLIER) cc_final: 0.7889 (t80) REVERT: E 269 GLU cc_start: 0.8324 (mt-10) cc_final: 0.8075 (tp30) REVERT: E 301 VAL cc_start: 0.9142 (OUTLIER) cc_final: 0.8846 (p) REVERT: E 364 PHE cc_start: 0.9288 (t80) cc_final: 0.8782 (t80) REVERT: E 413 MET cc_start: 0.8690 (ptp) cc_final: 0.8453 (ptp) REVERT: E 440 TRP cc_start: 0.7909 (m-10) cc_final: 0.7430 (m-10) REVERT: E 531 MET cc_start: 0.8659 (tpp) cc_final: 0.8434 (tpp) REVERT: E 878 ARG cc_start: 0.7879 (mmm-85) cc_final: 0.7672 (tpt170) REVERT: E 1188 ASP cc_start: 0.9050 (t0) cc_final: 0.8754 (t0) REVERT: E 1193 ASP cc_start: 0.8583 (t0) cc_final: 0.8279 (t0) REVERT: E 1251 ARG cc_start: 0.9017 (OUTLIER) cc_final: 0.8419 (mpt180) REVERT: E 1253 GLU cc_start: 0.8474 (mt-10) cc_final: 0.8251 (mt-10) REVERT: E 1258 CYS cc_start: 0.9009 (t) cc_final: 0.8253 (m) REVERT: E 1444 ARG cc_start: 0.8237 (ttm-80) cc_final: 0.8005 (ttm-80) outliers start: 46 outliers final: 32 residues processed: 179 average time/residue: 0.2058 time to fit residues: 55.5768 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 : 1.211 ------------------------------------------------------------------------------- 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 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 442 MET 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 1005 LEU Chi-restraints excluded: chain E residue 1026 VAL Chi-restraints excluded: chain E residue 1105 ILE Chi-restraints excluded: chain E residue 1148 LEU Chi-restraints excluded: chain E residue 1251 ARG Chi-restraints excluded: chain E residue 1255 ILE Chi-restraints excluded: chain E residue 1347 ILE Chi-restraints excluded: chain E residue 1410 ILE Chi-restraints excluded: chain E residue 1539 ARG Chi-restraints excluded: chain E residue 1576 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 24 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 38 optimal weight: 0.4980 chunk 89 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 98 optimal weight: 0.4980 chunk 77 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 = 0.3303 r_free = 0.3303 target = 0.101986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.085964 restraints weight = 18082.372| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 2.06 r_work: 0.2951 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.2026 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= 0.178 Angle : 0.562 8.550 15218 Z= 0.280 Chirality : 0.042 0.264 1813 Planarity : 0.004 0.043 1872 Dihedral : 7.818 102.827 1552 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 4.79 % Allowed : 18.29 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.23), residues: 1379 helix: 0.12 (0.18), residues: 905 sheet: -1.05 (0.74), residues: 51 loop : -1.70 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E1247 HIS 0.007 0.001 HIS E 847 PHE 0.012 0.001 PHE E 315 TYR 0.015 0.001 TYR E 125 ARG 0.003 0.000 ARG E 599 Details of bonding type rmsd hydrogen bonds : bond 0.03372 ( 568) hydrogen bonds : angle 3.97223 ( 1665) covalent geometry : bond 0.00407 (11195) covalent geometry : angle 0.56183 (15218) *********************** 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: 56 poor density : 135 time to evaluate : 1.333 Fit side-chains REVERT: E 95 LEU cc_start: 0.7662 (OUTLIER) cc_final: 0.7378 (tt) REVERT: E 146 LEU cc_start: 0.7145 (OUTLIER) cc_final: 0.6578 (pt) REVERT: E 222 PHE cc_start: 0.9083 (OUTLIER) cc_final: 0.8332 (m-80) REVERT: E 237 PHE cc_start: 0.8820 (OUTLIER) cc_final: 0.7983 (t80) REVERT: E 301 VAL cc_start: 0.9196 (OUTLIER) cc_final: 0.8909 (p) REVERT: E 364 PHE cc_start: 0.9266 (t80) cc_final: 0.8761 (t80) REVERT: E 440 TRP cc_start: 0.7906 (m-10) cc_final: 0.7434 (m-10) REVERT: E 491 GLU cc_start: 0.8616 (tt0) cc_final: 0.8409 (tp30) REVERT: E 586 ILE cc_start: 0.9276 (OUTLIER) cc_final: 0.9053 (tt) REVERT: E 878 ARG cc_start: 0.7864 (mmm-85) cc_final: 0.7662 (tpt170) REVERT: E 1188 ASP cc_start: 0.9089 (t0) cc_final: 0.8788 (t0) REVERT: E 1193 ASP cc_start: 0.8634 (t0) cc_final: 0.8302 (t0) REVERT: E 1251 ARG cc_start: 0.9022 (OUTLIER) cc_final: 0.8431 (mpt180) REVERT: E 1413 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8318 (mp) outliers start: 56 outliers final: 40 residues processed: 179 average time/residue: 0.2033 time to fit residues: 54.8804 Evaluate side-chains 178 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 130 time to evaluate : 1.216 ------------------------------------------------------------------------------- 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 152 THR Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 191 ILE Chi-restraints excluded: chain E residue 222 PHE Chi-restraints excluded: chain E residue 235 ASN Chi-restraints excluded: chain E residue 237 PHE Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 347 VAL Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 377 SER Chi-restraints excluded: chain E residue 388 LEU Chi-restraints excluded: chain E residue 421 LEU Chi-restraints excluded: chain E residue 422 VAL Chi-restraints excluded: chain E residue 442 MET 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 616 SER 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 1026 VAL Chi-restraints excluded: chain E residue 1091 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 1255 ILE Chi-restraints excluded: chain E residue 1318 LEU Chi-restraints excluded: chain E residue 1347 ILE Chi-restraints excluded: chain E residue 1410 ILE Chi-restraints excluded: chain E residue 1413 LEU Chi-restraints excluded: chain E residue 1539 ARG Chi-restraints excluded: chain E residue 1576 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 4 optimal weight: 0.0470 chunk 12 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 78 optimal weight: 0.7980 chunk 41 optimal weight: 0.6980 chunk 130 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 58 optimal weight: 0.4980 overall best weight: 0.5478 ------------------------------------------------------------------------------- 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 = 0.3334 r_free = 0.3334 target = 0.104118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.088107 restraints weight = 18046.784| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 2.08 r_work: 0.2983 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.2159 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 : 0.527 8.792 15218 Z= 0.262 Chirality : 0.041 0.247 1813 Planarity : 0.003 0.045 1872 Dihedral : 7.630 107.352 1552 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 4.10 % Allowed : 19.06 % Favored : 76.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.23), residues: 1379 helix: 0.34 (0.18), residues: 905 sheet: -0.88 (0.77), residues: 51 loop : -1.61 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E1247 HIS 0.007 0.001 HIS E 847 PHE 0.009 0.001 PHE E 315 TYR 0.024 0.001 TYR E 125 ARG 0.006 0.000 ARG E 599 Details of bonding type rmsd hydrogen bonds : bond 0.03074 ( 568) hydrogen bonds : angle 3.78385 ( 1665) covalent geometry : bond 0.00275 (11195) covalent geometry : angle 0.52716 (15218) *********************** 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 200 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 152 time to evaluate : 1.282 Fit side-chains revert: symmetry clash REVERT: E 95 LEU cc_start: 0.7697 (OUTLIER) cc_final: 0.7400 (tt) REVERT: E 146 LEU cc_start: 0.7197 (OUTLIER) cc_final: 0.6676 (pt) REVERT: E 152 THR cc_start: 0.7513 (m) cc_final: 0.7154 (m) REVERT: E 222 PHE cc_start: 0.9068 (OUTLIER) cc_final: 0.8404 (m-80) REVERT: E 237 PHE cc_start: 0.8774 (OUTLIER) cc_final: 0.7794 (t80) REVERT: E 301 VAL cc_start: 0.9137 (OUTLIER) cc_final: 0.8842 (p) REVERT: E 413 MET cc_start: 0.8686 (ptp) cc_final: 0.8462 (ptp) REVERT: E 440 TRP cc_start: 0.7804 (m-10) cc_final: 0.7354 (m-10) REVERT: E 491 GLU cc_start: 0.8716 (tt0) cc_final: 0.8391 (tp30) REVERT: E 586 ILE cc_start: 0.9243 (OUTLIER) cc_final: 0.9021 (tt) REVERT: E 903 MET cc_start: 0.8904 (mtp) cc_final: 0.8587 (mtp) REVERT: E 1188 ASP cc_start: 0.9059 (t0) cc_final: 0.8762 (t0) REVERT: E 1193 ASP cc_start: 0.8768 (t0) cc_final: 0.8431 (t0) REVERT: E 1251 ARG cc_start: 0.9006 (OUTLIER) cc_final: 0.8386 (mpt180) REVERT: E 1253 GLU cc_start: 0.8577 (mt-10) cc_final: 0.8356 (mt-10) REVERT: E 1413 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8303 (mp) outliers start: 48 outliers final: 36 residues processed: 187 average time/residue: 0.1997 time to fit residues: 56.6897 Evaluate side-chains 189 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 145 time to evaluate : 1.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 81 MET Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 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 442 MET 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 1255 ILE Chi-restraints excluded: chain E residue 1318 LEU Chi-restraints excluded: chain E residue 1347 ILE Chi-restraints excluded: chain E residue 1352 VAL Chi-restraints excluded: chain E residue 1410 ILE Chi-restraints excluded: chain E residue 1413 LEU Chi-restraints excluded: chain E residue 1539 ARG Chi-restraints excluded: chain E residue 1576 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 33 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 14 optimal weight: 0.0000 chunk 91 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 40 optimal weight: 0.0010 chunk 15 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 overall best weight: 0.4590 ------------------------------------------------------------------------------- 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 = 0.3346 r_free = 0.3346 target = 0.104997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.088949 restraints weight = 17814.916| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 2.07 r_work: 0.2992 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.2289 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= 0.111 Angle : 0.526 8.841 15218 Z= 0.259 Chirality : 0.040 0.180 1813 Planarity : 0.003 0.039 1872 Dihedral : 7.448 112.896 1552 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.23), residues: 1379 helix: 0.54 (0.18), residues: 901 sheet: -0.72 (0.78), residues: 51 loop : -1.57 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E1247 HIS 0.007 0.001 HIS E 847 PHE 0.012 0.001 PHE E1223 TYR 0.018 0.001 TYR E 125 ARG 0.005 0.000 ARG E 599 Details of bonding type rmsd hydrogen bonds : bond 0.02970 ( 568) hydrogen bonds : angle 3.68154 ( 1665) covalent geometry : bond 0.00250 (11195) covalent geometry : angle 0.52626 (15218) *********************** 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 200 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 150 time to evaluate : 1.280 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 95 LEU cc_start: 0.7593 (OUTLIER) cc_final: 0.7328 (tt) REVERT: E 146 LEU cc_start: 0.7286 (OUTLIER) cc_final: 0.6843 (pt) REVERT: E 152 THR cc_start: 0.7494 (m) cc_final: 0.7138 (m) REVERT: E 182 MET cc_start: 0.8451 (mmm) cc_final: 0.7981 (mmp) REVERT: E 222 PHE cc_start: 0.9057 (OUTLIER) cc_final: 0.8399 (m-80) REVERT: E 237 PHE cc_start: 0.8745 (OUTLIER) cc_final: 0.7737 (t80) REVERT: E 301 VAL cc_start: 0.9120 (OUTLIER) cc_final: 0.8828 (p) REVERT: E 440 TRP cc_start: 0.7845 (m-10) cc_final: 0.7398 (m-10) REVERT: E 491 GLU cc_start: 0.8725 (tt0) cc_final: 0.8341 (tp30) REVERT: E 586 ILE cc_start: 0.9233 (OUTLIER) cc_final: 0.9019 (tt) REVERT: E 903 MET cc_start: 0.8973 (mtp) cc_final: 0.8643 (mtp) REVERT: E 1165 LEU cc_start: 0.8830 (mt) cc_final: 0.8618 (mt) REVERT: E 1188 ASP cc_start: 0.9050 (t0) cc_final: 0.8597 (t0) REVERT: E 1193 ASP cc_start: 0.8771 (t0) cc_final: 0.8428 (t0) REVERT: E 1251 ARG cc_start: 0.8996 (OUTLIER) cc_final: 0.8360 (mpt180) REVERT: E 1322 GLU cc_start: 0.8605 (mp0) cc_final: 0.8155 (mp0) REVERT: E 1413 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8284 (mp) REVERT: E 1443 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.8163 (pm20) REVERT: E 1444 ARG cc_start: 0.8345 (ttm-80) cc_final: 0.8123 (ttm-80) outliers start: 50 outliers final: 36 residues processed: 187 average time/residue: 0.2342 time to fit residues: 66.4930 Evaluate side-chains 187 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 142 time to evaluate : 1.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 75 ARG Chi-restraints excluded: chain E residue 81 MET Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 191 ILE Chi-restraints excluded: chain E residue 222 PHE Chi-restraints excluded: chain E residue 235 ASN Chi-restraints excluded: chain E residue 237 PHE Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 347 VAL Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 377 SER Chi-restraints excluded: chain E residue 388 LEU Chi-restraints excluded: chain E residue 421 LEU Chi-restraints excluded: chain E residue 422 VAL Chi-restraints excluded: chain E residue 442 MET 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 943 THR Chi-restraints excluded: chain E residue 998 TRP Chi-restraints excluded: chain E residue 1105 ILE Chi-restraints excluded: chain E residue 1148 LEU Chi-restraints excluded: chain E residue 1251 ARG Chi-restraints excluded: chain E residue 1255 ILE Chi-restraints excluded: chain E residue 1318 LEU Chi-restraints excluded: chain E residue 1347 ILE Chi-restraints excluded: chain E residue 1352 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 125 optimal weight: 0.0040 chunk 128 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 123 optimal weight: 1.9990 chunk 74 optimal weight: 0.0050 chunk 9 optimal weight: 0.7980 chunk 77 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 chunk 69 optimal weight: 0.7980 chunk 102 optimal weight: 0.9980 overall best weight: 0.4606 ------------------------------------------------------------------------------- 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 = 0.3354 r_free = 0.3354 target = 0.105464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.089290 restraints weight = 17960.220| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 2.09 r_work: 0.2998 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.2366 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= 0.111 Angle : 0.526 8.898 15218 Z= 0.259 Chirality : 0.040 0.288 1813 Planarity : 0.003 0.040 1872 Dihedral : 7.357 119.696 1552 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 4.02 % Allowed : 19.91 % Favored : 76.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.23), residues: 1379 helix: 0.67 (0.18), residues: 907 sheet: -0.70 (0.78), residues: 51 loop : -1.58 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E1247 HIS 0.007 0.001 HIS E 847 PHE 0.014 0.001 PHE E1223 TYR 0.026 0.001 TYR E 125 ARG 0.004 0.000 ARG E 599 Details of bonding type rmsd hydrogen bonds : bond 0.02957 ( 568) hydrogen bonds : angle 3.64839 ( 1665) covalent geometry : bond 0.00251 (11195) covalent geometry : angle 0.52611 (15218) *********************** 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 195 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 148 time to evaluate : 1.433 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 95 LEU cc_start: 0.7532 (OUTLIER) cc_final: 0.7289 (tt) REVERT: E 146 LEU cc_start: 0.7244 (OUTLIER) cc_final: 0.6854 (pt) REVERT: E 152 THR cc_start: 0.7440 (m) cc_final: 0.7086 (m) REVERT: E 182 MET cc_start: 0.8450 (mmm) cc_final: 0.7992 (mmp) REVERT: E 222 PHE cc_start: 0.9061 (OUTLIER) cc_final: 0.8379 (m-80) REVERT: E 237 PHE cc_start: 0.8760 (OUTLIER) cc_final: 0.7742 (t80) REVERT: E 301 VAL cc_start: 0.9091 (OUTLIER) cc_final: 0.8802 (p) REVERT: E 440 TRP cc_start: 0.7735 (m-10) cc_final: 0.7286 (m-10) REVERT: E 491 GLU cc_start: 0.8732 (tt0) cc_final: 0.8342 (tp30) REVERT: E 586 ILE cc_start: 0.9217 (OUTLIER) cc_final: 0.9011 (tt) REVERT: E 903 MET cc_start: 0.8978 (mtp) cc_final: 0.8646 (mtp) REVERT: E 1188 ASP cc_start: 0.9035 (t0) cc_final: 0.8581 (t0) REVERT: E 1193 ASP cc_start: 0.8972 (t0) cc_final: 0.8648 (t0) REVERT: E 1251 ARG cc_start: 0.8987 (OUTLIER) cc_final: 0.8289 (mpt90) REVERT: E 1322 GLU cc_start: 0.8586 (mp0) cc_final: 0.8138 (mp0) REVERT: E 1413 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8270 (mp) REVERT: E 1443 GLU cc_start: 0.8458 (OUTLIER) cc_final: 0.8122 (pm20) REVERT: E 1444 ARG cc_start: 0.8342 (ttm-80) cc_final: 0.8115 (ttm-80) outliers start: 47 outliers final: 37 residues processed: 184 average time/residue: 0.2492 time to fit residues: 68.6386 Evaluate side-chains 188 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 142 time to evaluate : 1.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 75 ARG Chi-restraints excluded: chain E residue 81 MET Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 191 ILE Chi-restraints excluded: chain E residue 222 PHE Chi-restraints excluded: chain E residue 235 ASN Chi-restraints excluded: chain E residue 237 PHE Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 347 VAL Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 377 SER Chi-restraints excluded: chain E residue 388 LEU Chi-restraints excluded: chain E residue 421 LEU Chi-restraints excluded: chain E residue 422 VAL Chi-restraints excluded: chain E residue 442 MET 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 1105 ILE Chi-restraints excluded: chain E residue 1148 LEU Chi-restraints excluded: chain E residue 1251 ARG Chi-restraints excluded: chain E residue 1255 ILE Chi-restraints excluded: chain E residue 1318 LEU Chi-restraints excluded: chain E residue 1347 ILE Chi-restraints excluded: chain E residue 1352 VAL 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 67 optimal weight: 0.0980 chunk 90 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 121 optimal weight: 0.4980 chunk 6 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 101 optimal weight: 0.9990 chunk 76 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 57 optimal weight: 0.6980 chunk 42 optimal weight: 5.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3350 r_free = 0.3350 target = 0.105197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.089065 restraints weight = 17821.356| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 2.08 r_work: 0.2995 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.2390 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= 0.122 Angle : 0.536 8.855 15218 Z= 0.264 Chirality : 0.041 0.279 1813 Planarity : 0.003 0.040 1872 Dihedral : 7.292 124.846 1552 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.76 % Allowed : 20.85 % Favored : 75.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.23), residues: 1379 helix: 0.75 (0.18), residues: 902 sheet: -0.67 (0.78), residues: 51 loop : -1.43 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E1247 HIS 0.007 0.001 HIS E 847 PHE 0.014 0.001 PHE E1223 TYR 0.018 0.001 TYR E 125 ARG 0.004 0.000 ARG E 599 Details of bonding type rmsd hydrogen bonds : bond 0.02998 ( 568) hydrogen bonds : angle 3.66498 ( 1665) covalent geometry : bond 0.00278 (11195) covalent geometry : angle 0.53580 (15218) ********************** 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 193 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 149 time to evaluate : 1.282 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 95 LEU cc_start: 0.7544 (OUTLIER) cc_final: 0.7298 (tt) REVERT: E 146 LEU cc_start: 0.7260 (OUTLIER) cc_final: 0.6868 (pt) REVERT: E 152 THR cc_start: 0.7473 (m) cc_final: 0.7121 (m) REVERT: E 182 MET cc_start: 0.8444 (mmm) cc_final: 0.7996 (mmp) REVERT: E 222 PHE cc_start: 0.9071 (OUTLIER) cc_final: 0.8358 (m-80) REVERT: E 237 PHE cc_start: 0.8761 (OUTLIER) cc_final: 0.7753 (t80) REVERT: E 301 VAL cc_start: 0.9108 (OUTLIER) cc_final: 0.8818 (p) REVERT: E 440 TRP cc_start: 0.7726 (m-10) cc_final: 0.7276 (m-10) REVERT: E 491 GLU cc_start: 0.8738 (tt0) cc_final: 0.8348 (tp30) REVERT: E 586 ILE cc_start: 0.9204 (OUTLIER) cc_final: 0.8992 (tt) REVERT: E 903 MET cc_start: 0.8978 (mtp) cc_final: 0.8631 (mtp) REVERT: E 1188 ASP cc_start: 0.9037 (t0) cc_final: 0.8586 (t0) REVERT: E 1193 ASP cc_start: 0.9014 (t0) cc_final: 0.8695 (t0) REVERT: E 1251 ARG cc_start: 0.8985 (OUTLIER) cc_final: 0.8331 (mpt180) REVERT: E 1322 GLU cc_start: 0.8590 (mp0) cc_final: 0.8146 (mp0) REVERT: E 1413 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8261 (mp) REVERT: E 1443 GLU cc_start: 0.8478 (OUTLIER) cc_final: 0.8138 (pm20) REVERT: E 1444 ARG cc_start: 0.8326 (ttm-80) cc_final: 0.8111 (ttm-80) outliers start: 44 outliers final: 34 residues processed: 182 average time/residue: 0.2056 time to fit residues: 56.0647 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 : 1.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 75 ARG Chi-restraints excluded: chain E residue 81 MET Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 191 ILE Chi-restraints excluded: chain E residue 222 PHE Chi-restraints excluded: chain E residue 235 ASN Chi-restraints excluded: chain E residue 237 PHE Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 347 VAL Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 377 SER Chi-restraints excluded: chain E residue 388 LEU Chi-restraints excluded: chain E residue 421 LEU Chi-restraints excluded: chain E residue 422 VAL Chi-restraints excluded: chain E residue 442 MET 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 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 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 1352 VAL 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 60 optimal weight: 0.0770 chunk 9 optimal weight: 0.4980 chunk 99 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 28 optimal weight: 0.5980 chunk 125 optimal weight: 0.0870 chunk 44 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 overall best weight: 0.3916 ------------------------------------------------------------------------------- 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 = 0.3366 r_free = 0.3366 target = 0.106239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.090194 restraints weight = 17723.642| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 2.07 r_work: 0.3014 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11195 Z= 0.106 Angle : 0.528 8.957 15218 Z= 0.259 Chirality : 0.040 0.262 1813 Planarity : 0.003 0.039 1872 Dihedral : 7.133 126.508 1552 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 3.93 % Allowed : 21.11 % Favored : 74.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.23), residues: 1379 helix: 0.87 (0.18), residues: 900 sheet: -0.65 (0.78), residues: 51 loop : -1.40 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E1339 HIS 0.007 0.001 HIS E 847 PHE 0.014 0.001 PHE E1223 TYR 0.019 0.001 TYR E 125 ARG 0.004 0.000 ARG E 599 Details of bonding type rmsd hydrogen bonds : bond 0.02906 ( 568) hydrogen bonds : angle 3.58370 ( 1665) covalent geometry : bond 0.00239 (11195) covalent geometry : angle 0.52802 (15218) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5709.98 seconds wall clock time: 100 minutes 52.97 seconds (6052.97 seconds total)