Starting phenix.real_space_refine on Mon Mar 18 13:55:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s5y_24843/03_2024/7s5y_24843_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s5y_24843/03_2024/7s5y_24843.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s5y_24843/03_2024/7s5y_24843.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s5y_24843/03_2024/7s5y_24843.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s5y_24843/03_2024/7s5y_24843_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s5y_24843/03_2024/7s5y_24843_updated.pdb" } resolution = 3.9 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= 0.075 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 119 5.16 5 C 13639 2.51 5 N 3594 2.21 5 O 3747 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 32": "NH1" <-> "NH2" Residue "A PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 51": "OE1" <-> "OE2" Residue "A ASP 65": "OD1" <-> "OD2" Residue "A GLU 141": "OE1" <-> "OE2" Residue "A PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 195": "NH1" <-> "NH2" Residue "A ASP 237": "OD1" <-> "OD2" Residue "A ASP 280": "OD1" <-> "OD2" Residue "A GLU 282": "OE1" <-> "OE2" Residue "A ASP 323": "OD1" <-> "OD2" Residue "A TYR 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 32": "NH1" <-> "NH2" Residue "B PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 51": "OE1" <-> "OE2" Residue "B ASP 65": "OD1" <-> "OD2" Residue "B GLU 141": "OE1" <-> "OE2" Residue "B PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 195": "NH1" <-> "NH2" Residue "B ASP 237": "OD1" <-> "OD2" Residue "B ASP 280": "OD1" <-> "OD2" Residue "B GLU 282": "OE1" <-> "OE2" Residue "B ASP 323": "OD1" <-> "OD2" Residue "B TYR 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 32": "NH1" <-> "NH2" Residue "C PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 51": "OE1" <-> "OE2" Residue "C ASP 65": "OD1" <-> "OD2" Residue "C GLU 141": "OE1" <-> "OE2" Residue "C PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 195": "NH1" <-> "NH2" Residue "C ASP 237": "OD1" <-> "OD2" Residue "C ASP 280": "OD1" <-> "OD2" Residue "C GLU 282": "OE1" <-> "OE2" Residue "C ASP 323": "OD1" <-> "OD2" Residue "C TYR 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 32": "NH1" <-> "NH2" Residue "D PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 51": "OE1" <-> "OE2" Residue "D ASP 65": "OD1" <-> "OD2" Residue "D GLU 141": "OE1" <-> "OE2" Residue "D PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 195": "NH1" <-> "NH2" Residue "D ASP 237": "OD1" <-> "OD2" Residue "D ASP 280": "OD1" <-> "OD2" Residue "D GLU 282": "OE1" <-> "OE2" Residue "D ASP 323": "OD1" <-> "OD2" Residue "D TYR 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 10": "OE1" <-> "OE2" Residue "E ARG 17": "NH1" <-> "NH2" Residue "E ASP 30": "OD1" <-> "OD2" Residue "E ARG 75": "NH1" <-> "NH2" Residue "E PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 89": "OE1" <-> "OE2" Residue "E ASP 97": "OD1" <-> "OD2" Residue "E TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 155": "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 GLU 269": "OE1" <-> "OE2" Residue "E PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 307": "NH1" <-> "NH2" Residue "E PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 425": "OD1" <-> "OD2" 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 GLU 524": "OE1" <-> "OE2" Residue "E ARG 528": "NH1" <-> "NH2" Residue "E PHE 560": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 613": "OE1" <-> "OE2" Residue "E TYR 686": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 703": "NH1" <-> "NH2" Residue "E PHE 790": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 794": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 842": "NH1" <-> "NH2" Residue "E ASP 854": "OD1" <-> "OD2" Residue "E ASP 855": "OD1" <-> "OD2" Residue "E ASP 866": "OD1" <-> "OD2" Residue "E ASP 916": "OD1" <-> "OD2" Residue "E PHE 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 938": "OE1" <-> "OE2" Residue "E GLU 940": "OE1" <-> "OE2" Residue "E TYR 1004": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 1031": "OD1" <-> "OD2" Residue "E TYR 1064": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 1124": "NH1" <-> "NH2" Residue "E ASP 1128": "OD1" <-> "OD2" Residue "E GLU 1141": "OE1" <-> "OE2" Residue "E ASP 1194": "OD1" <-> "OD2" Residue "E PHE 1204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 1222": "NH1" <-> "NH2" Residue "E GLU 1229": "OE1" <-> "OE2" Residue "E ASP 1232": "OD1" <-> "OD2" Residue "E TYR 1294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 1314": "NH1" <-> "NH2" Residue "E TYR 1326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 1327": "OE1" <-> "OE2" Residue "E TYR 1354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 1406": "OD1" <-> "OD2" Residue "E ARG 1419": "NH1" <-> "NH2" Residue "E ARG 1437": "NH1" <-> "NH2" Residue "E ASP 1441": "OD1" <-> "OD2" 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 ASP 1530": "OD1" <-> "OD2" Residue "E PHE 1560": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 21106 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2519 Classifications: {'peptide': 321} Link IDs: {'PTRANS': 13, 'TRANS': 307} Chain: "B" Number of atoms: 2519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2519 Classifications: {'peptide': 321} Link IDs: {'PTRANS': 13, 'TRANS': 307} Chain: "C" Number of atoms: 2519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2519 Classifications: {'peptide': 321} Link IDs: {'PTRANS': 13, 'TRANS': 307} Chain: "D" Number of atoms: 2519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2519 Classifications: {'peptide': 321} Link IDs: {'PTRANS': 13, 'TRANS': 307} Chain: "E" Number of atoms: 11030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1406, 11030 Unusual residues: {' MG': 2, 'ADP': 1, 'ATP': 1} Classifications: {'peptide': 1402, 'undetermined': 4} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 42, 'TRANS': 1359, 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: 7 Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 128 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 64 Time building chain proxies: 10.68, per 1000 atoms: 0.51 Number of scatterers: 21106 At special positions: 0 Unit cell: (143, 145.6, 136.5, 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 119 16.00 P 5 15.00 Mg 2 11.99 O 3747 8.00 N 3594 7.00 C 13639 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS E 7 " - pdb=" SG CYS E 27 " distance=2.03 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: 8.31 Conformation dependent library (CDL) restraints added in 4.2 seconds 5324 Ramachandran restraints generated. 2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5068 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 78 helices and 15 sheets defined 43.3% alpha, 9.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.91 Creating SS restraints... Processing helix chain 'A' and resid 60 through 64 Processing helix chain 'A' and resid 68 through 96 Processing helix chain 'A' and resid 117 through 128 Processing helix chain 'A' and resid 144 through 171 Processing helix chain 'A' and resid 174 through 180 Processing helix chain 'A' and resid 272 through 274 No H-bonds generated for 'chain 'A' and resid 272 through 274' Processing helix chain 'B' and resid 60 through 64 Processing helix chain 'B' and resid 68 through 96 Processing helix chain 'B' and resid 117 through 128 Processing helix chain 'B' and resid 144 through 171 Processing helix chain 'B' and resid 174 through 180 Processing helix chain 'B' and resid 272 through 274 No H-bonds generated for 'chain 'B' and resid 272 through 274' Processing helix chain 'C' and resid 60 through 64 Processing helix chain 'C' and resid 68 through 96 Processing helix chain 'C' and resid 117 through 128 Processing helix chain 'C' and resid 144 through 171 Processing helix chain 'C' and resid 174 through 180 Processing helix chain 'C' and resid 272 through 274 No H-bonds generated for 'chain 'C' and resid 272 through 274' Processing helix chain 'D' and resid 60 through 64 Processing helix chain 'D' and resid 68 through 96 Processing helix chain 'D' and resid 117 through 128 Processing helix chain 'D' and resid 144 through 171 Processing helix chain 'D' and resid 174 through 180 Processing helix chain 'D' and resid 272 through 274 No H-bonds generated for 'chain 'D' and resid 272 through 274' Processing helix chain 'E' and resid 22 through 24 No H-bonds generated for 'chain 'E' and resid 22 through 24' Processing helix chain 'E' and resid 26 through 50 removed outlier: 4.238A pdb=" N VAL E 34 " --> pdb=" O ASP E 30 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N VAL E 35 " --> pdb=" O ALA E 31 " (cutoff:3.500A) Proline residue: E 36 - end of helix Proline residue: E 46 - end of helix Processing helix chain 'E' and resid 75 through 93 removed outlier: 3.812A pdb=" N CYS E 88 " --> pdb=" O PHE E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 129 Processing helix chain 'E' and resid 138 through 160 removed outlier: 5.941A pdb=" N PHE E 148 " --> pdb=" O THR E 145 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N VAL E 156 " --> pdb=" O ILE E 153 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ASP E 160 " --> pdb=" O LYS E 157 " (cutoff:3.500A) Processing helix chain 'E' and resid 168 through 193 removed outlier: 3.656A pdb=" N LEU E 175 " --> pdb=" O CYS E 171 " (cutoff:3.500A) Processing helix chain 'E' and resid 225 through 229 Processing helix chain 'E' and resid 239 through 243 removed outlier: 3.975A pdb=" N LYS E 243 " --> pdb=" O LYS E 239 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 239 through 243' Processing helix chain 'E' and resid 260 through 273 removed outlier: 3.711A pdb=" N ALA E 273 " --> pdb=" O GLU E 269 " (cutoff:3.500A) Processing helix chain 'E' and resid 285 through 312 removed outlier: 6.294A pdb=" N ARG E 298 " --> pdb=" O HIS E 294 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ARG E 299 " --> pdb=" O ALA E 295 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N ASP E 311 " --> pdb=" O ARG E 307 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU E 312 " --> pdb=" O ILE E 308 " (cutoff:3.500A) Processing helix chain 'E' and resid 314 through 329 Proline residue: E 318 - end of helix removed outlier: 3.612A pdb=" N PHE E 322 " --> pdb=" O LEU E 319 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL E 325 " --> pdb=" O PHE E 322 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ASP E 326 " --> pdb=" O GLY E 323 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU E 328 " --> pdb=" O VAL E 325 " (cutoff:3.500A) Processing helix chain 'E' and resid 349 through 354 Processing helix chain 'E' and resid 356 through 400 Processing helix chain 'E' and resid 406 through 409 No H-bonds generated for 'chain 'E' and resid 406 through 409' Processing helix chain 'E' and resid 415 through 423 Processing helix chain 'E' and resid 427 through 460 Proline residue: E 437 - end of helix Proline residue: E 443 - end of helix removed outlier: 3.654A pdb=" N VAL E 448 " --> pdb=" O VAL E 444 " (cutoff:3.500A) removed outlier: 8.348A pdb=" N VAL E 459 " --> pdb=" O TYR E 455 " (cutoff:3.500A) removed outlier: 8.632A pdb=" N SER E 460 " --> pdb=" O ILE E 456 " (cutoff:3.500A) Processing helix chain 'E' and resid 466 through 505 removed outlier: 5.963A pdb=" N ALA E 472 " --> pdb=" O ILE E 468 " (cutoff:3.500A) Proline residue: E 473 - end of helix Processing helix chain 'E' and resid 507 through 511 Processing helix chain 'E' and resid 516 through 564 Proline residue: E 552 - end of helix removed outlier: 3.519A pdb=" N VAL E 564 " --> pdb=" O PHE E 560 " (cutoff:3.500A) Processing helix chain 'E' and resid 575 through 599 Proline residue: E 590 - end of helix removed outlier: 4.478A pdb=" N LEU E 593 " --> pdb=" O THR E 589 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER E 595 " --> pdb=" O LEU E 591 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N SER E 596 " --> pdb=" O PHE E 592 " (cutoff:3.500A) Processing helix chain 'E' and resid 602 through 615 Processing helix chain 'E' and resid 720 through 727 removed outlier: 4.156A pdb=" N LEU E 724 " --> pdb=" O LYS E 720 " (cutoff:3.500A) 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 813 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 833 through 841 Processing helix chain 'E' and resid 862 through 870 Processing helix chain 'E' and resid 891 through 895 Proline residue: E 895 - end of helix Processing helix chain 'E' and resid 914 through 919 Processing helix chain 'E' and resid 924 through 931 Processing helix chain 'E' and resid 1000 through 1008 Processing helix chain 'E' and resid 1010 through 1038 Processing helix chain 'E' and resid 1063 through 1096 Processing helix chain 'E' and resid 1101 through 1105 Processing helix chain 'E' and resid 1110 through 1115 Processing helix chain 'E' and resid 1118 through 1133 removed outlier: 4.160A pdb=" N ASP E1128 " --> pdb=" O ARG E1124 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N CYS E1129 " --> pdb=" O PHE E1125 " (cutoff:3.500A) Processing helix chain 'E' and resid 1136 through 1160 removed outlier: 3.538A pdb=" N VAL E1160 " --> pdb=" O VAL E1156 " (cutoff:3.500A) Processing helix chain 'E' and resid 1162 through 1169 Processing helix chain 'E' and resid 1171 through 1196 removed outlier: 4.338A pdb=" N VAL E1184 " --> pdb=" O LYS E1180 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N ALA E1185 " --> pdb=" O TYR E1181 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N GLN E1191 " --> pdb=" O ARG E1187 " (cutoff:3.500A) Processing helix chain 'E' and resid 1200 through 1206 Processing helix chain 'E' and resid 1211 through 1217 Processing helix chain 'E' and resid 1220 through 1272 Processing helix chain 'E' and resid 1280 through 1319 removed outlier: 5.926A pdb=" N ASN E1296 " --> pdb=" O SER E1292 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N TRP E1297 " --> pdb=" O ASN E1293 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ALA E1311 " --> pdb=" O LEU E1307 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL E1312 " --> pdb=" O GLN E1308 " (cutoff:3.500A) Processing helix chain 'E' and resid 1385 through 1392 removed outlier: 3.848A pdb=" N LEU E1390 " --> pdb=" O SER E1386 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N PHE E1392 " --> pdb=" O PHE E1388 " (cutoff:3.500A) Processing helix chain 'E' and resid 1415 through 1420 Processing helix chain 'E' and resid 1436 through 1440 Processing helix chain 'E' and resid 1448 through 1456 Processing helix chain 'E' and resid 1461 through 1466 Processing helix chain 'E' and resid 1484 through 1495 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 Processing helix chain 'E' and resid 1563 through 1568 Processing helix chain 'E' and resid 1573 through 1581 Processing sheet with id= A, first strand: chain 'A' and resid 309 through 311 removed outlier: 6.707A pdb=" N ALA A 187 " --> pdb=" O LEU A 310 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 234 through 238 removed outlier: 4.364A pdb=" N MET A 217 " --> pdb=" O ILE A 238 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 319 through 322 Processing sheet with id= D, first strand: chain 'B' and resid 309 through 311 removed outlier: 6.707A pdb=" N ALA B 187 " --> pdb=" O LEU B 310 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 234 through 238 removed outlier: 4.364A pdb=" N MET B 217 " --> pdb=" O ILE B 238 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 319 through 322 Processing sheet with id= G, first strand: chain 'C' and resid 309 through 311 removed outlier: 6.708A pdb=" N ALA C 187 " --> pdb=" O LEU C 310 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 234 through 238 removed outlier: 4.363A pdb=" N MET C 217 " --> pdb=" O ILE C 238 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 319 through 322 Processing sheet with id= J, first strand: chain 'D' and resid 309 through 311 removed outlier: 6.707A pdb=" N ALA D 187 " --> pdb=" O LEU D 310 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 234 through 238 removed outlier: 4.364A pdb=" N MET D 217 " --> pdb=" O ILE D 238 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 319 through 322 Processing sheet with id= M, first strand: chain 'E' and resid 907 through 912 removed outlier: 3.606A pdb=" N THR E 907 " --> pdb=" O LYS E 904 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N ALA E 902 " --> pdb=" O GLN E 909 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N GLU E 911 " --> pdb=" O ILE E 900 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ILE E 900 " --> pdb=" O GLU E 911 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL E 887 " --> pdb=" O LEU E 853 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ALA E 771 " --> pdb=" O PHE E 852 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 1345 through 1348 Processing sheet with id= O, first strand: chain 'E' and resid 1533 through 1536 removed outlier: 6.926A pdb=" N LEU E1548 " --> pdb=" O GLY E1376 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N CYS E1378 " --> pdb=" O LEU E1548 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ILE E1550 " --> pdb=" O CYS E1378 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ASP E1561 " --> pdb=" O VAL E1549 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLU E1559 " --> pdb=" O VAL E1551 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LYS E1553 " --> pdb=" O ILE E1557 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N ILE E1557 " --> pdb=" O LYS E1553 " (cutoff:3.500A) 973 hydrogen bonds defined for protein. 2706 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: 7.00 Time building geometry restraints manager: 9.02 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: 6091 1.34 - 1.46: 5348 1.46 - 1.58: 9925 1.58 - 1.71: 13 1.71 - 1.83: 190 Bond restraints: 21567 Sorted by residual: bond pdb=" C4 ATP E1604 " pdb=" C5 ATP E1604 " ideal model delta sigma weight residual 1.388 1.460 -0.072 1.00e-02 1.00e+04 5.17e+01 bond pdb=" C4 ATP E1604 " pdb=" N9 ATP E1604 " ideal model delta sigma weight residual 1.374 1.319 0.055 1.00e-02 1.00e+04 3.02e+01 bond pdb=" C5 ATP E1604 " pdb=" N7 ATP E1604 " ideal model delta sigma weight residual 1.387 1.333 0.054 1.00e-02 1.00e+04 2.89e+01 bond pdb=" C5 ATP E1604 " pdb=" C6 ATP E1604 " ideal model delta sigma weight residual 1.409 1.462 -0.053 1.00e-02 1.00e+04 2.86e+01 bond pdb=" C ILE E1136 " pdb=" N PRO E1137 " ideal model delta sigma weight residual 1.334 1.453 -0.119 2.34e-02 1.83e+03 2.59e+01 ... (remaining 21562 not shown) Histogram of bond angle deviations from ideal: 97.24 - 105.61: 477 105.61 - 113.97: 12367 113.97 - 122.34: 12754 122.34 - 130.70: 3526 130.70 - 139.07: 186 Bond angle restraints: 29310 Sorted by residual: angle pdb=" PB ATP E1604 " pdb=" O3B ATP E1604 " pdb=" PG ATP E1604 " ideal model delta sigma weight residual 139.87 122.05 17.82 1.00e+00 1.00e+00 3.18e+02 angle pdb=" PA ATP E1604 " pdb=" O3A ATP E1604 " pdb=" PB ATP E1604 " ideal model delta sigma weight residual 136.83 124.59 12.24 1.00e+00 1.00e+00 1.50e+02 angle pdb=" C ALA E 310 " pdb=" N ASP E 311 " pdb=" CA ASP E 311 " ideal model delta sigma weight residual 121.54 135.64 -14.10 1.91e+00 2.74e-01 5.45e+01 angle pdb=" C5 ATP E1604 " pdb=" C4 ATP E1604 " pdb=" N3 ATP E1604 " ideal model delta sigma weight residual 126.80 119.74 7.06 1.00e+00 1.00e+00 4.98e+01 angle pdb=" N3 ATP E1604 " pdb=" C4 ATP E1604 " pdb=" N9 ATP E1604 " ideal model delta sigma weight residual 127.04 134.86 -7.82 1.15e+00 7.59e-01 4.64e+01 ... (remaining 29305 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.98: 11728 24.98 - 49.96: 916 49.96 - 74.93: 159 74.93 - 99.91: 5 99.91 - 124.89: 1 Dihedral angle restraints: 12809 sinusoidal: 5009 harmonic: 7800 Sorted by residual: dihedral pdb=" CA GLY E 343 " pdb=" C GLY E 343 " pdb=" N VAL E 344 " pdb=" CA VAL E 344 " ideal model delta harmonic sigma weight residual -180.00 -118.48 -61.52 0 5.00e+00 4.00e-02 1.51e+02 dihedral pdb=" CA PHE E1182 " pdb=" C PHE E1182 " pdb=" N ARG E1183 " pdb=" CA ARG E1183 " ideal model delta harmonic sigma weight residual -180.00 -129.32 -50.68 0 5.00e+00 4.00e-02 1.03e+02 dihedral pdb=" CA LEU E 137 " pdb=" C LEU E 137 " pdb=" N ILE E 138 " pdb=" CA ILE E 138 " ideal model delta harmonic sigma weight residual -180.00 -136.18 -43.82 0 5.00e+00 4.00e-02 7.68e+01 ... (remaining 12806 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.141: 3193 0.141 - 0.282: 244 0.282 - 0.422: 23 0.422 - 0.563: 5 0.563 - 0.704: 4 Chirality restraints: 3469 Sorted by residual: chirality pdb=" CB VAL D 337 " pdb=" CA VAL D 337 " pdb=" CG1 VAL D 337 " pdb=" CG2 VAL D 337 " both_signs ideal model delta sigma weight residual False -2.63 -1.93 -0.70 2.00e-01 2.50e+01 1.24e+01 chirality pdb=" CB VAL C 337 " pdb=" CA VAL C 337 " pdb=" CG1 VAL C 337 " pdb=" CG2 VAL C 337 " both_signs ideal model delta sigma weight residual False -2.63 -1.93 -0.70 2.00e-01 2.50e+01 1.23e+01 chirality pdb=" CB VAL A 337 " pdb=" CA VAL A 337 " pdb=" CG1 VAL A 337 " pdb=" CG2 VAL A 337 " both_signs ideal model delta sigma weight residual False -2.63 -1.93 -0.70 2.00e-01 2.50e+01 1.23e+01 ... (remaining 3466 not shown) Planarity restraints: 3646 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS E1180 " 0.023 2.00e-02 2.50e+03 4.64e-02 2.16e+01 pdb=" C LYS E1180 " -0.080 2.00e-02 2.50e+03 pdb=" O LYS E1180 " 0.030 2.00e-02 2.50e+03 pdb=" N TYR E1181 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE E 149 " -0.023 2.00e-02 2.50e+03 4.62e-02 2.14e+01 pdb=" C ILE E 149 " 0.080 2.00e-02 2.50e+03 pdb=" O ILE E 149 " -0.030 2.00e-02 2.50e+03 pdb=" N THR E 150 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP E 144 " -0.022 2.00e-02 2.50e+03 4.49e-02 2.01e+01 pdb=" C TRP E 144 " 0.078 2.00e-02 2.50e+03 pdb=" O TRP E 144 " -0.029 2.00e-02 2.50e+03 pdb=" N THR E 145 " -0.026 2.00e-02 2.50e+03 ... (remaining 3643 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 951 2.71 - 3.26: 19201 3.26 - 3.80: 36524 3.80 - 4.35: 43921 4.35 - 4.90: 71303 Nonbonded interactions: 171900 Sorted by model distance: nonbonded pdb=" O1B ADP E1601 " pdb="MG MG E1603 " model vdw 2.160 2.170 nonbonded pdb=" OE1 GLN E 775 " pdb="MG MG E1602 " model vdw 2.166 2.170 nonbonded pdb="MG MG E1602 " pdb=" O2B ATP E1604 " model vdw 2.166 2.170 nonbonded pdb=" OG SER E1386 " pdb="MG MG E1603 " model vdw 2.172 2.170 nonbonded pdb="MG MG E1602 " pdb=" O3B ATP E1604 " model vdw 2.175 2.170 ... (remaining 171895 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.840 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: 11.110 Check model and map are aligned: 0.280 Set scattering table: 0.170 Process input model: 56.410 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.100 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 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 : 0.010 0.119 21567 Z= 0.624 Angle : 1.484 19.636 29310 Z= 0.813 Chirality : 0.083 0.704 3469 Planarity : 0.012 0.095 3646 Dihedral : 17.699 124.888 7738 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.26 % Favored : 94.67 % Rotamer: Outliers : 7.41 % Allowed : 12.39 % Favored : 80.20 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.62 % 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: -5.12 (0.11), residues: 2662 helix: -4.11 (0.07), residues: 1321 sheet: -1.57 (0.30), residues: 271 loop : -2.65 (0.15), residues: 1070 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP E1033 HIS 0.014 0.002 HIS A 276 PHE 0.042 0.004 PHE E 373 TYR 0.029 0.003 TYR E 379 ARG 0.009 0.001 ARG B 177 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5324 Ramachandran restraints generated. 2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5324 Ramachandran restraints generated. 2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 722 residues out of total 2323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 552 time to evaluate : 2.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ASN cc_start: 0.8287 (t0) cc_final: 0.7708 (t0) REVERT: A 52 GLN cc_start: 0.8107 (tt0) cc_final: 0.7254 (pp30) REVERT: A 65 ASP cc_start: 0.8661 (t0) cc_final: 0.8398 (t0) REVERT: A 83 TRP cc_start: 0.9431 (m-10) cc_final: 0.9031 (m-90) REVERT: A 84 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8928 (mt) REVERT: A 126 GLU cc_start: 0.8886 (mt-10) cc_final: 0.8276 (mp0) REVERT: A 160 ASN cc_start: 0.9121 (m-40) cc_final: 0.8913 (t0) REVERT: A 163 MET cc_start: 0.9091 (mmm) cc_final: 0.8829 (mmm) REVERT: A 247 ASN cc_start: 0.8498 (p0) cc_final: 0.8175 (p0) REVERT: A 250 PHE cc_start: 0.8791 (t80) cc_final: 0.8490 (t80) REVERT: B 48 ASN cc_start: 0.8944 (m-40) cc_final: 0.7627 (m-40) REVERT: B 57 GLN cc_start: 0.8793 (mt0) cc_final: 0.8261 (tp-100) REVERT: B 86 PHE cc_start: 0.9255 (m-80) cc_final: 0.9052 (m-10) REVERT: B 151 VAL cc_start: 0.9619 (OUTLIER) cc_final: 0.9416 (t) REVERT: B 152 GLN cc_start: 0.9213 (tp40) cc_final: 0.8556 (tp-100) REVERT: B 170 LYS cc_start: 0.8524 (tptt) cc_final: 0.8271 (tptt) REVERT: B 262 ASP cc_start: 0.8649 (p0) cc_final: 0.8020 (p0) REVERT: B 292 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7880 (tm-30) REVERT: B 316 VAL cc_start: 0.8543 (OUTLIER) cc_final: 0.8306 (m) REVERT: B 331 SER cc_start: 0.9069 (OUTLIER) cc_final: 0.8212 (p) REVERT: C 65 ASP cc_start: 0.7489 (t0) cc_final: 0.7253 (t0) REVERT: C 77 MET cc_start: 0.8432 (tpp) cc_final: 0.8158 (ttt) REVERT: C 170 LYS cc_start: 0.8870 (tptt) cc_final: 0.8434 (tptm) REVERT: C 179 GLU cc_start: 0.7952 (mt-10) cc_final: 0.7566 (tp30) REVERT: C 185 LYS cc_start: 0.8546 (ttpp) cc_final: 0.7813 (ttpt) REVERT: C 214 THR cc_start: 0.8889 (m) cc_final: 0.8545 (p) REVERT: C 237 ASP cc_start: 0.8726 (m-30) cc_final: 0.7836 (m-30) REVERT: C 281 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8641 (tt) REVERT: C 286 ILE cc_start: 0.9396 (mp) cc_final: 0.9113 (tp) REVERT: C 292 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7429 (tm-30) REVERT: C 313 GLN cc_start: 0.8829 (mt0) cc_final: 0.8234 (mm110) REVERT: C 316 VAL cc_start: 0.9150 (OUTLIER) cc_final: 0.8932 (p) REVERT: D 43 ASN cc_start: 0.8027 (t0) cc_final: 0.7325 (t0) REVERT: D 150 ILE cc_start: 0.9606 (mt) cc_final: 0.9391 (mt) REVERT: D 163 MET cc_start: 0.8653 (mmm) cc_final: 0.8013 (mmm) REVERT: D 173 GLN cc_start: 0.8518 (pt0) cc_final: 0.7921 (mt0) REVERT: D 179 GLU cc_start: 0.8268 (mt-10) cc_final: 0.7971 (mt-10) REVERT: D 185 LYS cc_start: 0.8891 (ttpp) cc_final: 0.8634 (ttpt) REVERT: D 216 HIS cc_start: 0.7753 (m170) cc_final: 0.7473 (m-70) REVERT: D 240 MET cc_start: 0.8822 (ptm) cc_final: 0.8354 (ppp) REVERT: D 280 ASP cc_start: 0.8005 (t70) cc_final: 0.7695 (t0) REVERT: D 281 LEU cc_start: 0.9204 (OUTLIER) cc_final: 0.8974 (tt) REVERT: D 286 ILE cc_start: 0.9309 (mp) cc_final: 0.9007 (mp) REVERT: D 331 SER cc_start: 0.8437 (OUTLIER) cc_final: 0.8096 (p) REVERT: D 334 ASP cc_start: 0.8424 (p0) cc_final: 0.7782 (t0) REVERT: D 348 GLN cc_start: 0.9240 (mt0) cc_final: 0.8616 (tm-30) REVERT: E 32 LEU cc_start: 0.9585 (mt) cc_final: 0.9252 (mp) REVERT: E 39 PHE cc_start: 0.9006 (t80) cc_final: 0.8675 (t80) REVERT: E 75 ARG cc_start: 0.8264 (mtp85) cc_final: 0.8058 (ttm-80) REVERT: E 80 PHE cc_start: 0.8761 (m-10) cc_final: 0.8142 (m-80) REVERT: E 113 MET cc_start: 0.8855 (mmp) cc_final: 0.8587 (mmp) REVERT: E 146 LEU cc_start: 0.9518 (mm) cc_final: 0.9285 (mm) REVERT: E 153 ILE cc_start: 0.9343 (mm) cc_final: 0.9107 (mm) REVERT: E 168 LEU cc_start: 0.8712 (pt) cc_final: 0.8273 (tp) REVERT: E 353 LEU cc_start: 0.9389 (mm) cc_final: 0.8795 (pp) REVERT: E 364 PHE cc_start: 0.8955 (t80) cc_final: 0.8170 (t80) REVERT: E 368 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8571 (mm) REVERT: E 425 ASP cc_start: 0.7733 (m-30) cc_final: 0.7272 (m-30) REVERT: E 446 ILE cc_start: 0.9496 (pt) cc_final: 0.9275 (tp) REVERT: E 508 LYS cc_start: 0.9353 (tttt) cc_final: 0.9069 (ttmm) REVERT: E 546 PHE cc_start: 0.8872 (t80) cc_final: 0.8643 (t80) REVERT: E 723 LEU cc_start: 0.9285 (mt) cc_final: 0.9044 (mt) REVERT: E 857 PHE cc_start: 0.8465 (m-80) cc_final: 0.8132 (m-80) REVERT: E 903 MET cc_start: 0.7799 (ptm) cc_final: 0.7331 (ptm) REVERT: E 1074 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8948 (mp) REVERT: E 1232 ASP cc_start: 0.8126 (t70) cc_final: 0.7894 (t70) REVERT: E 1261 LEU cc_start: 0.8847 (tp) cc_final: 0.8597 (tp) REVERT: E 1290 MET cc_start: 0.9269 (tpp) cc_final: 0.9020 (tpp) REVERT: E 1293 ASN cc_start: 0.9021 (m-40) cc_final: 0.8613 (t0) REVERT: E 1305 MET cc_start: 0.8618 (tpp) cc_final: 0.8277 (mmt) REVERT: E 1395 MET cc_start: 0.8461 (mmt) cc_final: 0.7961 (mmp) REVERT: E 1428 ASP cc_start: 0.8535 (t0) cc_final: 0.8239 (m-30) outliers start: 170 outliers final: 39 residues processed: 669 average time/residue: 0.3144 time to fit residues: 326.5521 Evaluate side-chains 400 residues out of total 2323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 349 time to evaluate : 2.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 292 GLU Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 292 GLU Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 288 GLU Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 331 SER Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 941 LYS Chi-restraints excluded: chain E residue 942 GLU Chi-restraints excluded: chain E residue 943 THR Chi-restraints excluded: chain E residue 1074 LEU Chi-restraints excluded: chain E residue 1175 CYS Chi-restraints excluded: chain E residue 1509 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 226 optimal weight: 4.9990 chunk 203 optimal weight: 7.9990 chunk 112 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 137 optimal weight: 4.9990 chunk 108 optimal weight: 1.9990 chunk 210 optimal weight: 7.9990 chunk 81 optimal weight: 0.9990 chunk 127 optimal weight: 7.9990 chunk 156 optimal weight: 1.9990 chunk 243 optimal weight: 30.0000 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 HIS A 153 ASN ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 46 HIS B 48 ASN B 313 GLN C 46 HIS ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 HIS ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 24 ASN E 127 ASN E 375 GLN E 486 GLN E 609 GLN ** E 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 787 ASN ** E 817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 867 HIS E1301 ASN E1402 HIS E1486 GLN E1518 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 21567 Z= 0.248 Angle : 0.723 11.789 29310 Z= 0.375 Chirality : 0.045 0.268 3469 Planarity : 0.006 0.061 3646 Dihedral : 9.087 99.274 2987 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.57 % Favored : 96.39 % Rotamer: Outliers : 4.19 % Allowed : 18.97 % Favored : 76.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -2.57 (0.14), residues: 2662 helix: -1.61 (0.12), residues: 1312 sheet: -0.62 (0.32), residues: 255 loop : -1.93 (0.17), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E1033 HIS 0.005 0.001 HIS C 259 PHE 0.019 0.002 PHE E 6 TYR 0.018 0.001 TYR E1181 ARG 0.008 0.000 ARG C 221 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5324 Ramachandran restraints generated. 2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5324 Ramachandran restraints generated. 2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 2323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 386 time to evaluate : 2.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LYS cc_start: 0.8704 (tttp) cc_final: 0.7836 (ttpp) REVERT: A 43 ASN cc_start: 0.8267 (t0) cc_final: 0.7889 (t0) REVERT: A 65 ASP cc_start: 0.8832 (t0) cc_final: 0.8414 (t0) REVERT: A 158 MET cc_start: 0.8008 (tmm) cc_final: 0.7764 (tmm) REVERT: A 163 MET cc_start: 0.9268 (mmm) cc_final: 0.8900 (mmm) REVERT: A 247 ASN cc_start: 0.8368 (p0) cc_final: 0.8090 (p0) REVERT: B 56 LEU cc_start: 0.9437 (OUTLIER) cc_final: 0.9147 (mm) REVERT: B 163 MET cc_start: 0.9176 (mmm) cc_final: 0.8905 (mmm) REVERT: B 170 LYS cc_start: 0.8654 (tptt) cc_final: 0.8264 (tptt) REVERT: B 240 MET cc_start: 0.8482 (tmm) cc_final: 0.8203 (tmm) REVERT: B 247 ASN cc_start: 0.7772 (p0) cc_final: 0.7496 (p0) REVERT: B 287 LEU cc_start: 0.9518 (tt) cc_final: 0.9088 (pt) REVERT: B 313 GLN cc_start: 0.7614 (OUTLIER) cc_final: 0.7197 (mp10) REVERT: C 65 ASP cc_start: 0.7908 (t0) cc_final: 0.7468 (t0) REVERT: C 77 MET cc_start: 0.8646 (tpp) cc_final: 0.8055 (ttt) REVERT: C 170 LYS cc_start: 0.8965 (tptt) cc_final: 0.8719 (tptm) REVERT: C 209 MET cc_start: 0.8820 (tpp) cc_final: 0.8549 (mmm) REVERT: C 237 ASP cc_start: 0.8199 (m-30) cc_final: 0.7702 (m-30) REVERT: C 240 MET cc_start: 0.7997 (tmm) cc_final: 0.7759 (tmm) REVERT: C 247 ASN cc_start: 0.8355 (p0) cc_final: 0.8055 (p0) REVERT: C 292 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7481 (tm-30) REVERT: C 313 GLN cc_start: 0.8894 (mt0) cc_final: 0.8165 (mm110) REVERT: D 43 ASN cc_start: 0.7786 (t0) cc_final: 0.7248 (t0) REVERT: D 160 ASN cc_start: 0.8454 (m-40) cc_final: 0.8219 (m-40) REVERT: D 163 MET cc_start: 0.9089 (mmm) cc_final: 0.8325 (mmm) REVERT: D 166 SER cc_start: 0.9415 (t) cc_final: 0.9075 (p) REVERT: D 185 LYS cc_start: 0.8984 (ttpp) cc_final: 0.8665 (ttpt) REVERT: D 198 PHE cc_start: 0.8792 (t80) cc_final: 0.8395 (t80) REVERT: D 199 MET cc_start: 0.7962 (mtm) cc_final: 0.6732 (mpp) REVERT: D 280 ASP cc_start: 0.8010 (t70) cc_final: 0.7766 (t0) REVERT: D 286 ILE cc_start: 0.9549 (mp) cc_final: 0.9328 (mp) REVERT: D 288 GLU cc_start: 0.7721 (pt0) cc_final: 0.7394 (pt0) REVERT: D 334 ASP cc_start: 0.8646 (p0) cc_final: 0.7673 (t0) REVERT: E 75 ARG cc_start: 0.8480 (mtp85) cc_final: 0.8267 (ttm-80) REVERT: E 146 LEU cc_start: 0.9619 (mm) cc_final: 0.9331 (mm) REVERT: E 168 LEU cc_start: 0.8827 (pt) cc_final: 0.8473 (tp) REVERT: E 170 PHE cc_start: 0.8489 (t80) cc_final: 0.8155 (t80) REVERT: E 258 MET cc_start: 0.8589 (ptp) cc_final: 0.8376 (ptp) REVERT: E 353 LEU cc_start: 0.9391 (mm) cc_final: 0.8902 (pp) REVERT: E 364 PHE cc_start: 0.8808 (t80) cc_final: 0.8328 (t80) REVERT: E 546 PHE cc_start: 0.8933 (t80) cc_final: 0.8657 (t80) REVERT: E 603 LYS cc_start: 0.7464 (OUTLIER) cc_final: 0.4990 (mtmm) REVERT: E 1020 GLN cc_start: 0.8976 (mm110) cc_final: 0.8387 (mm-40) REVERT: E 1066 MET cc_start: 0.6951 (tpt) cc_final: 0.6423 (ptm) REVERT: E 1140 LEU cc_start: 0.9573 (OUTLIER) cc_final: 0.9285 (mm) REVERT: E 1194 ASP cc_start: 0.8771 (OUTLIER) cc_final: 0.8420 (t0) REVERT: E 1261 LEU cc_start: 0.8845 (tp) cc_final: 0.8618 (tp) REVERT: E 1290 MET cc_start: 0.9346 (tpp) cc_final: 0.9110 (tpp) REVERT: E 1293 ASN cc_start: 0.9061 (m-40) cc_final: 0.8588 (t0) REVERT: E 1298 MET cc_start: 0.9180 (tmm) cc_final: 0.8862 (tmm) REVERT: E 1389 SER cc_start: 0.9487 (t) cc_final: 0.9190 (p) REVERT: E 1395 MET cc_start: 0.8693 (mmt) cc_final: 0.8084 (mmp) REVERT: E 1428 ASP cc_start: 0.8593 (t0) cc_final: 0.8305 (m-30) outliers start: 96 outliers final: 53 residues processed: 452 average time/residue: 0.3075 time to fit residues: 218.1271 Evaluate side-chains 381 residues out of total 2323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 322 time to evaluate : 2.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 313 GLN Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 292 GLU Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 303 SER Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 110 CYS Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 169 MET Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 196 TYR Chi-restraints excluded: chain E residue 222 PHE Chi-restraints excluded: chain E residue 306 PHE Chi-restraints excluded: chain E residue 358 VAL Chi-restraints excluded: chain E residue 497 LEU Chi-restraints excluded: chain E residue 557 LEU Chi-restraints excluded: chain E residue 603 LYS Chi-restraints excluded: chain E residue 844 LEU Chi-restraints excluded: chain E residue 941 LYS Chi-restraints excluded: chain E residue 1140 LEU Chi-restraints excluded: chain E residue 1194 ASP Chi-restraints excluded: chain E residue 1259 VAL Chi-restraints excluded: chain E residue 1494 ARG Chi-restraints excluded: chain E residue 1509 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 135 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 202 optimal weight: 4.9990 chunk 165 optimal weight: 7.9990 chunk 67 optimal weight: 0.0870 chunk 243 optimal weight: 9.9990 chunk 263 optimal weight: 3.9990 chunk 217 optimal weight: 0.9980 chunk 241 optimal weight: 9.9990 chunk 83 optimal weight: 6.9990 chunk 195 optimal weight: 9.9990 overall best weight: 1.6164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 ASN A 57 GLN ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 GLN ** C 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 216 HIS E 60 HIS ** E 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 428 GLN E 681 GLN E 817 HIS ** E 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1427 GLN E1439 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.3311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21567 Z= 0.229 Angle : 0.676 10.620 29310 Z= 0.344 Chirality : 0.044 0.226 3469 Planarity : 0.004 0.040 3646 Dihedral : 7.753 88.266 2941 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.36 % Favored : 95.60 % Rotamer: Outliers : 3.84 % Allowed : 22.02 % Favored : 74.14 % 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: -1.45 (0.15), residues: 2662 helix: -0.47 (0.14), residues: 1335 sheet: -0.30 (0.33), residues: 259 loop : -1.67 (0.18), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 83 HIS 0.004 0.001 HIS E 242 PHE 0.015 0.001 PHE E 578 TYR 0.016 0.001 TYR E1176 ARG 0.008 0.000 ARG E 703 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5324 Ramachandran restraints generated. 2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5324 Ramachandran restraints generated. 2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 2323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 338 time to evaluate : 2.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ASN cc_start: 0.8172 (t0) cc_final: 0.7886 (t0) REVERT: A 48 ASN cc_start: 0.8616 (t0) cc_final: 0.8383 (t0) REVERT: A 60 PHE cc_start: 0.8927 (t80) cc_final: 0.8649 (t80) REVERT: A 65 ASP cc_start: 0.8927 (t0) cc_final: 0.8423 (t0) REVERT: A 158 MET cc_start: 0.8034 (tmm) cc_final: 0.7664 (tmm) REVERT: A 163 MET cc_start: 0.9125 (mmm) cc_final: 0.8765 (mmm) REVERT: A 209 MET cc_start: 0.9008 (tpp) cc_final: 0.8669 (tpp) REVERT: B 170 LYS cc_start: 0.8707 (tptt) cc_final: 0.8420 (tptt) REVERT: B 240 MET cc_start: 0.8535 (OUTLIER) cc_final: 0.8190 (tmm) REVERT: B 247 ASN cc_start: 0.8413 (p0) cc_final: 0.7971 (p0) REVERT: B 292 GLU cc_start: 0.8301 (tm-30) cc_final: 0.7944 (tm-30) REVERT: B 313 GLN cc_start: 0.8365 (OUTLIER) cc_final: 0.8095 (mp10) REVERT: C 65 ASP cc_start: 0.8112 (t0) cc_final: 0.7579 (t0) REVERT: C 85 LEU cc_start: 0.9390 (tt) cc_final: 0.9103 (tp) REVERT: C 199 MET cc_start: 0.8256 (mtt) cc_final: 0.7985 (mtt) REVERT: C 240 MET cc_start: 0.8023 (tmm) cc_final: 0.7775 (tmm) REVERT: C 247 ASN cc_start: 0.8537 (p0) cc_final: 0.8089 (p0) REVERT: C 292 GLU cc_start: 0.7845 (tm-30) cc_final: 0.7531 (tm-30) REVERT: D 43 ASN cc_start: 0.7790 (t0) cc_final: 0.7221 (t0) REVERT: D 110 CYS cc_start: 0.8254 (m) cc_final: 0.7937 (m) REVERT: D 122 LEU cc_start: 0.9293 (OUTLIER) cc_final: 0.9081 (mm) REVERT: D 137 MET cc_start: 0.8066 (ttp) cc_final: 0.7858 (ttp) REVERT: D 163 MET cc_start: 0.9243 (mmm) cc_final: 0.8522 (mmm) REVERT: D 166 SER cc_start: 0.9484 (t) cc_final: 0.9178 (p) REVERT: D 185 LYS cc_start: 0.8998 (ttpp) cc_final: 0.8771 (ttpt) REVERT: D 199 MET cc_start: 0.8123 (mtm) cc_final: 0.6786 (mpp) REVERT: D 280 ASP cc_start: 0.8055 (t70) cc_final: 0.7716 (t0) REVERT: D 286 ILE cc_start: 0.9663 (mp) cc_final: 0.9378 (mt) REVERT: D 288 GLU cc_start: 0.7817 (pt0) cc_final: 0.7370 (pt0) REVERT: D 334 ASP cc_start: 0.8555 (p0) cc_final: 0.7658 (t70) REVERT: E 146 LEU cc_start: 0.9730 (mm) cc_final: 0.9514 (mm) REVERT: E 353 LEU cc_start: 0.9403 (mm) cc_final: 0.8956 (pp) REVERT: E 368 LEU cc_start: 0.9243 (mm) cc_final: 0.8648 (mm) REVERT: E 531 MET cc_start: 0.8791 (tpp) cc_final: 0.8531 (tpp) REVERT: E 603 LYS cc_start: 0.7174 (OUTLIER) cc_final: 0.5317 (mtmm) REVERT: E 1020 GLN cc_start: 0.9045 (mm110) cc_final: 0.8430 (mm-40) REVERT: E 1066 MET cc_start: 0.7009 (tpt) cc_final: 0.6500 (ptm) REVERT: E 1293 ASN cc_start: 0.9018 (m-40) cc_final: 0.8447 (t0) REVERT: E 1298 MET cc_start: 0.9284 (tmm) cc_final: 0.8903 (tmm) REVERT: E 1389 SER cc_start: 0.9440 (t) cc_final: 0.9200 (p) REVERT: E 1395 MET cc_start: 0.8724 (mmt) cc_final: 0.8158 (mmm) REVERT: E 1428 ASP cc_start: 0.8569 (t0) cc_final: 0.8345 (m-30) REVERT: E 1507 GLU cc_start: 0.8311 (mt-10) cc_final: 0.7874 (mp0) outliers start: 88 outliers final: 50 residues processed: 395 average time/residue: 0.3135 time to fit residues: 197.2405 Evaluate side-chains 356 residues out of total 2323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 302 time to evaluate : 2.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 313 GLN Chi-restraints excluded: chain B residue 334 ASP Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 303 SER Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 169 MET Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 222 PHE Chi-restraints excluded: chain E residue 306 PHE Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 358 VAL Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 497 LEU Chi-restraints excluded: chain E residue 557 LEU Chi-restraints excluded: chain E residue 603 LYS Chi-restraints excluded: chain E residue 817 HIS Chi-restraints excluded: chain E residue 941 LYS Chi-restraints excluded: chain E residue 1016 LEU Chi-restraints excluded: chain E residue 1193 ASP Chi-restraints excluded: chain E residue 1509 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 240 optimal weight: 8.9990 chunk 183 optimal weight: 1.9990 chunk 126 optimal weight: 0.9990 chunk 26 optimal weight: 9.9990 chunk 116 optimal weight: 0.7980 chunk 163 optimal weight: 3.9990 chunk 244 optimal weight: 2.9990 chunk 259 optimal weight: 5.9990 chunk 127 optimal weight: 2.9990 chunk 231 optimal weight: 6.9990 chunk 69 optimal weight: 0.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 GLN ** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 160 ASN D 242 ASN E 220 GLN E 708 GLN ** E 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1197 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.3753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21567 Z= 0.218 Angle : 0.653 11.418 29310 Z= 0.328 Chirality : 0.043 0.231 3469 Planarity : 0.004 0.048 3646 Dihedral : 7.068 79.607 2927 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.13 % Favored : 95.83 % Rotamer: Outliers : 4.23 % Allowed : 22.76 % Favored : 73.00 % 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 (0.16), residues: 2662 helix: 0.18 (0.14), residues: 1312 sheet: -0.16 (0.33), residues: 259 loop : -1.36 (0.18), residues: 1091 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E1033 HIS 0.017 0.001 HIS E 817 PHE 0.016 0.001 PHE E 84 TYR 0.018 0.001 TYR B 258 ARG 0.003 0.000 ARG E 703 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5324 Ramachandran restraints generated. 2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5324 Ramachandran restraints generated. 2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 2323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 322 time to evaluate : 2.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ASN cc_start: 0.8264 (t0) cc_final: 0.7986 (t0) REVERT: A 47 LYS cc_start: 0.8142 (tppt) cc_final: 0.7920 (tppt) REVERT: A 65 ASP cc_start: 0.8984 (t0) cc_final: 0.8438 (t0) REVERT: A 158 MET cc_start: 0.8197 (tmm) cc_final: 0.7829 (tmm) REVERT: A 163 MET cc_start: 0.9116 (mmm) cc_final: 0.8786 (mmm) REVERT: A 209 MET cc_start: 0.8943 (tpp) cc_final: 0.8630 (tpp) REVERT: A 250 PHE cc_start: 0.8834 (t80) cc_final: 0.8596 (t80) REVERT: B 67 LYS cc_start: 0.7721 (tptt) cc_final: 0.7492 (tptt) REVERT: B 77 MET cc_start: 0.9225 (tpp) cc_final: 0.8935 (tpp) REVERT: B 159 ILE cc_start: 0.9021 (pt) cc_final: 0.8699 (mm) REVERT: B 163 MET cc_start: 0.9093 (mmm) cc_final: 0.8878 (mmt) REVERT: B 170 LYS cc_start: 0.8808 (tptt) cc_final: 0.8481 (tptt) REVERT: B 240 MET cc_start: 0.8643 (OUTLIER) cc_final: 0.8304 (tmm) REVERT: B 247 ASN cc_start: 0.8593 (p0) cc_final: 0.7994 (p0) REVERT: B 292 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7929 (tm-30) REVERT: C 65 ASP cc_start: 0.8169 (t0) cc_final: 0.7726 (t0) REVERT: C 81 CYS cc_start: 0.9377 (m) cc_final: 0.8944 (m) REVERT: C 85 LEU cc_start: 0.9438 (OUTLIER) cc_final: 0.9166 (tp) REVERT: C 199 MET cc_start: 0.8486 (mtt) cc_final: 0.8170 (mtt) REVERT: C 240 MET cc_start: 0.8167 (tmm) cc_final: 0.7882 (tmm) REVERT: C 247 ASN cc_start: 0.8631 (p0) cc_final: 0.8110 (p0) REVERT: C 292 GLU cc_start: 0.7886 (tm-30) cc_final: 0.7614 (tm-30) REVERT: D 163 MET cc_start: 0.9260 (mmm) cc_final: 0.8625 (mmm) REVERT: D 166 SER cc_start: 0.9523 (t) cc_final: 0.9235 (p) REVERT: D 185 LYS cc_start: 0.9045 (ttpp) cc_final: 0.8779 (ttpt) REVERT: D 199 MET cc_start: 0.8151 (mtm) cc_final: 0.6632 (mpp) REVERT: D 240 MET cc_start: 0.8983 (ppp) cc_final: 0.8398 (ppp) REVERT: D 286 ILE cc_start: 0.9709 (mp) cc_final: 0.9492 (mp) REVERT: D 288 GLU cc_start: 0.7825 (pt0) cc_final: 0.7394 (pt0) REVERT: E 146 LEU cc_start: 0.9737 (mm) cc_final: 0.9530 (mm) REVERT: E 353 LEU cc_start: 0.9423 (mm) cc_final: 0.8962 (pp) REVERT: E 364 PHE cc_start: 0.8949 (t80) cc_final: 0.8550 (t80) REVERT: E 368 LEU cc_start: 0.9217 (mm) cc_final: 0.8533 (mm) REVERT: E 429 LEU cc_start: 0.9189 (OUTLIER) cc_final: 0.8914 (tt) REVERT: E 503 MET cc_start: 0.9244 (tpp) cc_final: 0.9011 (tpp) REVERT: E 603 LYS cc_start: 0.7210 (OUTLIER) cc_final: 0.4832 (mtmm) REVERT: E 608 VAL cc_start: 0.9290 (OUTLIER) cc_final: 0.9070 (p) REVERT: E 1020 GLN cc_start: 0.8969 (mm110) cc_final: 0.8262 (mm-40) REVERT: E 1066 MET cc_start: 0.7170 (tpt) cc_final: 0.6755 (ptm) REVERT: E 1173 ILE cc_start: 0.9247 (mm) cc_final: 0.8908 (pt) REVERT: E 1252 MET cc_start: 0.8436 (mpp) cc_final: 0.8227 (mpp) REVERT: E 1293 ASN cc_start: 0.9023 (m-40) cc_final: 0.8483 (t0) REVERT: E 1298 MET cc_start: 0.9261 (tmm) cc_final: 0.8926 (tmm) REVERT: E 1389 SER cc_start: 0.9410 (t) cc_final: 0.9206 (p) REVERT: E 1395 MET cc_start: 0.8771 (mmt) cc_final: 0.8142 (mmp) outliers start: 97 outliers final: 62 residues processed: 389 average time/residue: 0.3069 time to fit residues: 189.9511 Evaluate side-chains 371 residues out of total 2323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 303 time to evaluate : 2.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 292 GLU Chi-restraints excluded: chain B residue 334 ASP Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 303 SER Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 169 MET Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 274 ASP Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 222 PHE Chi-restraints excluded: chain E residue 300 LEU Chi-restraints excluded: chain E residue 306 PHE Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 311 ASP Chi-restraints excluded: chain E residue 358 VAL Chi-restraints excluded: chain E residue 429 LEU Chi-restraints excluded: chain E residue 439 LEU Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 497 LEU Chi-restraints excluded: chain E residue 547 MET Chi-restraints excluded: chain E residue 557 LEU Chi-restraints excluded: chain E residue 603 LYS Chi-restraints excluded: chain E residue 608 VAL Chi-restraints excluded: chain E residue 817 HIS Chi-restraints excluded: chain E residue 941 LYS Chi-restraints excluded: chain E residue 1016 LEU Chi-restraints excluded: chain E residue 1283 LEU Chi-restraints excluded: chain E residue 1286 THR Chi-restraints excluded: chain E residue 1390 LEU Chi-restraints excluded: chain E residue 1509 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 215 optimal weight: 8.9990 chunk 147 optimal weight: 5.9990 chunk 3 optimal weight: 4.9990 chunk 192 optimal weight: 10.0000 chunk 106 optimal weight: 4.9990 chunk 221 optimal weight: 6.9990 chunk 179 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 132 optimal weight: 7.9990 chunk 232 optimal weight: 1.9990 chunk 65 optimal weight: 20.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 ASN ** A 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 97 HIS D 115 HIS ** D 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 235 ASN ** E 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 817 HIS E 846 GLN ** E 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1342 GLN E1521 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.4548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 21567 Z= 0.445 Angle : 0.779 11.327 29310 Z= 0.400 Chirality : 0.047 0.222 3469 Planarity : 0.004 0.061 3646 Dihedral : 7.173 96.125 2925 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 19.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 5.28 % Allowed : 23.59 % Favored : 71.13 % 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 (0.16), residues: 2662 helix: 0.23 (0.14), residues: 1324 sheet: -0.67 (0.29), residues: 321 loop : -1.38 (0.19), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP E1033 HIS 0.008 0.001 HIS E 242 PHE 0.024 0.002 PHE E 578 TYR 0.036 0.002 TYR D 258 ARG 0.006 0.001 ARG D 192 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5324 Ramachandran restraints generated. 2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5324 Ramachandran restraints generated. 2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 2323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 284 time to evaluate : 2.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ASN cc_start: 0.8393 (t0) cc_final: 0.7950 (t0) REVERT: A 47 LYS cc_start: 0.8401 (tppt) cc_final: 0.8196 (tppt) REVERT: A 65 ASP cc_start: 0.9072 (t0) cc_final: 0.8592 (t0) REVERT: A 158 MET cc_start: 0.8089 (tmm) cc_final: 0.7713 (tmm) REVERT: A 163 MET cc_start: 0.9033 (mmm) cc_final: 0.8689 (mmm) REVERT: A 257 ILE cc_start: 0.9631 (mm) cc_final: 0.9414 (mm) REVERT: B 152 GLN cc_start: 0.9575 (OUTLIER) cc_final: 0.8383 (tp40) REVERT: B 159 ILE cc_start: 0.9239 (pt) cc_final: 0.8842 (mm) REVERT: B 240 MET cc_start: 0.9037 (OUTLIER) cc_final: 0.8634 (tmm) REVERT: B 292 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.8193 (tm-30) REVERT: C 65 ASP cc_start: 0.8356 (t0) cc_final: 0.8075 (t0) REVERT: C 81 CYS cc_start: 0.9518 (m) cc_final: 0.9086 (m) REVERT: C 85 LEU cc_start: 0.9521 (OUTLIER) cc_final: 0.9281 (tp) REVERT: C 88 MET cc_start: 0.8589 (tmm) cc_final: 0.8055 (tmm) REVERT: C 199 MET cc_start: 0.8540 (mtt) cc_final: 0.8281 (mtt) REVERT: C 240 MET cc_start: 0.8262 (tmm) cc_final: 0.7982 (tmm) REVERT: C 247 ASN cc_start: 0.8796 (p0) cc_final: 0.8376 (p0) REVERT: C 292 GLU cc_start: 0.8109 (tm-30) cc_final: 0.7792 (tm-30) REVERT: D 115 HIS cc_start: 0.7878 (OUTLIER) cc_final: 0.6993 (p-80) REVERT: D 163 MET cc_start: 0.9354 (mmm) cc_final: 0.8658 (mmm) REVERT: D 185 LYS cc_start: 0.9169 (ttpp) cc_final: 0.8952 (ttpt) REVERT: D 240 MET cc_start: 0.9307 (ppp) cc_final: 0.8803 (ppp) REVERT: E 146 LEU cc_start: 0.9745 (mm) cc_final: 0.9482 (mt) REVERT: E 364 PHE cc_start: 0.9072 (t80) cc_final: 0.8685 (t80) REVERT: E 368 LEU cc_start: 0.9244 (mm) cc_final: 0.8613 (mm) REVERT: E 413 MET cc_start: 0.8467 (tpp) cc_final: 0.8139 (tpp) REVERT: E 429 LEU cc_start: 0.9332 (OUTLIER) cc_final: 0.9063 (tt) REVERT: E 1016 LEU cc_start: 0.9472 (OUTLIER) cc_final: 0.9126 (tp) REVERT: E 1020 GLN cc_start: 0.8947 (mm110) cc_final: 0.8474 (mm-40) REVERT: E 1066 MET cc_start: 0.7446 (tpt) cc_final: 0.7153 (ptm) REVERT: E 1173 ILE cc_start: 0.9275 (mm) cc_final: 0.8937 (pt) REVERT: E 1252 MET cc_start: 0.8614 (mpp) cc_final: 0.8385 (mpp) REVERT: E 1293 ASN cc_start: 0.9054 (m-40) cc_final: 0.8570 (t0) REVERT: E 1298 MET cc_start: 0.9401 (tmm) cc_final: 0.9070 (tmm) REVERT: E 1305 MET cc_start: 0.8740 (mmt) cc_final: 0.8501 (mmt) REVERT: E 1389 SER cc_start: 0.9430 (t) cc_final: 0.9085 (p) REVERT: E 1395 MET cc_start: 0.8677 (mmt) cc_final: 0.8056 (mmp) REVERT: E 1507 GLU cc_start: 0.8377 (mt-10) cc_final: 0.8033 (mp0) outliers start: 121 outliers final: 88 residues processed: 373 average time/residue: 0.2976 time to fit residues: 176.8376 Evaluate side-chains 362 residues out of total 2323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 267 time to evaluate : 2.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 334 ASP Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 115 HIS Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 152 GLN Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 292 GLU Chi-restraints excluded: chain B residue 334 ASP Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 303 SER Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain D residue 43 ASN Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 115 HIS Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 169 MET Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 274 ASP Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 307 ASP Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 334 ASP Chi-restraints excluded: chain D residue 335 ASN Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 196 TYR Chi-restraints excluded: chain E residue 222 PHE Chi-restraints excluded: chain E residue 232 TRP Chi-restraints excluded: chain E residue 300 LEU Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 311 ASP Chi-restraints excluded: chain E residue 358 VAL Chi-restraints excluded: chain E residue 429 LEU Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 497 LEU Chi-restraints excluded: chain E residue 523 VAL Chi-restraints excluded: chain E residue 547 MET Chi-restraints excluded: chain E residue 557 LEU Chi-restraints excluded: chain E residue 603 LYS Chi-restraints excluded: chain E residue 941 LYS Chi-restraints excluded: chain E residue 943 THR Chi-restraints excluded: chain E residue 1013 LEU Chi-restraints excluded: chain E residue 1016 LEU Chi-restraints excluded: chain E residue 1175 CYS Chi-restraints excluded: chain E residue 1193 ASP Chi-restraints excluded: chain E residue 1232 ASP Chi-restraints excluded: chain E residue 1259 VAL Chi-restraints excluded: chain E residue 1265 VAL Chi-restraints excluded: chain E residue 1286 THR Chi-restraints excluded: chain E residue 1334 LEU Chi-restraints excluded: chain E residue 1390 LEU Chi-restraints excluded: chain E residue 1428 ASP Chi-restraints excluded: chain E residue 1509 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 87 optimal weight: 3.9990 chunk 233 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 152 optimal weight: 0.9980 chunk 63 optimal weight: 0.0670 chunk 259 optimal weight: 5.9990 chunk 215 optimal weight: 5.9990 chunk 120 optimal weight: 6.9990 chunk 21 optimal weight: 7.9990 chunk 85 optimal weight: 0.9980 chunk 136 optimal weight: 0.9990 overall best weight: 1.2122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 279 GLN D 115 HIS ** D 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 708 GLN ** E 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.4579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21567 Z= 0.200 Angle : 0.664 12.258 29310 Z= 0.328 Chirality : 0.044 0.255 3469 Planarity : 0.003 0.039 3646 Dihedral : 6.817 103.451 2925 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 4.14 % Allowed : 25.38 % Favored : 70.48 % 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: -0.25 (0.16), residues: 2662 helix: 0.62 (0.15), residues: 1299 sheet: -0.22 (0.33), residues: 269 loop : -1.04 (0.19), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E1037 HIS 0.022 0.001 HIS D 115 PHE 0.021 0.001 PHE E1164 TYR 0.014 0.001 TYR E 379 ARG 0.003 0.000 ARG D 192 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5324 Ramachandran restraints generated. 2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5324 Ramachandran restraints generated. 2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 2323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 306 time to evaluate : 2.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ASN cc_start: 0.8373 (t0) cc_final: 0.8006 (t0) REVERT: A 65 ASP cc_start: 0.8979 (t0) cc_final: 0.8510 (t0) REVERT: A 152 GLN cc_start: 0.9444 (OUTLIER) cc_final: 0.8738 (tm-30) REVERT: A 158 MET cc_start: 0.8232 (tmm) cc_final: 0.7860 (tmm) REVERT: A 163 MET cc_start: 0.9130 (mmm) cc_final: 0.8761 (mmm) REVERT: B 65 ASP cc_start: 0.8599 (t0) cc_final: 0.8157 (t0) REVERT: B 81 CYS cc_start: 0.8633 (m) cc_final: 0.7790 (t) REVERT: B 152 GLN cc_start: 0.9505 (OUTLIER) cc_final: 0.8378 (tp40) REVERT: B 159 ILE cc_start: 0.9145 (pt) cc_final: 0.8917 (mm) REVERT: B 160 ASN cc_start: 0.9410 (t0) cc_final: 0.9168 (t0) REVERT: B 240 MET cc_start: 0.8982 (OUTLIER) cc_final: 0.8727 (tmm) REVERT: B 247 ASN cc_start: 0.8744 (p0) cc_final: 0.8063 (p0) REVERT: B 292 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7994 (tm-30) REVERT: B 316 VAL cc_start: 0.9007 (OUTLIER) cc_final: 0.8759 (m) REVERT: C 81 CYS cc_start: 0.9434 (m) cc_final: 0.9033 (m) REVERT: C 88 MET cc_start: 0.8548 (tmm) cc_final: 0.8011 (tmm) REVERT: C 199 MET cc_start: 0.8590 (mtt) cc_final: 0.8345 (mtt) REVERT: C 247 ASN cc_start: 0.8794 (p0) cc_final: 0.8471 (p0) REVERT: C 292 GLU cc_start: 0.7969 (tm-30) cc_final: 0.7679 (tm-30) REVERT: D 115 HIS cc_start: 0.7761 (OUTLIER) cc_final: 0.7175 (p-80) REVERT: D 163 MET cc_start: 0.9220 (mmm) cc_final: 0.8856 (mmm) REVERT: D 185 LYS cc_start: 0.9134 (ttpp) cc_final: 0.8880 (ttpt) REVERT: D 240 MET cc_start: 0.9326 (ppp) cc_final: 0.8778 (ppp) REVERT: D 258 TYR cc_start: 0.8720 (p90) cc_final: 0.8443 (p90) REVERT: E 146 LEU cc_start: 0.9745 (mm) cc_final: 0.9541 (mm) REVERT: E 364 PHE cc_start: 0.9061 (t80) cc_final: 0.8829 (t80) REVERT: E 368 LEU cc_start: 0.9227 (mm) cc_final: 0.8593 (mm) REVERT: E 413 MET cc_start: 0.8469 (tpp) cc_final: 0.8034 (tpp) REVERT: E 429 LEU cc_start: 0.9177 (OUTLIER) cc_final: 0.8945 (tt) REVERT: E 503 MET cc_start: 0.9264 (tpp) cc_final: 0.9058 (tpp) REVERT: E 602 VAL cc_start: 0.9037 (OUTLIER) cc_final: 0.8702 (m) REVERT: E 603 LYS cc_start: 0.6989 (OUTLIER) cc_final: 0.5159 (mtmm) REVERT: E 869 MET cc_start: 0.9295 (mmm) cc_final: 0.8843 (mmm) REVERT: E 1016 LEU cc_start: 0.9542 (OUTLIER) cc_final: 0.9297 (pp) REVERT: E 1020 GLN cc_start: 0.8889 (mm110) cc_final: 0.8311 (mm-40) REVERT: E 1066 MET cc_start: 0.7353 (tpt) cc_final: 0.7036 (ptm) REVERT: E 1173 ILE cc_start: 0.9227 (mm) cc_final: 0.8867 (pt) REVERT: E 1252 MET cc_start: 0.8579 (mpp) cc_final: 0.8218 (mpp) REVERT: E 1293 ASN cc_start: 0.8924 (m-40) cc_final: 0.8580 (t0) REVERT: E 1298 MET cc_start: 0.9365 (tmm) cc_final: 0.9074 (tmm) REVERT: E 1389 SER cc_start: 0.9371 (t) cc_final: 0.9011 (p) REVERT: E 1395 MET cc_start: 0.8771 (mmt) cc_final: 0.8209 (mmp) REVERT: E 1507 GLU cc_start: 0.8480 (mt-10) cc_final: 0.7948 (mp0) outliers start: 95 outliers final: 63 residues processed: 370 average time/residue: 0.3113 time to fit residues: 184.6978 Evaluate side-chains 348 residues out of total 2323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 275 time to evaluate : 2.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 152 GLN Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 152 GLN Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 292 GLU Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 152 GLN Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 303 SER Chi-restraints excluded: chain C residue 334 ASP Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 115 HIS Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 169 MET Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 335 ASN Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 196 TYR Chi-restraints excluded: chain E residue 222 PHE Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 232 TRP Chi-restraints excluded: chain E residue 300 LEU Chi-restraints excluded: chain E residue 306 PHE Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 311 ASP Chi-restraints excluded: chain E residue 358 VAL Chi-restraints excluded: chain E residue 429 LEU Chi-restraints excluded: chain E residue 497 LEU Chi-restraints excluded: chain E residue 523 VAL Chi-restraints excluded: chain E residue 547 MET Chi-restraints excluded: chain E residue 557 LEU Chi-restraints excluded: chain E residue 602 VAL Chi-restraints excluded: chain E residue 603 LYS Chi-restraints excluded: chain E residue 830 LEU Chi-restraints excluded: chain E residue 885 VAL Chi-restraints excluded: chain E residue 1016 LEU Chi-restraints excluded: chain E residue 1283 LEU Chi-restraints excluded: chain E residue 1286 THR Chi-restraints excluded: chain E residue 1341 ASP Chi-restraints excluded: chain E residue 1428 ASP Chi-restraints excluded: chain E residue 1509 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 249 optimal weight: 0.0870 chunk 29 optimal weight: 10.0000 chunk 147 optimal weight: 8.9990 chunk 189 optimal weight: 0.0170 chunk 146 optimal weight: 3.9990 chunk 218 optimal weight: 2.9990 chunk 144 optimal weight: 7.9990 chunk 258 optimal weight: 1.9990 chunk 161 optimal weight: 2.9990 chunk 157 optimal weight: 0.9980 chunk 119 optimal weight: 5.9990 overall best weight: 1.2200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 97 HIS D 115 HIS ** D 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 708 GLN ** E 797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 892 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1541 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.4729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21567 Z= 0.201 Angle : 0.673 12.400 29310 Z= 0.328 Chirality : 0.044 0.260 3469 Planarity : 0.003 0.031 3646 Dihedral : 6.578 107.225 2919 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 3.88 % Allowed : 26.34 % Favored : 69.78 % 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: -0.07 (0.16), residues: 2662 helix: 0.77 (0.15), residues: 1299 sheet: -0.15 (0.33), residues: 269 loop : -0.95 (0.19), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E1037 HIS 0.012 0.001 HIS D 115 PHE 0.022 0.001 PHE E 84 TYR 0.013 0.001 TYR E 379 ARG 0.004 0.000 ARG C 177 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5324 Ramachandran restraints generated. 2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5324 Ramachandran restraints generated. 2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 2323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 304 time to evaluate : 3.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ASN cc_start: 0.8456 (t0) cc_final: 0.8052 (t0) REVERT: A 65 ASP cc_start: 0.8957 (t0) cc_final: 0.8463 (t0) REVERT: A 158 MET cc_start: 0.8411 (tmm) cc_final: 0.7964 (tmm) REVERT: A 163 MET cc_start: 0.9093 (mmm) cc_final: 0.8738 (mmm) REVERT: A 250 PHE cc_start: 0.8857 (t80) cc_final: 0.8544 (t80) REVERT: B 81 CYS cc_start: 0.8524 (m) cc_final: 0.7705 (t) REVERT: B 152 GLN cc_start: 0.9493 (OUTLIER) cc_final: 0.8240 (tp40) REVERT: B 159 ILE cc_start: 0.9161 (pt) cc_final: 0.8942 (mm) REVERT: B 240 MET cc_start: 0.8970 (OUTLIER) cc_final: 0.8737 (tmm) REVERT: B 247 ASN cc_start: 0.8784 (p0) cc_final: 0.8083 (p0) REVERT: B 292 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7799 (tm-30) REVERT: B 304 TYR cc_start: 0.8776 (m-10) cc_final: 0.8116 (m-10) REVERT: B 316 VAL cc_start: 0.8954 (OUTLIER) cc_final: 0.8688 (m) REVERT: C 81 CYS cc_start: 0.9413 (m) cc_final: 0.9024 (m) REVERT: C 88 MET cc_start: 0.8512 (tmm) cc_final: 0.8026 (tmm) REVERT: C 148 ILE cc_start: 0.9695 (tp) cc_final: 0.9434 (tp) REVERT: C 185 LYS cc_start: 0.9158 (tptp) cc_final: 0.8900 (tptp) REVERT: C 199 MET cc_start: 0.8574 (mtt) cc_final: 0.8344 (mtt) REVERT: C 240 MET cc_start: 0.8035 (tmm) cc_final: 0.7748 (tmm) REVERT: C 247 ASN cc_start: 0.8800 (p0) cc_final: 0.8506 (p0) REVERT: C 292 GLU cc_start: 0.8151 (tm-30) cc_final: 0.7811 (tm-30) REVERT: D 110 CYS cc_start: 0.8211 (m) cc_final: 0.7972 (m) REVERT: D 115 HIS cc_start: 0.7740 (OUTLIER) cc_final: 0.7025 (p-80) REVERT: D 163 MET cc_start: 0.9271 (mmm) cc_final: 0.8923 (mmm) REVERT: D 185 LYS cc_start: 0.9124 (ttpp) cc_final: 0.8873 (ttpt) REVERT: D 240 MET cc_start: 0.9273 (ppp) cc_final: 0.8694 (ppp) REVERT: D 258 TYR cc_start: 0.8709 (p90) cc_final: 0.8492 (p90) REVERT: E 60 HIS cc_start: 0.8192 (m-70) cc_final: 0.7720 (m-70) REVERT: E 63 HIS cc_start: 0.7851 (p90) cc_final: 0.7074 (p90) REVERT: E 146 LEU cc_start: 0.9745 (mm) cc_final: 0.9500 (mt) REVERT: E 364 PHE cc_start: 0.9072 (t80) cc_final: 0.8793 (t80) REVERT: E 368 LEU cc_start: 0.9225 (mm) cc_final: 0.8598 (mm) REVERT: E 503 MET cc_start: 0.9295 (tpp) cc_final: 0.9067 (tpp) REVERT: E 531 MET cc_start: 0.8610 (tpp) cc_final: 0.8353 (tpp) REVERT: E 602 VAL cc_start: 0.9035 (OUTLIER) cc_final: 0.8728 (m) REVERT: E 603 LYS cc_start: 0.7027 (OUTLIER) cc_final: 0.5313 (mtmm) REVERT: E 869 MET cc_start: 0.9315 (mmm) cc_final: 0.8879 (mmm) REVERT: E 1016 LEU cc_start: 0.9532 (OUTLIER) cc_final: 0.9295 (pp) REVERT: E 1020 GLN cc_start: 0.8897 (mm110) cc_final: 0.8362 (mm-40) REVERT: E 1066 MET cc_start: 0.7392 (tpt) cc_final: 0.7065 (ptm) REVERT: E 1173 ILE cc_start: 0.9204 (mm) cc_final: 0.8893 (pt) REVERT: E 1293 ASN cc_start: 0.8949 (m-40) cc_final: 0.8566 (t0) REVERT: E 1298 MET cc_start: 0.9355 (tmm) cc_final: 0.9044 (tmm) REVERT: E 1389 SER cc_start: 0.9381 (t) cc_final: 0.9059 (p) REVERT: E 1395 MET cc_start: 0.8744 (mmt) cc_final: 0.8243 (mmp) REVERT: E 1507 GLU cc_start: 0.8496 (mt-10) cc_final: 0.7971 (mp0) outliers start: 89 outliers final: 67 residues processed: 371 average time/residue: 0.3051 time to fit residues: 182.9282 Evaluate side-chains 362 residues out of total 2323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 287 time to evaluate : 2.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 152 GLN Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 115 HIS Chi-restraints excluded: chain B residue 152 GLN Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 292 GLU Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 334 ASP Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 152 GLN Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 303 SER Chi-restraints excluded: chain C residue 334 ASP Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 115 HIS Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 169 MET Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 274 ASP Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 335 ASN Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 196 TYR Chi-restraints excluded: chain E residue 222 PHE Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 232 TRP Chi-restraints excluded: chain E residue 271 PHE Chi-restraints excluded: chain E residue 300 LEU Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 311 ASP Chi-restraints excluded: chain E residue 358 VAL Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 497 LEU Chi-restraints excluded: chain E residue 523 VAL Chi-restraints excluded: chain E residue 547 MET Chi-restraints excluded: chain E residue 557 LEU Chi-restraints excluded: chain E residue 602 VAL Chi-restraints excluded: chain E residue 603 LYS Chi-restraints excluded: chain E residue 885 VAL Chi-restraints excluded: chain E residue 1016 LEU Chi-restraints excluded: chain E residue 1283 LEU Chi-restraints excluded: chain E residue 1286 THR Chi-restraints excluded: chain E residue 1341 ASP Chi-restraints excluded: chain E residue 1390 LEU Chi-restraints excluded: chain E residue 1509 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 159 optimal weight: 7.9990 chunk 103 optimal weight: 0.6980 chunk 154 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 chunk 50 optimal weight: 6.9990 chunk 164 optimal weight: 0.7980 chunk 175 optimal weight: 7.9990 chunk 127 optimal weight: 9.9990 chunk 24 optimal weight: 7.9990 chunk 203 optimal weight: 7.9990 chunk 234 optimal weight: 1.9990 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 889 HIS ** E 892 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.4992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 21567 Z= 0.336 Angle : 0.736 12.286 29310 Z= 0.366 Chirality : 0.045 0.247 3469 Planarity : 0.004 0.035 3646 Dihedral : 6.644 111.565 2917 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 17.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 4.80 % Allowed : 25.86 % Favored : 69.34 % 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: -0.13 (0.16), residues: 2662 helix: 0.70 (0.15), residues: 1299 sheet: -0.29 (0.31), residues: 281 loop : -0.91 (0.19), residues: 1082 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E1033 HIS 0.021 0.001 HIS D 115 PHE 0.023 0.002 PHE E 84 TYR 0.014 0.001 TYR B 326 ARG 0.006 0.000 ARG C 177 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5324 Ramachandran restraints generated. 2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5324 Ramachandran restraints generated. 2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 2323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 276 time to evaluate : 2.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ASN cc_start: 0.8577 (t0) cc_final: 0.8206 (t0) REVERT: A 65 ASP cc_start: 0.9047 (t0) cc_final: 0.8494 (t0) REVERT: A 152 GLN cc_start: 0.9535 (OUTLIER) cc_final: 0.8726 (tp40) REVERT: A 158 MET cc_start: 0.8436 (tmm) cc_final: 0.7983 (tmm) REVERT: A 163 MET cc_start: 0.9010 (mmm) cc_final: 0.8643 (mmm) REVERT: A 209 MET cc_start: 0.9123 (mmm) cc_final: 0.8804 (mmm) REVERT: A 257 ILE cc_start: 0.9631 (mm) cc_final: 0.9418 (mm) REVERT: B 152 GLN cc_start: 0.9562 (OUTLIER) cc_final: 0.8311 (tp40) REVERT: B 159 ILE cc_start: 0.9288 (pt) cc_final: 0.9013 (mm) REVERT: B 240 MET cc_start: 0.9098 (OUTLIER) cc_final: 0.8749 (tmm) REVERT: B 292 GLU cc_start: 0.8346 (OUTLIER) cc_final: 0.7891 (tm-30) REVERT: B 304 TYR cc_start: 0.8806 (m-10) cc_final: 0.8150 (m-10) REVERT: B 316 VAL cc_start: 0.9014 (OUTLIER) cc_final: 0.8764 (m) REVERT: C 39 LYS cc_start: 0.8866 (tttp) cc_final: 0.8663 (ttpp) REVERT: C 81 CYS cc_start: 0.9496 (m) cc_final: 0.9051 (m) REVERT: C 88 MET cc_start: 0.8586 (tmm) cc_final: 0.8032 (tmm) REVERT: C 152 GLN cc_start: 0.9521 (OUTLIER) cc_final: 0.8714 (tp-100) REVERT: C 199 MET cc_start: 0.8593 (mtt) cc_final: 0.8344 (mtt) REVERT: C 247 ASN cc_start: 0.8950 (p0) cc_final: 0.8570 (p0) REVERT: C 292 GLU cc_start: 0.8044 (tm-30) cc_final: 0.7694 (tm-30) REVERT: D 43 ASN cc_start: 0.8000 (OUTLIER) cc_final: 0.7365 (p0) REVERT: D 115 HIS cc_start: 0.7493 (OUTLIER) cc_final: 0.6871 (p90) REVERT: D 126 GLU cc_start: 0.8269 (mt-10) cc_final: 0.7702 (mp0) REVERT: D 163 MET cc_start: 0.9163 (mmm) cc_final: 0.8805 (mmm) REVERT: D 185 LYS cc_start: 0.9163 (ttpp) cc_final: 0.8950 (ttpt) REVERT: D 209 MET cc_start: 0.8779 (tpp) cc_final: 0.8537 (tpp) REVERT: D 240 MET cc_start: 0.9327 (ppp) cc_final: 0.8724 (ppp) REVERT: D 258 TYR cc_start: 0.8699 (p90) cc_final: 0.8491 (p90) REVERT: E 16 TYR cc_start: 0.8712 (OUTLIER) cc_final: 0.8285 (m-10) REVERT: E 146 LEU cc_start: 0.9762 (mm) cc_final: 0.9498 (mt) REVERT: E 364 PHE cc_start: 0.9098 (t80) cc_final: 0.8806 (t80) REVERT: E 368 LEU cc_start: 0.9251 (mm) cc_final: 0.8600 (mm) REVERT: E 388 LEU cc_start: 0.9525 (tp) cc_final: 0.9181 (tt) REVERT: E 442 MET cc_start: 0.8190 (tpp) cc_final: 0.7885 (tpt) REVERT: E 503 MET cc_start: 0.9305 (tpp) cc_final: 0.9034 (tpp) REVERT: E 531 MET cc_start: 0.8653 (tpp) cc_final: 0.8388 (tpp) REVERT: E 602 VAL cc_start: 0.9138 (OUTLIER) cc_final: 0.8795 (m) REVERT: E 603 LYS cc_start: 0.7370 (OUTLIER) cc_final: 0.5657 (mtmm) REVERT: E 869 MET cc_start: 0.9392 (mmm) cc_final: 0.8974 (mmm) REVERT: E 1016 LEU cc_start: 0.9550 (OUTLIER) cc_final: 0.9139 (tp) REVERT: E 1020 GLN cc_start: 0.8928 (mm110) cc_final: 0.8361 (mm-40) REVERT: E 1066 MET cc_start: 0.7522 (tpt) cc_final: 0.7240 (ptm) REVERT: E 1140 LEU cc_start: 0.9542 (OUTLIER) cc_final: 0.9332 (mm) REVERT: E 1173 ILE cc_start: 0.9226 (mm) cc_final: 0.8882 (pt) REVERT: E 1293 ASN cc_start: 0.9046 (m-40) cc_final: 0.8592 (t0) REVERT: E 1298 MET cc_start: 0.9323 (tmm) cc_final: 0.9034 (tmm) REVERT: E 1395 MET cc_start: 0.8742 (mmt) cc_final: 0.8223 (mmp) REVERT: E 1432 PHE cc_start: 0.8953 (m-80) cc_final: 0.8598 (m-10) REVERT: E 1507 GLU cc_start: 0.8484 (mt-10) cc_final: 0.8006 (mp0) outliers start: 110 outliers final: 81 residues processed: 356 average time/residue: 0.3091 time to fit residues: 175.0843 Evaluate side-chains 360 residues out of total 2323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 266 time to evaluate : 2.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 152 GLN Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 334 ASP Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 115 HIS Chi-restraints excluded: chain B residue 152 GLN Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 292 GLU Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 334 ASP Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 152 GLN Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 303 SER Chi-restraints excluded: chain C residue 334 ASP Chi-restraints excluded: chain D residue 43 ASN Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 115 HIS Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 169 MET Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 274 ASP Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 335 ASN Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain E residue 16 TYR Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 97 ASP Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 196 TYR Chi-restraints excluded: chain E residue 222 PHE Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 232 TRP Chi-restraints excluded: chain E residue 300 LEU Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 311 ASP Chi-restraints excluded: chain E residue 358 VAL Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 497 LEU Chi-restraints excluded: chain E residue 523 VAL Chi-restraints excluded: chain E residue 547 MET Chi-restraints excluded: chain E residue 602 VAL Chi-restraints excluded: chain E residue 603 LYS Chi-restraints excluded: chain E residue 817 HIS Chi-restraints excluded: chain E residue 830 LEU Chi-restraints excluded: chain E residue 847 HIS Chi-restraints excluded: chain E residue 885 VAL Chi-restraints excluded: chain E residue 1016 LEU Chi-restraints excluded: chain E residue 1140 LEU Chi-restraints excluded: chain E residue 1193 ASP Chi-restraints excluded: chain E residue 1232 ASP Chi-restraints excluded: chain E residue 1259 VAL Chi-restraints excluded: chain E residue 1274 ARG Chi-restraints excluded: chain E residue 1286 THR Chi-restraints excluded: chain E residue 1341 ASP Chi-restraints excluded: chain E residue 1390 LEU Chi-restraints excluded: chain E residue 1428 ASP Chi-restraints excluded: chain E residue 1509 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 247 optimal weight: 0.3980 chunk 225 optimal weight: 10.0000 chunk 240 optimal weight: 3.9990 chunk 144 optimal weight: 7.9990 chunk 104 optimal weight: 0.0070 chunk 189 optimal weight: 8.9990 chunk 73 optimal weight: 0.9980 chunk 217 optimal weight: 3.9990 chunk 227 optimal weight: 0.8980 chunk 239 optimal weight: 0.9990 chunk 158 optimal weight: 1.9990 overall best weight: 0.6600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 242 ASN ** D 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 708 GLN E 892 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.5014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 21567 Z= 0.179 Angle : 0.692 13.111 29310 Z= 0.331 Chirality : 0.043 0.239 3469 Planarity : 0.003 0.031 3646 Dihedral : 6.456 108.967 2917 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 3.79 % Allowed : 26.78 % Favored : 69.43 % 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: 0.11 (0.17), residues: 2662 helix: 0.88 (0.15), residues: 1291 sheet: -0.06 (0.33), residues: 261 loop : -0.78 (0.19), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 90 HIS 0.007 0.001 HIS D 115 PHE 0.030 0.001 PHE E 584 TYR 0.014 0.001 TYR E1176 ARG 0.003 0.000 ARG C 176 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5324 Ramachandran restraints generated. 2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5324 Ramachandran restraints generated. 2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 2323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 314 time to evaluate : 2.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LYS cc_start: 0.8903 (tttt) cc_final: 0.8643 (tttp) REVERT: A 43 ASN cc_start: 0.8566 (t0) cc_final: 0.8271 (t0) REVERT: A 65 ASP cc_start: 0.8959 (t0) cc_final: 0.8325 (t0) REVERT: A 152 GLN cc_start: 0.9375 (OUTLIER) cc_final: 0.8892 (tm-30) REVERT: A 158 MET cc_start: 0.8608 (tmm) cc_final: 0.8137 (tmm) REVERT: A 163 MET cc_start: 0.9127 (mmm) cc_final: 0.8751 (mmm) REVERT: A 250 PHE cc_start: 0.8872 (t80) cc_final: 0.8517 (t80) REVERT: B 81 CYS cc_start: 0.8521 (m) cc_final: 0.7716 (t) REVERT: B 152 GLN cc_start: 0.9459 (OUTLIER) cc_final: 0.8614 (tp40) REVERT: B 163 MET cc_start: 0.9049 (mmt) cc_final: 0.8834 (mmm) REVERT: B 240 MET cc_start: 0.8982 (tmm) cc_final: 0.8757 (tmm) REVERT: B 292 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7858 (tm-30) REVERT: B 304 TYR cc_start: 0.8782 (m-10) cc_final: 0.8276 (m-10) REVERT: B 316 VAL cc_start: 0.8933 (OUTLIER) cc_final: 0.8655 (m) REVERT: C 81 CYS cc_start: 0.9423 (m) cc_final: 0.8988 (m) REVERT: C 88 MET cc_start: 0.8484 (tmm) cc_final: 0.7955 (tmm) REVERT: C 128 GLN cc_start: 0.8522 (OUTLIER) cc_final: 0.8317 (tt0) REVERT: C 148 ILE cc_start: 0.9682 (tp) cc_final: 0.9432 (tp) REVERT: C 152 GLN cc_start: 0.9425 (OUTLIER) cc_final: 0.9045 (tp40) REVERT: C 170 LYS cc_start: 0.9308 (tptm) cc_final: 0.9069 (tptm) REVERT: C 199 MET cc_start: 0.8493 (mtt) cc_final: 0.8274 (mtt) REVERT: C 247 ASN cc_start: 0.8910 (p0) cc_final: 0.8447 (p0) REVERT: C 292 GLU cc_start: 0.8159 (tm-30) cc_final: 0.7808 (tm-30) REVERT: D 163 MET cc_start: 0.9263 (mmm) cc_final: 0.8841 (mmm) REVERT: D 185 LYS cc_start: 0.9154 (ttpp) cc_final: 0.8894 (ttpt) REVERT: D 240 MET cc_start: 0.9245 (ppp) cc_final: 0.8623 (ppp) REVERT: D 258 TYR cc_start: 0.8643 (p90) cc_final: 0.8378 (p90) REVERT: E 16 TYR cc_start: 0.8512 (OUTLIER) cc_final: 0.7997 (m-10) REVERT: E 146 LEU cc_start: 0.9760 (mm) cc_final: 0.9501 (mt) REVERT: E 364 PHE cc_start: 0.9066 (t80) cc_final: 0.8810 (t80) REVERT: E 368 LEU cc_start: 0.9344 (mm) cc_final: 0.8715 (mm) REVERT: E 433 PHE cc_start: 0.9248 (m-10) cc_final: 0.9030 (m-10) REVERT: E 442 MET cc_start: 0.8204 (tpp) cc_final: 0.7885 (tpt) REVERT: E 503 MET cc_start: 0.9260 (tpp) cc_final: 0.9043 (tpp) REVERT: E 584 PHE cc_start: 0.8604 (m-80) cc_final: 0.8339 (m-80) REVERT: E 602 VAL cc_start: 0.8986 (OUTLIER) cc_final: 0.8676 (m) REVERT: E 603 LYS cc_start: 0.7463 (OUTLIER) cc_final: 0.5866 (mtmm) REVERT: E 869 MET cc_start: 0.9335 (mmm) cc_final: 0.8925 (mmm) REVERT: E 1016 LEU cc_start: 0.9593 (OUTLIER) cc_final: 0.9303 (pp) REVERT: E 1020 GLN cc_start: 0.8895 (mm110) cc_final: 0.8363 (mm-40) REVERT: E 1066 MET cc_start: 0.7469 (tpt) cc_final: 0.7141 (ptm) REVERT: E 1140 LEU cc_start: 0.9468 (OUTLIER) cc_final: 0.9062 (mm) REVERT: E 1173 ILE cc_start: 0.9267 (mm) cc_final: 0.8924 (pt) REVERT: E 1293 ASN cc_start: 0.8930 (m-40) cc_final: 0.8541 (t0) REVERT: E 1298 MET cc_start: 0.9285 (tmm) cc_final: 0.8950 (tmm) REVERT: E 1389 SER cc_start: 0.9380 (t) cc_final: 0.8978 (p) REVERT: E 1395 MET cc_start: 0.8674 (mmt) cc_final: 0.8188 (mmp) REVERT: E 1432 PHE cc_start: 0.8868 (m-80) cc_final: 0.8618 (m-10) REVERT: E 1507 GLU cc_start: 0.8466 (mt-10) cc_final: 0.7963 (mp0) outliers start: 87 outliers final: 57 residues processed: 380 average time/residue: 0.3036 time to fit residues: 183.4284 Evaluate side-chains 362 residues out of total 2323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 294 time to evaluate : 2.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 152 GLN Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 334 ASP Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 152 GLN Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 274 ASP Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 292 GLU Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 128 GLN Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 152 GLN Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 303 SER Chi-restraints excluded: chain C residue 334 ASP Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 274 ASP Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain E residue 16 TYR Chi-restraints excluded: chain E residue 97 ASP Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 196 TYR Chi-restraints excluded: chain E residue 222 PHE Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 232 TRP Chi-restraints excluded: chain E residue 300 LEU Chi-restraints excluded: chain E residue 311 ASP Chi-restraints excluded: chain E residue 358 VAL Chi-restraints excluded: chain E residue 497 LEU Chi-restraints excluded: chain E residue 523 VAL Chi-restraints excluded: chain E residue 547 MET Chi-restraints excluded: chain E residue 602 VAL Chi-restraints excluded: chain E residue 603 LYS Chi-restraints excluded: chain E residue 830 LEU Chi-restraints excluded: chain E residue 885 VAL Chi-restraints excluded: chain E residue 1016 LEU Chi-restraints excluded: chain E residue 1140 LEU Chi-restraints excluded: chain E residue 1175 CYS Chi-restraints excluded: chain E residue 1193 ASP Chi-restraints excluded: chain E residue 1274 ARG Chi-restraints excluded: chain E residue 1283 LEU Chi-restraints excluded: chain E residue 1286 THR Chi-restraints excluded: chain E residue 1390 LEU Chi-restraints excluded: chain E residue 1509 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 254 optimal weight: 0.8980 chunk 155 optimal weight: 0.7980 chunk 120 optimal weight: 8.9990 chunk 176 optimal weight: 0.9990 chunk 266 optimal weight: 0.0570 chunk 245 optimal weight: 9.9990 chunk 212 optimal weight: 4.9990 chunk 22 optimal weight: 0.0670 chunk 164 optimal weight: 3.9990 chunk 130 optimal weight: 0.8980 chunk 168 optimal weight: 0.5980 overall best weight: 0.4836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 48 ASN B 128 GLN ** D 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 708 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.5111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 21567 Z= 0.173 Angle : 0.700 13.614 29310 Z= 0.333 Chirality : 0.043 0.281 3469 Planarity : 0.003 0.036 3646 Dihedral : 6.341 106.226 2917 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.83 % Allowed : 28.26 % Favored : 68.91 % 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: 0.17 (0.16), residues: 2662 helix: 0.94 (0.15), residues: 1280 sheet: 0.05 (0.33), residues: 261 loop : -0.79 (0.18), residues: 1121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E1037 HIS 0.005 0.001 HIS E 889 PHE 0.029 0.001 PHE E 584 TYR 0.022 0.001 TYR E 124 ARG 0.010 0.000 ARG E 266 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5324 Ramachandran restraints generated. 2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5324 Ramachandran restraints generated. 2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 310 time to evaluate : 2.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LYS cc_start: 0.8831 (tttt) cc_final: 0.8549 (tttp) REVERT: A 43 ASN cc_start: 0.8623 (t0) cc_final: 0.8342 (t0) REVERT: A 65 ASP cc_start: 0.8928 (t0) cc_final: 0.8236 (t0) REVERT: A 152 GLN cc_start: 0.9398 (OUTLIER) cc_final: 0.8885 (tm-30) REVERT: A 158 MET cc_start: 0.8628 (tmm) cc_final: 0.8254 (tmm) REVERT: A 163 MET cc_start: 0.9146 (mmm) cc_final: 0.8735 (mmm) REVERT: A 207 LYS cc_start: 0.8025 (pttt) cc_final: 0.7542 (ptpt) REVERT: B 47 LYS cc_start: 0.9430 (mmtm) cc_final: 0.9225 (ptmm) REVERT: B 48 ASN cc_start: 0.9271 (OUTLIER) cc_final: 0.8724 (m110) REVERT: B 152 GLN cc_start: 0.9551 (OUTLIER) cc_final: 0.8604 (tp40) REVERT: B 240 MET cc_start: 0.8924 (tmm) cc_final: 0.8723 (tmm) REVERT: B 292 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7842 (tm-30) REVERT: B 304 TYR cc_start: 0.8783 (m-10) cc_final: 0.8308 (m-10) REVERT: C 81 CYS cc_start: 0.9373 (m) cc_final: 0.8974 (m) REVERT: C 88 MET cc_start: 0.8426 (tmm) cc_final: 0.7958 (tmm) REVERT: C 148 ILE cc_start: 0.9666 (tp) cc_final: 0.9441 (tp) REVERT: C 152 GLN cc_start: 0.9388 (OUTLIER) cc_final: 0.8934 (tp40) REVERT: C 179 GLU cc_start: 0.7966 (mt-10) cc_final: 0.7347 (tp30) REVERT: C 199 MET cc_start: 0.8477 (mtt) cc_final: 0.8254 (mtt) REVERT: C 222 LYS cc_start: 0.9020 (ttpp) cc_final: 0.8818 (ttpp) REVERT: C 247 ASN cc_start: 0.8904 (p0) cc_final: 0.8464 (p0) REVERT: C 292 GLU cc_start: 0.8103 (tm-30) cc_final: 0.7816 (tm-30) REVERT: D 163 MET cc_start: 0.9199 (mmm) cc_final: 0.8821 (mmm) REVERT: D 185 LYS cc_start: 0.9120 (ttpp) cc_final: 0.8858 (tmtt) REVERT: D 240 MET cc_start: 0.9194 (ppp) cc_final: 0.8559 (ppp) REVERT: D 258 TYR cc_start: 0.8628 (p90) cc_final: 0.8379 (p90) REVERT: E 16 TYR cc_start: 0.8498 (OUTLIER) cc_final: 0.8013 (m-80) REVERT: E 146 LEU cc_start: 0.9745 (mm) cc_final: 0.9484 (mt) REVERT: E 364 PHE cc_start: 0.9117 (t80) cc_final: 0.8870 (t80) REVERT: E 368 LEU cc_start: 0.9216 (mm) cc_final: 0.8577 (mm) REVERT: E 433 PHE cc_start: 0.9203 (m-10) cc_final: 0.9002 (m-10) REVERT: E 442 MET cc_start: 0.8190 (tpp) cc_final: 0.7881 (tpt) REVERT: E 503 MET cc_start: 0.9277 (tpp) cc_final: 0.9076 (tpp) REVERT: E 584 PHE cc_start: 0.8603 (m-80) cc_final: 0.8347 (m-80) REVERT: E 602 VAL cc_start: 0.8935 (OUTLIER) cc_final: 0.8667 (m) REVERT: E 603 LYS cc_start: 0.7481 (OUTLIER) cc_final: 0.6018 (mtmm) REVERT: E 869 MET cc_start: 0.9324 (mmm) cc_final: 0.8905 (mmm) REVERT: E 932 MET cc_start: 0.7998 (ttp) cc_final: 0.7435 (ttp) REVERT: E 1016 LEU cc_start: 0.9567 (OUTLIER) cc_final: 0.9287 (pp) REVERT: E 1020 GLN cc_start: 0.8932 (mm110) cc_final: 0.8414 (mm-40) REVERT: E 1066 MET cc_start: 0.7238 (tpt) cc_final: 0.6910 (ptm) REVERT: E 1140 LEU cc_start: 0.9474 (OUTLIER) cc_final: 0.9198 (mm) REVERT: E 1173 ILE cc_start: 0.9219 (mm) cc_final: 0.8900 (pt) REVERT: E 1298 MET cc_start: 0.9235 (tmm) cc_final: 0.8916 (tmm) REVERT: E 1389 SER cc_start: 0.9376 (t) cc_final: 0.8969 (p) REVERT: E 1395 MET cc_start: 0.8639 (mmt) cc_final: 0.8174 (mmp) REVERT: E 1507 GLU cc_start: 0.8447 (mt-10) cc_final: 0.7970 (mp0) outliers start: 65 outliers final: 46 residues processed: 360 average time/residue: 0.3172 time to fit residues: 182.8341 Evaluate side-chains 345 residues out of total 2323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 289 time to evaluate : 2.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 152 GLN Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 334 ASP Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain B residue 48 ASN Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 115 HIS Chi-restraints excluded: chain B residue 152 GLN Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 274 ASP Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 292 GLU Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 152 GLN Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 303 SER Chi-restraints excluded: chain C residue 334 ASP Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain E residue 16 TYR Chi-restraints excluded: chain E residue 97 ASP Chi-restraints excluded: chain E residue 196 TYR Chi-restraints excluded: chain E residue 222 PHE Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 232 TRP Chi-restraints excluded: chain E residue 311 ASP Chi-restraints excluded: chain E residue 358 VAL Chi-restraints excluded: chain E residue 497 LEU Chi-restraints excluded: chain E residue 547 MET Chi-restraints excluded: chain E residue 602 VAL Chi-restraints excluded: chain E residue 603 LYS Chi-restraints excluded: chain E residue 885 VAL Chi-restraints excluded: chain E residue 1016 LEU Chi-restraints excluded: chain E residue 1140 LEU Chi-restraints excluded: chain E residue 1274 ARG Chi-restraints excluded: chain E residue 1283 LEU Chi-restraints excluded: chain E residue 1509 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 226 optimal weight: 6.9990 chunk 65 optimal weight: 8.9990 chunk 196 optimal weight: 0.7980 chunk 31 optimal weight: 0.0670 chunk 59 optimal weight: 0.3980 chunk 212 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 218 optimal weight: 0.9980 chunk 26 optimal weight: 4.9990 chunk 39 optimal weight: 0.4980 chunk 186 optimal weight: 6.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 186 HIS ** D 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 708 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.068338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.056570 restraints weight = 89364.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.058313 restraints weight = 45640.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.059483 restraints weight = 28786.249| |-----------------------------------------------------------------------------| r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.5133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.214 21567 Z= 0.265 Angle : 0.831 59.195 29310 Z= 0.440 Chirality : 0.044 0.318 3469 Planarity : 0.003 0.035 3646 Dihedral : 6.325 106.221 2916 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 15.75 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.58 % Favored : 95.38 % Rotamer: Outliers : 2.70 % Allowed : 28.22 % Favored : 69.08 % 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: 0.16 (0.16), residues: 2662 helix: 0.93 (0.15), residues: 1280 sheet: 0.06 (0.33), residues: 261 loop : -0.78 (0.19), residues: 1121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E1037 HIS 0.006 0.001 HIS B 186 PHE 0.051 0.001 PHE C 168 TYR 0.021 0.001 TYR E 124 ARG 0.009 0.000 ARG E 266 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4457.24 seconds wall clock time: 82 minutes 7.03 seconds (4927.03 seconds total)