Starting phenix.real_space_refine (version: 1.21rc1) on Sat Apr 22 00:13:19 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s5v_24840/04_2023/7s5v_24840_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s5v_24840/04_2023/7s5v_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s5v_24840/04_2023/7s5v_24840.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s5v_24840/04_2023/7s5v_24840.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s5v_24840/04_2023/7s5v_24840_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s5v_24840/04_2023/7s5v_24840_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 Residue "E TYR 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 19": "OD1" <-> "OD2" Residue "E PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 75": "NH1" <-> "NH2" Residue "E GLU 101": "OE1" <-> "OE2" Residue "E TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 307": "NH1" <-> "NH2" Residue "E ASP 311": "OD1" <-> "OD2" Residue "E PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 351": "OE1" <-> "OE2" Residue "E PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 425": "OD1" <-> "OD2" Residue "E PHE 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 528": "NH1" <-> "NH2" Residue "E PHE 560": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 571": "OD1" <-> "OD2" Residue "E PHE 578": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 613": "OE1" <-> "OE2" Residue "E TYR 686": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 687": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 703": "NH1" <-> "NH2" Residue "E ASP 811": "OD1" <-> "OD2" Residue "E ARG 842": "NH1" <-> "NH2" Residue "E TYR 845": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 898": "OD1" <-> "OD2" Residue "E TYR 1004": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1018": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 1031": "OD1" <-> "OD2" Residue "E ASP 1039": "OD1" <-> "OD2" Residue "E ARG 1124": "NH1" <-> "NH2" Residue "E ASP 1188": "OD1" <-> "OD2" Residue "E ARG 1222": "NH1" <-> "NH2" Residue "E ASP 1232": "OD1" <-> "OD2" Residue "E PHE 1240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 1253": "OE1" <-> "OE2" Residue "E TYR 1287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 1306": "OE1" <-> "OE2" Residue "E ARG 1314": "NH1" <-> "NH2" Residue "E TYR 1354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 1397": "OD1" <-> "OD2" Residue "E ARG 1419": "NH1" <-> "NH2" Residue "E ARG 1437": "NH1" <-> "NH2" Residue "E ARG 1487": "NH1" <-> "NH2" Residue "E ARG 1494": "NH1" <-> "NH2" Residue "E ARG 1498": "NH1" <-> "NH2" Residue "E PHE 1503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 1507": "OE1" <-> "OE2" Residue "E GLU 1559": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 10964 Number of models: 1 Model: "" Number of chains: 1 Chain: "E" Number of atoms: 10964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1401, 10964 Unusual residues: {' MG': 2, 'ADP': 1, 'ATP': 1} Classifications: {'peptide': 1397, 'undetermined': 4} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 45, 'TRANS': 1351, None: 4} Not linked: pdbres="LYS E1582 " pdbres="ADP E1601 " Not linked: pdbres="ADP E1601 " pdbres=" MG E1602 " Not linked: pdbres=" MG E1602 " pdbres=" MG E1603 " Not linked: pdbres=" MG E1603 " pdbres="ATP E1604 " 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 Time building chain proxies: 6.22, per 1000 atoms: 0.57 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.40 Conformation dependent library (CDL) restraints added in 1.6 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... running ksdssp... Secondary structure from input PDB file: 57 helices and 4 sheets defined 57.1% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.29 Creating SS restraints... Processing helix chain 'E' and resid 35 through 50 Proline residue: E 46 - end of helix Processing helix chain 'E' and resid 72 through 99 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) Processing helix chain 'E' and resid 109 through 129 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 134 through 156 removed outlier: 4.147A pdb=" N ALA E 139 " --> pdb=" O LEU E 136 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N TYR E 143 " --> pdb=" O LEU E 140 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N TRP E 144 " --> pdb=" O LEU E 141 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N LEU E 146 " --> pdb=" O TYR E 143 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N ALA E 147 " --> pdb=" O TRP E 144 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ILE E 153 " --> pdb=" O THR E 150 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS E 154 " --> pdb=" O LYS E 151 " (cutoff:3.500A) Processing helix chain 'E' and resid 168 through 191 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) Processing helix chain 'E' and resid 225 through 229 Processing helix chain 'E' and resid 232 through 239 removed outlier: 3.613A pdb=" N ALA E 236 " --> pdb=" O TRP E 233 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ILE E 238 " --> pdb=" O ASN E 235 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS E 239 " --> pdb=" O ALA E 236 " (cutoff:3.500A) Processing helix chain 'E' and resid 260 through 274 removed outlier: 3.752A pdb=" N ARG E 266 " --> pdb=" O THR E 262 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLN E 274 " --> pdb=" O ALA E 270 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 295 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 297 through 328 removed outlier: 4.186A pdb=" N ALA E 316 " --> pdb=" O LEU E 312 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N GLY E 317 " --> pdb=" O LEU E 313 " (cutoff:3.500A) Proline residue: E 318 - end of helix removed outlier: 3.519A pdb=" N VAL E 325 " --> pdb=" O ILE E 321 " (cutoff:3.500A) Processing helix chain 'E' and resid 349 through 352 No H-bonds generated for 'chain 'E' and resid 349 through 352' Processing helix chain 'E' and resid 357 through 402 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) removed outlier: 3.816A pdb=" N HIS E 402 " --> pdb=" O ASN E 398 " (cutoff:3.500A) Processing helix chain 'E' and resid 415 through 423 Processing helix chain 'E' and resid 425 through 433 Processing helix chain 'E' and resid 436 through 456 Proline residue: E 443 - end of helix Processing helix chain 'E' and resid 459 through 510 removed outlier: 4.575A pdb=" N ALA E 466 " --> pdb=" O ILE E 463 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N VAL E 467 " --> pdb=" O GLY E 464 " (cutoff:3.500A) Proline residue: E 473 - end of helix removed outlier: 4.648A pdb=" N VAL E 478 " --> pdb=" O GLN E 475 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N GLN E 486 " --> pdb=" O SER E 483 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N THR E 489 " --> pdb=" O GLN E 486 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N LEU E 490 " --> pdb=" O ARG E 487 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N SER E 493 " --> pdb=" O LEU E 490 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N THR E 500 " --> pdb=" O LEU E 497 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N GLU E 502 " --> pdb=" O GLN E 499 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ARG E 505 " --> pdb=" O GLU E 502 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N LYS E 508 " --> pdb=" O ARG E 505 " (cutoff:3.500A) Processing helix chain 'E' and resid 516 through 564 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 574 through 586 removed outlier: 3.731A pdb=" N SER E 582 " --> pdb=" O PHE E 578 " (cutoff:3.500A) Processing helix chain 'E' and resid 591 through 600 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 606 through 615 Processing helix chain 'E' and resid 720 through 727 Processing helix chain 'E' and resid 784 through 789 Processing helix chain 'E' and resid 796 through 805 Processing helix chain 'E' and resid 809 through 814 removed outlier: 3.579A pdb=" N ILE E 814 " --> pdb=" O PRO E 810 " (cutoff:3.500A) Processing helix chain 'E' and resid 818 through 820 No H-bonds generated for 'chain 'E' and resid 818 through 820' Processing helix chain 'E' and resid 832 through 843 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 862 through 870 removed outlier: 3.869A pdb=" N HIS E 867 " --> pdb=" O HIS E 863 " (cutoff:3.500A) Processing helix chain 'E' and resid 891 through 896 Proline residue: E 895 - end of helix Processing helix chain 'E' and resid 914 through 919 Processing helix chain 'E' and resid 924 through 929 Processing helix chain 'E' and resid 999 through 1006 Processing helix chain 'E' and resid 1010 through 1017 Processing helix chain 'E' and resid 1021 through 1032 removed outlier: 3.785A pdb=" N ALA E1029 " --> pdb=" O MET E1025 " (cutoff:3.500A) Processing helix chain 'E' and resid 1038 through 1041 Processing helix chain 'E' and resid 1069 through 1072 No H-bonds generated for 'chain 'E' and resid 1069 through 1072' Processing helix chain 'E' and resid 1080 through 1105 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) Processing helix chain 'E' and resid 1110 through 1115 Processing helix chain 'E' and resid 1118 through 1126 removed outlier: 3.598A pdb=" N PHE E1125 " --> pdb=" O ILE E1121 " (cutoff:3.500A) Processing helix chain 'E' and resid 1128 through 1134 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 1136 through 1154 removed outlier: 3.908A pdb=" N GLU E1141 " --> pdb=" O PRO E1137 " (cutoff:3.500A) Processing helix chain 'E' and resid 1162 through 1191 removed outlier: 4.341A pdb=" N LEU E1169 " --> pdb=" O VAL E1166 " (cutoff:3.500A) Proline residue: E1170 - end of helix removed outlier: 5.777A pdb=" N ILE E1173 " --> pdb=" O PRO E1170 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N LYS E1180 " --> pdb=" O PHE E1177 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N VAL E1184 " --> pdb=" O TYR E1181 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N ARG E1187 " --> pdb=" O VAL E1184 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ASP E1188 " --> pdb=" O ALA E1185 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLN E1190 " --> pdb=" O ARG E1187 " (cutoff:3.500A) Processing helix chain 'E' and resid 1197 through 1209 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) Processing helix chain 'E' and resid 1211 through 1216 Processing helix chain 'E' and resid 1220 through 1272 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) Processing helix chain 'E' and resid 1279 through 1294 Processing helix chain 'E' and resid 1296 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 1385 through 1392 removed outlier: 4.185A pdb=" N PHE E1392 " --> pdb=" O PHE E1388 " (cutoff:3.500A) Processing helix chain 'E' and resid 1415 through 1421 removed outlier: 3.928A pdb=" N SER E1420 " --> pdb=" O HIS E1416 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ARG E1421 " --> pdb=" O THR E1417 " (cutoff:3.500A) Processing helix chain 'E' and resid 1436 through 1440 Processing helix chain 'E' and resid 1449 through 1456 removed outlier: 4.119A pdb=" N GLU E1453 " --> pdb=" O THR E1450 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N ALA E1454 " --> pdb=" O LEU E1451 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLU E1456 " --> pdb=" O GLU E1453 " (cutoff:3.500A) Processing helix chain 'E' and resid 1461 through 1464 No H-bonds generated for 'chain 'E' and resid 1461 through 1464' Processing helix chain 'E' and resid 1477 through 1479 No H-bonds generated for 'chain 'E' and resid 1477 through 1479' Processing helix chain 'E' and resid 1485 through 1497 removed outlier: 3.626A pdb=" N VAL E1497 " --> pdb=" O ALA E1493 " (cutoff:3.500A) Processing helix chain 'E' and resid 1508 through 1510 No H-bonds generated for 'chain 'E' and resid 1508 through 1510' Processing helix chain 'E' and resid 1514 through 1527 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 1563 through 1567 Processing helix chain 'E' and resid 1573 through 1577 Processing sheet with id= A, first strand: chain 'E' and resid 907 through 912 removed outlier: 6.933A pdb=" N ALA E 902 " --> pdb=" O GLN E 909 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N GLU E 911 " --> pdb=" O ILE E 900 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ILE E 900 " --> pdb=" O GLU E 911 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TRP E 899 " --> pdb=" O LEU E 709 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N VAL E 884 " --> pdb=" O THR E 710 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N ILE E 712 " --> pdb=" O VAL E 884 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N LEU E 886 " --> pdb=" O ILE E 712 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ALA E 771 " --> pdb=" O PHE E 852 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'E' and resid 1346 through 1348 Processing sheet with id= C, first strand: chain 'E' and resid 1376 through 1379 Processing sheet with id= D, first strand: chain 'E' and resid 1423 through 1425 removed outlier: 6.459A pdb=" N THR E1532 " --> pdb=" O PHE E1503 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N MET E1505 " --> pdb=" O THR E1532 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N VAL E1534 " --> pdb=" O MET E1505 " (cutoff:3.500A) 495 hydrogen bonds defined for protein. 1257 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: 4.21 Time building geometry restraints manager: 4.78 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: 98.82 - 106.24: 253 106.24 - 113.66: 6498 113.66 - 121.08: 5685 121.08 - 128.51: 2675 128.51 - 135.93: 107 Bond angle restraints: 15218 Sorted by residual: angle pdb=" PB ATP E1604 " pdb=" O3B ATP E1604 " pdb=" PG ATP E1604 " ideal model delta sigma weight residual 139.87 118.40 21.47 1.00e+00 1.00e+00 4.61e+02 angle pdb=" PA ATP E1604 " pdb=" O3A ATP E1604 " pdb=" PB ATP E1604 " ideal model delta sigma weight residual 136.83 119.81 17.02 1.00e+00 1.00e+00 2.90e+02 angle pdb=" C5 ATP E1604 " pdb=" C4 ATP E1604 " pdb=" N3 ATP E1604 " ideal model delta sigma weight residual 126.80 118.81 7.99 1.00e+00 1.00e+00 6.38e+01 angle pdb=" N3 ATP E1604 " pdb=" C4 ATP E1604 " pdb=" N9 ATP E1604 " ideal model delta sigma weight residual 127.04 135.19 -8.15 1.15e+00 7.59e-01 5.04e+01 angle pdb=" N1 ATP E1604 " pdb=" C2 ATP E1604 " pdb=" N3 ATP E1604 " ideal model delta sigma weight residual 128.69 123.69 5.00 1.00e+00 1.00e+00 2.50e+01 ... (remaining 15213 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.19: 6156 24.19 - 48.38: 414 48.38 - 72.56: 42 72.56 - 96.75: 4 96.75 - 120.94: 1 Dihedral angle restraints: 6617 sinusoidal: 2547 harmonic: 4070 Sorted by residual: dihedral pdb=" O1B ADP E1601 " pdb=" O3A ADP E1601 " pdb=" PB ADP E1601 " pdb=" PA ADP E1601 " ideal model delta sinusoidal sigma weight residual -60.00 60.94 -120.94 1 2.00e+01 2.50e-03 3.63e+01 dihedral pdb=" CA GLY E 411 " pdb=" C GLY E 411 " pdb=" N GLU E 412 " pdb=" CA GLU E 412 " ideal model delta harmonic sigma weight residual -180.00 -150.01 -29.99 0 5.00e+00 4.00e-02 3.60e+01 dihedral pdb=" CA ASP E 854 " pdb=" C ASP E 854 " pdb=" N ASP E 855 " pdb=" CA ASP E 855 " ideal model delta harmonic sigma weight residual -180.00 -152.05 -27.95 0 5.00e+00 4.00e-02 3.12e+01 ... (remaining 6614 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1537 0.069 - 0.139: 251 0.139 - 0.208: 23 0.208 - 0.278: 1 0.278 - 0.347: 1 Chirality restraints: 1813 Sorted by residual: chirality pdb=" CG LEU E1227 " pdb=" CB LEU E1227 " pdb=" CD1 LEU E1227 " pdb=" CD2 LEU E1227 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.35 2.00e-01 2.50e+01 3.02e+00 chirality pdb=" CB ILE E 138 " pdb=" CA ILE E 138 " pdb=" CG1 ILE E 138 " pdb=" CG2 ILE E 138 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" CB VAL E 598 " pdb=" CA VAL E 598 " pdb=" CG1 VAL E 598 " pdb=" CG2 VAL E 598 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 1.01e+00 ... (remaining 1810 not shown) Planarity restraints: 1872 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU E 894 " 0.050 5.00e-02 4.00e+02 7.51e-02 9.02e+00 pdb=" N PRO E 895 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO E 895 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO E 895 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE E 45 " -0.046 5.00e-02 4.00e+02 6.88e-02 7.58e+00 pdb=" N PRO E 46 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO E 46 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO E 46 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA E1370 " -0.042 5.00e-02 4.00e+02 6.36e-02 6.47e+00 pdb=" N PRO E1371 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO E1371 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO E1371 " -0.035 5.00e-02 4.00e+02 ... (remaining 1869 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 170 2.65 - 3.22: 9795 3.22 - 3.78: 17314 3.78 - 4.34: 23907 4.34 - 4.90: 38924 Nonbonded interactions: 90110 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 90105 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: 2.080 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: 10.760 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 31.360 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.750 ------------------------------------------------------------------------------- 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= 0.393 Angle : 0.876 21.467 15218 Z= 0.518 Chirality : 0.051 0.347 1813 Planarity : 0.007 0.075 1872 Dihedral : 15.450 120.941 3973 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer Outliers : 4.27 % 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 *********************** 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 fitting. rotamer outliers: 50 poor density : 172 time to evaluate : 1.316 Fit side-chains outliers start: 50 outliers final: 31 residues processed: 220 average time/residue: 0.2437 time to fit residues: 76.0454 Evaluate side-chains 162 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 131 time to evaluate : 1.173 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.1139 time to fit residues: 7.7985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 118 optimal weight: 0.9980 chunk 106 optimal weight: 0.5980 chunk 58 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 109 optimal weight: 0.6980 chunk 42 optimal weight: 0.3980 chunk 66 optimal weight: 0.6980 chunk 81 optimal weight: 2.9990 chunk 127 optimal weight: 0.1980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 73 ASN E 104 HIS E 212 GLN E 220 GLN E 327 HIS E 350 GLN E 375 GLN E 475 GLN E 499 GLN E 708 GLN E 732 GLN E 781 ASN E 836 GLN E 933 ASN E1020 GLN E1061 GLN E1134 GLN E1518 ASN E1541 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.1290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 11195 Z= 0.168 Angle : 0.554 10.321 15218 Z= 0.275 Chirality : 0.039 0.181 1813 Planarity : 0.004 0.050 1872 Dihedral : 6.328 98.266 1507 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer Outliers : 1.37 % 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: -2.84 (0.20), residues: 1379 helix: -1.56 (0.15), residues: 895 sheet: -1.82 (0.71), residues: 51 loop : -2.24 (0.27), residues: 433 *********************** 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 165 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 149 time to evaluate : 1.346 Fit side-chains outliers start: 16 outliers final: 8 residues processed: 161 average time/residue: 0.2218 time to fit residues: 53.1718 Evaluate side-chains 137 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 129 time to evaluate : 1.285 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1165 time to fit residues: 3.6969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 70 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 105 optimal weight: 0.7980 chunk 86 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 127 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 126 optimal weight: 0.8980 chunk 43 optimal weight: 0.6980 chunk 102 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 836 GLN E 933 ASN E1541 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.1509 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= 0.225 Angle : 0.548 8.134 15218 Z= 0.273 Chirality : 0.040 0.150 1813 Planarity : 0.004 0.040 1872 Dihedral : 6.106 100.964 1507 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer Outliers : 2.05 % 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: -2.04 (0.22), residues: 1379 helix: -0.89 (0.17), residues: 905 sheet: -1.57 (0.75), residues: 51 loop : -2.08 (0.28), residues: 423 *********************** 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 159 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 135 time to evaluate : 1.324 Fit side-chains outliers start: 24 outliers final: 11 residues processed: 153 average time/residue: 0.2076 time to fit residues: 48.0848 Evaluate side-chains 137 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 126 time to evaluate : 1.238 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1140 time to fit residues: 4.0031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 125 optimal weight: 0.1980 chunk 95 optimal weight: 0.7980 chunk 66 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 135 optimal weight: 0.0980 chunk 121 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 chunk 112 optimal weight: 0.6980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 836 GLN E1541 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.036 11195 Z= 0.156 Angle : 0.509 7.011 15218 Z= 0.254 Chirality : 0.039 0.145 1813 Planarity : 0.003 0.039 1872 Dihedral : 5.795 103.569 1507 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer Outliers : 1.54 % 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: -1.43 (0.23), residues: 1379 helix: -0.38 (0.18), residues: 901 sheet: -1.50 (0.76), residues: 50 loop : -1.90 (0.28), residues: 428 *********************** 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 157 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 139 time to evaluate : 1.488 Fit side-chains outliers start: 18 outliers final: 3 residues processed: 155 average time/residue: 0.2241 time to fit residues: 53.4816 Evaluate side-chains 135 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 132 time to evaluate : 1.304 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1286 time to fit residues: 2.5359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 76 optimal weight: 1.9990 chunk 1 optimal weight: 20.0000 chunk 100 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 115 optimal weight: 0.0010 chunk 93 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 69 optimal weight: 2.9990 chunk 121 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 overall best weight: 0.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 836 GLN E1541 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.1795 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= 0.205 Angle : 0.534 7.093 15218 Z= 0.264 Chirality : 0.040 0.240 1813 Planarity : 0.003 0.042 1872 Dihedral : 5.741 107.096 1507 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer Outliers : 1.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.23), residues: 1379 helix: -0.19 (0.18), residues: 903 sheet: -1.33 (0.78), residues: 50 loop : -1.83 (0.29), residues: 426 *********************** 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 156 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 137 time to evaluate : 1.193 Fit side-chains outliers start: 19 outliers final: 8 residues processed: 151 average time/residue: 0.2119 time to fit residues: 48.2225 Evaluate side-chains 139 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 131 time to evaluate : 1.332 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1137 time to fit residues: 3.5012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 121 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 79 optimal weight: 3.9990 chunk 33 optimal weight: 0.0980 chunk 135 optimal weight: 0.9990 chunk 112 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 71 optimal weight: 0.4980 chunk 130 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 836 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 11195 Z= 0.179 Angle : 0.525 7.985 15218 Z= 0.258 Chirality : 0.040 0.295 1813 Planarity : 0.003 0.041 1872 Dihedral : 5.640 111.049 1507 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer Outliers : 0.60 % 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: -0.99 (0.23), residues: 1379 helix: 0.00 (0.18), residues: 898 sheet: -1.29 (0.78), residues: 50 loop : -1.83 (0.28), residues: 431 *********************** 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 145 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 138 time to evaluate : 1.178 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 144 average time/residue: 0.2096 time to fit residues: 46.2719 Evaluate side-chains 134 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 130 time to evaluate : 1.276 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1052 time to fit residues: 2.5368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 15 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 98 optimal weight: 0.0170 chunk 76 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 75 optimal weight: 0.0670 chunk 134 optimal weight: 0.9980 chunk 84 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 83 optimal weight: 0.0670 overall best weight: 0.4094 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 420 ASN E 836 GLN E1541 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 11195 Z= 0.149 Angle : 0.509 7.204 15218 Z= 0.250 Chirality : 0.039 0.271 1813 Planarity : 0.003 0.040 1872 Dihedral : 5.500 117.408 1507 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer Outliers : 0.26 % 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: -0.76 (0.23), residues: 1379 helix: 0.20 (0.18), residues: 896 sheet: -1.27 (0.78), residues: 50 loop : -1.75 (0.29), residues: 433 *********************** 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 150 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 147 time to evaluate : 1.374 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 149 average time/residue: 0.2184 time to fit residues: 49.3793 Evaluate side-chains 141 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 140 time to evaluate : 1.231 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1424 time to fit residues: 2.2252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 53 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 26 optimal weight: 0.0770 chunk 85 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 106 optimal weight: 1.9990 chunk 122 optimal weight: 0.7980 chunk 129 optimal weight: 2.9990 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 104 HIS E 681 GLN E 836 GLN ** E 933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.2017 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= 0.199 Angle : 0.531 7.379 15218 Z= 0.261 Chirality : 0.041 0.264 1813 Planarity : 0.003 0.041 1872 Dihedral : 5.537 124.044 1507 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer Outliers : 0.94 % 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: -0.66 (0.23), residues: 1379 helix: 0.27 (0.18), residues: 890 sheet: -1.29 (0.78), residues: 50 loop : -1.68 (0.29), residues: 439 *********************** 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 150 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 139 time to evaluate : 1.197 Fit side-chains outliers start: 11 outliers final: 4 residues processed: 144 average time/residue: 0.2146 time to fit residues: 46.8368 Evaluate side-chains 140 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 136 time to evaluate : 1.247 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1135 time to fit residues: 2.5384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 117 optimal weight: 0.7980 chunk 125 optimal weight: 0.7980 chunk 129 optimal weight: 0.5980 chunk 75 optimal weight: 0.0980 chunk 54 optimal weight: 0.8980 chunk 98 optimal weight: 0.6980 chunk 38 optimal weight: 0.5980 chunk 113 optimal weight: 3.9990 chunk 118 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 132 optimal weight: 0.7980 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.2082 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= 0.176 Angle : 0.524 7.296 15218 Z= 0.257 Chirality : 0.040 0.312 1813 Planarity : 0.003 0.041 1872 Dihedral : 5.482 124.086 1507 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer Outliers : 0.60 % 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: -0.57 (0.23), residues: 1379 helix: 0.33 (0.18), residues: 890 sheet: -1.32 (0.78), residues: 50 loop : -1.59 (0.29), residues: 439 *********************** 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 148 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 141 time to evaluate : 1.378 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 146 average time/residue: 0.2195 time to fit residues: 48.2915 Evaluate side-chains 142 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 139 time to evaluate : 1.302 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1170 time to fit residues: 2.4204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 81 optimal weight: 0.8980 chunk 63 optimal weight: 0.7980 chunk 92 optimal weight: 1.9990 chunk 139 optimal weight: 1.9990 chunk 128 optimal weight: 0.0870 chunk 111 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 88 optimal weight: 2.9990 chunk 118 optimal weight: 0.8980 overall best weight: 0.6758 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 11195 Z= 0.199 Angle : 0.538 7.337 15218 Z= 0.264 Chirality : 0.041 0.288 1813 Planarity : 0.003 0.041 1872 Dihedral : 5.448 120.633 1507 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer Outliers : 0.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.23), residues: 1379 helix: 0.38 (0.18), residues: 884 sheet: -1.34 (0.78), residues: 50 loop : -1.46 (0.29), residues: 445 ********************** 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 145 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 141 time to evaluate : 1.268 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 143 average time/residue: 0.2266 time to fit residues: 48.7679 Evaluate side-chains 140 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 138 time to evaluate : 1.245 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1099 time to fit residues: 2.2205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 34 optimal weight: 1.9990 chunk 102 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 114 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 6 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.105517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.089646 restraints weight = 17659.580| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 2.04 r_work: 0.3006 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2882 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 11195 Z= 0.195 Angle : 0.534 7.218 15218 Z= 0.263 Chirality : 0.041 0.277 1813 Planarity : 0.003 0.041 1872 Dihedral : 5.374 115.501 1507 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer Outliers : 0.17 % 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: -0.42 (0.23), residues: 1379 helix: 0.42 (0.18), residues: 885 sheet: -1.35 (0.78), residues: 50 loop : -1.45 (0.29), residues: 444 =============================================================================== Job complete usr+sys time: 2370.82 seconds wall clock time: 43 minutes 41.16 seconds (2621.16 seconds total)