Starting phenix.real_space_refine on Mon Mar 18 11:15:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8we9_37475/03_2024/8we9_37475_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8we9_37475/03_2024/8we9_37475.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8we9_37475/03_2024/8we9_37475_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8we9_37475/03_2024/8we9_37475_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8we9_37475/03_2024/8we9_37475_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8we9_37475/03_2024/8we9_37475.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8we9_37475/03_2024/8we9_37475.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8we9_37475/03_2024/8we9_37475_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8we9_37475/03_2024/8we9_37475_updated.pdb" } resolution = 3.0 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= -0.001 sd= 0.075 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 2 9.91 5 P 4 5.49 5 S 104 5.16 5 C 13388 2.51 5 N 3412 2.21 5 O 3820 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 407": "OE1" <-> "OE2" Residue "A GLU 411": "OE1" <-> "OE2" Residue "A GLU 432": "OE1" <-> "OE2" Residue "A PHE 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 570": "OE1" <-> "OE2" Residue "A ASP 592": "OD1" <-> "OD2" Residue "A ASP 680": "OD1" <-> "OD2" Residue "A PHE 689": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 707": "OD1" <-> "OD2" Residue "A GLU 771": "OE1" <-> "OE2" Residue "A ASP 1098": "OD1" <-> "OD2" Residue "A GLU 1112": "OE1" <-> "OE2" Residue "A GLU 1139": "OE1" <-> "OE2" Residue "A TYR 1240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1242": "OE1" <-> "OE2" Residue "A TYR 1243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1437": "OD1" <-> "OD2" Residue "A GLU 1544": "OE1" <-> "OE2" Residue "D GLU 115": "OE1" <-> "OE2" Residue "D GLU 199": "OE1" <-> "OE2" Residue "D TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 278": "OE1" <-> "OE2" Residue "D TYR 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 496": "OD1" <-> "OD2" Residue "D TYR 599": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 601": "OD1" <-> "OD2" Residue "D TYR 666": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 686": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 750": "OE1" <-> "OE2" Residue "D GLU 754": "OE1" <-> "OE2" Residue "D TYR 779": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 780": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 788": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 854": "OD1" <-> "OD2" Residue "D ASP 855": "OD1" <-> "OD2" Residue "D ASP 984": "OD1" <-> "OD2" Residue "D PHE 1003": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1015": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1068": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 209": "OD1" <-> "OD2" Residue "C ASP 220": "OD1" <-> "OD2" Residue "C GLU 331": "OE1" <-> "OE2" Residue "C PHE 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 20730 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 10172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1260, 10172 Classifications: {'peptide': 1260} Link IDs: {'PTRANS': 39, 'TRANS': 1220} Chain breaks: 7 Chain: "D" Number of atoms: 7570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 948, 7570 Classifications: {'peptide': 948} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 907} Chain breaks: 5 Chain: "C" Number of atoms: 2575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2575 Classifications: {'peptide': 324} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 304} Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 202 Unusual residues: {' CA': 1, '3PE': 1, 'CLR': 3, 'NAG': 1, 'PT5': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PT5:plan-6': 1} Unresolved non-hydrogen planarities: 2 Chain: "D" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' CA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 11.60, per 1000 atoms: 0.56 Number of scatterers: 20730 At special positions: 0 Unit cell: (170.442, 176.012, 181.582, 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) Ca 2 19.99 S 104 16.00 P 4 15.00 O 3820 8.00 N 3412 7.00 C 13388 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 298 " - pdb=" SG CYS A 326 " distance=2.03 Simple disulfide: pdb=" SG CYS A 316 " - pdb=" SG CYS A 332 " distance=2.03 Simple disulfide: pdb=" SG CYS A1078 " - pdb=" SG CYS A1089 " distance=2.03 Simple disulfide: pdb=" SG CYS A1479 " - pdb=" SG CYS A1495 " distance=2.03 Simple disulfide: pdb=" SG CYS D 303 " - pdb=" SG CYS D1044 " distance=2.03 Simple disulfide: pdb=" SG CYS D 404 " - pdb=" SG CYS D1071 " distance=2.03 Simple disulfide: pdb=" SG CYS D 667 " - pdb=" SG CYS D 697 " distance=2.03 Simple disulfide: pdb=" SG CYS D 904 " - pdb=" SG CYS D 974 " distance=2.03 Simple disulfide: pdb=" SG CYS D 996 " - pdb=" SG CYS D1026 " distance=2.03 Simple disulfide: pdb=" SG CYS D 999 " - pdb=" SG CYS D1024 " 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 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " NAG B 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " NAG F 3 " " NAG F 3 " - " NAG F 4 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG A2306 " - " ASN A1436 " " NAG B 1 " - " ASN D 184 " " NAG D1202 " - " ASN D 92 " " NAG D1203 " - " ASN D 781 " " NAG E 1 " - " ASN D 348 " " NAG F 1 " - " ASN D 468 " " NAG G 1 " - " ASN D 613 " " NAG H 1 " - " ASN D 895 " Time building additional restraints: 9.13 Conformation dependent library (CDL) restraints added in 3.9 seconds 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4796 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 102 helices and 13 sheets defined 46.8% alpha, 6.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.35 Creating SS restraints... Processing helix chain 'A' and resid 127 through 143 Processing helix chain 'A' and resid 154 through 181 removed outlier: 3.555A pdb=" N ARG A 161 " --> pdb=" O SER A 157 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N TYR A 164 " --> pdb=" O GLU A 160 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU A 165 " --> pdb=" O ARG A 161 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA A 180 " --> pdb=" O LEU A 176 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N TYR A 181 " --> pdb=" O LYS A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 216 Processing helix chain 'A' and resid 240 through 250 Proline residue: A 244 - end of helix Processing helix chain 'A' and resid 252 through 263 removed outlier: 3.590A pdb=" N VAL A 256 " --> pdb=" O PRO A 252 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N VAL A 257 " --> pdb=" O SER A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 285 removed outlier: 3.794A pdb=" N HIS A 270 " --> pdb=" O PRO A 267 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N ILE A 271 " --> pdb=" O LEU A 268 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA A 272 " --> pdb=" O LEU A 269 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N LEU A 273 " --> pdb=" O HIS A 270 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LEU A 274 " --> pdb=" O ILE A 271 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N VAL A 275 " --> pdb=" O ALA A 272 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE A 279 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TYR A 282 " --> pdb=" O ILE A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 360 Processing helix chain 'A' and resid 365 through 376 Processing helix chain 'A' and resid 381 through 392 removed outlier: 3.644A pdb=" N PHE A 385 " --> pdb=" O PRO A 381 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE A 389 " --> pdb=" O PHE A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 418 removed outlier: 3.749A pdb=" N SER A 409 " --> pdb=" O SER A 405 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS A 410 " --> pdb=" O GLY A 406 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLU A 411 " --> pdb=" O GLU A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 436 Processing helix chain 'A' and resid 438 through 445 Processing helix chain 'A' and resid 510 through 522 removed outlier: 3.532A pdb=" N ARG A 514 " --> pdb=" O ARG A 511 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N ARG A 515 " --> pdb=" O PHE A 512 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N CYS A 517 " --> pdb=" O ARG A 514 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N ARG A 518 " --> pdb=" O ARG A 515 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N VAL A 521 " --> pdb=" O ARG A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 541 Processing helix chain 'A' and resid 550 through 578 removed outlier: 3.644A pdb=" N GLU A 554 " --> pdb=" O ASN A 550 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LYS A 561 " --> pdb=" O ASP A 557 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU A 564 " --> pdb=" O ASN A 560 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU A 566 " --> pdb=" O ALA A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 583 No H-bonds generated for 'chain 'A' and resid 580 through 583' Processing helix chain 'A' and resid 587 through 607 removed outlier: 3.787A pdb=" N CYS A 593 " --> pdb=" O ASN A 589 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ILE A 604 " --> pdb=" O ILE A 600 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LEU A 605 " --> pdb=" O LEU A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 617 through 630 Processing helix chain 'A' and resid 635 through 646 Processing helix chain 'A' and resid 651 through 673 removed outlier: 3.619A pdb=" N LEU A 656 " --> pdb=" O ALA A 652 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU A 657 " --> pdb=" O SER A 653 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU A 658 " --> pdb=" O LEU A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 692 through 704 Processing helix chain 'A' and resid 708 through 719 removed outlier: 3.522A pdb=" N MET A 712 " --> pdb=" O TRP A 708 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N MET A 717 " --> pdb=" O TYR A 713 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N TYR A 719 " --> pdb=" O GLY A 715 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 746 removed outlier: 3.701A pdb=" N LEU A 728 " --> pdb=" O PHE A 724 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N VAL A 729 " --> pdb=" O PRO A 725 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N CYS A 730 " --> pdb=" O GLY A 726 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N ILE A 731 " --> pdb=" O MET A 727 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N TYR A 732 " --> pdb=" O LEU A 728 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N PHE A 733 " --> pdb=" O VAL A 729 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N TYR A 742 " --> pdb=" O ILE A 738 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ILE A 743 " --> pdb=" O CYS A 739 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU A 745 " --> pdb=" O ASN A 741 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 781 removed outlier: 4.090A pdb=" N ASP A 758 " --> pdb=" O ASP A 754 " (cutoff:3.500A) Processing helix chain 'A' and resid 900 through 918 Processing helix chain 'A' and resid 929 through 974 removed outlier: 3.596A pdb=" N LEU A 953 " --> pdb=" O ARG A 929 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLY A 954 " --> pdb=" O ASN A 930 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ASP A 957 " --> pdb=" O LEU A 953 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N TYR A 958 " --> pdb=" O GLY A 954 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL A 959 " --> pdb=" O ASN A 955 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER A 962 " --> pdb=" O TYR A 958 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N THR A 973 " --> pdb=" O ILE A 969 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ALA A 974 " --> pdb=" O LEU A 970 " (cutoff:3.500A) Processing helix chain 'A' and resid 988 through 1004 Processing helix chain 'A' and resid 1013 through 1016 Processing helix chain 'A' and resid 1018 through 1020 No H-bonds generated for 'chain 'A' and resid 1018 through 1020' Processing helix chain 'A' and resid 1024 through 1028 Processing helix chain 'A' and resid 1035 through 1048 Processing helix chain 'A' and resid 1051 through 1071 Processing helix chain 'A' and resid 1097 through 1099 No H-bonds generated for 'chain 'A' and resid 1097 through 1099' Processing helix chain 'A' and resid 1121 through 1132 Processing helix chain 'A' and resid 1137 through 1146 removed outlier: 3.726A pdb=" N ASP A1146 " --> pdb=" O TYR A1142 " (cutoff:3.500A) Processing helix chain 'A' and resid 1160 through 1173 removed outlier: 4.070A pdb=" N ILE A1173 " --> pdb=" O ILE A1170 " (cutoff:3.500A) Processing helix chain 'A' and resid 1177 through 1193 removed outlier: 3.997A pdb=" N VAL A1182 " --> pdb=" O MET A1178 " (cutoff:3.500A) Processing helix chain 'A' and resid 1206 through 1214 Processing helix chain 'A' and resid 1227 through 1237 Processing helix chain 'A' and resid 1239 through 1257 removed outlier: 3.708A pdb=" N LEU A1250 " --> pdb=" O PHE A1246 " (cutoff:3.500A) Processing helix chain 'A' and resid 1265 through 1300 Proline residue: A1295 - end of helix Processing helix chain 'A' and resid 1302 through 1320 removed outlier: 3.900A pdb=" N PHE A1306 " --> pdb=" O PRO A1302 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE A1308 " --> pdb=" O ASN A1304 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU A1309 " --> pdb=" O VAL A1305 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL A1318 " --> pdb=" O SER A1314 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ILE A1319 " --> pdb=" O ILE A1315 " (cutoff:3.500A) Processing helix chain 'A' and resid 1381 through 1389 Processing helix chain 'A' and resid 1394 through 1407 removed outlier: 3.525A pdb=" N TRP A1399 " --> pdb=" O ARG A1395 " (cutoff:3.500A) Processing helix chain 'A' and resid 1411 through 1429 removed outlier: 4.341A pdb=" N ILE A1415 " --> pdb=" O VAL A1411 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL A1416 " --> pdb=" O ALA A1412 " (cutoff:3.500A) Processing helix chain 'A' and resid 1450 through 1462 Processing helix chain 'A' and resid 1466 through 1472 Processing helix chain 'A' and resid 1498 through 1525 removed outlier: 3.934A pdb=" N VAL A1501 " --> pdb=" O SER A1498 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ILE A1505 " --> pdb=" O PHE A1502 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER A1506 " --> pdb=" O TYR A1503 " (cutoff:3.500A) Processing helix chain 'A' and resid 1539 through 1541 No H-bonds generated for 'chain 'A' and resid 1539 through 1541' Processing helix chain 'A' and resid 1543 through 1552 removed outlier: 3.745A pdb=" N ALA A1550 " --> pdb=" O LYS A1546 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N GLU A1551 " --> pdb=" O ARG A1547 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N TYR A1552 " --> pdb=" O ILE A1548 " (cutoff:3.500A) Processing helix chain 'A' and resid 1568 through 1570 No H-bonds generated for 'chain 'A' and resid 1568 through 1570' Processing helix chain 'A' and resid 1586 through 1593 Processing helix chain 'A' and resid 1607 through 1617 Processing helix chain 'A' and resid 1627 through 1634 Processing helix chain 'A' and resid 1643 through 1645 No H-bonds generated for 'chain 'A' and resid 1643 through 1645' Processing helix chain 'D' and resid 30 through 52 removed outlier: 3.836A pdb=" N ASP D 43 " --> pdb=" O LYS D 39 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU D 44 " --> pdb=" O MET D 40 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA D 48 " --> pdb=" O LEU D 44 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA D 51 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 54 through 58 removed outlier: 3.929A pdb=" N VAL D 58 " --> pdb=" O VAL D 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 54 through 58' Processing helix chain 'D' and resid 60 through 63 No H-bonds generated for 'chain 'D' and resid 60 through 63' Processing helix chain 'D' and resid 65 through 67 No H-bonds generated for 'chain 'D' and resid 65 through 67' Processing helix chain 'D' and resid 75 through 109 removed outlier: 3.520A pdb=" N VAL D 79 " --> pdb=" O ALA D 75 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA D 82 " --> pdb=" O LEU D 78 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE D 86 " --> pdb=" O ALA D 82 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG D 93 " --> pdb=" O LEU D 89 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER D 94 " --> pdb=" O LEU D 90 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N GLU D 103 " --> pdb=" O ARG D 99 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LYS D 106 " --> pdb=" O LEU D 102 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N VAL D 107 " --> pdb=" O GLU D 103 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLN D 108 " --> pdb=" O ALA D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 120 No H-bonds generated for 'chain 'D' and resid 118 through 120' Processing helix chain 'D' and resid 177 through 185 Processing helix chain 'D' and resid 189 through 199 removed outlier: 3.968A pdb=" N ARG D 197 " --> pdb=" O PHE D 193 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N GLU D 198 " --> pdb=" O LYS D 194 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N GLU D 199 " --> pdb=" O LYS D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 240 No H-bonds generated for 'chain 'D' and resid 238 through 240' Processing helix chain 'D' and resid 242 through 248 removed outlier: 4.040A pdb=" N GLY D 247 " --> pdb=" O TRP D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 262 through 264 No H-bonds generated for 'chain 'D' and resid 262 through 264' Processing helix chain 'D' and resid 267 through 282 removed outlier: 4.046A pdb=" N GLU D 281 " --> pdb=" O SER D 277 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N THR D 282 " --> pdb=" O GLU D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 312 through 324 removed outlier: 3.794A pdb=" N ASN D 323 " --> pdb=" O LYS D 319 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ASN D 324 " --> pdb=" O ASP D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 343 removed outlier: 3.587A pdb=" N PHE D 339 " --> pdb=" O LYS D 335 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA D 340 " --> pdb=" O GLY D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 375 Processing helix chain 'D' and resid 397 through 405 removed outlier: 3.638A pdb=" N ALA D 403 " --> pdb=" O ILE D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 422 removed outlier: 4.447A pdb=" N ARG D 420 " --> pdb=" O GLY D 417 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE D 421 " --> pdb=" O ALA D 418 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASN D 422 " --> pdb=" O ILE D 419 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 430 removed outlier: 3.542A pdb=" N VAL D 429 " --> pdb=" O TYR D 426 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU D 430 " --> pdb=" O LEU D 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 435 No H-bonds generated for 'chain 'D' and resid 432 through 435' Processing helix chain 'D' and resid 438 through 441 Processing helix chain 'D' and resid 494 through 497 No H-bonds generated for 'chain 'D' and resid 494 through 497' Processing helix chain 'D' and resid 561 through 564 No H-bonds generated for 'chain 'D' and resid 561 through 564' Processing helix chain 'D' and resid 570 through 579 Processing helix chain 'D' and resid 638 through 648 removed outlier: 4.029A pdb=" N TYR D 644 " --> pdb=" O THR D 640 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR D 647 " --> pdb=" O ARG D 643 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU D 648 " --> pdb=" O TYR D 644 " (cutoff:3.500A) Processing helix chain 'D' and resid 652 through 656 Processing helix chain 'D' and resid 676 through 688 removed outlier: 3.751A pdb=" N ASP D 688 " --> pdb=" O ASN D 684 " (cutoff:3.500A) Processing helix chain 'D' and resid 700 through 718 removed outlier: 3.569A pdb=" N GLY D 710 " --> pdb=" O LEU D 706 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE D 711 " --> pdb=" O LEU D 707 " (cutoff:3.500A) Processing helix chain 'D' and resid 749 through 751 No H-bonds generated for 'chain 'D' and resid 749 through 751' Processing helix chain 'D' and resid 758 through 760 No H-bonds generated for 'chain 'D' and resid 758 through 760' Processing helix chain 'D' and resid 762 through 769 Processing helix chain 'D' and resid 819 through 826 removed outlier: 3.573A pdb=" N GLU D 823 " --> pdb=" O ASN D 819 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASN D 824 " --> pdb=" O SER D 820 " (cutoff:3.500A) Processing helix chain 'D' and resid 865 through 869 Processing helix chain 'D' and resid 875 through 878 No H-bonds generated for 'chain 'D' and resid 875 through 878' Processing helix chain 'D' and resid 880 through 888 Processing helix chain 'D' and resid 1021 through 1023 No H-bonds generated for 'chain 'D' and resid 1021 through 1023' Processing helix chain 'D' and resid 1043 through 1045 No H-bonds generated for 'chain 'D' and resid 1043 through 1045' Processing helix chain 'D' and resid 1047 through 1049 No H-bonds generated for 'chain 'D' and resid 1047 through 1049' Processing helix chain 'C' and resid 39 through 45 removed outlier: 4.056A pdb=" N VAL C 44 " --> pdb=" O ALA C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 51 No H-bonds generated for 'chain 'C' and resid 48 through 51' Processing helix chain 'C' and resid 121 through 127 Processing helix chain 'C' and resid 192 through 208 removed outlier: 3.732A pdb=" N GLN C 197 " --> pdb=" O THR C 193 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA C 199 " --> pdb=" O MET C 195 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LEU C 200 " --> pdb=" O MET C 196 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ASP C 202 " --> pdb=" O LYS C 198 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N PHE C 203 " --> pdb=" O ALA C 199 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LEU C 204 " --> pdb=" O LEU C 200 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS C 205 " --> pdb=" O PHE C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 253 removed outlier: 4.708A pdb=" N GLU C 253 " --> pdb=" O GLU C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 263 removed outlier: 4.205A pdb=" N SER C 263 " --> pdb=" O LEU C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 299 through 307 removed outlier: 5.383A pdb=" N ARG C 307 " --> pdb=" O LEU C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 325 removed outlier: 4.301A pdb=" N MET C 320 " --> pdb=" O VAL C 317 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ALA C 321 " --> pdb=" O GLN C 318 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N TYR C 322 " --> pdb=" O MET C 319 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS C 324 " --> pdb=" O ALA C 321 " (cutoff:3.500A) 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 342 through 359 removed outlier: 4.410A pdb=" N GLU C 347 " --> pdb=" O GLU C 343 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL C 355 " --> pdb=" O GLU C 351 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ARG C 358 " --> pdb=" O GLU C 354 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 296 through 300 Processing sheet with id= B, first strand: chain 'A' and resid 1076 through 1078 Processing sheet with id= C, first strand: chain 'A' and resid 1092 through 1096 Processing sheet with id= D, first strand: chain 'D' and resid 68 through 72 Processing sheet with id= E, first strand: chain 'D' and resid 165 through 167 removed outlier: 7.020A pdb=" N VAL D 466 " --> pdb=" O LEU D 485 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N VAL D 487 " --> pdb=" O LEU D 464 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N LEU D 464 " --> pdb=" O VAL D 487 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 410 through 413 removed outlier: 8.220A pdb=" N TYR D 411 " --> pdb=" O VAL D 384 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N THR D 386 " --> pdb=" O TYR D 411 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N ILE D 413 " --> pdb=" O THR D 386 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N SER D 388 " --> pdb=" O ILE D 413 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N LYS D 356 " --> pdb=" O ARG D 383 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N PHE D 385 " --> pdb=" O LYS D 356 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N ILE D 358 " --> pdb=" O PHE D 385 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N PHE D 387 " --> pdb=" O ILE D 358 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N LEU D 360 " --> pdb=" O PHE D 387 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N VAL D 389 " --> pdb=" O LEU D 360 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N THR D 362 " --> pdb=" O VAL D 389 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LEU D 255 " --> pdb=" O MET D 359 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N PHE D 361 " --> pdb=" O LEU D 255 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N LEU D 257 " --> pdb=" O PHE D 361 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ASN D 290 " --> pdb=" O ILE D 256 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N VAL D 258 " --> pdb=" O ASN D 290 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ALA D 292 " --> pdb=" O VAL D 258 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 459 through 461 Processing sheet with id= H, first strand: chain 'D' and resid 511 through 515 Processing sheet with id= I, first strand: chain 'D' and resid 732 through 736 removed outlier: 4.059A pdb=" N MET D 793 " --> pdb=" O THR D 776 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 989 through 994 removed outlier: 7.583A pdb=" N ILE D1002 " --> pdb=" O GLU D1019 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N GLU D1019 " --> pdb=" O ILE D1002 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N VAL D 851 " --> pdb=" O ILE D1016 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N VAL D1018 " --> pdb=" O ASP D 849 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ILE D 852 " --> pdb=" O MET D 861 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N MET D 861 " --> pdb=" O ILE D 852 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ASP D 854 " --> pdb=" O LEU D 859 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LEU D 859 " --> pdb=" O ASP D 854 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 892 through 899 removed outlier: 3.820A pdb=" N GLN D 980 " --> pdb=" O ASN D 895 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 103 through 107 Processing sheet with id= M, first strand: chain 'C' and resid 180 through 183 removed outlier: 5.873A pdb=" N ILE C 288 " --> pdb=" O VAL C 181 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N VAL C 183 " --> pdb=" O ILE C 288 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N VAL C 290 " --> pdb=" O VAL C 183 " (cutoff:3.500A) No H-bonds generated for sheet with id= M 757 hydrogen bonds defined for protein. 2004 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: 6.79 Time building geometry restraints manager: 9.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 3355 1.29 - 1.42: 5469 1.42 - 1.56: 12168 1.56 - 1.69: 21 1.69 - 1.82: 160 Bond restraints: 21173 Sorted by residual: bond pdb=" CA TRP D 223 " pdb=" C TRP D 223 " ideal model delta sigma weight residual 1.528 1.421 0.106 1.37e-02 5.33e+03 6.03e+01 bond pdb=" CA TYR D 217 " pdb=" C TYR D 217 " ideal model delta sigma weight residual 1.526 1.422 0.103 1.42e-02 4.96e+03 5.28e+01 bond pdb=" CA ALA D 215 " pdb=" C ALA D 215 " ideal model delta sigma weight residual 1.523 1.452 0.071 1.18e-02 7.18e+03 3.60e+01 bond pdb=" CA GLU A 122 " pdb=" C GLU A 122 " ideal model delta sigma weight residual 1.523 1.446 0.077 1.34e-02 5.57e+03 3.34e+01 bond pdb=" C TYR D 217 " pdb=" O TYR D 217 " ideal model delta sigma weight residual 1.233 1.161 0.073 1.28e-02 6.10e+03 3.21e+01 ... (remaining 21168 not shown) Histogram of bond angle deviations from ideal: 94.68 - 106.30: 533 106.30 - 117.91: 15285 117.91 - 129.52: 12746 129.52 - 141.13: 120 141.13 - 152.74: 3 Bond angle restraints: 28687 Sorted by residual: angle pdb=" C18 PT5 A2307 " pdb=" C19 PT5 A2307 " pdb=" C20 PT5 A2307 " ideal model delta sigma weight residual 85.86 152.74 -66.88 3.00e+00 1.11e-01 4.97e+02 angle pdb=" N LEU A1017 " pdb=" CA LEU A1017 " pdb=" C LEU A1017 " ideal model delta sigma weight residual 114.56 103.17 11.39 1.27e+00 6.20e-01 8.04e+01 angle pdb=" N ARG A1021 " pdb=" CA ARG A1021 " pdb=" C ARG A1021 " ideal model delta sigma weight residual 113.23 103.04 10.19 1.24e+00 6.50e-01 6.76e+01 angle pdb=" N ARG A 237 " pdb=" CA ARG A 237 " pdb=" C ARG A 237 " ideal model delta sigma weight residual 112.92 103.26 9.66 1.23e+00 6.61e-01 6.17e+01 angle pdb=" N LYS A1589 " pdb=" CA LYS A1589 " pdb=" C LYS A1589 " ideal model delta sigma weight residual 111.82 103.19 8.63 1.16e+00 7.43e-01 5.53e+01 ... (remaining 28682 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.56: 11271 23.56 - 47.12: 1373 47.12 - 70.67: 312 70.67 - 94.23: 56 94.23 - 117.79: 58 Dihedral angle restraints: 13070 sinusoidal: 5661 harmonic: 7409 Sorted by residual: dihedral pdb=" CB CYS D 999 " pdb=" SG CYS D 999 " pdb=" SG CYS D1024 " pdb=" CB CYS D1024 " ideal model delta sinusoidal sigma weight residual -86.00 -171.97 85.97 1 1.00e+01 1.00e-02 8.93e+01 dihedral pdb=" CA ILE A 262 " pdb=" C ILE A 262 " pdb=" N LYS A 263 " pdb=" CA LYS A 263 " ideal model delta harmonic sigma weight residual 180.00 151.55 28.45 0 5.00e+00 4.00e-02 3.24e+01 dihedral pdb=" CB CYS D 667 " pdb=" SG CYS D 667 " pdb=" SG CYS D 697 " pdb=" CB CYS D 697 " ideal model delta sinusoidal sigma weight residual 93.00 48.34 44.66 1 1.00e+01 1.00e-02 2.77e+01 ... (remaining 13067 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.114: 3217 0.114 - 0.228: 64 0.228 - 0.342: 4 0.342 - 0.455: 0 0.455 - 0.569: 1 Chirality restraints: 3286 Sorted by residual: chirality pdb=" C1 NAG D1203 " pdb=" ND2 ASN D 781 " pdb=" C2 NAG D1203 " pdb=" O5 NAG D1203 " both_signs ideal model delta sigma weight residual False -2.40 -2.97 0.57 2.00e-01 2.50e+01 8.10e+00 chirality pdb=" CA PHE D 780 " pdb=" N PHE D 780 " pdb=" C PHE D 780 " pdb=" CB PHE D 780 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.11e+00 chirality pdb=" C1 NAG D1202 " pdb=" ND2 ASN D 92 " pdb=" C2 NAG D1202 " pdb=" O5 NAG D1202 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.72e+00 ... (remaining 3283 not shown) Planarity restraints: 3610 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP A1543 " -0.022 2.00e-02 2.50e+03 4.47e-02 2.00e+01 pdb=" C ASP A1543 " 0.077 2.00e-02 2.50e+03 pdb=" O ASP A1543 " -0.029 2.00e-02 2.50e+03 pdb=" N GLU A1544 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 781 " -0.023 2.00e-02 2.50e+03 3.26e-02 1.33e+01 pdb=" CG ASN D 781 " 0.008 2.00e-02 2.50e+03 pdb=" OD1 ASN D 781 " -0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN D 781 " 0.058 2.00e-02 2.50e+03 pdb=" C1 NAG D1203 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP D 879 " 0.055 5.00e-02 4.00e+02 8.37e-02 1.12e+01 pdb=" N PRO D 880 " -0.145 5.00e-02 4.00e+02 pdb=" CA PRO D 880 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO D 880 " 0.046 5.00e-02 4.00e+02 ... (remaining 3607 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1925 2.74 - 3.28: 21385 3.28 - 3.82: 33977 3.82 - 4.36: 40980 4.36 - 4.90: 69111 Nonbonded interactions: 167378 Sorted by model distance: nonbonded pdb=" O ASN D 295 " pdb=" ND2 ASN D 295 " model vdw 2.195 2.520 nonbonded pdb=" O GLN C 50 " pdb=" NE2 GLN C 50 " model vdw 2.222 2.520 nonbonded pdb=" OD1 ASP D 596 " pdb=" OG SER D 762 " model vdw 2.222 2.440 nonbonded pdb=" N GLU D 199 " pdb=" OE1 GLU D 199 " model vdw 2.225 2.520 nonbonded pdb=" OH TYR A 546 " pdb=" OD1 ASP A1151 " model vdw 2.235 2.440 ... (remaining 167373 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 'E' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.830 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: 6.180 Check model and map are aligned: 0.320 Set scattering table: 0.200 Process input model: 56.910 Find NCS groups from input model: 0.480 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: 0.010 Load rotamer database and sin/cos tables:11.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.106 21173 Z= 0.364 Angle : 0.901 66.877 28687 Z= 0.485 Chirality : 0.046 0.569 3286 Planarity : 0.005 0.084 3602 Dihedral : 22.122 117.789 8244 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 15.78 Ramachandran Plot: Outliers : 1.44 % Allowed : 9.15 % Favored : 89.41 % Rotamer: Outliers : 8.57 % Allowed : 33.87 % Favored : 57.56 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.17), residues: 2502 helix: -0.67 (0.15), residues: 1160 sheet: -0.73 (0.36), residues: 212 loop : -2.41 (0.18), residues: 1130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A1233 HIS 0.004 0.001 HIS C 314 PHE 0.022 0.001 PHE D1003 TYR 0.045 0.001 TYR D 217 ARG 0.006 0.000 ARG D 643 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 2241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 266 time to evaluate : 2.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 LYS cc_start: 0.8101 (OUTLIER) cc_final: 0.7848 (tptm) REVERT: A 304 ILE cc_start: 0.6352 (OUTLIER) cc_final: 0.6064 (mp) REVERT: A 306 ASP cc_start: 0.8835 (t70) cc_final: 0.8560 (t70) REVERT: A 405 SER cc_start: 0.8738 (OUTLIER) cc_final: 0.8481 (m) REVERT: A 407 GLU cc_start: 0.8212 (tp30) cc_final: 0.7867 (tp30) REVERT: A 1007 GLN cc_start: 0.6072 (OUTLIER) cc_final: 0.5757 (tp40) REVERT: A 1546 LYS cc_start: 0.7649 (OUTLIER) cc_final: 0.7398 (tptt) REVERT: A 1548 ILE cc_start: 0.7917 (OUTLIER) cc_final: 0.7646 (pp) REVERT: A 1551 GLU cc_start: 0.6732 (OUTLIER) cc_final: 0.6447 (pm20) REVERT: A 1569 LEU cc_start: 0.7066 (OUTLIER) cc_final: 0.6149 (tp) REVERT: A 1578 PHE cc_start: 0.5425 (OUTLIER) cc_final: 0.4610 (t80) REVERT: D 115 GLU cc_start: 0.7678 (tm-30) cc_final: 0.7455 (tm-30) REVERT: D 199 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7972 (mp0) REVERT: D 439 ASP cc_start: 0.8128 (OUTLIER) cc_final: 0.7924 (p0) REVERT: D 861 MET cc_start: 0.7053 (tpp) cc_final: 0.6802 (mmm) REVERT: D 883 MET cc_start: 0.7851 (tpt) cc_final: 0.7644 (mmp) REVERT: C 201 PHE cc_start: 0.7631 (OUTLIER) cc_final: 0.7258 (m-80) REVERT: C 205 LYS cc_start: 0.6858 (OUTLIER) cc_final: 0.5675 (tppt) outliers start: 192 outliers final: 123 residues processed: 438 average time/residue: 0.9775 time to fit residues: 505.4267 Evaluate side-chains 380 residues out of total 2241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 244 time to evaluate : 2.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 152 SER Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 322 HIS Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 412 ARG Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain A residue 431 GLU Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 561 LYS Chi-restraints excluded: chain A residue 590 ARG Chi-restraints excluded: chain A residue 593 CYS Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 610 ILE Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 647 SER Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 687 SER Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 764 SER Chi-restraints excluded: chain A residue 768 GLU Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain A residue 912 LEU Chi-restraints excluded: chain A residue 914 SER Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 1007 GLN Chi-restraints excluded: chain A residue 1042 VAL Chi-restraints excluded: chain A residue 1051 ASN Chi-restraints excluded: chain A residue 1079 SER Chi-restraints excluded: chain A residue 1160 VAL Chi-restraints excluded: chain A residue 1219 LEU Chi-restraints excluded: chain A residue 1255 CYS Chi-restraints excluded: chain A residue 1263 GLN Chi-restraints excluded: chain A residue 1274 LEU Chi-restraints excluded: chain A residue 1284 VAL Chi-restraints excluded: chain A residue 1291 ILE Chi-restraints excluded: chain A residue 1306 PHE Chi-restraints excluded: chain A residue 1311 VAL Chi-restraints excluded: chain A residue 1315 ILE Chi-restraints excluded: chain A residue 1372 SER Chi-restraints excluded: chain A residue 1386 LYS Chi-restraints excluded: chain A residue 1394 ILE Chi-restraints excluded: chain A residue 1408 LEU Chi-restraints excluded: chain A residue 1449 THR Chi-restraints excluded: chain A residue 1493 THR Chi-restraints excluded: chain A residue 1495 CYS Chi-restraints excluded: chain A residue 1531 THR Chi-restraints excluded: chain A residue 1536 ILE Chi-restraints excluded: chain A residue 1540 HIS Chi-restraints excluded: chain A residue 1546 LYS Chi-restraints excluded: chain A residue 1547 ARG Chi-restraints excluded: chain A residue 1548 ILE Chi-restraints excluded: chain A residue 1551 GLU Chi-restraints excluded: chain A residue 1564 ASP Chi-restraints excluded: chain A residue 1565 VAL Chi-restraints excluded: chain A residue 1568 LEU Chi-restraints excluded: chain A residue 1569 LEU Chi-restraints excluded: chain A residue 1573 GLN Chi-restraints excluded: chain A residue 1578 PHE Chi-restraints excluded: chain A residue 1582 CYS Chi-restraints excluded: chain A residue 1623 GLU Chi-restraints excluded: chain A residue 1636 ILE Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 66 ASP Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 142 SER Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain D residue 199 GLU Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 366 GLU Chi-restraints excluded: chain D residue 371 GLU Chi-restraints excluded: chain D residue 372 ILE Chi-restraints excluded: chain D residue 379 ASP Chi-restraints excluded: chain D residue 393 ASN Chi-restraints excluded: chain D residue 439 ASP Chi-restraints excluded: chain D residue 463 THR Chi-restraints excluded: chain D residue 481 ASN Chi-restraints excluded: chain D residue 500 LEU Chi-restraints excluded: chain D residue 507 CYS Chi-restraints excluded: chain D residue 522 LEU Chi-restraints excluded: chain D residue 530 LYS Chi-restraints excluded: chain D residue 532 ILE Chi-restraints excluded: chain D residue 587 THR Chi-restraints excluded: chain D residue 590 THR Chi-restraints excluded: chain D residue 618 SER Chi-restraints excluded: chain D residue 631 ILE Chi-restraints excluded: chain D residue 670 LEU Chi-restraints excluded: chain D residue 687 ILE Chi-restraints excluded: chain D residue 691 THR Chi-restraints excluded: chain D residue 721 SER Chi-restraints excluded: chain D residue 743 VAL Chi-restraints excluded: chain D residue 783 SER Chi-restraints excluded: chain D residue 795 SER Chi-restraints excluded: chain D residue 897 SER Chi-restraints excluded: chain D residue 903 VAL Chi-restraints excluded: chain D residue 975 ILE Chi-restraints excluded: chain D residue 985 ASN Chi-restraints excluded: chain D residue 989 SER Chi-restraints excluded: chain D residue 995 ASP Chi-restraints excluded: chain D residue 1026 CYS Chi-restraints excluded: chain D residue 1028 THR Chi-restraints excluded: chain D residue 1037 THR Chi-restraints excluded: chain D residue 1058 VAL Chi-restraints excluded: chain D residue 1069 THR Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 201 PHE Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 205 LYS Chi-restraints excluded: chain C residue 208 PHE Chi-restraints excluded: chain C residue 211 ARG Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 333 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 212 optimal weight: 5.9990 chunk 191 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 65 optimal weight: 7.9990 chunk 128 optimal weight: 8.9990 chunk 102 optimal weight: 0.3980 chunk 197 optimal weight: 4.9990 chunk 76 optimal weight: 4.9990 chunk 120 optimal weight: 6.9990 chunk 147 optimal weight: 0.9980 chunk 228 optimal weight: 20.0000 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 ASN A 429 GLN ** A 925 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN ** D 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 265 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.1297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 21173 Z= 0.413 Angle : 0.755 11.773 28687 Z= 0.373 Chirality : 0.048 0.306 3286 Planarity : 0.005 0.069 3602 Dihedral : 16.315 111.018 3584 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.52 % Allowed : 9.35 % Favored : 90.13 % Rotamer: Outliers : 9.50 % Allowed : 30.92 % Favored : 59.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.15 (0.17), residues: 2502 helix: -0.59 (0.15), residues: 1175 sheet: -1.07 (0.34), residues: 231 loop : -2.43 (0.19), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A1549 HIS 0.006 0.001 HIS A1260 PHE 0.024 0.002 PHE A1306 TYR 0.015 0.002 TYR D 217 ARG 0.007 0.001 ARG A1571 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 2241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 213 poor density : 247 time to evaluate : 2.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 LYS cc_start: 0.8297 (OUTLIER) cc_final: 0.7634 (tptp) REVERT: A 163 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7428 (tp30) REVERT: A 176 LEU cc_start: 0.7280 (OUTLIER) cc_final: 0.7063 (mp) REVERT: A 240 ARG cc_start: 0.7894 (OUTLIER) cc_final: 0.6958 (mtm180) REVERT: A 319 GLU cc_start: 0.7298 (OUTLIER) cc_final: 0.7054 (mm-30) REVERT: A 362 MET cc_start: 0.8814 (mtm) cc_final: 0.8588 (mtm) REVERT: A 405 SER cc_start: 0.8755 (OUTLIER) cc_final: 0.8485 (m) REVERT: A 407 GLU cc_start: 0.8056 (tp30) cc_final: 0.7739 (tp30) REVERT: A 581 GLN cc_start: 0.7748 (pm20) cc_final: 0.7122 (mm-40) REVERT: A 912 LEU cc_start: 0.8363 (OUTLIER) cc_final: 0.8127 (mt) REVERT: A 916 SER cc_start: 0.8307 (OUTLIER) cc_final: 0.7696 (p) REVERT: A 1007 GLN cc_start: 0.5244 (OUTLIER) cc_final: 0.4954 (tp40) REVERT: A 1307 ASP cc_start: 0.8326 (m-30) cc_final: 0.8010 (m-30) REVERT: A 1623 GLU cc_start: 0.6317 (OUTLIER) cc_final: 0.6101 (pm20) REVERT: A 1632 GLU cc_start: 0.7722 (mm-30) cc_final: 0.7317 (mm-30) REVERT: D 39 LYS cc_start: 0.6960 (OUTLIER) cc_final: 0.6690 (tppp) REVERT: D 42 GLU cc_start: 0.8165 (mp0) cc_final: 0.7890 (mp0) REVERT: D 102 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.7921 (mp) REVERT: D 199 GLU cc_start: 0.8263 (mp0) cc_final: 0.7813 (mp0) REVERT: D 523 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8861 (tp) REVERT: D 601 ASP cc_start: 0.8221 (t0) cc_final: 0.8005 (t0) REVERT: D 879 ASP cc_start: 0.6944 (t0) cc_final: 0.6665 (t0) REVERT: C 200 LEU cc_start: 0.8353 (pp) cc_final: 0.8104 (tm) REVERT: C 205 LYS cc_start: 0.6936 (ttpt) cc_final: 0.6436 (pttm) REVERT: C 268 VAL cc_start: 0.7722 (m) cc_final: 0.7489 (p) outliers start: 213 outliers final: 100 residues processed: 432 average time/residue: 0.9615 time to fit residues: 490.3001 Evaluate side-chains 351 residues out of total 2241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 238 time to evaluate : 2.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 240 ARG Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain A residue 322 HIS Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 590 ARG Chi-restraints excluded: chain A residue 593 CYS Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 764 SER Chi-restraints excluded: chain A residue 768 GLU Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain A residue 912 LEU Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 1007 GLN Chi-restraints excluded: chain A residue 1015 LYS Chi-restraints excluded: chain A residue 1017 LEU Chi-restraints excluded: chain A residue 1042 VAL Chi-restraints excluded: chain A residue 1051 ASN Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1160 VAL Chi-restraints excluded: chain A residue 1219 LEU Chi-restraints excluded: chain A residue 1255 CYS Chi-restraints excluded: chain A residue 1263 GLN Chi-restraints excluded: chain A residue 1274 LEU Chi-restraints excluded: chain A residue 1277 LEU Chi-restraints excluded: chain A residue 1284 VAL Chi-restraints excluded: chain A residue 1306 PHE Chi-restraints excluded: chain A residue 1315 ILE Chi-restraints excluded: chain A residue 1372 SER Chi-restraints excluded: chain A residue 1394 ILE Chi-restraints excluded: chain A residue 1408 LEU Chi-restraints excluded: chain A residue 1493 THR Chi-restraints excluded: chain A residue 1531 THR Chi-restraints excluded: chain A residue 1540 HIS Chi-restraints excluded: chain A residue 1547 ARG Chi-restraints excluded: chain A residue 1565 VAL Chi-restraints excluded: chain A residue 1586 VAL Chi-restraints excluded: chain A residue 1623 GLU Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 66 ASP Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 142 SER Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 326 THR Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 335 LYS Chi-restraints excluded: chain D residue 366 GLU Chi-restraints excluded: chain D residue 371 GLU Chi-restraints excluded: chain D residue 372 ILE Chi-restraints excluded: chain D residue 379 ASP Chi-restraints excluded: chain D residue 393 ASN Chi-restraints excluded: chain D residue 463 THR Chi-restraints excluded: chain D residue 516 ASP Chi-restraints excluded: chain D residue 522 LEU Chi-restraints excluded: chain D residue 523 LEU Chi-restraints excluded: chain D residue 532 ILE Chi-restraints excluded: chain D residue 587 THR Chi-restraints excluded: chain D residue 631 ILE Chi-restraints excluded: chain D residue 670 LEU Chi-restraints excluded: chain D residue 691 THR Chi-restraints excluded: chain D residue 740 ILE Chi-restraints excluded: chain D residue 743 VAL Chi-restraints excluded: chain D residue 783 SER Chi-restraints excluded: chain D residue 792 ILE Chi-restraints excluded: chain D residue 795 SER Chi-restraints excluded: chain D residue 798 VAL Chi-restraints excluded: chain D residue 806 LEU Chi-restraints excluded: chain D residue 845 SER Chi-restraints excluded: chain D residue 846 ASP Chi-restraints excluded: chain D residue 903 VAL Chi-restraints excluded: chain D residue 975 ILE Chi-restraints excluded: chain D residue 985 ASN Chi-restraints excluded: chain D residue 995 ASP Chi-restraints excluded: chain D residue 1028 THR Chi-restraints excluded: chain D residue 1032 ILE Chi-restraints excluded: chain D residue 1037 THR Chi-restraints excluded: chain D residue 1046 MET Chi-restraints excluded: chain D residue 1058 VAL Chi-restraints excluded: chain D residue 1069 THR Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 294 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 127 optimal weight: 8.9990 chunk 71 optimal weight: 0.9980 chunk 190 optimal weight: 3.9990 chunk 155 optimal weight: 0.8980 chunk 63 optimal weight: 9.9990 chunk 229 optimal weight: 50.0000 chunk 247 optimal weight: 8.9990 chunk 204 optimal weight: 2.9990 chunk 227 optimal weight: 30.0000 chunk 78 optimal weight: 1.9990 chunk 183 optimal weight: 5.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 ASN A 691 ASN ** A 925 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN ** D 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 652 ASN C 265 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 21173 Z= 0.322 Angle : 0.675 11.397 28687 Z= 0.332 Chirality : 0.045 0.305 3286 Planarity : 0.005 0.067 3602 Dihedral : 13.569 111.115 3477 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.44 % Allowed : 8.71 % Favored : 90.85 % Rotamer: Outliers : 8.70 % Allowed : 31.41 % Favored : 59.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: -1.93 (0.17), residues: 2502 helix: -0.37 (0.15), residues: 1175 sheet: -1.14 (0.33), residues: 231 loop : -2.32 (0.19), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A1549 HIS 0.004 0.001 HIS A1260 PHE 0.022 0.002 PHE A1545 TYR 0.019 0.001 TYR C 356 ARG 0.005 0.000 ARG A1585 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 2241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 195 poor density : 263 time to evaluate : 2.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 ASP cc_start: 0.8268 (t0) cc_final: 0.8057 (t0) REVERT: A 163 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7528 (tp30) REVERT: A 176 LEU cc_start: 0.7418 (OUTLIER) cc_final: 0.7192 (mp) REVERT: A 319 GLU cc_start: 0.7331 (OUTLIER) cc_final: 0.7031 (mm-30) REVERT: A 362 MET cc_start: 0.8790 (mtm) cc_final: 0.8574 (mtm) REVERT: A 401 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.8026 (mp) REVERT: A 407 GLU cc_start: 0.8015 (tp30) cc_final: 0.7683 (tp30) REVERT: A 413 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7679 (mm-30) REVERT: A 431 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.7487 (tp30) REVERT: A 581 GLN cc_start: 0.7877 (pm20) cc_final: 0.7210 (mm-40) REVERT: A 590 ARG cc_start: 0.7702 (OUTLIER) cc_final: 0.7444 (ptp90) REVERT: A 775 ARG cc_start: 0.7166 (OUTLIER) cc_final: 0.6917 (tmm-80) REVERT: A 916 SER cc_start: 0.8432 (OUTLIER) cc_final: 0.7823 (p) REVERT: A 1162 ILE cc_start: 0.8341 (OUTLIER) cc_final: 0.8089 (tp) REVERT: A 1296 LYS cc_start: 0.7021 (OUTLIER) cc_final: 0.6605 (mmtt) REVERT: A 1307 ASP cc_start: 0.8405 (m-30) cc_final: 0.8076 (m-30) REVERT: A 1549 TRP cc_start: 0.6313 (t-100) cc_final: 0.6101 (t60) REVERT: A 1578 PHE cc_start: 0.5994 (OUTLIER) cc_final: 0.5534 (t80) REVERT: A 1605 MET cc_start: 0.6613 (OUTLIER) cc_final: 0.6115 (ppp) REVERT: A 1623 GLU cc_start: 0.6253 (OUTLIER) cc_final: 0.6030 (pm20) REVERT: A 1632 GLU cc_start: 0.7752 (mm-30) cc_final: 0.7302 (mm-30) REVERT: D 39 LYS cc_start: 0.7045 (OUTLIER) cc_final: 0.6664 (tppp) REVERT: D 42 GLU cc_start: 0.8167 (mp0) cc_final: 0.7916 (mp0) REVERT: D 77 GLN cc_start: 0.8053 (OUTLIER) cc_final: 0.7404 (mp10) REVERT: D 199 GLU cc_start: 0.8332 (mp0) cc_final: 0.7722 (mp0) REVERT: D 366 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.8264 (pm20) REVERT: D 523 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8771 (tp) REVERT: D 601 ASP cc_start: 0.8214 (t0) cc_final: 0.7969 (t0) REVERT: D 704 ARG cc_start: 0.8162 (OUTLIER) cc_final: 0.7571 (ttt90) REVERT: D 708 ASP cc_start: 0.8369 (OUTLIER) cc_final: 0.7901 (t0) REVERT: D 860 LEU cc_start: 0.7471 (OUTLIER) cc_final: 0.7117 (mt) REVERT: D 861 MET cc_start: 0.7324 (OUTLIER) cc_final: 0.6821 (mmm) REVERT: D 879 ASP cc_start: 0.7171 (t0) cc_final: 0.6834 (t0) REVERT: D 895 ASN cc_start: 0.8477 (OUTLIER) cc_final: 0.8221 (m-40) REVERT: D 986 ASP cc_start: 0.8763 (OUTLIER) cc_final: 0.8413 (t0) REVERT: C 181 VAL cc_start: 0.4559 (t) cc_final: 0.4349 (p) REVERT: C 200 LEU cc_start: 0.8313 (pp) cc_final: 0.7977 (tm) REVERT: C 205 LYS cc_start: 0.6882 (ttpt) cc_final: 0.6508 (ptpp) REVERT: C 268 VAL cc_start: 0.7603 (m) cc_final: 0.7326 (p) REVERT: C 269 LEU cc_start: 0.6907 (pp) cc_final: 0.6596 (pp) REVERT: C 289 ILE cc_start: 0.5739 (OUTLIER) cc_final: 0.5354 (tt) outliers start: 195 outliers final: 94 residues processed: 425 average time/residue: 0.9990 time to fit residues: 500.4748 Evaluate side-chains 366 residues out of total 2241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 247 time to evaluate : 2.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain A residue 431 GLU Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 590 ARG Chi-restraints excluded: chain A residue 593 CYS Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 616 ILE Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 775 ARG Chi-restraints excluded: chain A residue 776 LYS Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 1039 VAL Chi-restraints excluded: chain A residue 1042 VAL Chi-restraints excluded: chain A residue 1051 ASN Chi-restraints excluded: chain A residue 1160 VAL Chi-restraints excluded: chain A residue 1162 ILE Chi-restraints excluded: chain A residue 1219 LEU Chi-restraints excluded: chain A residue 1255 CYS Chi-restraints excluded: chain A residue 1265 CYS Chi-restraints excluded: chain A residue 1274 LEU Chi-restraints excluded: chain A residue 1277 LEU Chi-restraints excluded: chain A residue 1284 VAL Chi-restraints excluded: chain A residue 1296 LYS Chi-restraints excluded: chain A residue 1306 PHE Chi-restraints excluded: chain A residue 1315 ILE Chi-restraints excluded: chain A residue 1449 THR Chi-restraints excluded: chain A residue 1493 THR Chi-restraints excluded: chain A residue 1531 THR Chi-restraints excluded: chain A residue 1540 HIS Chi-restraints excluded: chain A residue 1564 ASP Chi-restraints excluded: chain A residue 1565 VAL Chi-restraints excluded: chain A residue 1573 GLN Chi-restraints excluded: chain A residue 1578 PHE Chi-restraints excluded: chain A residue 1586 VAL Chi-restraints excluded: chain A residue 1605 MET Chi-restraints excluded: chain A residue 1623 GLU Chi-restraints excluded: chain A residue 1636 ILE Chi-restraints excluded: chain A residue 1645 SER Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 66 ASP Chi-restraints excluded: chain D residue 77 GLN Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 335 LYS Chi-restraints excluded: chain D residue 366 GLU Chi-restraints excluded: chain D residue 371 GLU Chi-restraints excluded: chain D residue 372 ILE Chi-restraints excluded: chain D residue 379 ASP Chi-restraints excluded: chain D residue 393 ASN Chi-restraints excluded: chain D residue 463 THR Chi-restraints excluded: chain D residue 481 ASN Chi-restraints excluded: chain D residue 500 LEU Chi-restraints excluded: chain D residue 516 ASP Chi-restraints excluded: chain D residue 522 LEU Chi-restraints excluded: chain D residue 523 LEU Chi-restraints excluded: chain D residue 587 THR Chi-restraints excluded: chain D residue 645 SER Chi-restraints excluded: chain D residue 670 LEU Chi-restraints excluded: chain D residue 691 THR Chi-restraints excluded: chain D residue 704 ARG Chi-restraints excluded: chain D residue 708 ASP Chi-restraints excluded: chain D residue 740 ILE Chi-restraints excluded: chain D residue 743 VAL Chi-restraints excluded: chain D residue 783 SER Chi-restraints excluded: chain D residue 795 SER Chi-restraints excluded: chain D residue 798 VAL Chi-restraints excluded: chain D residue 806 LEU Chi-restraints excluded: chain D residue 845 SER Chi-restraints excluded: chain D residue 860 LEU Chi-restraints excluded: chain D residue 861 MET Chi-restraints excluded: chain D residue 890 SER Chi-restraints excluded: chain D residue 895 ASN Chi-restraints excluded: chain D residue 897 SER Chi-restraints excluded: chain D residue 903 VAL Chi-restraints excluded: chain D residue 985 ASN Chi-restraints excluded: chain D residue 986 ASP Chi-restraints excluded: chain D residue 1015 PHE Chi-restraints excluded: chain D residue 1028 THR Chi-restraints excluded: chain D residue 1032 ILE Chi-restraints excluded: chain D residue 1037 THR Chi-restraints excluded: chain D residue 1058 VAL Chi-restraints excluded: chain D residue 1069 THR Chi-restraints excluded: chain D residue 1075 SER Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 208 PHE Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 356 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 226 optimal weight: 30.0000 chunk 172 optimal weight: 1.9990 chunk 118 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 109 optimal weight: 0.0270 chunk 153 optimal weight: 0.6980 chunk 230 optimal weight: 30.0000 chunk 243 optimal weight: 0.7980 chunk 120 optimal weight: 8.9990 chunk 218 optimal weight: 0.4980 chunk 65 optimal weight: 8.9990 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 925 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN ** D 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1062 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 21173 Z= 0.181 Angle : 0.621 9.812 28687 Z= 0.306 Chirality : 0.041 0.319 3286 Planarity : 0.004 0.064 3602 Dihedral : 11.642 109.994 3435 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.95 % Favored : 91.69 % Rotamer: Outliers : 7.05 % Allowed : 33.47 % Favored : 59.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: -1.65 (0.17), residues: 2502 helix: -0.13 (0.15), residues: 1177 sheet: -0.92 (0.33), residues: 229 loop : -2.22 (0.19), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A1233 HIS 0.004 0.001 HIS D 885 PHE 0.048 0.001 PHE D1015 TYR 0.015 0.001 TYR D 719 ARG 0.005 0.000 ARG A1570 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 2241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 266 time to evaluate : 2.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 GLU cc_start: 0.7484 (OUTLIER) cc_final: 0.6851 (mp0) REVERT: A 150 ASP cc_start: 0.8199 (t0) cc_final: 0.7956 (t0) REVERT: A 163 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7518 (tp30) REVERT: A 319 GLU cc_start: 0.7259 (OUTLIER) cc_final: 0.6954 (mm-30) REVERT: A 362 MET cc_start: 0.8760 (mtm) cc_final: 0.8512 (mtm) REVERT: A 407 GLU cc_start: 0.7988 (tp30) cc_final: 0.7703 (tp30) REVERT: A 583 TYR cc_start: 0.7099 (t80) cc_final: 0.6616 (t80) REVERT: A 775 ARG cc_start: 0.7115 (OUTLIER) cc_final: 0.6873 (tmm-80) REVERT: A 928 PHE cc_start: 0.8345 (t80) cc_final: 0.8099 (t80) REVERT: A 929 ARG cc_start: 0.8090 (OUTLIER) cc_final: 0.6597 (ttp-110) REVERT: A 1307 ASP cc_start: 0.8211 (m-30) cc_final: 0.7913 (m-30) REVERT: A 1526 ASN cc_start: 0.8459 (t0) cc_final: 0.8137 (t0) REVERT: A 1549 TRP cc_start: 0.6354 (t-100) cc_final: 0.6028 (t60) REVERT: A 1578 PHE cc_start: 0.5814 (OUTLIER) cc_final: 0.5407 (t80) REVERT: A 1605 MET cc_start: 0.6448 (OUTLIER) cc_final: 0.6109 (ppp) REVERT: A 1611 PHE cc_start: 0.8500 (t80) cc_final: 0.7957 (m-80) REVERT: A 1615 ARG cc_start: 0.7948 (tpp80) cc_final: 0.7437 (tpm170) REVERT: A 1623 GLU cc_start: 0.6146 (OUTLIER) cc_final: 0.5897 (pm20) REVERT: D 39 LYS cc_start: 0.6966 (OUTLIER) cc_final: 0.6695 (tppp) REVERT: D 42 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7924 (mp0) REVERT: D 77 GLN cc_start: 0.8108 (OUTLIER) cc_final: 0.7458 (mp10) REVERT: D 102 LEU cc_start: 0.8228 (OUTLIER) cc_final: 0.7806 (mp) REVERT: D 198 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.8035 (mp0) REVERT: D 199 GLU cc_start: 0.8337 (mp0) cc_final: 0.7798 (mp0) REVERT: D 366 GLU cc_start: 0.8585 (OUTLIER) cc_final: 0.8219 (pm20) REVERT: D 601 ASP cc_start: 0.8184 (t0) cc_final: 0.7939 (t0) REVERT: D 704 ARG cc_start: 0.8083 (OUTLIER) cc_final: 0.7468 (ttt90) REVERT: D 708 ASP cc_start: 0.8256 (OUTLIER) cc_final: 0.7880 (t0) REVERT: D 879 ASP cc_start: 0.7114 (t0) cc_final: 0.6726 (t0) REVERT: D 883 MET cc_start: 0.7712 (tpt) cc_final: 0.7459 (mmp) REVERT: D 986 ASP cc_start: 0.8723 (OUTLIER) cc_final: 0.8392 (t0) REVERT: D 1010 ASN cc_start: 0.8764 (m110) cc_final: 0.8530 (m-40) REVERT: C 200 LEU cc_start: 0.8376 (pp) cc_final: 0.8152 (tm) REVERT: C 201 PHE cc_start: 0.7557 (OUTLIER) cc_final: 0.7213 (m-10) REVERT: C 205 LYS cc_start: 0.6954 (ttpt) cc_final: 0.6571 (ptpp) REVERT: C 266 LEU cc_start: 0.7022 (OUTLIER) cc_final: 0.6663 (mm) REVERT: C 268 VAL cc_start: 0.7617 (m) cc_final: 0.7248 (p) REVERT: C 269 LEU cc_start: 0.6733 (pp) cc_final: 0.6467 (pp) REVERT: C 356 TYR cc_start: 0.7344 (OUTLIER) cc_final: 0.6755 (m-80) outliers start: 158 outliers final: 71 residues processed: 393 average time/residue: 1.0545 time to fit residues: 484.0153 Evaluate side-chains 335 residues out of total 2241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 244 time to evaluate : 2.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 592 ASP Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 775 ARG Chi-restraints excluded: chain A residue 776 LYS Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain A residue 929 ARG Chi-restraints excluded: chain A residue 1042 VAL Chi-restraints excluded: chain A residue 1051 ASN Chi-restraints excluded: chain A residue 1160 VAL Chi-restraints excluded: chain A residue 1219 LEU Chi-restraints excluded: chain A residue 1255 CYS Chi-restraints excluded: chain A residue 1274 LEU Chi-restraints excluded: chain A residue 1277 LEU Chi-restraints excluded: chain A residue 1284 VAL Chi-restraints excluded: chain A residue 1291 ILE Chi-restraints excluded: chain A residue 1315 ILE Chi-restraints excluded: chain A residue 1385 VAL Chi-restraints excluded: chain A residue 1449 THR Chi-restraints excluded: chain A residue 1493 THR Chi-restraints excluded: chain A residue 1531 THR Chi-restraints excluded: chain A residue 1564 ASP Chi-restraints excluded: chain A residue 1578 PHE Chi-restraints excluded: chain A residue 1605 MET Chi-restraints excluded: chain A residue 1609 THR Chi-restraints excluded: chain A residue 1623 GLU Chi-restraints excluded: chain A residue 1636 ILE Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 66 ASP Chi-restraints excluded: chain D residue 77 GLN Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 160 SER Chi-restraints excluded: chain D residue 198 GLU Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 366 GLU Chi-restraints excluded: chain D residue 379 ASP Chi-restraints excluded: chain D residue 393 ASN Chi-restraints excluded: chain D residue 463 THR Chi-restraints excluded: chain D residue 500 LEU Chi-restraints excluded: chain D residue 516 ASP Chi-restraints excluded: chain D residue 587 THR Chi-restraints excluded: chain D residue 590 THR Chi-restraints excluded: chain D residue 670 LEU Chi-restraints excluded: chain D residue 691 THR Chi-restraints excluded: chain D residue 704 ARG Chi-restraints excluded: chain D residue 708 ASP Chi-restraints excluded: chain D residue 740 ILE Chi-restraints excluded: chain D residue 743 VAL Chi-restraints excluded: chain D residue 895 ASN Chi-restraints excluded: chain D residue 903 VAL Chi-restraints excluded: chain D residue 975 ILE Chi-restraints excluded: chain D residue 985 ASN Chi-restraints excluded: chain D residue 986 ASP Chi-restraints excluded: chain D residue 995 ASP Chi-restraints excluded: chain D residue 1028 THR Chi-restraints excluded: chain D residue 1032 ILE Chi-restraints excluded: chain D residue 1037 THR Chi-restraints excluded: chain D residue 1046 MET Chi-restraints excluded: chain D residue 1069 THR Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 201 PHE Chi-restraints excluded: chain C residue 208 PHE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 356 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 202 optimal weight: 0.5980 chunk 138 optimal weight: 3.9990 chunk 3 optimal weight: 0.1980 chunk 181 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 207 optimal weight: 1.9990 chunk 168 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 124 optimal weight: 20.0000 chunk 218 optimal weight: 4.9990 chunk 61 optimal weight: 0.9980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 589 ASN ** A 925 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 652 ASN D 682 ASN D1062 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 21173 Z= 0.216 Angle : 0.619 9.642 28687 Z= 0.306 Chirality : 0.042 0.297 3286 Planarity : 0.004 0.062 3602 Dihedral : 10.814 108.815 3404 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.28 % Allowed : 8.19 % Favored : 91.53 % Rotamer: Outliers : 6.83 % Allowed : 33.60 % Favored : 59.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: -1.53 (0.17), residues: 2502 helix: -0.03 (0.15), residues: 1170 sheet: -0.84 (0.33), residues: 229 loop : -2.15 (0.19), residues: 1103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A1233 HIS 0.004 0.001 HIS D 885 PHE 0.024 0.001 PHE A 591 TYR 0.011 0.001 TYR A1222 ARG 0.008 0.000 ARG C 107 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 2241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 261 time to evaluate : 2.535 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 127 GLU cc_start: 0.7444 (OUTLIER) cc_final: 0.6832 (mp0) REVERT: A 150 ASP cc_start: 0.8292 (t0) cc_final: 0.8029 (t0) REVERT: A 163 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7551 (tp30) REVERT: A 319 GLU cc_start: 0.7268 (OUTLIER) cc_final: 0.6957 (mm-30) REVERT: A 362 MET cc_start: 0.8771 (mtm) cc_final: 0.8569 (mtm) REVERT: A 407 GLU cc_start: 0.8010 (tp30) cc_final: 0.7702 (tp30) REVERT: A 583 TYR cc_start: 0.7413 (t80) cc_final: 0.6759 (t80) REVERT: A 686 ARG cc_start: 0.8191 (OUTLIER) cc_final: 0.7792 (mmt90) REVERT: A 775 ARG cc_start: 0.7129 (OUTLIER) cc_final: 0.6882 (tmm-80) REVERT: A 928 PHE cc_start: 0.8393 (t80) cc_final: 0.8173 (t80) REVERT: A 929 ARG cc_start: 0.8108 (OUTLIER) cc_final: 0.6588 (ttp-110) REVERT: A 1051 ASN cc_start: 0.8328 (OUTLIER) cc_final: 0.7795 (p0) REVERT: A 1207 ARG cc_start: 0.7439 (mpp80) cc_final: 0.7204 (pmm-80) REVERT: A 1307 ASP cc_start: 0.8246 (m-30) cc_final: 0.7935 (m-30) REVERT: A 1526 ASN cc_start: 0.8432 (t0) cc_final: 0.8118 (t0) REVERT: A 1549 TRP cc_start: 0.6387 (t-100) cc_final: 0.6052 (t60) REVERT: A 1578 PHE cc_start: 0.5910 (OUTLIER) cc_final: 0.5572 (t80) REVERT: A 1596 MET cc_start: 0.4130 (mmp) cc_final: 0.3636 (mtp) REVERT: A 1605 MET cc_start: 0.6542 (ptp) cc_final: 0.6155 (ppp) REVERT: A 1611 PHE cc_start: 0.8518 (t80) cc_final: 0.7969 (m-80) REVERT: A 1615 ARG cc_start: 0.8024 (tpp80) cc_final: 0.7456 (tpm170) REVERT: A 1648 LEU cc_start: 0.6418 (OUTLIER) cc_final: 0.6218 (mm) REVERT: D 39 LYS cc_start: 0.6998 (OUTLIER) cc_final: 0.6711 (tppp) REVERT: D 42 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7937 (mp0) REVERT: D 77 GLN cc_start: 0.8100 (OUTLIER) cc_final: 0.7449 (mp10) REVERT: D 102 LEU cc_start: 0.8198 (OUTLIER) cc_final: 0.7722 (mp) REVERT: D 103 GLU cc_start: 0.7584 (mp0) cc_final: 0.7190 (mp0) REVERT: D 198 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.8065 (mp0) REVERT: D 199 GLU cc_start: 0.8360 (mp0) cc_final: 0.7928 (mp0) REVERT: D 366 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.8105 (pm20) REVERT: D 523 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8641 (tp) REVERT: D 601 ASP cc_start: 0.8178 (t0) cc_final: 0.7940 (t0) REVERT: D 704 ARG cc_start: 0.8077 (OUTLIER) cc_final: 0.7482 (ttt90) REVERT: D 708 ASP cc_start: 0.8233 (OUTLIER) cc_final: 0.7871 (t0) REVERT: D 861 MET cc_start: 0.7421 (OUTLIER) cc_final: 0.7204 (tpp) REVERT: D 879 ASP cc_start: 0.7113 (t0) cc_final: 0.6863 (t0) REVERT: D 986 ASP cc_start: 0.8693 (OUTLIER) cc_final: 0.7735 (t70) REVERT: D 1010 ASN cc_start: 0.8736 (m110) cc_final: 0.8502 (m-40) REVERT: C 200 LEU cc_start: 0.8375 (pp) cc_final: 0.8172 (tm) REVERT: C 201 PHE cc_start: 0.7652 (OUTLIER) cc_final: 0.7373 (m-10) REVERT: C 205 LYS cc_start: 0.6946 (ttpt) cc_final: 0.6494 (ptpp) REVERT: C 266 LEU cc_start: 0.6961 (OUTLIER) cc_final: 0.6653 (mm) REVERT: C 268 VAL cc_start: 0.7604 (m) cc_final: 0.7242 (p) REVERT: C 269 LEU cc_start: 0.6623 (pp) cc_final: 0.6421 (pp) outliers start: 153 outliers final: 80 residues processed: 385 average time/residue: 1.0260 time to fit residues: 464.3651 Evaluate side-chains 353 residues out of total 2241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 251 time to evaluate : 2.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 686 ARG Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 775 ARG Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 929 ARG Chi-restraints excluded: chain A residue 1011 ILE Chi-restraints excluded: chain A residue 1049 ILE Chi-restraints excluded: chain A residue 1051 ASN Chi-restraints excluded: chain A residue 1058 LEU Chi-restraints excluded: chain A residue 1219 LEU Chi-restraints excluded: chain A residue 1255 CYS Chi-restraints excluded: chain A residue 1274 LEU Chi-restraints excluded: chain A residue 1277 LEU Chi-restraints excluded: chain A residue 1291 ILE Chi-restraints excluded: chain A residue 1385 VAL Chi-restraints excluded: chain A residue 1394 ILE Chi-restraints excluded: chain A residue 1449 THR Chi-restraints excluded: chain A residue 1493 THR Chi-restraints excluded: chain A residue 1531 THR Chi-restraints excluded: chain A residue 1564 ASP Chi-restraints excluded: chain A residue 1573 GLN Chi-restraints excluded: chain A residue 1578 PHE Chi-restraints excluded: chain A residue 1636 ILE Chi-restraints excluded: chain A residue 1648 LEU Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 66 ASP Chi-restraints excluded: chain D residue 77 GLN Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 198 GLU Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 328 LYS Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 366 GLU Chi-restraints excluded: chain D residue 372 ILE Chi-restraints excluded: chain D residue 379 ASP Chi-restraints excluded: chain D residue 393 ASN Chi-restraints excluded: chain D residue 463 THR Chi-restraints excluded: chain D residue 481 ASN Chi-restraints excluded: chain D residue 500 LEU Chi-restraints excluded: chain D residue 516 ASP Chi-restraints excluded: chain D residue 522 LEU Chi-restraints excluded: chain D residue 523 LEU Chi-restraints excluded: chain D residue 532 ILE Chi-restraints excluded: chain D residue 587 THR Chi-restraints excluded: chain D residue 590 THR Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 645 SER Chi-restraints excluded: chain D residue 670 LEU Chi-restraints excluded: chain D residue 687 ILE Chi-restraints excluded: chain D residue 691 THR Chi-restraints excluded: chain D residue 704 ARG Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain D residue 708 ASP Chi-restraints excluded: chain D residue 740 ILE Chi-restraints excluded: chain D residue 743 VAL Chi-restraints excluded: chain D residue 811 VAL Chi-restraints excluded: chain D residue 861 MET Chi-restraints excluded: chain D residue 890 SER Chi-restraints excluded: chain D residue 895 ASN Chi-restraints excluded: chain D residue 903 VAL Chi-restraints excluded: chain D residue 975 ILE Chi-restraints excluded: chain D residue 985 ASN Chi-restraints excluded: chain D residue 986 ASP Chi-restraints excluded: chain D residue 995 ASP Chi-restraints excluded: chain D residue 1028 THR Chi-restraints excluded: chain D residue 1032 ILE Chi-restraints excluded: chain D residue 1037 THR Chi-restraints excluded: chain D residue 1046 MET Chi-restraints excluded: chain D residue 1058 VAL Chi-restraints excluded: chain D residue 1069 THR Chi-restraints excluded: chain D residue 1075 SER Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 201 PHE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 294 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 81 optimal weight: 4.9990 chunk 219 optimal weight: 4.9990 chunk 48 optimal weight: 0.9980 chunk 143 optimal weight: 1.9990 chunk 60 optimal weight: 6.9990 chunk 243 optimal weight: 0.4980 chunk 202 optimal weight: 1.9990 chunk 112 optimal weight: 0.6980 chunk 20 optimal weight: 0.4980 chunk 80 optimal weight: 0.6980 chunk 128 optimal weight: 10.0000 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 925 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN D 295 ASN ** D 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1062 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21173 Z= 0.172 Angle : 0.602 9.932 28687 Z= 0.296 Chirality : 0.041 0.274 3286 Planarity : 0.004 0.064 3602 Dihedral : 10.112 107.606 3395 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.55 % Favored : 92.21 % Rotamer: Outliers : 6.20 % Allowed : 33.82 % Favored : 59.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: -1.37 (0.17), residues: 2502 helix: 0.14 (0.16), residues: 1159 sheet: -0.64 (0.34), residues: 217 loop : -2.12 (0.19), residues: 1126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A1233 HIS 0.004 0.001 HIS D 885 PHE 0.029 0.001 PHE A 591 TYR 0.011 0.001 TYR A1222 ARG 0.006 0.000 ARG A1570 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 2241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 275 time to evaluate : 2.453 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 127 GLU cc_start: 0.7313 (OUTLIER) cc_final: 0.6751 (mp0) REVERT: A 150 ASP cc_start: 0.8230 (t0) cc_final: 0.7968 (t0) REVERT: A 163 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7530 (tp30) REVERT: A 173 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.7140 (tt0) REVERT: A 212 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8388 (mp) REVERT: A 319 GLU cc_start: 0.7245 (OUTLIER) cc_final: 0.6912 (mm-30) REVERT: A 362 MET cc_start: 0.8765 (mtm) cc_final: 0.8498 (mtm) REVERT: A 401 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.8187 (mp) REVERT: A 407 GLU cc_start: 0.7977 (tp30) cc_final: 0.7703 (tp30) REVERT: A 583 TYR cc_start: 0.7244 (t80) cc_final: 0.6743 (t80) REVERT: A 683 GLN cc_start: 0.7728 (pm20) cc_final: 0.7525 (pm20) REVERT: A 916 SER cc_start: 0.8349 (OUTLIER) cc_final: 0.7695 (p) REVERT: A 928 PHE cc_start: 0.8405 (t80) cc_final: 0.8163 (t80) REVERT: A 929 ARG cc_start: 0.8115 (OUTLIER) cc_final: 0.6629 (ttp-110) REVERT: A 1011 ILE cc_start: 0.5827 (OUTLIER) cc_final: 0.5484 (pp) REVERT: A 1051 ASN cc_start: 0.8227 (OUTLIER) cc_final: 0.7687 (p0) REVERT: A 1162 ILE cc_start: 0.8294 (OUTLIER) cc_final: 0.8033 (tp) REVERT: A 1207 ARG cc_start: 0.7514 (mpp80) cc_final: 0.7287 (pmm-80) REVERT: A 1307 ASP cc_start: 0.8177 (m-30) cc_final: 0.7877 (m-30) REVERT: A 1526 ASN cc_start: 0.8366 (t0) cc_final: 0.8053 (t0) REVERT: A 1549 TRP cc_start: 0.6647 (t-100) cc_final: 0.6299 (t60) REVERT: A 1578 PHE cc_start: 0.5915 (OUTLIER) cc_final: 0.5631 (t80) REVERT: A 1596 MET cc_start: 0.4030 (mmp) cc_final: 0.3559 (mtt) REVERT: A 1605 MET cc_start: 0.6977 (OUTLIER) cc_final: 0.6569 (ppp) REVERT: A 1615 ARG cc_start: 0.8160 (tpp80) cc_final: 0.7717 (tpm170) REVERT: D 39 LYS cc_start: 0.6885 (OUTLIER) cc_final: 0.6658 (tppp) REVERT: D 42 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7920 (mp0) REVERT: D 77 GLN cc_start: 0.8125 (OUTLIER) cc_final: 0.7495 (mp10) REVERT: D 103 GLU cc_start: 0.7565 (mp0) cc_final: 0.7102 (mp0) REVERT: D 199 GLU cc_start: 0.8360 (mp0) cc_final: 0.7922 (mp0) REVERT: D 601 ASP cc_start: 0.8148 (t0) cc_final: 0.7906 (t0) REVERT: D 704 ARG cc_start: 0.8049 (OUTLIER) cc_final: 0.7407 (ttt90) REVERT: D 708 ASP cc_start: 0.8177 (OUTLIER) cc_final: 0.7956 (t0) REVERT: D 879 ASP cc_start: 0.7121 (t0) cc_final: 0.6846 (t0) REVERT: D 883 MET cc_start: 0.7719 (tpt) cc_final: 0.7515 (mmp) REVERT: D 985 ASN cc_start: 0.8677 (OUTLIER) cc_final: 0.8162 (p0) REVERT: D 986 ASP cc_start: 0.8690 (OUTLIER) cc_final: 0.7739 (t70) REVERT: D 1010 ASN cc_start: 0.8751 (m110) cc_final: 0.8519 (m-40) REVERT: C 201 PHE cc_start: 0.7695 (OUTLIER) cc_final: 0.7339 (m-10) REVERT: C 205 LYS cc_start: 0.6923 (ttpt) cc_final: 0.6573 (ptpp) REVERT: C 266 LEU cc_start: 0.7105 (OUTLIER) cc_final: 0.6711 (mm) REVERT: C 268 VAL cc_start: 0.7603 (m) cc_final: 0.7258 (p) REVERT: C 347 GLU cc_start: 0.7624 (tp30) cc_final: 0.7344 (mp0) REVERT: C 356 TYR cc_start: 0.7107 (OUTLIER) cc_final: 0.6551 (m-80) outliers start: 139 outliers final: 72 residues processed: 388 average time/residue: 1.0044 time to fit residues: 457.4236 Evaluate side-chains 346 residues out of total 2241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 251 time to evaluate : 2.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 592 ASP Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 929 ARG Chi-restraints excluded: chain A residue 1011 ILE Chi-restraints excluded: chain A residue 1042 VAL Chi-restraints excluded: chain A residue 1051 ASN Chi-restraints excluded: chain A residue 1162 ILE Chi-restraints excluded: chain A residue 1219 LEU Chi-restraints excluded: chain A residue 1255 CYS Chi-restraints excluded: chain A residue 1274 LEU Chi-restraints excluded: chain A residue 1291 ILE Chi-restraints excluded: chain A residue 1315 ILE Chi-restraints excluded: chain A residue 1385 VAL Chi-restraints excluded: chain A residue 1449 THR Chi-restraints excluded: chain A residue 1493 THR Chi-restraints excluded: chain A residue 1531 THR Chi-restraints excluded: chain A residue 1564 ASP Chi-restraints excluded: chain A residue 1565 VAL Chi-restraints excluded: chain A residue 1578 PHE Chi-restraints excluded: chain A residue 1582 CYS Chi-restraints excluded: chain A residue 1605 MET Chi-restraints excluded: chain A residue 1609 THR Chi-restraints excluded: chain A residue 1636 ILE Chi-restraints excluded: chain A residue 1645 SER Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 66 ASP Chi-restraints excluded: chain D residue 77 GLN Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 210 SER Chi-restraints excluded: chain D residue 263 SER Chi-restraints excluded: chain D residue 372 ILE Chi-restraints excluded: chain D residue 393 ASN Chi-restraints excluded: chain D residue 463 THR Chi-restraints excluded: chain D residue 500 LEU Chi-restraints excluded: chain D residue 516 ASP Chi-restraints excluded: chain D residue 587 THR Chi-restraints excluded: chain D residue 670 LEU Chi-restraints excluded: chain D residue 691 THR Chi-restraints excluded: chain D residue 704 ARG Chi-restraints excluded: chain D residue 708 ASP Chi-restraints excluded: chain D residue 743 VAL Chi-restraints excluded: chain D residue 795 SER Chi-restraints excluded: chain D residue 811 VAL Chi-restraints excluded: chain D residue 890 SER Chi-restraints excluded: chain D residue 895 ASN Chi-restraints excluded: chain D residue 897 SER Chi-restraints excluded: chain D residue 975 ILE Chi-restraints excluded: chain D residue 985 ASN Chi-restraints excluded: chain D residue 986 ASP Chi-restraints excluded: chain D residue 995 ASP Chi-restraints excluded: chain D residue 1015 PHE Chi-restraints excluded: chain D residue 1032 ILE Chi-restraints excluded: chain D residue 1046 MET Chi-restraints excluded: chain D residue 1058 VAL Chi-restraints excluded: chain D residue 1069 THR Chi-restraints excluded: chain D residue 1075 SER Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 201 PHE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 356 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 235 optimal weight: 8.9990 chunk 27 optimal weight: 1.9990 chunk 138 optimal weight: 1.9990 chunk 178 optimal weight: 6.9990 chunk 137 optimal weight: 3.9990 chunk 205 optimal weight: 7.9990 chunk 136 optimal weight: 0.0170 chunk 242 optimal weight: 7.9990 chunk 152 optimal weight: 0.6980 chunk 148 optimal weight: 1.9990 chunk 112 optimal weight: 0.8980 overall best weight: 1.1222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 925 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 295 ASN ** D 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1062 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 21173 Z= 0.214 Angle : 0.630 10.831 28687 Z= 0.308 Chirality : 0.042 0.264 3286 Planarity : 0.004 0.066 3602 Dihedral : 9.856 106.788 3387 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.99 % Favored : 91.81 % Rotamer: Outliers : 5.89 % Allowed : 34.54 % Favored : 59.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: -1.30 (0.17), residues: 2502 helix: 0.21 (0.16), residues: 1155 sheet: -0.60 (0.34), residues: 217 loop : -2.08 (0.19), residues: 1130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A1233 HIS 0.004 0.001 HIS D 885 PHE 0.028 0.001 PHE A 594 TYR 0.011 0.001 TYR D 788 ARG 0.004 0.000 ARG D 313 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 2241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 260 time to evaluate : 2.603 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 127 GLU cc_start: 0.7344 (OUTLIER) cc_final: 0.6811 (mp0) REVERT: A 150 ASP cc_start: 0.8280 (t0) cc_final: 0.8021 (t0) REVERT: A 163 GLU cc_start: 0.7969 (OUTLIER) cc_final: 0.7572 (tp30) REVERT: A 173 GLU cc_start: 0.7634 (OUTLIER) cc_final: 0.7239 (tt0) REVERT: A 212 LEU cc_start: 0.8589 (mp) cc_final: 0.8358 (mp) REVERT: A 319 GLU cc_start: 0.7239 (OUTLIER) cc_final: 0.6898 (mm-30) REVERT: A 362 MET cc_start: 0.8772 (mtm) cc_final: 0.8506 (mtm) REVERT: A 401 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.8186 (mp) REVERT: A 407 GLU cc_start: 0.7986 (tp30) cc_final: 0.7632 (mm-30) REVERT: A 580 LEU cc_start: 0.7468 (tp) cc_final: 0.6943 (pt) REVERT: A 583 TYR cc_start: 0.7495 (t80) cc_final: 0.6970 (t80) REVERT: A 621 CYS cc_start: 0.8624 (m) cc_final: 0.8084 (p) REVERT: A 683 GLN cc_start: 0.7723 (pm20) cc_final: 0.7516 (pm20) REVERT: A 775 ARG cc_start: 0.7227 (OUTLIER) cc_final: 0.7010 (tmm-80) REVERT: A 916 SER cc_start: 0.8356 (OUTLIER) cc_final: 0.7699 (p) REVERT: A 928 PHE cc_start: 0.8439 (t80) cc_final: 0.8180 (t80) REVERT: A 929 ARG cc_start: 0.8113 (OUTLIER) cc_final: 0.6615 (ttp-110) REVERT: A 1011 ILE cc_start: 0.5788 (OUTLIER) cc_final: 0.5463 (pp) REVERT: A 1051 ASN cc_start: 0.8238 (OUTLIER) cc_final: 0.7685 (p0) REVERT: A 1219 LEU cc_start: 0.6654 (OUTLIER) cc_final: 0.6304 (tp) REVERT: A 1274 LEU cc_start: 0.7935 (OUTLIER) cc_final: 0.7650 (mt) REVERT: A 1307 ASP cc_start: 0.8163 (m-30) cc_final: 0.7869 (m-30) REVERT: A 1526 ASN cc_start: 0.8354 (t0) cc_final: 0.8034 (t0) REVERT: A 1549 TRP cc_start: 0.6758 (t-100) cc_final: 0.6469 (t-100) REVERT: A 1578 PHE cc_start: 0.5948 (OUTLIER) cc_final: 0.5664 (t80) REVERT: A 1596 MET cc_start: 0.3729 (mmp) cc_final: 0.3337 (mtp) REVERT: A 1605 MET cc_start: 0.6957 (OUTLIER) cc_final: 0.6551 (ppp) REVERT: A 1615 ARG cc_start: 0.8188 (tpp80) cc_final: 0.7707 (tpm170) REVERT: A 1623 GLU cc_start: 0.4057 (OUTLIER) cc_final: 0.3449 (pm20) REVERT: D 39 LYS cc_start: 0.6889 (OUTLIER) cc_final: 0.6674 (tppp) REVERT: D 42 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7932 (mp0) REVERT: D 77 GLN cc_start: 0.8111 (OUTLIER) cc_final: 0.7479 (mp10) REVERT: D 103 GLU cc_start: 0.7587 (mp0) cc_final: 0.7124 (mp0) REVERT: D 601 ASP cc_start: 0.8158 (t0) cc_final: 0.7923 (t0) REVERT: D 827 LYS cc_start: 0.7172 (mttt) cc_final: 0.6338 (mttp) REVERT: D 879 ASP cc_start: 0.7108 (t0) cc_final: 0.6845 (t0) REVERT: D 985 ASN cc_start: 0.8707 (OUTLIER) cc_final: 0.8188 (p0) REVERT: D 986 ASP cc_start: 0.8686 (OUTLIER) cc_final: 0.7742 (t70) REVERT: D 1010 ASN cc_start: 0.8749 (m110) cc_final: 0.8519 (m-40) REVERT: C 201 PHE cc_start: 0.7845 (OUTLIER) cc_final: 0.7352 (m-10) REVERT: C 205 LYS cc_start: 0.6958 (ttpt) cc_final: 0.6583 (ptpp) REVERT: C 266 LEU cc_start: 0.7026 (OUTLIER) cc_final: 0.6678 (mm) REVERT: C 268 VAL cc_start: 0.7704 (m) cc_final: 0.7375 (p) REVERT: C 285 LEU cc_start: 0.1388 (OUTLIER) cc_final: 0.0850 (pp) REVERT: C 347 GLU cc_start: 0.7567 (tp30) cc_final: 0.7257 (mp0) REVERT: C 356 TYR cc_start: 0.7100 (OUTLIER) cc_final: 0.6594 (m-80) outliers start: 132 outliers final: 76 residues processed: 372 average time/residue: 1.0106 time to fit residues: 445.5643 Evaluate side-chains 351 residues out of total 2241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 251 time to evaluate : 2.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 775 ARG Chi-restraints excluded: chain A residue 776 LYS Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 929 ARG Chi-restraints excluded: chain A residue 1011 ILE Chi-restraints excluded: chain A residue 1042 VAL Chi-restraints excluded: chain A residue 1051 ASN Chi-restraints excluded: chain A residue 1219 LEU Chi-restraints excluded: chain A residue 1255 CYS Chi-restraints excluded: chain A residue 1274 LEU Chi-restraints excluded: chain A residue 1277 LEU Chi-restraints excluded: chain A residue 1291 ILE Chi-restraints excluded: chain A residue 1315 ILE Chi-restraints excluded: chain A residue 1385 VAL Chi-restraints excluded: chain A residue 1449 THR Chi-restraints excluded: chain A residue 1493 THR Chi-restraints excluded: chain A residue 1531 THR Chi-restraints excluded: chain A residue 1564 ASP Chi-restraints excluded: chain A residue 1578 PHE Chi-restraints excluded: chain A residue 1582 CYS Chi-restraints excluded: chain A residue 1605 MET Chi-restraints excluded: chain A residue 1623 GLU Chi-restraints excluded: chain A residue 1636 ILE Chi-restraints excluded: chain A residue 1645 SER Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 66 ASP Chi-restraints excluded: chain D residue 77 GLN Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 160 SER Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 263 SER Chi-restraints excluded: chain D residue 372 ILE Chi-restraints excluded: chain D residue 393 ASN Chi-restraints excluded: chain D residue 463 THR Chi-restraints excluded: chain D residue 481 ASN Chi-restraints excluded: chain D residue 500 LEU Chi-restraints excluded: chain D residue 516 ASP Chi-restraints excluded: chain D residue 532 ILE Chi-restraints excluded: chain D residue 582 GLU Chi-restraints excluded: chain D residue 587 THR Chi-restraints excluded: chain D residue 590 THR Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 645 SER Chi-restraints excluded: chain D residue 670 LEU Chi-restraints excluded: chain D residue 687 ILE Chi-restraints excluded: chain D residue 691 THR Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain D residue 743 VAL Chi-restraints excluded: chain D residue 795 SER Chi-restraints excluded: chain D residue 811 VAL Chi-restraints excluded: chain D residue 890 SER Chi-restraints excluded: chain D residue 897 SER Chi-restraints excluded: chain D residue 975 ILE Chi-restraints excluded: chain D residue 985 ASN Chi-restraints excluded: chain D residue 986 ASP Chi-restraints excluded: chain D residue 995 ASP Chi-restraints excluded: chain D residue 1015 PHE Chi-restraints excluded: chain D residue 1032 ILE Chi-restraints excluded: chain D residue 1037 THR Chi-restraints excluded: chain D residue 1046 MET Chi-restraints excluded: chain D residue 1058 VAL Chi-restraints excluded: chain D residue 1069 THR Chi-restraints excluded: chain D residue 1075 SER Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 201 PHE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 356 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 150 optimal weight: 1.9990 chunk 96 optimal weight: 6.9990 chunk 145 optimal weight: 0.6980 chunk 73 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 154 optimal weight: 1.9990 chunk 165 optimal weight: 0.9990 chunk 120 optimal weight: 9.9990 chunk 22 optimal weight: 0.5980 chunk 190 optimal weight: 3.9990 chunk 220 optimal weight: 8.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 925 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN D 295 ASN ** D 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1062 ASN ** C 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 21173 Z= 0.204 Angle : 0.622 11.080 28687 Z= 0.304 Chirality : 0.042 0.261 3286 Planarity : 0.004 0.068 3602 Dihedral : 9.562 106.282 3387 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.87 % Favored : 91.97 % Rotamer: Outliers : 5.58 % Allowed : 35.21 % Favored : 59.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: -1.26 (0.17), residues: 2502 helix: 0.25 (0.16), residues: 1163 sheet: -0.54 (0.35), residues: 198 loop : -2.07 (0.18), residues: 1141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A1233 HIS 0.003 0.001 HIS D 885 PHE 0.030 0.001 PHE A 594 TYR 0.011 0.001 TYR A1222 ARG 0.004 0.000 ARG D 313 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 2241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 263 time to evaluate : 2.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 GLU cc_start: 0.7334 (OUTLIER) cc_final: 0.6807 (mp0) REVERT: A 150 ASP cc_start: 0.8260 (t0) cc_final: 0.8008 (t0) REVERT: A 163 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7550 (tp30) REVERT: A 173 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.7328 (tt0) REVERT: A 319 GLU cc_start: 0.7257 (OUTLIER) cc_final: 0.6923 (mm-30) REVERT: A 362 MET cc_start: 0.8759 (mtm) cc_final: 0.8551 (mtm) REVERT: A 401 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.8193 (mp) REVERT: A 407 GLU cc_start: 0.7980 (tp30) cc_final: 0.7643 (mm-30) REVERT: A 583 TYR cc_start: 0.7196 (t80) cc_final: 0.6834 (t80) REVERT: A 621 CYS cc_start: 0.8739 (m) cc_final: 0.8220 (p) REVERT: A 683 GLN cc_start: 0.7720 (pm20) cc_final: 0.7486 (pm20) REVERT: A 766 GLN cc_start: 0.6890 (mm-40) cc_final: 0.6580 (mp10) REVERT: A 775 ARG cc_start: 0.7202 (OUTLIER) cc_final: 0.6972 (tmm-80) REVERT: A 916 SER cc_start: 0.8347 (OUTLIER) cc_final: 0.7687 (p) REVERT: A 928 PHE cc_start: 0.8413 (t80) cc_final: 0.8170 (t80) REVERT: A 929 ARG cc_start: 0.8120 (OUTLIER) cc_final: 0.6622 (ttp-110) REVERT: A 1011 ILE cc_start: 0.5744 (OUTLIER) cc_final: 0.5438 (pp) REVERT: A 1051 ASN cc_start: 0.8219 (OUTLIER) cc_final: 0.7675 (p0) REVERT: A 1219 LEU cc_start: 0.6664 (OUTLIER) cc_final: 0.6439 (tp) REVERT: A 1274 LEU cc_start: 0.7755 (OUTLIER) cc_final: 0.7496 (mt) REVERT: A 1307 ASP cc_start: 0.8157 (m-30) cc_final: 0.7853 (m-30) REVERT: A 1526 ASN cc_start: 0.8321 (t0) cc_final: 0.7988 (t0) REVERT: A 1549 TRP cc_start: 0.6801 (t-100) cc_final: 0.6496 (t-100) REVERT: A 1578 PHE cc_start: 0.5922 (OUTLIER) cc_final: 0.5682 (t80) REVERT: A 1594 MET cc_start: 0.5702 (mmt) cc_final: 0.4524 (tpt) REVERT: A 1596 MET cc_start: 0.3964 (mmp) cc_final: 0.3569 (mtp) REVERT: A 1605 MET cc_start: 0.6980 (OUTLIER) cc_final: 0.6610 (ppp) REVERT: A 1623 GLU cc_start: 0.4152 (OUTLIER) cc_final: 0.3569 (pm20) REVERT: D 42 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7957 (mp0) REVERT: D 77 GLN cc_start: 0.8106 (OUTLIER) cc_final: 0.7473 (mp10) REVERT: D 103 GLU cc_start: 0.7518 (mp0) cc_final: 0.7027 (mp0) REVERT: D 366 GLU cc_start: 0.8387 (pt0) cc_final: 0.8126 (pm20) REVERT: D 601 ASP cc_start: 0.8174 (t0) cc_final: 0.7926 (t0) REVERT: D 704 ARG cc_start: 0.8044 (OUTLIER) cc_final: 0.7330 (ttt90) REVERT: D 708 ASP cc_start: 0.8237 (t0) cc_final: 0.7800 (t0) REVERT: D 827 LYS cc_start: 0.7261 (mttt) cc_final: 0.6440 (mttp) REVERT: D 879 ASP cc_start: 0.7119 (t0) cc_final: 0.6802 (t0) REVERT: D 985 ASN cc_start: 0.8571 (OUTLIER) cc_final: 0.8266 (p0) REVERT: C 201 PHE cc_start: 0.7822 (OUTLIER) cc_final: 0.7246 (m-10) REVERT: C 266 LEU cc_start: 0.7051 (OUTLIER) cc_final: 0.6675 (mm) REVERT: C 268 VAL cc_start: 0.7655 (m) cc_final: 0.7316 (p) REVERT: C 347 GLU cc_start: 0.7520 (tp30) cc_final: 0.7296 (mp0) outliers start: 125 outliers final: 81 residues processed: 368 average time/residue: 1.0323 time to fit residues: 445.7582 Evaluate side-chains 353 residues out of total 2241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 251 time to evaluate : 2.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 775 ARG Chi-restraints excluded: chain A residue 776 LYS Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 929 ARG Chi-restraints excluded: chain A residue 1011 ILE Chi-restraints excluded: chain A residue 1042 VAL Chi-restraints excluded: chain A residue 1051 ASN Chi-restraints excluded: chain A residue 1219 LEU Chi-restraints excluded: chain A residue 1274 LEU Chi-restraints excluded: chain A residue 1277 LEU Chi-restraints excluded: chain A residue 1291 ILE Chi-restraints excluded: chain A residue 1315 ILE Chi-restraints excluded: chain A residue 1385 VAL Chi-restraints excluded: chain A residue 1390 ARG Chi-restraints excluded: chain A residue 1449 THR Chi-restraints excluded: chain A residue 1493 THR Chi-restraints excluded: chain A residue 1531 THR Chi-restraints excluded: chain A residue 1564 ASP Chi-restraints excluded: chain A residue 1565 VAL Chi-restraints excluded: chain A residue 1578 PHE Chi-restraints excluded: chain A residue 1582 CYS Chi-restraints excluded: chain A residue 1605 MET Chi-restraints excluded: chain A residue 1623 GLU Chi-restraints excluded: chain A residue 1636 ILE Chi-restraints excluded: chain A residue 1645 SER Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 66 ASP Chi-restraints excluded: chain D residue 77 GLN Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 160 SER Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 263 SER Chi-restraints excluded: chain D residue 372 ILE Chi-restraints excluded: chain D residue 393 ASN Chi-restraints excluded: chain D residue 463 THR Chi-restraints excluded: chain D residue 481 ASN Chi-restraints excluded: chain D residue 500 LEU Chi-restraints excluded: chain D residue 516 ASP Chi-restraints excluded: chain D residue 532 ILE Chi-restraints excluded: chain D residue 582 GLU Chi-restraints excluded: chain D residue 587 THR Chi-restraints excluded: chain D residue 590 THR Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 645 SER Chi-restraints excluded: chain D residue 670 LEU Chi-restraints excluded: chain D residue 687 ILE Chi-restraints excluded: chain D residue 691 THR Chi-restraints excluded: chain D residue 704 ARG Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain D residue 795 SER Chi-restraints excluded: chain D residue 811 VAL Chi-restraints excluded: chain D residue 890 SER Chi-restraints excluded: chain D residue 891 VAL Chi-restraints excluded: chain D residue 975 ILE Chi-restraints excluded: chain D residue 985 ASN Chi-restraints excluded: chain D residue 995 ASP Chi-restraints excluded: chain D residue 1015 PHE Chi-restraints excluded: chain D residue 1028 THR Chi-restraints excluded: chain D residue 1032 ILE Chi-restraints excluded: chain D residue 1037 THR Chi-restraints excluded: chain D residue 1046 MET Chi-restraints excluded: chain D residue 1058 VAL Chi-restraints excluded: chain D residue 1069 THR Chi-restraints excluded: chain D residue 1075 SER Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 201 PHE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 294 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 232 optimal weight: 9.9990 chunk 212 optimal weight: 10.0000 chunk 226 optimal weight: 20.0000 chunk 136 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 177 optimal weight: 0.0980 chunk 69 optimal weight: 0.8980 chunk 204 optimal weight: 2.9990 chunk 214 optimal weight: 0.9980 chunk 225 optimal weight: 6.9990 chunk 148 optimal weight: 0.9980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 925 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1062 ASN ** C 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21173 Z= 0.220 Angle : 0.628 10.978 28687 Z= 0.308 Chirality : 0.042 0.264 3286 Planarity : 0.004 0.068 3602 Dihedral : 9.383 105.943 3385 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.83 % Favored : 92.01 % Rotamer: Outliers : 5.22 % Allowed : 35.65 % Favored : 59.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: -1.21 (0.17), residues: 2502 helix: 0.27 (0.16), residues: 1165 sheet: -0.64 (0.34), residues: 221 loop : -2.04 (0.19), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A1233 HIS 0.004 0.001 HIS D 885 PHE 0.029 0.001 PHE A 594 TYR 0.010 0.001 TYR A 384 ARG 0.005 0.000 ARG A 246 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 2241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 259 time to evaluate : 2.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 GLU cc_start: 0.7328 (OUTLIER) cc_final: 0.6626 (mp0) REVERT: A 131 LEU cc_start: 0.7798 (tt) cc_final: 0.7564 (mt) REVERT: A 150 ASP cc_start: 0.8296 (t0) cc_final: 0.8045 (t0) REVERT: A 163 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7555 (tp30) REVERT: A 319 GLU cc_start: 0.7250 (OUTLIER) cc_final: 0.6933 (mm-30) REVERT: A 362 MET cc_start: 0.8764 (mtm) cc_final: 0.8512 (mtm) REVERT: A 401 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.8164 (mp) REVERT: A 407 GLU cc_start: 0.7974 (tp30) cc_final: 0.7681 (mm-30) REVERT: A 583 TYR cc_start: 0.7273 (t80) cc_final: 0.6933 (t80) REVERT: A 621 CYS cc_start: 0.8734 (m) cc_final: 0.8224 (p) REVERT: A 766 GLN cc_start: 0.6877 (mm-40) cc_final: 0.6572 (mp10) REVERT: A 775 ARG cc_start: 0.7192 (OUTLIER) cc_final: 0.6980 (tmm-80) REVERT: A 916 SER cc_start: 0.8500 (OUTLIER) cc_final: 0.7857 (p) REVERT: A 928 PHE cc_start: 0.8417 (t80) cc_final: 0.8185 (t80) REVERT: A 929 ARG cc_start: 0.8122 (OUTLIER) cc_final: 0.6622 (ttp-110) REVERT: A 1011 ILE cc_start: 0.5697 (OUTLIER) cc_final: 0.5417 (pp) REVERT: A 1051 ASN cc_start: 0.8204 (OUTLIER) cc_final: 0.7646 (p0) REVERT: A 1219 LEU cc_start: 0.6629 (OUTLIER) cc_final: 0.6423 (tp) REVERT: A 1274 LEU cc_start: 0.7752 (OUTLIER) cc_final: 0.7506 (mt) REVERT: A 1307 ASP cc_start: 0.8165 (m-30) cc_final: 0.7851 (m-30) REVERT: A 1526 ASN cc_start: 0.8330 (t0) cc_final: 0.8004 (t0) REVERT: A 1549 TRP cc_start: 0.7118 (t-100) cc_final: 0.6875 (t-100) REVERT: A 1578 PHE cc_start: 0.5861 (OUTLIER) cc_final: 0.5620 (t80) REVERT: A 1605 MET cc_start: 0.7010 (OUTLIER) cc_final: 0.6637 (ppp) REVERT: A 1615 ARG cc_start: 0.8209 (tpp80) cc_final: 0.7803 (tpp80) REVERT: A 1623 GLU cc_start: 0.4144 (OUTLIER) cc_final: 0.3537 (pm20) REVERT: D 42 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7936 (mp0) REVERT: D 77 GLN cc_start: 0.8095 (OUTLIER) cc_final: 0.7455 (mp10) REVERT: D 102 LEU cc_start: 0.8021 (OUTLIER) cc_final: 0.7607 (mp) REVERT: D 103 GLU cc_start: 0.7740 (mp0) cc_final: 0.7237 (mp0) REVERT: D 366 GLU cc_start: 0.8390 (pt0) cc_final: 0.8140 (pm20) REVERT: D 506 LEU cc_start: 0.7360 (OUTLIER) cc_final: 0.7085 (mt) REVERT: D 601 ASP cc_start: 0.8201 (t0) cc_final: 0.7949 (t0) REVERT: D 704 ARG cc_start: 0.8070 (OUTLIER) cc_final: 0.7364 (ttt90) REVERT: D 708 ASP cc_start: 0.8130 (t0) cc_final: 0.7639 (t0) REVERT: D 985 ASN cc_start: 0.8604 (OUTLIER) cc_final: 0.8398 (p0) REVERT: C 201 PHE cc_start: 0.7871 (OUTLIER) cc_final: 0.7243 (m-10) REVERT: C 266 LEU cc_start: 0.7073 (OUTLIER) cc_final: 0.6633 (mm) REVERT: C 268 VAL cc_start: 0.7664 (m) cc_final: 0.7332 (p) outliers start: 117 outliers final: 76 residues processed: 357 average time/residue: 1.0308 time to fit residues: 431.6422 Evaluate side-chains 348 residues out of total 2241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 250 time to evaluate : 2.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 775 ARG Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 929 ARG Chi-restraints excluded: chain A residue 1011 ILE Chi-restraints excluded: chain A residue 1042 VAL Chi-restraints excluded: chain A residue 1051 ASN Chi-restraints excluded: chain A residue 1219 LEU Chi-restraints excluded: chain A residue 1274 LEU Chi-restraints excluded: chain A residue 1291 ILE Chi-restraints excluded: chain A residue 1385 VAL Chi-restraints excluded: chain A residue 1390 ARG Chi-restraints excluded: chain A residue 1449 THR Chi-restraints excluded: chain A residue 1493 THR Chi-restraints excluded: chain A residue 1531 THR Chi-restraints excluded: chain A residue 1564 ASP Chi-restraints excluded: chain A residue 1565 VAL Chi-restraints excluded: chain A residue 1578 PHE Chi-restraints excluded: chain A residue 1582 CYS Chi-restraints excluded: chain A residue 1605 MET Chi-restraints excluded: chain A residue 1609 THR Chi-restraints excluded: chain A residue 1623 GLU Chi-restraints excluded: chain A residue 1636 ILE Chi-restraints excluded: chain A residue 1645 SER Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 66 ASP Chi-restraints excluded: chain D residue 77 GLN Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 160 SER Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 263 SER Chi-restraints excluded: chain D residue 372 ILE Chi-restraints excluded: chain D residue 393 ASN Chi-restraints excluded: chain D residue 463 THR Chi-restraints excluded: chain D residue 481 ASN Chi-restraints excluded: chain D residue 500 LEU Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain D residue 516 ASP Chi-restraints excluded: chain D residue 532 ILE Chi-restraints excluded: chain D residue 582 GLU Chi-restraints excluded: chain D residue 587 THR Chi-restraints excluded: chain D residue 590 THR Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 645 SER Chi-restraints excluded: chain D residue 670 LEU Chi-restraints excluded: chain D residue 687 ILE Chi-restraints excluded: chain D residue 691 THR Chi-restraints excluded: chain D residue 704 ARG Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain D residue 795 SER Chi-restraints excluded: chain D residue 811 VAL Chi-restraints excluded: chain D residue 890 SER Chi-restraints excluded: chain D residue 975 ILE Chi-restraints excluded: chain D residue 985 ASN Chi-restraints excluded: chain D residue 995 ASP Chi-restraints excluded: chain D residue 1015 PHE Chi-restraints excluded: chain D residue 1028 THR Chi-restraints excluded: chain D residue 1032 ILE Chi-restraints excluded: chain D residue 1037 THR Chi-restraints excluded: chain D residue 1046 MET Chi-restraints excluded: chain D residue 1058 VAL Chi-restraints excluded: chain D residue 1075 SER Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 201 PHE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 294 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 239 optimal weight: 10.0000 chunk 146 optimal weight: 0.6980 chunk 113 optimal weight: 1.9990 chunk 166 optimal weight: 2.9990 chunk 251 optimal weight: 0.9990 chunk 231 optimal weight: 1.9990 chunk 199 optimal weight: 0.0170 chunk 20 optimal weight: 2.9990 chunk 154 optimal weight: 2.9990 chunk 122 optimal weight: 6.9990 chunk 158 optimal weight: 0.3980 overall best weight: 0.8222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 925 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN D 295 ASN D 481 ASN ** D 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1062 ASN ** C 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 21173 Z= 0.188 Angle : 0.631 15.286 28687 Z= 0.308 Chirality : 0.042 0.270 3286 Planarity : 0.004 0.071 3602 Dihedral : 9.139 105.656 3384 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.55 % Favored : 92.29 % Rotamer: Outliers : 4.46 % Allowed : 36.41 % Favored : 59.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: -1.12 (0.17), residues: 2502 helix: 0.37 (0.16), residues: 1163 sheet: -0.53 (0.35), residues: 202 loop : -2.00 (0.18), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A1233 HIS 0.003 0.001 HIS A1562 PHE 0.029 0.001 PHE A 594 TYR 0.017 0.001 TYR C 356 ARG 0.008 0.000 ARG C 211 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 257 time to evaluate : 2.515 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 127 GLU cc_start: 0.7347 (OUTLIER) cc_final: 0.6641 (mp0) REVERT: A 150 ASP cc_start: 0.8258 (t0) cc_final: 0.8018 (t0) REVERT: A 163 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7567 (tp30) REVERT: A 319 GLU cc_start: 0.7227 (OUTLIER) cc_final: 0.6913 (mm-30) REVERT: A 362 MET cc_start: 0.8755 (mtm) cc_final: 0.8550 (mtm) REVERT: A 401 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.8204 (mp) REVERT: A 407 GLU cc_start: 0.7946 (tp30) cc_final: 0.7668 (mm-30) REVERT: A 583 TYR cc_start: 0.7371 (t80) cc_final: 0.6995 (t80) REVERT: A 621 CYS cc_start: 0.8718 (m) cc_final: 0.8226 (p) REVERT: A 766 GLN cc_start: 0.6941 (mm-40) cc_final: 0.6602 (mp10) REVERT: A 916 SER cc_start: 0.8487 (OUTLIER) cc_final: 0.7843 (p) REVERT: A 928 PHE cc_start: 0.8403 (t80) cc_final: 0.8181 (t80) REVERT: A 929 ARG cc_start: 0.8140 (OUTLIER) cc_final: 0.6653 (ttp-110) REVERT: A 1011 ILE cc_start: 0.5581 (OUTLIER) cc_final: 0.5317 (pp) REVERT: A 1051 ASN cc_start: 0.8216 (OUTLIER) cc_final: 0.7661 (p0) REVERT: A 1307 ASP cc_start: 0.8163 (m-30) cc_final: 0.7827 (m-30) REVERT: A 1526 ASN cc_start: 0.8203 (t0) cc_final: 0.7858 (t0) REVERT: A 1549 TRP cc_start: 0.7151 (t-100) cc_final: 0.6907 (t-100) REVERT: A 1578 PHE cc_start: 0.5814 (OUTLIER) cc_final: 0.5609 (t80) REVERT: A 1594 MET cc_start: 0.5834 (mmt) cc_final: 0.4397 (tpt) REVERT: A 1596 MET cc_start: 0.4156 (mmp) cc_final: 0.3866 (mtm) REVERT: A 1605 MET cc_start: 0.7051 (OUTLIER) cc_final: 0.6742 (ppp) REVERT: A 1615 ARG cc_start: 0.8176 (tpp80) cc_final: 0.7900 (tpp80) REVERT: A 1623 GLU cc_start: 0.4125 (OUTLIER) cc_final: 0.3534 (pm20) REVERT: D 42 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7923 (mp0) REVERT: D 77 GLN cc_start: 0.8104 (OUTLIER) cc_final: 0.7478 (mp10) REVERT: D 103 GLU cc_start: 0.7524 (mp0) cc_final: 0.7018 (mp0) REVERT: D 366 GLU cc_start: 0.8362 (pt0) cc_final: 0.8096 (pm20) REVERT: D 506 LEU cc_start: 0.7294 (OUTLIER) cc_final: 0.7022 (mt) REVERT: D 601 ASP cc_start: 0.8181 (t0) cc_final: 0.7934 (t0) REVERT: D 704 ARG cc_start: 0.8056 (OUTLIER) cc_final: 0.7340 (ttt90) REVERT: D 708 ASP cc_start: 0.8112 (t0) cc_final: 0.7612 (t0) REVERT: C 201 PHE cc_start: 0.7849 (OUTLIER) cc_final: 0.7252 (m-10) REVERT: C 266 LEU cc_start: 0.6832 (OUTLIER) cc_final: 0.6616 (mm) outliers start: 100 outliers final: 70 residues processed: 344 average time/residue: 1.0480 time to fit residues: 424.1921 Evaluate side-chains 335 residues out of total 2241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 248 time to evaluate : 2.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 929 ARG Chi-restraints excluded: chain A residue 1011 ILE Chi-restraints excluded: chain A residue 1042 VAL Chi-restraints excluded: chain A residue 1051 ASN Chi-restraints excluded: chain A residue 1291 ILE Chi-restraints excluded: chain A residue 1385 VAL Chi-restraints excluded: chain A residue 1390 ARG Chi-restraints excluded: chain A residue 1449 THR Chi-restraints excluded: chain A residue 1493 THR Chi-restraints excluded: chain A residue 1531 THR Chi-restraints excluded: chain A residue 1564 ASP Chi-restraints excluded: chain A residue 1578 PHE Chi-restraints excluded: chain A residue 1582 CYS Chi-restraints excluded: chain A residue 1586 VAL Chi-restraints excluded: chain A residue 1605 MET Chi-restraints excluded: chain A residue 1609 THR Chi-restraints excluded: chain A residue 1623 GLU Chi-restraints excluded: chain A residue 1636 ILE Chi-restraints excluded: chain A residue 1645 SER Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 66 ASP Chi-restraints excluded: chain D residue 77 GLN Chi-restraints excluded: chain D residue 160 SER Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 263 SER Chi-restraints excluded: chain D residue 335 LYS Chi-restraints excluded: chain D residue 372 ILE Chi-restraints excluded: chain D residue 393 ASN Chi-restraints excluded: chain D residue 481 ASN Chi-restraints excluded: chain D residue 500 LEU Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain D residue 516 ASP Chi-restraints excluded: chain D residue 532 ILE Chi-restraints excluded: chain D residue 582 GLU Chi-restraints excluded: chain D residue 587 THR Chi-restraints excluded: chain D residue 590 THR Chi-restraints excluded: chain D residue 670 LEU Chi-restraints excluded: chain D residue 687 ILE Chi-restraints excluded: chain D residue 691 THR Chi-restraints excluded: chain D residue 704 ARG Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain D residue 811 VAL Chi-restraints excluded: chain D residue 975 ILE Chi-restraints excluded: chain D residue 995 ASP Chi-restraints excluded: chain D residue 1015 PHE Chi-restraints excluded: chain D residue 1032 ILE Chi-restraints excluded: chain D residue 1037 THR Chi-restraints excluded: chain D residue 1046 MET Chi-restraints excluded: chain D residue 1058 VAL Chi-restraints excluded: chain D residue 1075 SER Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 201 PHE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 294 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 212 optimal weight: 10.0000 chunk 61 optimal weight: 6.9990 chunk 184 optimal weight: 5.9990 chunk 29 optimal weight: 7.9990 chunk 55 optimal weight: 0.9980 chunk 200 optimal weight: 10.0000 chunk 83 optimal weight: 1.9990 chunk 205 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 175 optimal weight: 0.2980 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 925 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 295 ASN ** D 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 652 ASN D1062 ASN ** C 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.168081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.096627 restraints weight = 29060.278| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 2.53 r_work: 0.3002 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 21173 Z= 0.353 Angle : 0.685 13.730 28687 Z= 0.339 Chirality : 0.045 0.286 3286 Planarity : 0.005 0.068 3602 Dihedral : 9.287 105.778 3377 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.15 % Favored : 91.69 % Rotamer: Outliers : 4.42 % Allowed : 36.59 % Favored : 58.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: -1.31 (0.17), residues: 2502 helix: 0.22 (0.15), residues: 1165 sheet: -0.98 (0.34), residues: 214 loop : -2.04 (0.18), residues: 1123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A1233 HIS 0.005 0.001 HIS D 306 PHE 0.030 0.002 PHE A 594 TYR 0.020 0.002 TYR D1068 ARG 0.007 0.000 ARG D 643 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8563.36 seconds wall clock time: 152 minutes 7.99 seconds (9127.99 seconds total)