Starting phenix.real_space_refine on Sun Feb 18 07:09:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s5z_24844/02_2024/7s5z_24844_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s5z_24844/02_2024/7s5z_24844.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/7s5z_24844/02_2024/7s5z_24844.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s5z_24844/02_2024/7s5z_24844.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s5z_24844/02_2024/7s5z_24844_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s5z_24844/02_2024/7s5z_24844_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= 0.078 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 121 5.16 5 C 13673 2.51 5 N 3597 2.21 5 O 3750 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 PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 126": "OE1" <-> "OE2" Residue "A GLU 141": "OE1" <-> "OE2" Residue "A GLU 179": "OE1" <-> "OE2" Residue "A ARG 195": "NH1" <-> "NH2" Residue "A GLU 241": "OE1" <-> "OE2" Residue "A ASP 280": "OD1" <-> "OD2" Residue "A GLU 282": "OE1" <-> "OE2" Residue "A GLU 288": "OE1" <-> "OE2" Residue "B ARG 32": "NH1" <-> "NH2" Residue "B PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 126": "OE1" <-> "OE2" Residue "B GLU 141": "OE1" <-> "OE2" Residue "B GLU 179": "OE1" <-> "OE2" Residue "B ARG 195": "NH1" <-> "NH2" Residue "B GLU 241": "OE1" <-> "OE2" Residue "B ASP 280": "OD1" <-> "OD2" Residue "B GLU 282": "OE1" <-> "OE2" Residue "B GLU 288": "OE1" <-> "OE2" Residue "C ARG 32": "NH1" <-> "NH2" Residue "C PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 126": "OE1" <-> "OE2" Residue "C GLU 141": "OE1" <-> "OE2" Residue "C GLU 179": "OE1" <-> "OE2" Residue "C ARG 195": "NH1" <-> "NH2" Residue "C GLU 241": "OE1" <-> "OE2" Residue "C ASP 280": "OD1" <-> "OD2" Residue "C GLU 282": "OE1" <-> "OE2" Residue "C GLU 288": "OE1" <-> "OE2" Residue "D ARG 32": "NH1" <-> "NH2" Residue "D PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 126": "OE1" <-> "OE2" Residue "D GLU 141": "OE1" <-> "OE2" Residue "D GLU 179": "OE1" <-> "OE2" Residue "D ARG 195": "NH1" <-> "NH2" Residue "D GLU 241": "OE1" <-> "OE2" Residue "D ASP 280": "OD1" <-> "OD2" Residue "D GLU 282": "OE1" <-> "OE2" Residue "D GLU 288": "OE1" <-> "OE2" Residue "E GLU 10": "OE1" <-> "OE2" Residue "E ASP 30": "OD1" <-> "OD2" Residue "E ARG 75": "NH1" <-> "NH2" Residue "E GLU 92": "OE1" <-> "OE2" Residue "E GLU 101": "OE1" <-> "OE2" Residue "E TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 307": "NH1" <-> "NH2" Residue "E PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 516": "OE1" <-> "OE2" Residue "E PHE 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 528": "NH1" <-> "NH2" Residue "E PHE 560": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 569": "OE1" <-> "OE2" Residue "E ASP 571": "OD1" <-> "OD2" Residue "E ASP 676": "OD1" <-> "OD2" Residue "E ARG 703": "NH1" <-> "NH2" Residue "E PHE 739": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 819": "OD1" <-> "OD2" Residue "E ARG 842": "NH1" <-> "NH2" Residue "E ASP 854": "OD1" <-> "OD2" Residue "E ASP 861": "OD1" <-> "OD2" Residue "E ASP 905": "OD1" <-> "OD2" Residue "E GLU 911": "OE1" <-> "OE2" Residue "E ASP 916": "OD1" <-> "OD2" Residue "E GLU 938": "OE1" <-> "OE2" Residue "E GLU 942": "OE1" <-> "OE2" Residue "E ASP 1031": "OD1" <-> "OD2" Residue "E TYR 1064": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1068": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 1124": "NH1" <-> "NH2" Residue "E ASP 1133": "OD1" <-> "OD2" Residue "E GLU 1141": "OE1" <-> "OE2" Residue "E TYR 1181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 1206": "OE1" <-> "OE2" Residue "E PHE 1217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 1222": "NH1" <-> "NH2" Residue "E GLU 1275": "OE1" <-> "OE2" Residue "E TYR 1287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 1304": "OD1" <-> "OD2" Residue "E ARG 1314": "NH1" <-> "NH2" Residue "E GLU 1322": "OE1" <-> "OE2" Residue "E TYR 1326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 1327": "OE1" <-> "OE2" Residue "E PHE 1393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 1406": "OD1" <-> "OD2" Residue "E ARG 1419": "NH1" <-> "NH2" Residue "E ARG 1437": "NH1" <-> "NH2" Residue "E PHE 1438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 1480": "OE1" <-> "OE2" 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 1513": "OD1" <-> "OD2" Residue "E PHE 1528": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1560": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 21148 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: 11072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1407, 11072 Unusual residues: {' MG': 2, 'ADP': 1, 'ATP': 1} Classifications: {'peptide': 1403, 'undetermined': 4} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 42, 'TRANS': 1360, 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: 75 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 53 Time building chain proxies: 12.46, per 1000 atoms: 0.59 Number of scatterers: 21148 At special positions: 0 Unit cell: (130, 154.7, 141.7, 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 121 16.00 P 5 15.00 Mg 2 11.99 O 3750 8.00 N 3597 7.00 C 13673 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 110 " - pdb=" SG CYS A 142 " distance=2.03 Simple disulfide: pdb=" SG CYS B 110 " - pdb=" SG CYS B 142 " distance=2.03 Simple disulfide: pdb=" SG CYS C 110 " - pdb=" SG CYS C 142 " distance=2.03 Simple disulfide: pdb=" SG CYS D 110 " - pdb=" SG CYS D 142 " 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: 9.15 Conformation dependent library (CDL) restraints added in 4.2 seconds 5326 Ramachandran restraints generated. 2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5070 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 87 helices and 26 sheets defined 46.0% alpha, 10.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.59 Creating SS restraints... Processing helix chain 'A' and resid 53 through 56 No H-bonds generated for 'chain 'A' and resid 53 through 56' Processing helix chain 'A' and resid 59 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 143 through 172 Processing helix chain 'A' and resid 177 through 180 Processing helix chain 'A' and resid 306 through 308 No H-bonds generated for 'chain 'A' and resid 306 through 308' Processing helix chain 'A' and resid 330 through 332 No H-bonds generated for 'chain 'A' and resid 330 through 332' Processing helix chain 'A' and resid 346 through 350 removed outlier: 3.794A pdb=" N ASP A 350 " --> pdb=" O ALA A 346 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 346 through 350' Processing helix chain 'B' and resid 53 through 56 No H-bonds generated for 'chain 'B' and resid 53 through 56' Processing helix chain 'B' and resid 59 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 143 through 172 Processing helix chain 'B' and resid 177 through 180 Processing helix chain 'B' and resid 306 through 308 No H-bonds generated for 'chain 'B' and resid 306 through 308' Processing helix chain 'B' and resid 330 through 332 No H-bonds generated for 'chain 'B' and resid 330 through 332' Processing helix chain 'B' and resid 346 through 350 removed outlier: 3.794A pdb=" N ASP B 350 " --> pdb=" O ALA B 346 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 346 through 350' Processing helix chain 'C' and resid 53 through 56 No H-bonds generated for 'chain 'C' and resid 53 through 56' Processing helix chain 'C' and resid 59 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 143 through 172 Processing helix chain 'C' and resid 177 through 180 Processing helix chain 'C' and resid 306 through 308 No H-bonds generated for 'chain 'C' and resid 306 through 308' Processing helix chain 'C' and resid 330 through 332 No H-bonds generated for 'chain 'C' and resid 330 through 332' Processing helix chain 'C' and resid 346 through 350 removed outlier: 3.793A pdb=" N ASP C 350 " --> pdb=" O ALA C 346 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 346 through 350' Processing helix chain 'D' and resid 53 through 56 No H-bonds generated for 'chain 'D' and resid 53 through 56' Processing helix chain 'D' and resid 59 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 143 through 172 Processing helix chain 'D' and resid 177 through 180 Processing helix chain 'D' and resid 306 through 308 No H-bonds generated for 'chain 'D' and resid 306 through 308' Processing helix chain 'D' and resid 330 through 332 No H-bonds generated for 'chain 'D' and resid 330 through 332' Processing helix chain 'D' and resid 346 through 350 removed outlier: 3.793A pdb=" N ASP D 350 " --> pdb=" O ALA D 346 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 346 through 350' Processing helix chain 'E' and resid 14 through 16 No H-bonds generated for 'chain 'E' and resid 14 through 16' Processing helix chain 'E' and resid 26 through 51 removed outlier: 3.563A 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 72 through 96 Processing helix chain 'E' and resid 109 through 130 Processing helix chain 'E' and resid 138 through 161 Processing helix chain 'E' and resid 168 through 192 Processing helix chain 'E' and resid 225 through 230 Processing helix chain 'E' and resid 232 through 239 removed outlier: 3.568A pdb=" N ILE E 238 " --> pdb=" O ASN E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 262 through 274 removed outlier: 5.837A pdb=" N LEU E 267 " --> pdb=" O ASN E 263 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ALA E 273 " --> pdb=" O GLU E 269 " (cutoff:3.500A) Processing helix chain 'E' and resid 285 through 309 removed outlier: 5.631A pdb=" N ARG E 298 " --> pdb=" O HIS E 294 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N ARG E 299 " --> pdb=" O ALA E 295 " (cutoff:3.500A) Processing helix chain 'E' and resid 314 through 327 Proline residue: E 318 - end of helix removed outlier: 3.792A pdb=" N VAL E 325 " --> pdb=" O PHE E 322 " (cutoff:3.500A) Processing helix chain 'E' and resid 349 through 354 Processing helix chain 'E' and resid 356 through 401 removed outlier: 4.001A pdb=" N THR E 394 " --> pdb=" O GLY E 390 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 409 Processing helix chain 'E' and resid 415 through 455 removed outlier: 5.293A pdb=" N ASN E 427 " --> pdb=" O ALA E 423 " (cutoff:3.500A) Proline residue: E 437 - end of helix Proline residue: E 443 - end of helix Processing helix chain 'E' and resid 458 through 505 removed outlier: 3.613A pdb=" N ALA E 461 " --> pdb=" O GLY E 458 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ALA E 466 " --> pdb=" O ILE E 463 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N VAL E 467 " --> pdb=" O GLY E 464 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA E 472 " --> pdb=" O ILE E 469 " (cutoff:3.500A) Proline residue: E 473 - end of helix removed outlier: 3.599A pdb=" N VAL E 478 " --> pdb=" O GLN E 475 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU E 482 " --> pdb=" O ALA E 479 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LEU E 490 " --> pdb=" O ARG E 487 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG E 496 " --> pdb=" O SER E 493 " (cutoff:3.500A) Processing helix chain 'E' and resid 507 through 512 Processing helix chain 'E' and resid 516 through 548 removed outlier: 3.530A pdb=" N SER E 533 " --> pdb=" O LYS E 529 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ALA E 536 " --> pdb=" O THR E 532 " (cutoff:3.500A) Processing helix chain 'E' and resid 551 through 564 Processing helix chain 'E' and resid 574 through 588 Processing helix chain 'E' and resid 594 through 615 Processing helix chain 'E' and resid 720 through 727 removed outlier: 3.620A 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 814 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 846 removed outlier: 3.768A pdb=" N GLN E 846 " --> pdb=" O ARG E 842 " (cutoff:3.500A) Processing helix chain 'E' and resid 862 through 870 Processing helix chain 'E' and resid 894 through 896 No H-bonds generated for 'chain 'E' and resid 894 through 896' Processing helix chain 'E' and resid 914 through 919 Processing helix chain 'E' and resid 922 through 932 Processing helix chain 'E' and resid 999 through 1008 Processing helix chain 'E' and resid 1010 through 1038 Processing helix chain 'E' and resid 1067 through 1097 Processing helix chain 'E' and resid 1101 through 1106 Processing helix chain 'E' and resid 1110 through 1115 Processing helix chain 'E' and resid 1118 through 1134 removed outlier: 4.984A pdb=" N CYS E1129 " --> pdb=" O PHE E1125 " (cutoff:3.500A) Processing helix chain 'E' and resid 1136 through 1160 removed outlier: 3.544A pdb=" N SER E1146 " --> pdb=" O CYS E1142 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU E1148 " --> pdb=" O SER E1144 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU E1149 " --> pdb=" O ARG E1145 " (cutoff:3.500A) Processing helix chain 'E' and resid 1162 through 1216 removed outlier: 4.265A pdb=" N LEU E1165 " --> pdb=" O PRO E1162 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL E1166 " --> pdb=" O VAL E1163 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N LEU E1169 " --> pdb=" O VAL E1166 " (cutoff:3.500A) Proline residue: E1170 - end of helix removed outlier: 3.530A pdb=" N VAL E1174 " --> pdb=" O LEU E1171 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE E1178 " --> pdb=" O CYS E1175 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ARG E1183 " --> pdb=" O LYS E1180 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N VAL E1184 " --> pdb=" O TYR E1181 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG E1187 " --> pdb=" O VAL E1184 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU E1189 " --> pdb=" O SER E1186 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR E1196 " --> pdb=" O ASP E1193 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N LEU E1198 " --> pdb=" O THR E1195 " (cutoff:3.500A) Proline residue: E1199 - end of helix removed outlier: 3.911A pdb=" N VAL E1208 " --> pdb=" O ALA E1205 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLU E1209 " --> pdb=" O GLU E1206 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY E1210 " --> pdb=" O THR E1207 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LEU E1211 " --> pdb=" O VAL E1208 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N THR E1212 " --> pdb=" O GLU E1209 " (cutoff:3.500A) Processing helix chain 'E' and resid 1220 through 1272 removed outlier: 4.029A pdb=" N VAL E1260 " --> pdb=" O GLY E1256 " (cutoff:3.500A) Processing helix chain 'E' and resid 1280 through 1319 removed outlier: 5.342A pdb=" N ASN E1296 " --> pdb=" O SER E1292 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N TRP E1297 " --> pdb=" O ASN E1293 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ALA E1311 " --> pdb=" O LEU E1307 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL E1312 " --> pdb=" O GLN E1308 " (cutoff:3.500A) Processing helix chain 'E' and resid 1385 through 1392 removed outlier: 3.859A pdb=" N SER E1389 " --> pdb=" O LYS E1385 " (cutoff:3.500A) Processing helix chain 'E' and resid 1415 through 1421 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 1497 Processing helix chain 'E' and resid 1514 through 1523 Processing helix chain 'E' and resid 1540 through 1543 No H-bonds generated for 'chain 'E' and resid 1540 through 1543' Processing helix chain 'E' and resid 1563 through 1567 Processing helix chain 'E' and resid 1573 through 1581 Processing sheet with id= A, first strand: chain 'A' and resid 181 through 183 removed outlier: 3.670A pdb=" N VAL A 202 " --> pdb=" O LEU A 255 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU A 255 " --> pdb=" O VAL A 202 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 188 through 192 Processing sheet with id= C, first strand: chain 'A' and resid 234 through 238 removed outlier: 3.777A pdb=" N ARG A 221 " --> pdb=" O HIS A 234 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N MET A 217 " --> pdb=" O ILE A 238 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 313 through 315 Processing sheet with id= E, first strand: chain 'A' and resid 319 through 322 Processing sheet with id= F, first strand: chain 'B' and resid 181 through 183 removed outlier: 3.670A pdb=" N VAL B 202 " --> pdb=" O LEU B 255 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU B 255 " --> pdb=" O VAL B 202 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 188 through 192 Processing sheet with id= H, first strand: chain 'B' and resid 234 through 238 removed outlier: 3.777A pdb=" N ARG B 221 " --> pdb=" O HIS B 234 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N MET B 217 " --> pdb=" O ILE B 238 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 313 through 315 Processing sheet with id= J, first strand: chain 'B' and resid 319 through 322 Processing sheet with id= K, first strand: chain 'C' and resid 181 through 183 removed outlier: 3.670A pdb=" N VAL C 202 " --> pdb=" O LEU C 255 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU C 255 " --> pdb=" O VAL C 202 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 188 through 192 Processing sheet with id= M, first strand: chain 'C' and resid 234 through 238 removed outlier: 3.777A pdb=" N ARG C 221 " --> pdb=" O HIS C 234 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N MET C 217 " --> pdb=" O ILE C 238 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 313 through 315 Processing sheet with id= O, first strand: chain 'C' and resid 319 through 322 Processing sheet with id= P, first strand: chain 'D' and resid 181 through 183 removed outlier: 3.670A pdb=" N VAL D 202 " --> pdb=" O LEU D 255 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU D 255 " --> pdb=" O VAL D 202 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 188 through 192 Processing sheet with id= R, first strand: chain 'D' and resid 234 through 238 removed outlier: 3.777A pdb=" N ARG D 221 " --> pdb=" O HIS D 234 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N MET D 217 " --> pdb=" O ILE D 238 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 313 through 315 Processing sheet with id= T, first strand: chain 'D' and resid 319 through 322 Processing sheet with id= U, first strand: chain 'E' and resid 899 through 903 removed outlier: 6.733A pdb=" N VAL E 884 " --> pdb=" O THR E 710 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N ILE E 712 " --> pdb=" O VAL E 884 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N LEU E 886 " --> pdb=" O ILE E 712 " (cutoff:3.500A) removed outlier: 8.288A pdb=" N GLY E 714 " --> pdb=" O LEU E 886 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N ALA E 771 " --> pdb=" O PHE E 852 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'E' and resid 1376 through 1379 removed outlier: 3.528A pdb=" N VAL E1551 " --> pdb=" O GLU E1559 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N GLU E1559 " --> pdb=" O VAL E1551 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LYS E1553 " --> pdb=" O ILE E1557 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N ILE E1557 " --> pdb=" O LYS E1553 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'E' and resid 1502 through 1505 removed outlier: 6.154A pdb=" N THR E1532 " --> pdb=" O PHE E1503 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N MET E1505 " --> pdb=" O THR E1532 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N VAL E1534 " --> pdb=" O MET E1505 " (cutoff:3.500A) No H-bonds generated for sheet with id= W Processing sheet with id= X, first strand: chain 'E' and resid 686 through 688 removed outlier: 3.758A pdb=" N TYR E 686 " --> pdb=" O SER E 735 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER E 735 " --> pdb=" O TYR E 686 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N THR E 688 " --> pdb=" O LYS E 733 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N LYS E 733 " --> pdb=" O THR E 688 " (cutoff:3.500A) No H-bonds generated for sheet with id= X Processing sheet with id= Y, first strand: chain 'E' and resid 1345 through 1350 removed outlier: 5.368A pdb=" N VAL E1365 " --> pdb=" O ASN E1349 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'E' and resid 1351 through 1353 removed outlier: 3.670A pdb=" N SER E1351 " --> pdb=" O GLU E1400 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ARG E1353 " --> pdb=" O THR E1398 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N THR E1398 " --> pdb=" O ARG E1353 " (cutoff:3.500A) 996 hydrogen bonds defined for protein. 2682 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: 7.77 Time building geometry restraints manager: 9.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6588 1.34 - 1.46: 4241 1.46 - 1.58: 10580 1.58 - 1.70: 8 1.70 - 1.81: 194 Bond restraints: 21611 Sorted by residual: bond pdb=" C4 ATP E1604 " pdb=" C5 ATP E1604 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 5.98e+01 bond pdb=" C5 ATP E1604 " pdb=" C6 ATP E1604 " ideal model delta sigma weight residual 1.409 1.471 -0.062 1.00e-02 1.00e+04 3.87e+01 bond pdb=" C ILE E1136 " pdb=" N PRO E1137 " ideal model delta sigma weight residual 1.336 1.403 -0.067 1.20e-02 6.94e+03 3.09e+01 bond pdb=" C4 ATP E1604 " pdb=" N9 ATP E1604 " ideal model delta sigma weight residual 1.374 1.325 0.049 1.00e-02 1.00e+04 2.42e+01 bond pdb=" C5 ATP E1604 " pdb=" N7 ATP E1604 " ideal model delta sigma weight residual 1.387 1.339 0.048 1.00e-02 1.00e+04 2.31e+01 ... (remaining 21606 not shown) Histogram of bond angle deviations from ideal: 97.62 - 105.32: 388 105.32 - 113.03: 12143 113.03 - 120.73: 9921 120.73 - 128.43: 6695 128.43 - 136.13: 218 Bond angle restraints: 29365 Sorted by residual: angle pdb=" PA ATP E1604 " pdb=" O3A ATP E1604 " pdb=" PB ATP E1604 " ideal model delta sigma weight residual 136.83 117.99 18.84 1.00e+00 1.00e+00 3.55e+02 angle pdb=" PB ATP E1604 " pdb=" O3B ATP E1604 " pdb=" PG ATP E1604 " ideal model delta sigma weight residual 139.87 125.45 14.42 1.00e+00 1.00e+00 2.08e+02 angle pdb=" C5 ATP E1604 " pdb=" C4 ATP E1604 " pdb=" N3 ATP E1604 " ideal model delta sigma weight residual 126.80 119.32 7.48 1.00e+00 1.00e+00 5.59e+01 angle pdb=" N3 ATP E1604 " pdb=" C4 ATP E1604 " pdb=" N9 ATP E1604 " ideal model delta sigma weight residual 127.04 134.77 -7.73 1.15e+00 7.59e-01 4.54e+01 angle pdb=" C ASN E 263 " pdb=" N TYR E 264 " pdb=" CA TYR E 264 " ideal model delta sigma weight residual 121.54 131.73 -10.19 1.91e+00 2.74e-01 2.84e+01 ... (remaining 29360 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.38: 11957 26.38 - 52.75: 765 52.75 - 79.13: 116 79.13 - 105.50: 6 105.50 - 131.88: 1 Dihedral angle restraints: 12845 sinusoidal: 5042 harmonic: 7803 Sorted by residual: dihedral pdb=" CA ILE E 61 " pdb=" C ILE E 61 " pdb=" N HIS E 62 " pdb=" CA HIS E 62 " ideal model delta harmonic sigma weight residual 180.00 141.72 38.28 0 5.00e+00 4.00e-02 5.86e+01 dihedral pdb=" CB CYS B 110 " pdb=" SG CYS B 110 " pdb=" SG CYS B 142 " pdb=" CB CYS B 142 " ideal model delta sinusoidal sigma weight residual 93.00 29.23 63.77 1 1.00e+01 1.00e-02 5.36e+01 dihedral pdb=" CB CYS C 110 " pdb=" SG CYS C 110 " pdb=" SG CYS C 142 " pdb=" CB CYS C 142 " ideal model delta sinusoidal sigma weight residual 93.00 29.25 63.75 1 1.00e+01 1.00e-02 5.35e+01 ... (remaining 12842 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 2639 0.062 - 0.124: 717 0.124 - 0.186: 97 0.186 - 0.249: 18 0.249 - 0.311: 3 Chirality restraints: 3474 Sorted by residual: chirality pdb=" CB ILE E 712 " pdb=" CA ILE E 712 " pdb=" CG1 ILE E 712 " pdb=" CG2 ILE E 712 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.41e+00 chirality pdb=" CB ILE E 704 " pdb=" CA ILE E 704 " pdb=" CG1 ILE E 704 " pdb=" CG2 ILE E 704 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CB VAL E1396 " pdb=" CA VAL E1396 " pdb=" CG1 VAL E1396 " pdb=" CG2 VAL E1396 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.56e+00 ... (remaining 3471 not shown) Planarity restraints: 3650 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR E 264 " -0.020 2.00e-02 2.50e+03 3.94e-02 1.56e+01 pdb=" C TYR E 264 " 0.068 2.00e-02 2.50e+03 pdb=" O TYR E 264 " -0.025 2.00e-02 2.50e+03 pdb=" N GLN E 265 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU E 261 " -0.018 2.00e-02 2.50e+03 3.54e-02 1.25e+01 pdb=" C LEU E 261 " 0.061 2.00e-02 2.50e+03 pdb=" O LEU E 261 " -0.023 2.00e-02 2.50e+03 pdb=" N THR E 262 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL E 422 " 0.014 2.00e-02 2.50e+03 2.75e-02 7.58e+00 pdb=" C VAL E 422 " -0.048 2.00e-02 2.50e+03 pdb=" O VAL E 422 " 0.018 2.00e-02 2.50e+03 pdb=" N ALA E 423 " 0.016 2.00e-02 2.50e+03 ... (remaining 3647 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 342 2.64 - 3.20: 19222 3.20 - 3.77: 35768 3.77 - 4.33: 45783 4.33 - 4.90: 73806 Nonbonded interactions: 174921 Sorted by model distance: nonbonded pdb=" OE1 GLN E 775 " pdb="MG MG E1602 " model vdw 2.073 2.170 nonbonded pdb="MG MG E1602 " pdb=" O3A ATP E1604 " model vdw 2.085 2.170 nonbonded pdb=" OG SER E 721 " pdb="MG MG E1602 " model vdw 2.088 2.170 nonbonded pdb=" O1B ADP E1601 " pdb="MG MG E1603 " model vdw 2.118 2.170 nonbonded pdb=" NE2 GLN E 775 " pdb="MG MG E1602 " model vdw 2.169 2.250 ... (remaining 174916 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: 11.580 Check model and map are aligned: 0.320 Set scattering table: 0.220 Process input model: 61.640 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.110 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 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 : 0.005 0.077 21611 Z= 0.352 Angle : 0.960 18.839 29365 Z= 0.544 Chirality : 0.056 0.311 3474 Planarity : 0.007 0.069 3650 Dihedral : 16.842 131.879 7763 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 6.47 % Allowed : 8.33 % Favored : 85.20 % 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: -3.30 (0.13), residues: 2663 helix: -2.12 (0.10), residues: 1327 sheet: -2.27 (0.26), residues: 274 loop : -2.02 (0.17), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 289 HIS 0.010 0.001 HIS E 106 PHE 0.021 0.002 PHE E 578 TYR 0.023 0.002 TYR E 264 ARG 0.004 0.000 ARG E1421 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5326 Ramachandran restraints generated. 2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5326 Ramachandran restraints generated. 2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 681 residues out of total 2324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 532 time to evaluate : 2.914 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: symmetry clash REVERT: A 39 LYS cc_start: 0.9060 (OUTLIER) cc_final: 0.8690 (ttmt) REVERT: A 51 GLU cc_start: 0.8210 (tp30) cc_final: 0.7682 (tp30) REVERT: A 57 GLN cc_start: 0.8340 (tt0) cc_final: 0.7844 (tp40) REVERT: A 66 LEU cc_start: 0.9173 (mt) cc_final: 0.8878 (mt) REVERT: A 73 LEU cc_start: 0.9057 (OUTLIER) cc_final: 0.8751 (tt) REVERT: A 163 MET cc_start: 0.9473 (mmm) cc_final: 0.9263 (mmm) REVERT: A 170 LYS cc_start: 0.9414 (tptp) cc_final: 0.9157 (tptt) REVERT: A 237 ASP cc_start: 0.7724 (p0) cc_final: 0.7178 (p0) REVERT: A 311 TRP cc_start: 0.9026 (t-100) cc_final: 0.8821 (t60) REVERT: A 330 TYR cc_start: 0.8744 (m-80) cc_final: 0.8442 (m-80) REVERT: B 57 GLN cc_start: 0.8386 (tt0) cc_final: 0.8183 (tp40) REVERT: B 80 LEU cc_start: 0.9655 (mm) cc_final: 0.9439 (mp) REVERT: B 84 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.8859 (mt) REVERT: B 160 ASN cc_start: 0.9147 (m110) cc_final: 0.8896 (m110) REVERT: B 163 MET cc_start: 0.9506 (mmm) cc_final: 0.9102 (mmm) REVERT: B 169 MET cc_start: 0.8820 (ttm) cc_final: 0.8612 (ttm) REVERT: B 176 ARG cc_start: 0.7994 (mtm-85) cc_final: 0.7207 (mtp180) REVERT: B 179 GLU cc_start: 0.8803 (OUTLIER) cc_final: 0.8411 (mt-10) REVERT: B 181 LEU cc_start: 0.9530 (mt) cc_final: 0.9306 (mt) REVERT: B 202 VAL cc_start: 0.9675 (OUTLIER) cc_final: 0.9445 (p) REVERT: B 220 VAL cc_start: 0.9575 (OUTLIER) cc_final: 0.9358 (p) REVERT: B 231 VAL cc_start: 0.8899 (OUTLIER) cc_final: 0.8171 (m) REVERT: B 240 MET cc_start: 0.9076 (tmm) cc_final: 0.8763 (tmm) REVERT: B 302 THR cc_start: 0.9431 (OUTLIER) cc_final: 0.9025 (m) REVERT: B 305 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8633 (mm) REVERT: C 39 LYS cc_start: 0.9381 (OUTLIER) cc_final: 0.8798 (tmtt) REVERT: C 41 ASN cc_start: 0.9013 (m110) cc_final: 0.8778 (m110) REVERT: C 48 ASN cc_start: 0.8812 (m-40) cc_final: 0.7515 (m-40) REVERT: C 56 LEU cc_start: 0.9259 (OUTLIER) cc_final: 0.9054 (mt) REVERT: C 65 ASP cc_start: 0.8387 (t0) cc_final: 0.8073 (t0) REVERT: C 91 TRP cc_start: 0.9275 (t60) cc_final: 0.9029 (t60) REVERT: C 128 GLN cc_start: 0.9001 (tt0) cc_final: 0.8751 (tt0) REVERT: C 160 ASN cc_start: 0.9074 (m110) cc_final: 0.8519 (m110) REVERT: C 163 MET cc_start: 0.9272 (mmm) cc_final: 0.9053 (mmt) REVERT: C 169 MET cc_start: 0.8994 (ttm) cc_final: 0.8697 (ttm) REVERT: C 240 MET cc_start: 0.9158 (tmm) cc_final: 0.8645 (tmm) REVERT: C 279 GLN cc_start: 0.8925 (tp40) cc_final: 0.8116 (tm-30) REVERT: D 54 ARG cc_start: 0.8479 (ptp-110) cc_final: 0.8161 (ptm160) REVERT: D 64 VAL cc_start: 0.9750 (OUTLIER) cc_final: 0.9526 (t) REVERT: D 65 ASP cc_start: 0.9010 (t0) cc_final: 0.8611 (t70) REVERT: D 77 MET cc_start: 0.8749 (OUTLIER) cc_final: 0.8435 (tpp) REVERT: D 163 MET cc_start: 0.9107 (mmm) cc_final: 0.8698 (mmm) REVERT: D 170 LYS cc_start: 0.9073 (tptp) cc_final: 0.8469 (tptt) REVERT: D 262 ASP cc_start: 0.9209 (t0) cc_final: 0.8875 (t70) REVERT: D 265 SER cc_start: 0.9077 (m) cc_final: 0.8767 (p) REVERT: D 330 TYR cc_start: 0.8015 (m-80) cc_final: 0.7716 (m-80) REVERT: E 30 ASP cc_start: 0.8793 (m-30) cc_final: 0.8541 (m-30) REVERT: E 116 MET cc_start: 0.9425 (mmm) cc_final: 0.9111 (mmm) REVERT: E 153 ILE cc_start: 0.9492 (mm) cc_final: 0.9185 (mm) REVERT: E 508 LYS cc_start: 0.9468 (tttt) cc_final: 0.9217 (ttmm) REVERT: E 547 MET cc_start: 0.9016 (tmm) cc_final: 0.8793 (tmm) REVERT: E 584 PHE cc_start: 0.9022 (m-80) cc_final: 0.8735 (m-80) REVERT: E 591 LEU cc_start: 0.9332 (tp) cc_final: 0.8978 (tp) REVERT: E 1020 GLN cc_start: 0.9156 (mm-40) cc_final: 0.8817 (tt0) REVERT: E 1034 LEU cc_start: 0.9343 (tp) cc_final: 0.9128 (tt) REVERT: E 1188 ASP cc_start: 0.8658 (t70) cc_final: 0.8429 (t0) REVERT: E 1191 GLN cc_start: 0.8992 (tm-30) cc_final: 0.8701 (tp-100) REVERT: E 1229 GLU cc_start: 0.8088 (mt-10) cc_final: 0.7874 (mp0) REVERT: E 1290 MET cc_start: 0.8958 (tpp) cc_final: 0.8340 (mmp) REVERT: E 1305 MET cc_start: 0.9341 (tpt) cc_final: 0.9100 (tpp) REVERT: E 1496 PHE cc_start: 0.8602 (m-10) cc_final: 0.8307 (m-80) outliers start: 149 outliers final: 35 residues processed: 625 average time/residue: 0.3405 time to fit residues: 326.3914 Evaluate side-chains 397 residues out of total 2324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 349 time to evaluate : 2.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LYS Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 344 CYS Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 332 LYS Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain C residue 39 LYS Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 77 MET Chi-restraints excluded: chain D residue 116 SER Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 344 CYS Chi-restraints excluded: chain E residue 770 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 226 optimal weight: 8.9990 chunk 203 optimal weight: 1.9990 chunk 112 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 chunk 137 optimal weight: 9.9990 chunk 108 optimal weight: 1.9990 chunk 210 optimal weight: 3.9990 chunk 81 optimal weight: 10.0000 chunk 127 optimal weight: 10.0000 chunk 156 optimal weight: 0.9990 chunk 243 optimal weight: 0.8980 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 242 ASN ** A 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 160 ASN ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 242 ASN B 277 HIS B 279 GLN C 52 GLN ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 160 ASN C 175 HIS C 277 HIS C 278 HIS D 48 ASN D 52 GLN D 153 ASN D 277 HIS E 106 HIS E 167 GLN E 407 ASN E 438 ASN E 475 GLN E 715 GLN E 836 GLN E 923 GLN ** E 933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1020 GLN E1308 GLN E1348 GLN E1364 HIS E1427 GLN E1459 GLN E1486 GLN ** E1488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21611 Z= 0.218 Angle : 0.626 11.367 29365 Z= 0.327 Chirality : 0.043 0.220 3474 Planarity : 0.005 0.058 3650 Dihedral : 7.953 105.427 2979 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.77 % Favored : 95.19 % Rotamer: Outliers : 3.73 % Allowed : 17.45 % Favored : 78.82 % 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: -1.58 (0.15), residues: 2663 helix: -0.44 (0.13), residues: 1332 sheet: -1.47 (0.31), residues: 242 loop : -1.59 (0.18), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 83 HIS 0.005 0.001 HIS E1024 PHE 0.027 0.002 PHE B 75 TYR 0.012 0.001 TYR E 143 ARG 0.005 0.000 ARG E 266 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5326 Ramachandran restraints generated. 2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5326 Ramachandran restraints generated. 2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 2324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 371 time to evaluate : 2.753 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: 0.9189 (mmmm) cc_final: 0.8965 (ttpt) REVERT: A 57 GLN cc_start: 0.8179 (tt0) cc_final: 0.7744 (tp40) REVERT: A 73 LEU cc_start: 0.8972 (tp) cc_final: 0.8747 (tt) REVERT: A 83 TRP cc_start: 0.9572 (m-10) cc_final: 0.8951 (m-90) REVERT: A 141 GLU cc_start: 0.8837 (tp30) cc_final: 0.8422 (tp30) REVERT: A 163 MET cc_start: 0.9547 (mmm) cc_final: 0.9295 (mmm) REVERT: A 170 LYS cc_start: 0.9487 (tptp) cc_final: 0.9015 (tptt) REVERT: A 268 TYR cc_start: 0.8830 (t80) cc_final: 0.8617 (t80) REVERT: A 292 GLU cc_start: 0.8468 (tm-30) cc_final: 0.8260 (tm-30) REVERT: A 311 TRP cc_start: 0.9142 (t-100) cc_final: 0.8852 (t60) REVERT: A 330 TYR cc_start: 0.8670 (m-80) cc_final: 0.8387 (m-80) REVERT: B 57 GLN cc_start: 0.8712 (tt0) cc_final: 0.8334 (tp40) REVERT: B 80 LEU cc_start: 0.9661 (mm) cc_final: 0.9447 (mp) REVERT: B 160 ASN cc_start: 0.9180 (m-40) cc_final: 0.8911 (m-40) REVERT: B 179 GLU cc_start: 0.8839 (OUTLIER) cc_final: 0.8161 (mt-10) REVERT: B 185 LYS cc_start: 0.9158 (ttmm) cc_final: 0.8597 (tptp) REVERT: B 231 VAL cc_start: 0.8945 (OUTLIER) cc_final: 0.8722 (m) REVERT: B 237 ASP cc_start: 0.8137 (p0) cc_final: 0.7443 (p0) REVERT: B 240 MET cc_start: 0.9269 (tmm) cc_final: 0.8709 (tmm) REVERT: B 296 ILE cc_start: 0.9175 (mp) cc_final: 0.8971 (tt) REVERT: C 39 LYS cc_start: 0.9313 (mmmm) cc_final: 0.8770 (tmtt) REVERT: C 47 LYS cc_start: 0.8198 (tppt) cc_final: 0.7856 (tppt) REVERT: C 63 LEU cc_start: 0.9650 (tp) cc_final: 0.9318 (tt) REVERT: C 65 ASP cc_start: 0.8562 (t0) cc_final: 0.8234 (t0) REVERT: C 84 LEU cc_start: 0.9239 (OUTLIER) cc_final: 0.8989 (tt) REVERT: C 160 ASN cc_start: 0.9188 (m-40) cc_final: 0.8742 (m110) REVERT: C 169 MET cc_start: 0.9029 (ttm) cc_final: 0.8720 (ttm) REVERT: C 170 LYS cc_start: 0.9328 (tptm) cc_final: 0.8987 (tttm) REVERT: C 179 GLU cc_start: 0.8428 (mp0) cc_final: 0.8065 (mp0) REVERT: C 185 LYS cc_start: 0.9351 (mmtm) cc_final: 0.8982 (mmtm) REVERT: C 214 THR cc_start: 0.9447 (OUTLIER) cc_final: 0.8783 (t) REVERT: C 240 MET cc_start: 0.8571 (tmm) cc_final: 0.8208 (tmm) REVERT: C 247 ASN cc_start: 0.8808 (p0) cc_final: 0.8508 (p0) REVERT: C 279 GLN cc_start: 0.9007 (tp40) cc_final: 0.8102 (tm-30) REVERT: D 65 ASP cc_start: 0.9027 (t0) cc_final: 0.8700 (t70) REVERT: D 77 MET cc_start: 0.8872 (OUTLIER) cc_final: 0.8323 (tpp) REVERT: D 163 MET cc_start: 0.9147 (mmm) cc_final: 0.8785 (mmm) REVERT: D 170 LYS cc_start: 0.9112 (tptp) cc_final: 0.8271 (tptt) REVERT: D 179 GLU cc_start: 0.8126 (tp30) cc_final: 0.7765 (tp30) REVERT: D 262 ASP cc_start: 0.9275 (t0) cc_final: 0.8839 (t70) REVERT: D 265 SER cc_start: 0.9130 (m) cc_final: 0.8717 (p) REVERT: D 288 GLU cc_start: 0.8240 (mt-10) cc_final: 0.7577 (tt0) REVERT: D 293 THR cc_start: 0.9336 (p) cc_final: 0.8933 (p) REVERT: E 30 ASP cc_start: 0.8802 (m-30) cc_final: 0.8492 (m-30) REVERT: E 80 PHE cc_start: 0.8680 (m-80) cc_final: 0.8346 (m-80) REVERT: E 82 LEU cc_start: 0.9756 (tp) cc_final: 0.9554 (tp) REVERT: E 116 MET cc_start: 0.9412 (mmm) cc_final: 0.9101 (mmm) REVERT: E 153 ILE cc_start: 0.9506 (mm) cc_final: 0.9236 (mm) REVERT: E 413 MET cc_start: 0.8021 (ptp) cc_final: 0.7809 (ptp) REVERT: E 442 MET cc_start: 0.8894 (tpt) cc_final: 0.8673 (tpt) REVERT: E 547 MET cc_start: 0.8902 (tmm) cc_final: 0.8584 (tmm) REVERT: E 584 PHE cc_start: 0.9008 (m-80) cc_final: 0.8696 (m-80) REVERT: E 591 LEU cc_start: 0.9147 (tp) cc_final: 0.8824 (tp) REVERT: E 790 PHE cc_start: 0.8721 (t80) cc_final: 0.8448 (t80) REVERT: E 1110 MET cc_start: 0.8520 (mtp) cc_final: 0.8299 (mmm) REVERT: E 1143 LEU cc_start: 0.9582 (tp) cc_final: 0.9239 (pp) REVERT: E 1290 MET cc_start: 0.8969 (tpp) cc_final: 0.8635 (mmp) REVERT: E 1395 MET cc_start: 0.8841 (mmm) cc_final: 0.8610 (mmm) outliers start: 86 outliers final: 50 residues processed: 432 average time/residue: 0.3176 time to fit residues: 218.1782 Evaluate side-chains 364 residues out of total 2324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 309 time to evaluate : 2.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 344 CYS Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain B residue 222 LYS Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 332 LYS Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain D residue 77 MET Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain D residue 153 ASN Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain E residue 12 HIS Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 306 PHE Chi-restraints excluded: chain E residue 429 LEU Chi-restraints excluded: chain E residue 439 LEU Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 770 VAL Chi-restraints excluded: chain E residue 884 VAL Chi-restraints excluded: chain E residue 1016 LEU Chi-restraints excluded: chain E residue 1198 LEU Chi-restraints excluded: chain E residue 1228 LEU Chi-restraints excluded: chain E residue 1260 VAL Chi-restraints excluded: chain E residue 1296 ASN Chi-restraints excluded: chain E residue 1362 LEU Chi-restraints excluded: chain E residue 1504 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 135 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 202 optimal weight: 5.9990 chunk 165 optimal weight: 9.9990 chunk 67 optimal weight: 0.7980 chunk 243 optimal weight: 6.9990 chunk 263 optimal weight: 0.9990 chunk 217 optimal weight: 7.9990 chunk 241 optimal weight: 7.9990 chunk 83 optimal weight: 10.0000 chunk 195 optimal weight: 5.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 GLN ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 278 HIS ** A 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 242 ASN C 153 ASN C 173 GLN C 242 ASN C 279 GLN ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 327 HIS E 494 ASN ** E 797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 889 HIS ** E 933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.2974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 21611 Z= 0.290 Angle : 0.642 11.674 29365 Z= 0.332 Chirality : 0.043 0.172 3474 Planarity : 0.004 0.062 3650 Dihedral : 7.196 102.935 2931 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 15.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 4.34 % Allowed : 20.40 % Favored : 75.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.16), residues: 2663 helix: 0.17 (0.14), residues: 1335 sheet: -1.05 (0.31), residues: 231 loop : -1.44 (0.19), residues: 1097 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E1033 HIS 0.005 0.001 HIS E 327 PHE 0.029 0.002 PHE E1496 TYR 0.020 0.001 TYR C 268 ARG 0.008 0.000 ARG E1579 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5326 Ramachandran restraints generated. 2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5326 Ramachandran restraints generated. 2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 2324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 328 time to evaluate : 2.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LEU cc_start: 0.9190 (mt) cc_final: 0.8963 (mt) REVERT: A 83 TRP cc_start: 0.9636 (m-10) cc_final: 0.9431 (m-10) REVERT: A 163 MET cc_start: 0.9564 (mmm) cc_final: 0.9307 (mmm) REVERT: A 170 LYS cc_start: 0.9560 (tptp) cc_final: 0.9137 (tptt) REVERT: A 268 TYR cc_start: 0.8835 (t80) cc_final: 0.8534 (t80) REVERT: A 332 LYS cc_start: 0.9407 (pttt) cc_final: 0.9100 (ptpp) REVERT: B 47 LYS cc_start: 0.9284 (tppt) cc_final: 0.9083 (tppt) REVERT: B 57 GLN cc_start: 0.8810 (tt0) cc_final: 0.8431 (tp40) REVERT: B 160 ASN cc_start: 0.9130 (m-40) cc_final: 0.8840 (m110) REVERT: B 169 MET cc_start: 0.9161 (ttm) cc_final: 0.8892 (ttm) REVERT: B 179 GLU cc_start: 0.8608 (mt-10) cc_final: 0.7977 (pt0) REVERT: B 185 LYS cc_start: 0.9336 (ttmm) cc_final: 0.8864 (tptt) REVERT: B 231 VAL cc_start: 0.9047 (OUTLIER) cc_final: 0.8818 (m) REVERT: B 240 MET cc_start: 0.9208 (tmm) cc_final: 0.8435 (tmm) REVERT: C 39 LYS cc_start: 0.9369 (mmmm) cc_final: 0.8895 (tmtt) REVERT: C 47 LYS cc_start: 0.8326 (tppt) cc_final: 0.8075 (tppt) REVERT: C 56 LEU cc_start: 0.9196 (pp) cc_final: 0.8984 (mm) REVERT: C 63 LEU cc_start: 0.9655 (tp) cc_final: 0.9401 (tt) REVERT: C 65 ASP cc_start: 0.8669 (t0) cc_final: 0.8262 (t0) REVERT: C 84 LEU cc_start: 0.9201 (OUTLIER) cc_final: 0.8983 (tt) REVERT: C 160 ASN cc_start: 0.9173 (m-40) cc_final: 0.8758 (m110) REVERT: C 169 MET cc_start: 0.9099 (ttm) cc_final: 0.8728 (ttm) REVERT: C 170 LYS cc_start: 0.9454 (tptm) cc_final: 0.9160 (tttm) REVERT: C 179 GLU cc_start: 0.8403 (mp0) cc_final: 0.8101 (mp0) REVERT: C 214 THR cc_start: 0.9470 (OUTLIER) cc_final: 0.8713 (t) REVERT: C 240 MET cc_start: 0.8332 (tmm) cc_final: 0.8097 (tmm) REVERT: C 247 ASN cc_start: 0.8946 (p0) cc_final: 0.8531 (p0) REVERT: C 332 LYS cc_start: 0.9311 (OUTLIER) cc_final: 0.8995 (pttp) REVERT: D 55 PHE cc_start: 0.9094 (OUTLIER) cc_final: 0.8754 (t80) REVERT: D 65 ASP cc_start: 0.9079 (t0) cc_final: 0.8774 (t70) REVERT: D 77 MET cc_start: 0.8856 (OUTLIER) cc_final: 0.8448 (tpp) REVERT: D 88 MET cc_start: 0.8616 (tmm) cc_final: 0.8023 (tmm) REVERT: D 137 MET cc_start: 0.8961 (tmm) cc_final: 0.8747 (tmm) REVERT: D 163 MET cc_start: 0.9196 (mmm) cc_final: 0.8785 (mmm) REVERT: D 170 LYS cc_start: 0.9238 (tptp) cc_final: 0.8729 (tptt) REVERT: D 179 GLU cc_start: 0.8024 (tp30) cc_final: 0.7565 (tp30) REVERT: D 209 MET cc_start: 0.8883 (mmm) cc_final: 0.8661 (mmm) REVERT: D 262 ASP cc_start: 0.9258 (t0) cc_final: 0.8736 (t70) REVERT: D 265 SER cc_start: 0.9070 (m) cc_final: 0.8637 (p) REVERT: E 30 ASP cc_start: 0.8884 (m-30) cc_final: 0.8656 (m-30) REVERT: E 83 LEU cc_start: 0.9601 (mt) cc_final: 0.9321 (mt) REVERT: E 108 TYR cc_start: 0.8509 (OUTLIER) cc_final: 0.7813 (m-80) REVERT: E 116 MET cc_start: 0.9428 (mmm) cc_final: 0.9135 (mmm) REVERT: E 153 ILE cc_start: 0.9532 (mm) cc_final: 0.9242 (mm) REVERT: E 226 LEU cc_start: 0.8861 (tt) cc_final: 0.8552 (tp) REVERT: E 413 MET cc_start: 0.8198 (ptp) cc_final: 0.7991 (ptp) REVERT: E 442 MET cc_start: 0.8965 (tpt) cc_final: 0.8754 (tpt) REVERT: E 547 MET cc_start: 0.8863 (tmm) cc_final: 0.8371 (tmm) REVERT: E 584 PHE cc_start: 0.8929 (m-80) cc_final: 0.8729 (m-80) REVERT: E 790 PHE cc_start: 0.8755 (t80) cc_final: 0.8412 (t80) REVERT: E 1402 HIS cc_start: 0.8299 (m-70) cc_final: 0.7934 (t-170) REVERT: E 1525 MET cc_start: 0.8416 (ptp) cc_final: 0.7899 (ppp) outliers start: 100 outliers final: 59 residues processed: 399 average time/residue: 0.3148 time to fit residues: 199.9391 Evaluate side-chains 356 residues out of total 2324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 290 time to evaluate : 2.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 242 ASN Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain C residue 42 CYS Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 153 ASN Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 332 LYS Chi-restraints excluded: chain D residue 55 PHE Chi-restraints excluded: chain D residue 77 MET Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 258 TYR Chi-restraints excluded: chain D residue 273 SER Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 108 TYR Chi-restraints excluded: chain E residue 109 MET Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 306 PHE Chi-restraints excluded: chain E residue 353 LEU Chi-restraints excluded: chain E residue 365 LEU Chi-restraints excluded: chain E residue 429 LEU Chi-restraints excluded: chain E residue 439 LEU Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 702 ILE Chi-restraints excluded: chain E residue 770 VAL Chi-restraints excluded: chain E residue 804 GLU Chi-restraints excluded: chain E residue 884 VAL Chi-restraints excluded: chain E residue 1016 LEU Chi-restraints excluded: chain E residue 1039 ASP Chi-restraints excluded: chain E residue 1168 LEU Chi-restraints excluded: chain E residue 1198 LEU Chi-restraints excluded: chain E residue 1228 LEU Chi-restraints excluded: chain E residue 1258 CYS Chi-restraints excluded: chain E residue 1260 VAL Chi-restraints excluded: chain E residue 1296 ASN Chi-restraints excluded: chain E residue 1362 LEU Chi-restraints excluded: chain E residue 1396 VAL Chi-restraints excluded: chain E residue 1504 ILE Chi-restraints excluded: chain E residue 1509 THR Chi-restraints excluded: chain E residue 1532 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 240 optimal weight: 5.9990 chunk 183 optimal weight: 8.9990 chunk 126 optimal weight: 0.6980 chunk 26 optimal weight: 8.9990 chunk 116 optimal weight: 0.8980 chunk 163 optimal weight: 0.8980 chunk 244 optimal weight: 6.9990 chunk 259 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 231 optimal weight: 0.9990 chunk 69 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 153 ASN D 52 GLN ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 153 ASN ** E 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1197 GLN ** E1488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1541 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.3193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21611 Z= 0.168 Angle : 0.590 11.728 29365 Z= 0.295 Chirality : 0.042 0.173 3474 Planarity : 0.003 0.064 3650 Dihedral : 6.763 107.397 2924 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.82 % Allowed : 22.31 % Favored : 73.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.16), residues: 2663 helix: 0.52 (0.14), residues: 1320 sheet: -0.78 (0.31), residues: 253 loop : -1.34 (0.19), residues: 1090 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 83 HIS 0.005 0.000 HIS E1024 PHE 0.024 0.001 PHE E1496 TYR 0.022 0.001 TYR C 268 ARG 0.006 0.000 ARG E1579 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5326 Ramachandran restraints generated. 2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5326 Ramachandran restraints generated. 2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 2324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 335 time to evaluate : 2.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LEU cc_start: 0.9103 (mt) cc_final: 0.8800 (pp) REVERT: A 77 MET cc_start: 0.8761 (OUTLIER) cc_final: 0.8554 (mmm) REVERT: A 83 TRP cc_start: 0.9582 (m-10) cc_final: 0.9039 (m-90) REVERT: A 163 MET cc_start: 0.9517 (mmm) cc_final: 0.9269 (mmm) REVERT: A 268 TYR cc_start: 0.8669 (t80) cc_final: 0.8420 (t80) REVERT: A 292 GLU cc_start: 0.8468 (tm-30) cc_final: 0.8243 (tm-30) REVERT: A 332 LYS cc_start: 0.9360 (pttt) cc_final: 0.9087 (ptpp) REVERT: B 57 GLN cc_start: 0.8800 (tt0) cc_final: 0.8512 (tp40) REVERT: B 160 ASN cc_start: 0.9114 (m-40) cc_final: 0.8866 (m-40) REVERT: B 169 MET cc_start: 0.9118 (ttm) cc_final: 0.8644 (ttm) REVERT: B 185 LYS cc_start: 0.9304 (ttmm) cc_final: 0.9027 (tptt) REVERT: B 231 VAL cc_start: 0.9030 (OUTLIER) cc_final: 0.8807 (m) REVERT: B 240 MET cc_start: 0.9202 (tmm) cc_final: 0.8331 (tmm) REVERT: B 296 ILE cc_start: 0.9251 (mp) cc_final: 0.8893 (tt) REVERT: B 330 TYR cc_start: 0.8134 (m-80) cc_final: 0.7912 (m-80) REVERT: C 39 LYS cc_start: 0.9273 (mmmm) cc_final: 0.8726 (tmtt) REVERT: C 47 LYS cc_start: 0.8496 (tppt) cc_final: 0.8227 (tppt) REVERT: C 63 LEU cc_start: 0.9647 (tp) cc_final: 0.9436 (tt) REVERT: C 65 ASP cc_start: 0.8619 (t0) cc_final: 0.8231 (t0) REVERT: C 84 LEU cc_start: 0.9190 (OUTLIER) cc_final: 0.8927 (tt) REVERT: C 160 ASN cc_start: 0.9161 (m-40) cc_final: 0.8790 (m110) REVERT: C 169 MET cc_start: 0.9087 (ttm) cc_final: 0.8652 (ttm) REVERT: C 170 LYS cc_start: 0.9410 (tptm) cc_final: 0.9109 (tttm) REVERT: C 179 GLU cc_start: 0.8398 (mp0) cc_final: 0.8066 (mp0) REVERT: C 214 THR cc_start: 0.9466 (OUTLIER) cc_final: 0.8877 (t) REVERT: C 240 MET cc_start: 0.7859 (tmm) cc_final: 0.6846 (tmm) REVERT: C 247 ASN cc_start: 0.8781 (p0) cc_final: 0.8502 (p0) REVERT: C 332 LYS cc_start: 0.9247 (OUTLIER) cc_final: 0.8901 (pttp) REVERT: C 338 LYS cc_start: 0.9115 (tppt) cc_final: 0.8848 (tppt) REVERT: D 50 ARG cc_start: 0.7351 (mmp-170) cc_final: 0.6948 (mmp80) REVERT: D 55 PHE cc_start: 0.9108 (OUTLIER) cc_final: 0.8778 (t80) REVERT: D 65 ASP cc_start: 0.9041 (t0) cc_final: 0.8832 (t70) REVERT: D 77 MET cc_start: 0.8751 (ttp) cc_final: 0.8547 (tpp) REVERT: D 88 MET cc_start: 0.8610 (tmm) cc_final: 0.7959 (tmm) REVERT: D 137 MET cc_start: 0.8871 (tmm) cc_final: 0.8591 (tmm) REVERT: D 163 MET cc_start: 0.9162 (mmm) cc_final: 0.8780 (mmm) REVERT: D 170 LYS cc_start: 0.9176 (tptp) cc_final: 0.8623 (tptt) REVERT: D 179 GLU cc_start: 0.8005 (tp30) cc_final: 0.7559 (tp30) REVERT: D 209 MET cc_start: 0.8710 (mmm) cc_final: 0.8493 (mmm) REVERT: D 262 ASP cc_start: 0.9226 (t0) cc_final: 0.8864 (t70) REVERT: D 292 GLU cc_start: 0.8452 (tm-30) cc_final: 0.8133 (tm-30) REVERT: D 293 THR cc_start: 0.9241 (p) cc_final: 0.8967 (p) REVERT: E 30 ASP cc_start: 0.8860 (m-30) cc_final: 0.8614 (m-30) REVERT: E 73 ASN cc_start: 0.9131 (OUTLIER) cc_final: 0.8794 (p0) REVERT: E 83 LEU cc_start: 0.9604 (mt) cc_final: 0.9381 (mt) REVERT: E 108 TYR cc_start: 0.8394 (OUTLIER) cc_final: 0.7730 (m-80) REVERT: E 116 MET cc_start: 0.9458 (mmm) cc_final: 0.9135 (mmm) REVERT: E 153 ILE cc_start: 0.9529 (mm) cc_final: 0.9233 (mm) REVERT: E 413 MET cc_start: 0.8028 (ptp) cc_final: 0.7827 (ptp) REVERT: E 419 CYS cc_start: 0.9092 (m) cc_final: 0.8805 (t) REVERT: E 442 MET cc_start: 0.9006 (tpt) cc_final: 0.8805 (tpt) REVERT: E 503 MET cc_start: 0.9128 (tpp) cc_final: 0.8801 (tpt) REVERT: E 611 LEU cc_start: 0.9612 (OUTLIER) cc_final: 0.9370 (mm) REVERT: E 711 MET cc_start: 0.8145 (mpp) cc_final: 0.7678 (mpp) REVERT: E 790 PHE cc_start: 0.8691 (t80) cc_final: 0.8425 (t80) REVERT: E 1080 LEU cc_start: 0.9313 (tp) cc_final: 0.8951 (mt) REVERT: E 1143 LEU cc_start: 0.9600 (tp) cc_final: 0.9227 (pp) REVERT: E 1191 GLN cc_start: 0.9097 (tm-30) cc_final: 0.8824 (tm-30) REVERT: E 1280 LEU cc_start: 0.9258 (mp) cc_final: 0.9044 (mm) REVERT: E 1402 HIS cc_start: 0.8221 (m-70) cc_final: 0.7939 (t-170) REVERT: E 1455 LEU cc_start: 0.9452 (OUTLIER) cc_final: 0.9192 (pp) REVERT: E 1525 MET cc_start: 0.8500 (ptp) cc_final: 0.8196 (ptp) outliers start: 88 outliers final: 46 residues processed: 399 average time/residue: 0.3112 time to fit residues: 198.6195 Evaluate side-chains 369 residues out of total 2324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 313 time to evaluate : 2.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain C residue 42 CYS Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 115 HIS Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 166 SER Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 332 LYS Chi-restraints excluded: chain D residue 55 PHE Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 273 SER Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 73 ASN Chi-restraints excluded: chain E residue 108 TYR Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 311 ASP Chi-restraints excluded: chain E residue 353 LEU Chi-restraints excluded: chain E residue 365 LEU Chi-restraints excluded: chain E residue 429 LEU Chi-restraints excluded: chain E residue 439 LEU Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 611 LEU Chi-restraints excluded: chain E residue 704 ILE Chi-restraints excluded: chain E residue 712 ILE Chi-restraints excluded: chain E residue 770 VAL Chi-restraints excluded: chain E residue 884 VAL Chi-restraints excluded: chain E residue 1027 LEU Chi-restraints excluded: chain E residue 1071 LEU Chi-restraints excluded: chain E residue 1258 CYS Chi-restraints excluded: chain E residue 1260 VAL Chi-restraints excluded: chain E residue 1261 LEU Chi-restraints excluded: chain E residue 1296 ASN Chi-restraints excluded: chain E residue 1362 LEU Chi-restraints excluded: chain E residue 1396 VAL Chi-restraints excluded: chain E residue 1455 LEU Chi-restraints excluded: chain E residue 1504 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 215 optimal weight: 10.0000 chunk 147 optimal weight: 9.9990 chunk 3 optimal weight: 5.9990 chunk 192 optimal weight: 8.9990 chunk 106 optimal weight: 8.9990 chunk 221 optimal weight: 4.9990 chunk 179 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 132 optimal weight: 7.9990 chunk 232 optimal weight: 8.9990 chunk 65 optimal weight: 7.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 276 HIS A 277 HIS B 70 HIS C 46 HIS C 48 ASN C 335 ASN ** D 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 106 HIS E 161 HIS ** E 797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 896 HIS ** E 933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1024 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1316 HIS ** E1488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1541 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.3972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.093 21611 Z= 0.667 Angle : 0.873 10.941 29365 Z= 0.456 Chirality : 0.049 0.178 3474 Planarity : 0.005 0.054 3650 Dihedral : 7.527 125.266 2919 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 23.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 6.51 % Allowed : 21.96 % Favored : 71.53 % 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: -0.84 (0.16), residues: 2663 helix: 0.14 (0.14), residues: 1305 sheet: -0.99 (0.30), residues: 251 loop : -1.21 (0.19), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 83 HIS 0.008 0.002 HIS E1203 PHE 0.024 0.003 PHE E 80 TYR 0.022 0.002 TYR C 268 ARG 0.006 0.001 ARG E1099 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5326 Ramachandran restraints generated. 2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5326 Ramachandran restraints generated. 2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 2324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 272 time to evaluate : 2.921 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 56 LEU cc_start: 0.9318 (mt) cc_final: 0.8914 (pp) REVERT: A 83 TRP cc_start: 0.9725 (m-10) cc_final: 0.9067 (m-90) REVERT: A 292 GLU cc_start: 0.8635 (tm-30) cc_final: 0.8412 (tm-30) REVERT: A 332 LYS cc_start: 0.9486 (pttt) cc_final: 0.9283 (ptpp) REVERT: B 160 ASN cc_start: 0.9238 (m-40) cc_final: 0.8969 (m-40) REVERT: B 185 LYS cc_start: 0.9381 (ttmm) cc_final: 0.9035 (tptp) REVERT: B 231 VAL cc_start: 0.9011 (OUTLIER) cc_final: 0.8769 (m) REVERT: B 240 MET cc_start: 0.9192 (tmm) cc_final: 0.8292 (tmm) REVERT: B 296 ILE cc_start: 0.9379 (mp) cc_final: 0.8835 (tt) REVERT: C 39 LYS cc_start: 0.9407 (mmmm) cc_final: 0.8852 (tmtt) REVERT: C 47 LYS cc_start: 0.8449 (tppt) cc_final: 0.8140 (tppt) REVERT: C 49 ILE cc_start: 0.8033 (OUTLIER) cc_final: 0.7787 (mp) REVERT: C 63 LEU cc_start: 0.9678 (tp) cc_final: 0.9462 (tt) REVERT: C 65 ASP cc_start: 0.8862 (t0) cc_final: 0.8367 (t0) REVERT: C 84 LEU cc_start: 0.9373 (OUTLIER) cc_final: 0.9119 (tt) REVERT: C 160 ASN cc_start: 0.9173 (m-40) cc_final: 0.8837 (m-40) REVERT: C 169 MET cc_start: 0.9237 (ttm) cc_final: 0.9026 (ttm) REVERT: C 170 LYS cc_start: 0.9551 (tptm) cc_final: 0.9267 (tttm) REVERT: C 179 GLU cc_start: 0.8680 (mp0) cc_final: 0.8352 (mp0) REVERT: C 332 LYS cc_start: 0.9351 (OUTLIER) cc_final: 0.9136 (pttp) REVERT: C 338 LYS cc_start: 0.9174 (tppt) cc_final: 0.8967 (tppt) REVERT: D 50 ARG cc_start: 0.7431 (mmp-170) cc_final: 0.7049 (mmp80) REVERT: D 55 PHE cc_start: 0.9213 (OUTLIER) cc_final: 0.8785 (t80) REVERT: D 77 MET cc_start: 0.8954 (ttp) cc_final: 0.8698 (tpp) REVERT: D 88 MET cc_start: 0.8841 (tmm) cc_final: 0.8086 (tmm) REVERT: D 115 HIS cc_start: 0.8543 (OUTLIER) cc_final: 0.8224 (p90) REVERT: D 142 CYS cc_start: 0.7463 (m) cc_final: 0.6983 (m) REVERT: D 170 LYS cc_start: 0.9501 (tptp) cc_final: 0.9179 (tppt) REVERT: D 262 ASP cc_start: 0.9232 (t0) cc_final: 0.8537 (t70) REVERT: D 265 SER cc_start: 0.9159 (m) cc_final: 0.8696 (p) REVERT: D 288 GLU cc_start: 0.8370 (mt-10) cc_final: 0.8097 (mt-10) REVERT: E 83 LEU cc_start: 0.9634 (mt) cc_final: 0.9342 (mt) REVERT: E 108 TYR cc_start: 0.8754 (OUTLIER) cc_final: 0.8114 (m-80) REVERT: E 116 MET cc_start: 0.9429 (mmm) cc_final: 0.9140 (mmm) REVERT: E 251 ILE cc_start: 0.9611 (OUTLIER) cc_final: 0.9328 (tp) REVERT: E 311 ASP cc_start: 0.9000 (OUTLIER) cc_final: 0.8496 (p0) REVERT: E 413 MET cc_start: 0.8346 (ptp) cc_final: 0.7975 (pmm) REVERT: E 442 MET cc_start: 0.9056 (tpt) cc_final: 0.8775 (tpt) REVERT: E 547 MET cc_start: 0.8614 (ttt) cc_final: 0.7620 (tmm) REVERT: E 584 PHE cc_start: 0.9070 (m-80) cc_final: 0.8610 (m-80) REVERT: E 611 LEU cc_start: 0.9663 (OUTLIER) cc_final: 0.9253 (mm) REVERT: E 711 MET cc_start: 0.8092 (mpp) cc_final: 0.7599 (mpp) REVERT: E 1080 LEU cc_start: 0.9451 (tp) cc_final: 0.9232 (mt) REVERT: E 1395 MET cc_start: 0.9276 (mmm) cc_final: 0.8883 (tpt) REVERT: E 1525 MET cc_start: 0.8629 (ptp) cc_final: 0.8038 (ppp) outliers start: 150 outliers final: 95 residues processed: 398 average time/residue: 0.3080 time to fit residues: 198.9589 Evaluate side-chains 358 residues out of total 2324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 253 time to evaluate : 2.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 335 ASN Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain C residue 41 ASN Chi-restraints excluded: chain C residue 42 CYS Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 115 HIS Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 166 SER Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 332 LYS Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain D residue 43 ASN Chi-restraints excluded: chain D residue 55 PHE Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 115 HIS Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain D residue 258 TYR Chi-restraints excluded: chain D residue 273 SER Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain E residue 12 HIS Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 73 ASN Chi-restraints excluded: chain E residue 108 TYR Chi-restraints excluded: chain E residue 109 MET Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 211 LEU Chi-restraints excluded: chain E residue 251 ILE Chi-restraints excluded: chain E residue 306 PHE Chi-restraints excluded: chain E residue 311 ASP Chi-restraints excluded: chain E residue 353 LEU Chi-restraints excluded: chain E residue 365 LEU Chi-restraints excluded: chain E residue 394 THR Chi-restraints excluded: chain E residue 429 LEU Chi-restraints excluded: chain E residue 439 LEU Chi-restraints excluded: chain E residue 453 LEU Chi-restraints excluded: chain E residue 467 VAL Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 611 LEU Chi-restraints excluded: chain E residue 682 ILE Chi-restraints excluded: chain E residue 702 ILE Chi-restraints excluded: chain E residue 770 VAL Chi-restraints excluded: chain E residue 884 VAL Chi-restraints excluded: chain E residue 1016 LEU Chi-restraints excluded: chain E residue 1027 LEU Chi-restraints excluded: chain E residue 1064 TYR Chi-restraints excluded: chain E residue 1071 LEU Chi-restraints excluded: chain E residue 1136 ILE Chi-restraints excluded: chain E residue 1175 CYS Chi-restraints excluded: chain E residue 1198 LEU Chi-restraints excluded: chain E residue 1228 LEU Chi-restraints excluded: chain E residue 1259 VAL Chi-restraints excluded: chain E residue 1260 VAL Chi-restraints excluded: chain E residue 1261 LEU Chi-restraints excluded: chain E residue 1296 ASN Chi-restraints excluded: chain E residue 1362 LEU Chi-restraints excluded: chain E residue 1396 VAL Chi-restraints excluded: chain E residue 1455 LEU Chi-restraints excluded: chain E residue 1497 VAL Chi-restraints excluded: chain E residue 1504 ILE Chi-restraints excluded: chain E residue 1509 THR Chi-restraints excluded: chain E residue 1532 THR Chi-restraints excluded: chain E residue 1581 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 87 optimal weight: 0.6980 chunk 233 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 152 optimal weight: 0.2980 chunk 63 optimal weight: 8.9990 chunk 259 optimal weight: 0.9980 chunk 215 optimal weight: 6.9990 chunk 120 optimal weight: 0.5980 chunk 21 optimal weight: 0.9980 chunk 85 optimal weight: 3.9990 chunk 136 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 57 GLN D 97 HIS D 153 ASN ** E 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 499 GLN ** E 797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 923 GLN ** E 933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1541 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.3843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21611 Z= 0.183 Angle : 0.617 12.380 29365 Z= 0.308 Chirality : 0.043 0.305 3474 Planarity : 0.003 0.063 3650 Dihedral : 6.982 118.266 2919 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 4.21 % Allowed : 24.48 % Favored : 71.31 % 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: -0.50 (0.16), residues: 2663 helix: 0.51 (0.14), residues: 1324 sheet: -0.96 (0.31), residues: 253 loop : -1.15 (0.19), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 83 HIS 0.007 0.001 HIS E1024 PHE 0.032 0.001 PHE E 133 TYR 0.023 0.001 TYR C 268 ARG 0.004 0.000 ARG E1579 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5326 Ramachandran restraints generated. 2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5326 Ramachandran restraints generated. 2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 2324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 306 time to evaluate : 2.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LEU cc_start: 0.9294 (mt) cc_final: 0.8833 (pp) REVERT: A 77 MET cc_start: 0.8732 (OUTLIER) cc_final: 0.8481 (mmm) REVERT: A 83 TRP cc_start: 0.9647 (m-10) cc_final: 0.9097 (m-90) REVERT: A 179 GLU cc_start: 0.8402 (tp30) cc_final: 0.8090 (tp30) REVERT: A 268 TYR cc_start: 0.8589 (t80) cc_final: 0.8101 (t80) REVERT: A 332 LYS cc_start: 0.9395 (pttt) cc_final: 0.9127 (ptpp) REVERT: B 57 GLN cc_start: 0.8587 (OUTLIER) cc_final: 0.8100 (tp40) REVERT: B 160 ASN cc_start: 0.9138 (m-40) cc_final: 0.8854 (m110) REVERT: B 185 LYS cc_start: 0.9320 (ttmm) cc_final: 0.8967 (tptt) REVERT: B 231 VAL cc_start: 0.9039 (OUTLIER) cc_final: 0.8803 (m) REVERT: B 240 MET cc_start: 0.9266 (tmm) cc_final: 0.8468 (tmm) REVERT: B 296 ILE cc_start: 0.9392 (mp) cc_final: 0.8931 (tt) REVERT: B 330 TYR cc_start: 0.8260 (m-80) cc_final: 0.7813 (m-80) REVERT: C 39 LYS cc_start: 0.9293 (mmmm) cc_final: 0.8776 (tmtt) REVERT: C 47 LYS cc_start: 0.8450 (tppt) cc_final: 0.8100 (tppt) REVERT: C 65 ASP cc_start: 0.8746 (t0) cc_final: 0.8279 (t0) REVERT: C 84 LEU cc_start: 0.9368 (OUTLIER) cc_final: 0.9131 (tt) REVERT: C 160 ASN cc_start: 0.9157 (m-40) cc_final: 0.8794 (m110) REVERT: C 170 LYS cc_start: 0.9399 (tptm) cc_final: 0.9122 (tttm) REVERT: C 179 GLU cc_start: 0.8498 (mp0) cc_final: 0.8177 (mp0) REVERT: C 214 THR cc_start: 0.9326 (OUTLIER) cc_final: 0.8476 (t) REVERT: C 247 ASN cc_start: 0.8415 (p0) cc_final: 0.7591 (p0) REVERT: C 288 GLU cc_start: 0.8729 (mm-30) cc_final: 0.8134 (mm-30) REVERT: C 332 LYS cc_start: 0.9223 (OUTLIER) cc_final: 0.8944 (pttp) REVERT: C 338 LYS cc_start: 0.9129 (tppt) cc_final: 0.8919 (tppt) REVERT: D 50 ARG cc_start: 0.7208 (mmp-170) cc_final: 0.6915 (mmp80) REVERT: D 55 PHE cc_start: 0.9217 (OUTLIER) cc_final: 0.8794 (t80) REVERT: D 65 ASP cc_start: 0.9091 (t0) cc_final: 0.8861 (t70) REVERT: D 77 MET cc_start: 0.8809 (ttp) cc_final: 0.8478 (tpp) REVERT: D 88 MET cc_start: 0.8606 (tmm) cc_final: 0.7877 (tmm) REVERT: D 115 HIS cc_start: 0.8538 (OUTLIER) cc_final: 0.8164 (p90) REVERT: D 142 CYS cc_start: 0.7266 (m) cc_final: 0.6732 (m) REVERT: D 163 MET cc_start: 0.9058 (mmt) cc_final: 0.8719 (mmt) REVERT: D 170 LYS cc_start: 0.9296 (tptp) cc_final: 0.8661 (tptt) REVERT: D 240 MET cc_start: 0.8636 (tmm) cc_final: 0.7752 (tmm) REVERT: D 262 ASP cc_start: 0.9139 (t0) cc_final: 0.8838 (t70) REVERT: D 288 GLU cc_start: 0.8331 (mt-10) cc_final: 0.7851 (tt0) REVERT: E 30 ASP cc_start: 0.9026 (m-30) cc_final: 0.8164 (t0) REVERT: E 65 THR cc_start: 0.8409 (OUTLIER) cc_final: 0.8100 (p) REVERT: E 73 ASN cc_start: 0.9252 (OUTLIER) cc_final: 0.8857 (p0) REVERT: E 81 MET cc_start: 0.8941 (mtm) cc_final: 0.8727 (ptp) REVERT: E 105 LEU cc_start: 0.9431 (mt) cc_final: 0.9217 (mt) REVERT: E 108 TYR cc_start: 0.8536 (OUTLIER) cc_final: 0.7753 (m-80) REVERT: E 116 MET cc_start: 0.9445 (mmm) cc_final: 0.9147 (mmm) REVERT: E 226 LEU cc_start: 0.9081 (tt) cc_final: 0.8862 (tp) REVERT: E 413 MET cc_start: 0.8275 (ptp) cc_final: 0.7835 (pmm) REVERT: E 584 PHE cc_start: 0.9051 (m-80) cc_final: 0.8576 (m-80) REVERT: E 611 LEU cc_start: 0.9653 (OUTLIER) cc_final: 0.9248 (mm) REVERT: E 711 MET cc_start: 0.8342 (mpp) cc_final: 0.7772 (mpp) REVERT: E 790 PHE cc_start: 0.8764 (t80) cc_final: 0.8548 (t80) REVERT: E 1080 LEU cc_start: 0.9378 (tp) cc_final: 0.9089 (mt) REVERT: E 1395 MET cc_start: 0.9189 (tmm) cc_final: 0.8893 (tpt) REVERT: E 1402 HIS cc_start: 0.8303 (m-70) cc_final: 0.8065 (t-170) REVERT: E 1455 LEU cc_start: 0.9459 (OUTLIER) cc_final: 0.9248 (pp) REVERT: E 1525 MET cc_start: 0.8552 (ptp) cc_final: 0.7762 (ppp) outliers start: 97 outliers final: 58 residues processed: 382 average time/residue: 0.3006 time to fit residues: 185.6802 Evaluate side-chains 355 residues out of total 2324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 284 time to evaluate : 2.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain B residue 57 GLN Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 335 ASN Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 81 CYS Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 88 MET Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 115 HIS Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 166 SER Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 332 LYS Chi-restraints excluded: chain D residue 55 PHE Chi-restraints excluded: chain D residue 82 SER 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 181 LEU Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 273 SER Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain E residue 12 HIS Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 73 ASN Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 108 TYR Chi-restraints excluded: chain E residue 109 MET Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 211 LEU Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 306 PHE Chi-restraints excluded: chain E residue 353 LEU Chi-restraints excluded: chain E residue 429 LEU Chi-restraints excluded: chain E residue 439 LEU Chi-restraints excluded: chain E residue 467 VAL Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 611 LEU Chi-restraints excluded: chain E residue 682 ILE Chi-restraints excluded: chain E residue 702 ILE Chi-restraints excluded: chain E residue 704 ILE Chi-restraints excluded: chain E residue 770 VAL Chi-restraints excluded: chain E residue 884 VAL Chi-restraints excluded: chain E residue 1016 LEU Chi-restraints excluded: chain E residue 1027 LEU Chi-restraints excluded: chain E residue 1260 VAL Chi-restraints excluded: chain E residue 1261 LEU Chi-restraints excluded: chain E residue 1296 ASN Chi-restraints excluded: chain E residue 1396 VAL Chi-restraints excluded: chain E residue 1455 LEU Chi-restraints excluded: chain E residue 1497 VAL Chi-restraints excluded: chain E residue 1532 THR Chi-restraints excluded: chain E residue 1581 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 249 optimal weight: 10.0000 chunk 29 optimal weight: 0.4980 chunk 147 optimal weight: 0.0020 chunk 189 optimal weight: 2.9990 chunk 146 optimal weight: 0.9980 chunk 218 optimal weight: 10.0000 chunk 144 optimal weight: 0.0070 chunk 258 optimal weight: 5.9990 chunk 161 optimal weight: 4.9990 chunk 157 optimal weight: 0.7980 chunk 119 optimal weight: 5.9990 overall best weight: 0.4606 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN D 153 ASN ** E 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 445 GLN ** E 797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 923 GLN ** E 933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1521 GLN ** E1541 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.3985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 21611 Z= 0.158 Angle : 0.612 12.291 29365 Z= 0.301 Chirality : 0.042 0.185 3474 Planarity : 0.003 0.066 3650 Dihedral : 6.679 115.844 2917 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.47 % Favored : 95.49 % Rotamer: Outliers : 3.26 % Allowed : 26.26 % Favored : 70.49 % 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: -0.24 (0.17), residues: 2663 helix: 0.76 (0.15), residues: 1313 sheet: -0.80 (0.32), residues: 261 loop : -1.08 (0.19), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 83 HIS 0.007 0.000 HIS E1024 PHE 0.025 0.001 PHE E 364 TYR 0.012 0.001 TYR C 268 ARG 0.003 0.000 ARG E1579 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5326 Ramachandran restraints generated. 2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5326 Ramachandran restraints generated. 2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 2324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 345 time to evaluate : 2.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LEU cc_start: 0.9312 (mt) cc_final: 0.8851 (pp) REVERT: A 77 MET cc_start: 0.8722 (OUTLIER) cc_final: 0.8429 (mmm) REVERT: A 83 TRP cc_start: 0.9589 (m-10) cc_final: 0.9164 (m-90) REVERT: A 268 TYR cc_start: 0.8486 (t80) cc_final: 0.8158 (t80) REVERT: A 332 LYS cc_start: 0.9369 (pttt) cc_final: 0.9099 (ptpp) REVERT: B 148 ILE cc_start: 0.9668 (tt) cc_final: 0.9443 (tp) REVERT: B 160 ASN cc_start: 0.9122 (m-40) cc_final: 0.8876 (m110) REVERT: B 169 MET cc_start: 0.8829 (ttm) cc_final: 0.8625 (ttm) REVERT: B 185 LYS cc_start: 0.9289 (ttmm) cc_final: 0.9038 (tptt) REVERT: B 240 MET cc_start: 0.9230 (tmm) cc_final: 0.8617 (tmm) REVERT: B 296 ILE cc_start: 0.9324 (mp) cc_final: 0.8898 (tt) REVERT: C 39 LYS cc_start: 0.9251 (mmmm) cc_final: 0.8670 (tmtt) REVERT: C 47 LYS cc_start: 0.8746 (tppt) cc_final: 0.8386 (tppt) REVERT: C 65 ASP cc_start: 0.8465 (t0) cc_final: 0.8093 (t0) REVERT: C 84 LEU cc_start: 0.9325 (mt) cc_final: 0.9056 (tt) REVERT: C 160 ASN cc_start: 0.9117 (m-40) cc_final: 0.8744 (m110) REVERT: C 169 MET cc_start: 0.8978 (ttm) cc_final: 0.8567 (ttm) REVERT: C 170 LYS cc_start: 0.9379 (tptm) cc_final: 0.9051 (tttp) REVERT: C 179 GLU cc_start: 0.8497 (mp0) cc_final: 0.8113 (mp0) REVERT: C 214 THR cc_start: 0.9307 (OUTLIER) cc_final: 0.8325 (t) REVERT: C 247 ASN cc_start: 0.8410 (p0) cc_final: 0.7758 (p0) REVERT: C 288 GLU cc_start: 0.8639 (mm-30) cc_final: 0.7877 (mm-30) REVERT: C 332 LYS cc_start: 0.9202 (OUTLIER) cc_final: 0.8999 (pttp) REVERT: C 338 LYS cc_start: 0.9136 (tppt) cc_final: 0.8885 (tppt) REVERT: D 50 ARG cc_start: 0.7103 (mmp-170) cc_final: 0.6794 (mmp80) REVERT: D 55 PHE cc_start: 0.9188 (OUTLIER) cc_final: 0.8797 (t80) REVERT: D 65 ASP cc_start: 0.8982 (t0) cc_final: 0.8763 (t70) REVERT: D 77 MET cc_start: 0.8765 (ttp) cc_final: 0.8518 (tpp) REVERT: D 88 MET cc_start: 0.8547 (tmm) cc_final: 0.7814 (tmm) REVERT: D 115 HIS cc_start: 0.8493 (OUTLIER) cc_final: 0.8167 (p90) REVERT: D 142 CYS cc_start: 0.7307 (m) cc_final: 0.6633 (m) REVERT: D 163 MET cc_start: 0.9112 (mmt) cc_final: 0.8747 (mmt) REVERT: D 170 LYS cc_start: 0.9212 (tptp) cc_final: 0.8809 (tptt) REVERT: D 240 MET cc_start: 0.8486 (tmm) cc_final: 0.7615 (tmm) REVERT: D 262 ASP cc_start: 0.9112 (t0) cc_final: 0.8829 (t70) REVERT: D 288 GLU cc_start: 0.8257 (mt-10) cc_final: 0.7930 (tt0) REVERT: E 65 THR cc_start: 0.8348 (OUTLIER) cc_final: 0.8063 (p) REVERT: E 73 ASN cc_start: 0.9169 (OUTLIER) cc_final: 0.8812 (p0) REVERT: E 80 PHE cc_start: 0.8723 (m-80) cc_final: 0.8314 (m-80) REVERT: E 105 LEU cc_start: 0.9349 (mt) cc_final: 0.9109 (mt) REVERT: E 108 TYR cc_start: 0.8486 (OUTLIER) cc_final: 0.7730 (m-80) REVERT: E 116 MET cc_start: 0.9448 (mmm) cc_final: 0.9146 (mmm) REVERT: E 153 ILE cc_start: 0.9641 (mm) cc_final: 0.9346 (mm) REVERT: E 311 ASP cc_start: 0.8954 (p0) cc_final: 0.8547 (p0) REVERT: E 419 CYS cc_start: 0.9095 (m) cc_final: 0.8830 (t) REVERT: E 503 MET cc_start: 0.8970 (mmm) cc_final: 0.8753 (tpt) REVERT: E 584 PHE cc_start: 0.8960 (m-80) cc_final: 0.8527 (m-80) REVERT: E 711 MET cc_start: 0.8345 (mpp) cc_final: 0.7762 (mpp) REVERT: E 731 MET cc_start: 0.9057 (tpp) cc_final: 0.8746 (mmm) REVERT: E 790 PHE cc_start: 0.8731 (t80) cc_final: 0.8528 (t80) REVERT: E 1080 LEU cc_start: 0.9354 (tp) cc_final: 0.9062 (mt) REVERT: E 1226 LYS cc_start: 0.8721 (mmtp) cc_final: 0.8473 (mmtp) REVERT: E 1395 MET cc_start: 0.9261 (tmm) cc_final: 0.8749 (tpt) REVERT: E 1402 HIS cc_start: 0.8292 (m-70) cc_final: 0.7953 (t-170) REVERT: E 1455 LEU cc_start: 0.9408 (OUTLIER) cc_final: 0.9208 (pp) REVERT: E 1525 MET cc_start: 0.8388 (ptp) cc_final: 0.7991 (ptp) outliers start: 75 outliers final: 51 residues processed: 406 average time/residue: 0.3028 time to fit residues: 197.2335 Evaluate side-chains 371 residues out of total 2324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 311 time to evaluate : 2.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 335 ASN Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 115 HIS Chi-restraints excluded: chain C residue 166 SER Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 332 LYS Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain D residue 55 PHE Chi-restraints excluded: chain D residue 115 HIS Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 73 ASN Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 108 TYR Chi-restraints excluded: chain E residue 109 MET Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 211 LEU Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 306 PHE Chi-restraints excluded: chain E residue 353 LEU Chi-restraints excluded: chain E residue 429 LEU Chi-restraints excluded: chain E residue 439 LEU Chi-restraints excluded: chain E residue 445 GLN Chi-restraints excluded: chain E residue 467 VAL Chi-restraints excluded: chain E residue 682 ILE Chi-restraints excluded: chain E residue 704 ILE Chi-restraints excluded: chain E residue 712 ILE Chi-restraints excluded: chain E residue 770 VAL Chi-restraints excluded: chain E residue 1034 LEU Chi-restraints excluded: chain E residue 1064 TYR Chi-restraints excluded: chain E residue 1136 ILE Chi-restraints excluded: chain E residue 1261 LEU Chi-restraints excluded: chain E residue 1296 ASN Chi-restraints excluded: chain E residue 1396 VAL Chi-restraints excluded: chain E residue 1455 LEU Chi-restraints excluded: chain E residue 1497 VAL Chi-restraints excluded: chain E residue 1504 ILE Chi-restraints excluded: chain E residue 1521 GLN Chi-restraints excluded: chain E residue 1532 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: 10.0000 chunk 154 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 50 optimal weight: 6.9990 chunk 164 optimal weight: 0.8980 chunk 175 optimal weight: 1.9990 chunk 127 optimal weight: 0.0170 chunk 24 optimal weight: 3.9990 chunk 203 optimal weight: 8.9990 chunk 234 optimal weight: 5.9990 overall best weight: 1.5824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 153 ASN D 160 ASN E 20 GLN ** E 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1521 GLN ** E1541 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.4119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 21611 Z= 0.222 Angle : 0.637 12.356 29365 Z= 0.316 Chirality : 0.043 0.249 3474 Planarity : 0.004 0.063 3650 Dihedral : 6.621 119.642 2916 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 15.40 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.62 % Favored : 95.34 % Rotamer: Outliers : 3.78 % Allowed : 26.22 % Favored : 70.01 % 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: -0.18 (0.17), residues: 2663 helix: 0.80 (0.15), residues: 1318 sheet: -0.83 (0.31), residues: 271 loop : -1.01 (0.19), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 83 HIS 0.005 0.001 HIS E1024 PHE 0.023 0.001 PHE E 133 TYR 0.018 0.001 TYR D 330 ARG 0.003 0.000 ARG E1579 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5326 Ramachandran restraints generated. 2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5326 Ramachandran restraints generated. 2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 2324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 308 time to evaluate : 2.485 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 56 LEU cc_start: 0.9331 (mt) cc_final: 0.8875 (pp) REVERT: A 77 MET cc_start: 0.8661 (OUTLIER) cc_final: 0.8411 (mmm) REVERT: A 83 TRP cc_start: 0.9614 (m-10) cc_final: 0.9118 (m-90) REVERT: A 332 LYS cc_start: 0.9340 (pttt) cc_final: 0.9109 (ptpp) REVERT: B 148 ILE cc_start: 0.9689 (tt) cc_final: 0.9434 (tp) REVERT: B 160 ASN cc_start: 0.9150 (m-40) cc_final: 0.8824 (m110) REVERT: B 169 MET cc_start: 0.8876 (ttm) cc_final: 0.8655 (ttm) REVERT: B 185 LYS cc_start: 0.9313 (ttmm) cc_final: 0.9039 (tptt) REVERT: B 240 MET cc_start: 0.9218 (tmm) cc_final: 0.8497 (tmm) REVERT: B 296 ILE cc_start: 0.9249 (mp) cc_final: 0.8819 (tt) REVERT: C 39 LYS cc_start: 0.9276 (mmmm) cc_final: 0.8649 (tmtt) REVERT: C 47 LYS cc_start: 0.8731 (tppt) cc_final: 0.8377 (tppt) REVERT: C 65 ASP cc_start: 0.8587 (t0) cc_final: 0.8167 (t0) REVERT: C 84 LEU cc_start: 0.9352 (mt) cc_final: 0.9076 (tt) REVERT: C 160 ASN cc_start: 0.9125 (m-40) cc_final: 0.8760 (m110) REVERT: C 170 LYS cc_start: 0.9387 (tptm) cc_final: 0.9060 (tttp) REVERT: C 179 GLU cc_start: 0.8568 (mp0) cc_final: 0.8264 (mp0) REVERT: C 214 THR cc_start: 0.9403 (OUTLIER) cc_final: 0.8535 (t) REVERT: C 242 ASN cc_start: 0.8527 (t0) cc_final: 0.8152 (p0) REVERT: C 247 ASN cc_start: 0.8786 (p0) cc_final: 0.8436 (p0) REVERT: C 288 GLU cc_start: 0.8660 (mm-30) cc_final: 0.8042 (mm-30) REVERT: C 332 LYS cc_start: 0.9209 (OUTLIER) cc_final: 0.8926 (pttp) REVERT: C 338 LYS cc_start: 0.9167 (tppt) cc_final: 0.8905 (tppt) REVERT: D 50 ARG cc_start: 0.7121 (mmp-170) cc_final: 0.6819 (mmp80) REVERT: D 77 MET cc_start: 0.8753 (ttp) cc_final: 0.8493 (tpp) REVERT: D 88 MET cc_start: 0.8643 (tmm) cc_final: 0.7910 (tmm) REVERT: D 115 HIS cc_start: 0.8560 (OUTLIER) cc_final: 0.8162 (p90) REVERT: D 142 CYS cc_start: 0.7236 (m) cc_final: 0.6609 (m) REVERT: D 170 LYS cc_start: 0.9265 (tptp) cc_final: 0.8696 (tptt) REVERT: D 262 ASP cc_start: 0.9118 (t0) cc_final: 0.8814 (t70) REVERT: D 288 GLU cc_start: 0.8299 (mt-10) cc_final: 0.7750 (tt0) REVERT: E 65 THR cc_start: 0.8349 (OUTLIER) cc_final: 0.8048 (p) REVERT: E 73 ASN cc_start: 0.9221 (OUTLIER) cc_final: 0.8868 (p0) REVERT: E 75 ARG cc_start: 0.8904 (ttm110) cc_final: 0.8555 (ttm-80) REVERT: E 105 LEU cc_start: 0.9376 (mt) cc_final: 0.9139 (mt) REVERT: E 108 TYR cc_start: 0.8516 (OUTLIER) cc_final: 0.7729 (m-80) REVERT: E 116 MET cc_start: 0.9437 (mmm) cc_final: 0.9140 (mmm) REVERT: E 311 ASP cc_start: 0.8956 (p0) cc_final: 0.8593 (p0) REVERT: E 413 MET cc_start: 0.8373 (ptm) cc_final: 0.7842 (ptm) REVERT: E 584 PHE cc_start: 0.9000 (m-80) cc_final: 0.8598 (m-80) REVERT: E 611 LEU cc_start: 0.9639 (OUTLIER) cc_final: 0.9223 (mm) REVERT: E 711 MET cc_start: 0.8319 (mpp) cc_final: 0.7678 (mpp) REVERT: E 731 MET cc_start: 0.9050 (tpp) cc_final: 0.8813 (mmm) REVERT: E 1080 LEU cc_start: 0.9401 (tp) cc_final: 0.9156 (mt) REVERT: E 1395 MET cc_start: 0.9239 (tmm) cc_final: 0.8702 (tpt) REVERT: E 1402 HIS cc_start: 0.8421 (m-70) cc_final: 0.7933 (t-170) REVERT: E 1455 LEU cc_start: 0.9413 (OUTLIER) cc_final: 0.9176 (pp) REVERT: E 1521 GLN cc_start: 0.8734 (OUTLIER) cc_final: 0.8230 (tm-30) REVERT: E 1525 MET cc_start: 0.8454 (ptp) cc_final: 0.8101 (ptp) outliers start: 87 outliers final: 60 residues processed: 378 average time/residue: 0.2998 time to fit residues: 181.6303 Evaluate side-chains 366 residues out of total 2324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 296 time to evaluate : 2.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 335 ASN Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain C residue 42 CYS Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 115 HIS Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 166 SER Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 332 LYS Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain D residue 115 HIS Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 299 GLN Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 73 ASN Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 108 TYR Chi-restraints excluded: chain E residue 109 MET Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 306 PHE Chi-restraints excluded: chain E residue 353 LEU Chi-restraints excluded: chain E residue 365 LEU Chi-restraints excluded: chain E residue 422 VAL Chi-restraints excluded: chain E residue 429 LEU Chi-restraints excluded: chain E residue 439 LEU Chi-restraints excluded: chain E residue 444 VAL Chi-restraints excluded: chain E residue 467 VAL Chi-restraints excluded: chain E residue 611 LEU Chi-restraints excluded: chain E residue 682 ILE Chi-restraints excluded: chain E residue 702 ILE Chi-restraints excluded: chain E residue 704 ILE Chi-restraints excluded: chain E residue 712 ILE Chi-restraints excluded: chain E residue 770 VAL Chi-restraints excluded: chain E residue 1016 LEU Chi-restraints excluded: chain E residue 1064 TYR Chi-restraints excluded: chain E residue 1136 ILE Chi-restraints excluded: chain E residue 1261 LEU Chi-restraints excluded: chain E residue 1296 ASN Chi-restraints excluded: chain E residue 1396 VAL Chi-restraints excluded: chain E residue 1455 LEU Chi-restraints excluded: chain E residue 1497 VAL Chi-restraints excluded: chain E residue 1521 GLN Chi-restraints excluded: chain E residue 1532 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 247 optimal weight: 20.0000 chunk 225 optimal weight: 0.5980 chunk 240 optimal weight: 3.9990 chunk 144 optimal weight: 4.9990 chunk 104 optimal weight: 5.9990 chunk 189 optimal weight: 5.9990 chunk 73 optimal weight: 0.9990 chunk 217 optimal weight: 7.9990 chunk 227 optimal weight: 0.8980 chunk 239 optimal weight: 0.6980 chunk 158 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 153 ASN D 160 ASN ** E 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 923 GLN ** E 933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1521 GLN ** E1541 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.4218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 21611 Z= 0.175 Angle : 0.642 12.483 29365 Z= 0.311 Chirality : 0.043 0.210 3474 Planarity : 0.004 0.063 3650 Dihedral : 6.437 118.456 2916 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.26 % Allowed : 26.69 % Favored : 70.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.17), residues: 2663 helix: 0.90 (0.15), residues: 1312 sheet: -0.66 (0.31), residues: 261 loop : -1.02 (0.19), residues: 1090 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 83 HIS 0.005 0.001 HIS E1024 PHE 0.028 0.001 PHE E 364 TYR 0.015 0.001 TYR D 330 ARG 0.006 0.000 ARG E 259 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5326 Ramachandran restraints generated. 2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5326 Ramachandran restraints generated. 2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 2324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 327 time to evaluate : 2.701 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 56 LEU cc_start: 0.9326 (mt) cc_final: 0.8856 (pp) REVERT: A 77 MET cc_start: 0.8630 (OUTLIER) cc_final: 0.8375 (mmm) REVERT: A 83 TRP cc_start: 0.9575 (m-10) cc_final: 0.9143 (m-90) REVERT: A 332 LYS cc_start: 0.9319 (pttt) cc_final: 0.9074 (ptpp) REVERT: B 148 ILE cc_start: 0.9683 (tt) cc_final: 0.9430 (tp) REVERT: B 160 ASN cc_start: 0.9142 (m-40) cc_final: 0.8867 (m110) REVERT: B 169 MET cc_start: 0.8858 (ttm) cc_final: 0.8654 (ttm) REVERT: B 185 LYS cc_start: 0.9273 (ttmm) cc_final: 0.9046 (tptt) REVERT: B 240 MET cc_start: 0.9164 (tmm) cc_final: 0.8488 (tmm) REVERT: B 296 ILE cc_start: 0.9213 (mp) cc_final: 0.8777 (tt) REVERT: C 39 LYS cc_start: 0.9283 (mmmm) cc_final: 0.8739 (tttm) REVERT: C 47 LYS cc_start: 0.8672 (tppt) cc_final: 0.8384 (tppt) REVERT: C 65 ASP cc_start: 0.8498 (t0) cc_final: 0.8084 (t0) REVERT: C 84 LEU cc_start: 0.9338 (mt) cc_final: 0.9050 (tt) REVERT: C 160 ASN cc_start: 0.9057 (m-40) cc_final: 0.8668 (m110) REVERT: C 170 LYS cc_start: 0.9354 (tptm) cc_final: 0.9021 (tttp) REVERT: C 179 GLU cc_start: 0.8580 (mp0) cc_final: 0.8171 (mp0) REVERT: C 199 MET cc_start: 0.9036 (mtm) cc_final: 0.8328 (mpp) REVERT: C 214 THR cc_start: 0.9370 (OUTLIER) cc_final: 0.8200 (t) REVERT: C 247 ASN cc_start: 0.8551 (p0) cc_final: 0.7973 (p0) REVERT: C 288 GLU cc_start: 0.8620 (mm-30) cc_final: 0.8046 (mm-30) REVERT: C 338 LYS cc_start: 0.9155 (tppt) cc_final: 0.8902 (tppt) REVERT: D 50 ARG cc_start: 0.7074 (mmp-170) cc_final: 0.6801 (mmp80) REVERT: D 77 MET cc_start: 0.8716 (ttp) cc_final: 0.8396 (tpp) REVERT: D 88 MET cc_start: 0.8565 (tmm) cc_final: 0.7844 (tmm) REVERT: D 115 HIS cc_start: 0.8540 (OUTLIER) cc_final: 0.8200 (p90) REVERT: D 137 MET cc_start: 0.8641 (tmm) cc_final: 0.8428 (tmm) REVERT: D 142 CYS cc_start: 0.7274 (m) cc_final: 0.6622 (m) REVERT: D 163 MET cc_start: 0.9242 (mmt) cc_final: 0.8819 (mmt) REVERT: D 170 LYS cc_start: 0.9228 (tptp) cc_final: 0.8769 (tptt) REVERT: D 240 MET cc_start: 0.8450 (tmm) cc_final: 0.7566 (tmm) REVERT: D 262 ASP cc_start: 0.9107 (t0) cc_final: 0.8828 (t70) REVERT: D 288 GLU cc_start: 0.8158 (mt-10) cc_final: 0.7832 (tt0) REVERT: E 65 THR cc_start: 0.8320 (OUTLIER) cc_final: 0.8034 (p) REVERT: E 73 ASN cc_start: 0.9186 (OUTLIER) cc_final: 0.8923 (p0) REVERT: E 75 ARG cc_start: 0.8877 (ttm110) cc_final: 0.8503 (ttm-80) REVERT: E 80 PHE cc_start: 0.8741 (m-80) cc_final: 0.8496 (m-80) REVERT: E 105 LEU cc_start: 0.9351 (mt) cc_final: 0.9108 (mt) REVERT: E 108 TYR cc_start: 0.8502 (OUTLIER) cc_final: 0.7720 (m-80) REVERT: E 116 MET cc_start: 0.9450 (mmm) cc_final: 0.9179 (mmm) REVERT: E 153 ILE cc_start: 0.9626 (mm) cc_final: 0.9344 (mm) REVERT: E 311 ASP cc_start: 0.8898 (p0) cc_final: 0.8602 (p0) REVERT: E 419 CYS cc_start: 0.9145 (m) cc_final: 0.8854 (t) REVERT: E 503 MET cc_start: 0.8928 (mmm) cc_final: 0.8723 (tpt) REVERT: E 584 PHE cc_start: 0.8963 (m-80) cc_final: 0.8587 (m-80) REVERT: E 711 MET cc_start: 0.8304 (mpp) cc_final: 0.7619 (mpp) REVERT: E 731 MET cc_start: 0.9021 (tpp) cc_final: 0.8621 (mmm) REVERT: E 1080 LEU cc_start: 0.9393 (tp) cc_final: 0.9124 (mt) REVERT: E 1191 GLN cc_start: 0.9141 (tm-30) cc_final: 0.8884 (tm-30) REVERT: E 1395 MET cc_start: 0.9247 (tmm) cc_final: 0.8779 (tpt) REVERT: E 1455 LEU cc_start: 0.9438 (OUTLIER) cc_final: 0.9232 (pp) outliers start: 75 outliers final: 56 residues processed: 385 average time/residue: 0.2993 time to fit residues: 185.2663 Evaluate side-chains 377 residues out of total 2324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 314 time to evaluate : 2.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 335 ASN Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 115 HIS Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 166 SER Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain D residue 115 HIS Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain D residue 299 GLN Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 73 ASN Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 108 TYR Chi-restraints excluded: chain E residue 109 MET Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 306 PHE Chi-restraints excluded: chain E residue 353 LEU Chi-restraints excluded: chain E residue 365 LEU Chi-restraints excluded: chain E residue 422 VAL Chi-restraints excluded: chain E residue 429 LEU Chi-restraints excluded: chain E residue 439 LEU Chi-restraints excluded: chain E residue 467 VAL Chi-restraints excluded: chain E residue 682 ILE Chi-restraints excluded: chain E residue 704 ILE Chi-restraints excluded: chain E residue 712 ILE Chi-restraints excluded: chain E residue 770 VAL Chi-restraints excluded: chain E residue 1064 TYR Chi-restraints excluded: chain E residue 1136 ILE Chi-restraints excluded: chain E residue 1228 LEU Chi-restraints excluded: chain E residue 1261 LEU Chi-restraints excluded: chain E residue 1296 ASN Chi-restraints excluded: chain E residue 1396 VAL Chi-restraints excluded: chain E residue 1455 LEU Chi-restraints excluded: chain E residue 1497 VAL Chi-restraints excluded: chain E residue 1532 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 254 optimal weight: 0.0980 chunk 155 optimal weight: 7.9990 chunk 120 optimal weight: 0.3980 chunk 176 optimal weight: 0.8980 chunk 266 optimal weight: 0.5980 chunk 245 optimal weight: 6.9990 chunk 212 optimal weight: 9.9990 chunk 22 optimal weight: 0.5980 chunk 164 optimal weight: 1.9990 chunk 130 optimal weight: 5.9990 chunk 168 optimal weight: 6.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 153 ASN D 160 ASN ** E 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 563 HIS ** E 797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1541 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.4359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.064 21611 Z= 0.166 Angle : 0.642 12.363 29365 Z= 0.310 Chirality : 0.043 0.202 3474 Planarity : 0.004 0.066 3650 Dihedral : 6.262 117.274 2916 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.91 % Allowed : 27.21 % Favored : 69.88 % 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: 0.05 (0.17), residues: 2663 helix: 0.97 (0.15), residues: 1303 sheet: -0.33 (0.31), residues: 301 loop : -0.98 (0.19), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 83 HIS 0.004 0.000 HIS E1024 PHE 0.027 0.001 PHE E 364 TYR 0.011 0.001 TYR B 304 ARG 0.018 0.000 ARG E 259 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5326 Ramachandran restraints generated. 2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5326 Ramachandran restraints generated. 2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 2324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 339 time to evaluate : 2.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LEU cc_start: 0.9333 (mt) cc_final: 0.8891 (pp) REVERT: A 77 MET cc_start: 0.8615 (OUTLIER) cc_final: 0.8382 (mmm) REVERT: A 83 TRP cc_start: 0.9534 (m-10) cc_final: 0.9137 (m-90) REVERT: A 332 LYS cc_start: 0.9285 (pttt) cc_final: 0.9038 (ptpp) REVERT: B 77 MET cc_start: 0.8977 (tpp) cc_final: 0.8365 (ttt) REVERT: B 148 ILE cc_start: 0.9653 (tt) cc_final: 0.9419 (tp) REVERT: B 160 ASN cc_start: 0.9143 (m-40) cc_final: 0.8849 (m110) REVERT: B 162 ILE cc_start: 0.9495 (mm) cc_final: 0.9227 (tp) REVERT: B 169 MET cc_start: 0.8825 (ttm) cc_final: 0.8606 (ttm) REVERT: B 240 MET cc_start: 0.9147 (tmm) cc_final: 0.8385 (tmm) REVERT: B 296 ILE cc_start: 0.9170 (mp) cc_final: 0.8754 (tt) REVERT: C 39 LYS cc_start: 0.9244 (mmmm) cc_final: 0.8680 (tttm) REVERT: C 47 LYS cc_start: 0.8653 (tppt) cc_final: 0.8360 (tppt) REVERT: C 65 ASP cc_start: 0.8462 (t0) cc_final: 0.8062 (t0) REVERT: C 160 ASN cc_start: 0.9022 (m-40) cc_final: 0.8634 (m110) REVERT: C 170 LYS cc_start: 0.9324 (tptm) cc_final: 0.9008 (tttp) REVERT: C 179 GLU cc_start: 0.8558 (mp0) cc_final: 0.8237 (mp0) REVERT: C 199 MET cc_start: 0.8996 (mtm) cc_final: 0.8310 (mpp) REVERT: C 214 THR cc_start: 0.9357 (OUTLIER) cc_final: 0.8017 (t) REVERT: C 247 ASN cc_start: 0.8557 (p0) cc_final: 0.8128 (p0) REVERT: C 288 GLU cc_start: 0.8585 (mm-30) cc_final: 0.7988 (mm-30) REVERT: C 292 GLU cc_start: 0.8296 (tp30) cc_final: 0.7893 (tm-30) REVERT: C 338 LYS cc_start: 0.9176 (tppt) cc_final: 0.8926 (tppt) REVERT: D 50 ARG cc_start: 0.7143 (mmp-170) cc_final: 0.6883 (mmp80) REVERT: D 77 MET cc_start: 0.8742 (ttp) cc_final: 0.8421 (tpp) REVERT: D 88 MET cc_start: 0.8557 (tmm) cc_final: 0.7851 (tmm) REVERT: D 115 HIS cc_start: 0.8509 (OUTLIER) cc_final: 0.8216 (p90) REVERT: D 137 MET cc_start: 0.8613 (tmm) cc_final: 0.8411 (tmm) REVERT: D 163 MET cc_start: 0.9272 (mmt) cc_final: 0.8802 (mmt) REVERT: D 170 LYS cc_start: 0.9164 (tptp) cc_final: 0.8603 (tptt) REVERT: D 240 MET cc_start: 0.8354 (tmm) cc_final: 0.7497 (tmm) REVERT: D 262 ASP cc_start: 0.9131 (t0) cc_final: 0.8888 (t70) REVERT: D 288 GLU cc_start: 0.8233 (mt-10) cc_final: 0.7872 (tt0) REVERT: D 291 VAL cc_start: 0.9647 (t) cc_final: 0.9432 (m) REVERT: E 30 ASP cc_start: 0.9001 (m-30) cc_final: 0.8796 (m-30) REVERT: E 47 ILE cc_start: 0.9560 (mm) cc_final: 0.9348 (pt) REVERT: E 65 THR cc_start: 0.8276 (OUTLIER) cc_final: 0.7975 (p) REVERT: E 80 PHE cc_start: 0.8685 (m-80) cc_final: 0.8418 (m-80) REVERT: E 105 LEU cc_start: 0.9319 (mt) cc_final: 0.9078 (mt) REVERT: E 108 TYR cc_start: 0.8501 (OUTLIER) cc_final: 0.7810 (m-80) REVERT: E 116 MET cc_start: 0.9492 (mmm) cc_final: 0.9283 (mmm) REVERT: E 153 ILE cc_start: 0.9490 (mm) cc_final: 0.9208 (mm) REVERT: E 311 ASP cc_start: 0.8866 (p0) cc_final: 0.8590 (p0) REVERT: E 419 CYS cc_start: 0.9197 (m) cc_final: 0.8918 (t) REVERT: E 503 MET cc_start: 0.8913 (mmm) cc_final: 0.8707 (tpt) REVERT: E 584 PHE cc_start: 0.8936 (m-80) cc_final: 0.8630 (m-80) REVERT: E 711 MET cc_start: 0.8268 (mpp) cc_final: 0.7557 (mpp) REVERT: E 731 MET cc_start: 0.8975 (tpp) cc_final: 0.8580 (mmm) REVERT: E 869 MET cc_start: 0.8282 (tpt) cc_final: 0.7906 (mmm) REVERT: E 1025 MET cc_start: 0.8652 (tpt) cc_final: 0.8400 (mmm) REVERT: E 1080 LEU cc_start: 0.9385 (tp) cc_final: 0.9116 (mt) REVERT: E 1143 LEU cc_start: 0.9523 (tt) cc_final: 0.9191 (pp) REVERT: E 1191 GLN cc_start: 0.9163 (tm-30) cc_final: 0.8889 (tm-30) REVERT: E 1395 MET cc_start: 0.9226 (tmm) cc_final: 0.8747 (tpt) REVERT: E 1402 HIS cc_start: 0.8244 (m-70) cc_final: 0.7937 (t-170) outliers start: 67 outliers final: 54 residues processed: 389 average time/residue: 0.3003 time to fit residues: 188.3541 Evaluate side-chains 376 residues out of total 2324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 317 time to evaluate : 2.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 335 ASN Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 88 MET Chi-restraints excluded: chain C residue 115 HIS Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 166 SER Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 115 HIS Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 299 GLN Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 108 TYR Chi-restraints excluded: chain E residue 109 MET Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 306 PHE Chi-restraints excluded: chain E residue 353 LEU Chi-restraints excluded: chain E residue 365 LEU Chi-restraints excluded: chain E residue 429 LEU Chi-restraints excluded: chain E residue 439 LEU Chi-restraints excluded: chain E residue 467 VAL Chi-restraints excluded: chain E residue 682 ILE Chi-restraints excluded: chain E residue 704 ILE Chi-restraints excluded: chain E residue 712 ILE Chi-restraints excluded: chain E residue 770 VAL Chi-restraints excluded: chain E residue 1064 TYR Chi-restraints excluded: chain E residue 1136 ILE Chi-restraints excluded: chain E residue 1228 LEU Chi-restraints excluded: chain E residue 1261 LEU Chi-restraints excluded: chain E residue 1296 ASN Chi-restraints excluded: chain E residue 1396 VAL Chi-restraints excluded: chain E residue 1497 VAL Chi-restraints excluded: chain E residue 1532 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 226 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 196 optimal weight: 7.9990 chunk 31 optimal weight: 6.9990 chunk 59 optimal weight: 4.9990 chunk 212 optimal weight: 9.9990 chunk 89 optimal weight: 6.9990 chunk 218 optimal weight: 7.9990 chunk 26 optimal weight: 0.0040 chunk 39 optimal weight: 7.9990 chunk 186 optimal weight: 5.9990 overall best weight: 4.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 GLN D 153 ASN D 279 GLN E 60 HIS ** E 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 499 GLN ** E 797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 923 GLN E 933 ASN E1348 GLN ** E1488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1541 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.061056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.050548 restraints weight = 95284.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.052081 restraints weight = 49798.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.053071 restraints weight = 31977.204| |-----------------------------------------------------------------------------| r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.4471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 21611 Z= 0.443 Angle : 0.775 11.019 29365 Z= 0.392 Chirality : 0.046 0.206 3474 Planarity : 0.004 0.058 3650 Dihedral : 6.855 124.157 2916 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 20.79 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.16 % Favored : 93.80 % Rotamer: Outliers : 3.56 % Allowed : 27.00 % Favored : 69.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.16), residues: 2663 helix: 0.71 (0.14), residues: 1294 sheet: -0.57 (0.32), residues: 245 loop : -0.85 (0.19), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP B 83 HIS 0.020 0.001 HIS B 186 PHE 0.029 0.002 PHE E 133 TYR 0.022 0.002 TYR C 268 ARG 0.013 0.001 ARG E 259 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4587.50 seconds wall clock time: 84 minutes 30.08 seconds (5070.08 seconds total)